SYSTEMS AND METHODS FOR GENOMIC AND GENETIC ANALYSIS

Abstract

The present invention relates to a method for genomic and/or genetic analysis of a human nucleic acid sample, the method comprising the steps of providing a group of human reference genomes; testing of the human nucleic acid sample for sex and/or ancestry; selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis on the results of the sex and/or ancestry test; and aligning the human nucleic acid sample to the selected PHREGs; and variant calling against the selected PHREGs. The present invention also provides respective computer systems and computer programs.

Description

The present invention relates to systems and methods for genomic and genetic analysis of a human nucleic acid sample.

BACKGROUND OF THE INVENTION

Next-Generation Sequencing (NGS)

Next-generation sequencing, also known as high-throughput sequencing, is a routine method for the high-throughput and parallel sequencing of nucleic acid fragments which is well known to the person skilled in the art. The equipment and methodology of next-generation sequencing is commercially available from diverse suppliers (see, e.g., www.illumina.com).

Next-generation sequencing is the catch-all term used to describe a number of different modern sequencing technologies including:

• • Illumina (Solexa) sequencing
  • Ion torrent: Proton/PGM sequencing
  • SOLiD sequencing.

NGS technologies produce high-quality DNA sequences (“reads”). These reads are substantially shorter than the reads produced by the capillary-based Sanger sequencing technology (650-1000 bp), developed by Frederick Sanger and colleagues in 1977, which was the most widely used sequencing method for approximately 30 years. Sanger reads are produced in low-throughput with high costs, while the NGS methods produce much shorter reads (25-500 bases) at moderate costs. However, the total number of base pairs sequenced in a NGS run is orders of magnitude higher. These two factors cause many new informatics challenges, including the ability to process these millions or even billions of short NGS reads. The reads are usually processed in one of two ways: either they are mapped back to their correct locations in an existing backbone/reference sequence, building a sequence that is similar but not necessarily identical to the backbone sequence (called “read mapping”), or they are built into a new sequence (called “de novo assembly”).

The primary advantage of read mapping back to a reference genome as opposed to de-novo assembly is that it greatly simplifies the process of genome inference. While assembly needs to discover the entire genomic sequence and gives rise to many ambiguities, reference-based resequencing only needs to discover a sample's differences from the reference. In terms of complexity and time requirements, de novo assemblies are orders of magnitude slower and more memory intensive than mapping assemblies.

Read mapping is the first and most fundamental step in NGS analysis pipelines that aim to discover the variation of a newly sequenced human genome (or fractions of it, like the exome or a small targeted panel of genes) with respect to the previously sequenced human reference genome.

Read mapping is also used to align these millions or billions of short NGS reads to detect the coverage (the number of reads at a particular position/locus) which is a key quality parameter of the NGS experiment and all further derived conclusions.

The Human Reference Genome (HRG)

In February 2001 the Human Genome Project, a U.S. federal government effort, together with Celera Genomics, a private company, successfully completed drafts of the entire human genome, which was revised several times subsequently ^{[Lander et al. 2001, Venter et al. 2001, Church et al. 2011]}. Over a number of years, the genome assembly has steadily improved and new versions (“builds”) have been released, to the point that the current Genome Reference Consortium (GRC) human genome assembly, GRCh38 ^{[Schneider et al. 2017]}, is arguably the best assembled mammalian genome in existence, with just 875 remaining assembly gaps and fewer than 160 million unspecified “N” nucleotides (as of GRCh38.p8), whereas the first version had ˜150,000 gaps ^{[Editorial (October 2010). “E pluribus unum”. Nature Methods. 7 (5): 331. doi:10.1038/nmeth0510-331]}.

The HRG is the single most important resource used in human genetics and genomics today. It acts as a universal coordinate system and as such is the space in which annotations (genes, promoters, etc.) and genetic variants are described^{[Harrow et al. 2012; ENCODE, 2012; 1000 Genomes Project Consortium, 2012]}. It is also the reference for the read alignment step in next-generation sequencing analysis pipelines. Downstream of this mapping, it is used for functional assays and variant calling pipelines ^{[Li H & Durbin 2009; DePristo et al., 2011]}.

The initial build of the HRG was composed of DNA sequences from a small cohort of thirteen anonymous DNA donors who had volunteered in Buffalo, N.Y. with primarily European origins ^{[Snyder et al]}. Donors were recruited by advertisement in the Buffalo News, on Sunday, Mar. 23, 1997. The first ten male and ten female volunteers were invited to make an appointment with the project's genetic counselors and donated blood from which DNA was extracted. As a result of how the DNA samples were processed, about 80 percent of the reference genome came from eight people. One male, designated as RP11, accounted for 66 percent of the total.

To identify and resolve larger assembly issues, e.g. complex regions containing large-scale duplications and structural variations, sequence data from new genome mapping technologies and single haplotype resources originating from new donors have been brought into the most recent builds. At the time of filing the present application, GRCh38 contains sequences from about 50 different individuals, see http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html.

Limitations of the HRG

1. The HRG is Linear

The human DNA is packaged into physically separate units called chromosomes. Humans are diploid organisms, containing two sets of genetic information, one set inherited from the mother and one from the father. Thus, each somatic cell has 22 pairs of chromosomes called autosomes (one member of each pair from each parent) and two sex chromosomes (an X and a Y chromosome in males and two X chromosomes in females). Each chromosome contains a single very long, linear DNA molecule. In the smallest human chromosomes, this DNA molecule is composed of about 50 million nucleotide pairs; the largest chromosomes contain about 250 million nucleotide pairs.

The diploid human genome is thus composed of 46 single DNA molecules of 24 distinct types. Because human chromosomes exist in pairs that are almost identical, only 3 billion nucleotide pairs (the haploid genome) needed to be sequenced to gain complete information concerning a representative human genome. The human genome is thus said to contain 3 billion nucleotide pairs, even though most human cells contain 6 billion nucleotide pairs. The haploid human genome consists of 22 autosomal chromosomes and the Y and the X chromosomes.

Each of the chromosomes represents a single DNA molecule, a sequence of millions of nucleotide bases. These molecules are linear, so one might expect that each chromosome should be represented by a single, continuous/linear nucleic acid sequence. Unfortunately, this is not the case for two main reasons: 1) because of the nature of genomic DNA and the limitations of sequencing methods, some parts of the genome remain unsequenced, and 2) some regions of the genome vary so much between individual people that they cannot be represented as a single continuous sequence. However, the HRG is represented as 24 linear DNA sequences consisting of the normal bases (A, C, T or G) with gaps represented as a series of “N”s clearly showing the position of gaps in the assembly.

The primary goal of the Human Genome Project was to produce a single representative sequence albeit with regions of uncertainty—that is, a single “scaffold”—for each physical chromosome. It also included a handful of alternate scaffolds representing allelic variation (different versions of the DNA bases present at a SNP locus are referred to as alleles), but they had no formalized relationship to the main scaffold. Recognizing that some highly polymorphic regions of the genome were particularly poorly represented by a single reference sequence, a formal model to introduce representative alternate versions of highly variable regions was added starting with GRCh37 ^{[Church et al. 2011]}. Sequences in the form of kilobase to multi-megabase “alternate locus scaffolds” were described relative to the “primary” (haploid) assembly, anchored to locations along the primary scaffolds. In the assembly at the time of filing the present application (GRCh38.p9), these cover 178 regions and total 261 linear sequences ^{[Paten et al. 2017]}.

Another complicating factor is that the HRG was deduced in the original international genome sequencing project from a collection of DNAs from multiple anonymous individuals. Thus, the resulting HRG is really a randomly mixed conglomerate, a haploid mosaic of different DNA sequences, that, in some cases, may be impossible to represent correctly as a single linear sequence.

2. The HRG is Certainly not Disease Free

Chen & Butte (2011) identified 3,556 disease-susceptible variants including 15 rare variants (Major Allele Frequency <1%) in the HRG. Using a curated, high-quality quantitative human disease-SNP association database, the authors assessed the likelihood ratio of increased risk over healthy population on 104 diseases for the reference genome and found high risk for type 1 diabetes, hypertension and other disorders. This provides clear evidence that the HRG does not represent a regular person and is certainly not disease free. Although it has dramatically accelerated the analysis of personal genome sequencing efforts, focusing on variants different from the reference genome will likely miss many disease causal variants including rare variants ^{[Chen & Butte 2011]}.

3. Reference Allele Bias Towards European Ancestry

A major challenge in using the HRG assemblies in prior art NGS analysis pipelines is the fact that they are derived from DNA samples from a relatively small number of anonymous donors with a bias towards European ancestry and therefore represent a small sampling of the broad array of human genetic variation.

Despite the relative effectiveness and ubiquity of the reference as a coordinate system for the majority of the genome, there is increasing concern that using the HRG as a lens to study all other human genomes excludes a great deal of common human variation and introduces a pervasive reference allele bias ^{[Petrovski et al. 2016, Paten et al. 2017]}. Reference allele bias is the tendency to over-report alleles present in the reference genome and under-report other alleles whose underlying DNA does not match a reference allele ^{[Degner et al. 2009, Brandt et al. 2015]}.

This bias arises chiefly during the read mapping and alignment step in resequencing experiments. To map correctly, reads must derive from genomic sequence that is both represented in the reference and similar enough to the reference sequence to be identified as the same genomic element. When these conditions are not met, mapping errors introduce a systematic blindness to the true sequence ^{[Paten et al. 2017]}. Reference allele bias also has the potential to affect some genetic subpopulations and some regions of the genome more than others, depending on the ancestral history of the reference genome at each locus bias ^{[Petrovski et al. 2016, Paten et al. 2017]}. Highly polymorphic regions such as HLA genes are especially susceptible to the effects of reference allele bias ^{[Nielsen et al. 2011]}, particularly when a single reference genome is used as an index for the alignment of NGS reads. In this situation, many true variants fail to be identified because they are present in haplotypes that differ from the genome used as index, and thus reads generated from these regions are not aligned and are lost ^{[Brandt et al. 2015]}.

As described above, reference bias is a known issue in human genome resequencing using the HRG for variant detection, and modifications to the reference can improve calling accuracy and interpretability ^{[Fakhro et al. 2016]}. One approach to mitigate this issue is to modify variant prevalence information early on in the genome-interpretation process by modifying the reference genome, such that variants discovered in the genome are the minor allele in the population ^{[Dewey et al., 2011]}. This modification to the reference results in a streamlined analysis workflow, as the number of false positives can be reduced and fewer variants need to be interpreted ^{[Fakhro et al. 2016]}.

The Future: Graph-Based Reference Structures/Genome Graphs

There is increasing recognition that a single, haploid reference genome is a poor universal reference structure for human genetics and genomics, because it represents only a tiny fraction of human variation: there exist variants and annotations that can not easily be described with respect to the reference genome ^{[Horton et al. 2008, Pei et al. 2012]}. Furthermore, as a target for read mapping and interpretation, it introduces a reference allele bias as described above. To mitigate these issues, recent versions of the reference genome assembly, such as the human genome assembly at the time of filing the present application (GRCh38.p9), have included “alternate locus” sequences (“alts”): additional multiple sequence representations of regions of the human genome considered to be highly polymorphic, anchored at their ends to locations within the “primary” (haploid) reference assembly. Such a structure, which contains multiple partially-overlapping sequence paths, can be considered a form of a mathematical graph: a genome graph ^{[Novak et al. 2017]}.

Graphs have a longstanding place in biological sequence analysis, in which they have often been used to compactly represent an ensemble of possible sequences. As a rule, the sequences themselves are implicitly encoded as walks in the graph. This makes graphs a natural fit for representing reference cohorts, which are by their nature ensembles of related sequences ^{[Paten et al. 2017]}. The graph contains not only the sample's approximate sequence, but also many of its specific variants.

Genome graphs are expected to produce improvements in read mapping, variant calling, and haplotype determination. It is anticipated that graph-based references will supplant linear references in humans and in other applications where cohorts of sequenced individuals are available ^{[Novak et al. 2017]}. Various projects are underway to build and apply these genome graphs. Genome graphs can now be built from libraries of common variants, and some tools, though still experimental, illustrate the huge potential of the graph-based approach.

Despite the theoretical advantages, research on variant calling using genome graphs is still relatively nascent. There is a number of questions yet to be tackled. How should duplications and repeats be represented? How can one best map to a graph? How should short variants whose homologies are unclear be parsed? How can graphs be used to enable a more comprehensive taxonomy of variation? These questions all represent open avenues for future research.

To be useful in practice, genome graphs must be able to translate their promised reduction in reference bias into measurable improvements in variant calling over established methodologies. Accordingly, developing variant calling algorithms for genome graphs is currently an important research frontier.

The Qatar Genome (QTRG)

Qatar is a small peninsula on the Persian Gulf with a total population of approximately 300,000 Qatari citizens. Qataris have one of the highest rates of consanguineous marriages in the world, which is still increasing, and the rate of endogamous marriage in Qatar approaches ˜100%. All these factors together with the large family size are the main reasons for the high rate of indigenous genetic diseases, which represent a financial burden on the Qatari budget. These factors triggered the Qatari government to seek a means to protect their own people from the threat of genetic diseases ^{[Zayed 2016]}.

Government officials decided to launch the Qatar genome project (QGP) in 2013 (http://www.gulf-times.com/story/374345/Qatarlaunches-genome-project). The intent of the project was to sequence the genome of each Qatari citizen in an effort to protect Qataris from the high rate of indigenous genetic diseases by allowing the mapping of disease-causing variants/rare variants and establishing a Qatari reference genome as a path towards personalized medicine. The final goal of the project is to apply the information to clinical practice and to allow this approach to become a routine part of the Qatari healthcare system ^{[Zayed 2016]}. To achieve the expected clinical application promise of the QGP, several serious challenges must be met, including reaching high variant-calling sensitivity and accuracy ^{[Kobodt 2010]}.

To facilitate precision medicine in regions of the Middle East and North Africa, a population-specific genome, custom tailored to disease research in the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from whole genome sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single-nucleotide polymorphisms (SNPs) and 3.1 million inDels (insertions and deletions) were observed in Qatar, including an average of 1.79% novel variants per individual genome ^{[Fakhr et al. 2016]}.

1000 Genomes Project (1 kG)

The 1000 Genomes Project was formed in 2008 to sequence and generate a catalog of human genetic variation (with respect to HRG GRCh37) and haplotypes from the genomes of at least 1,000 people around the world (hence the name the 1000 Genomes Project). The current phase 3 analysis of the project contains 2,504 individuals from 26 populations and defined 5 so-called super-populations, which are formed as unions of 4 to 7 populations each ^{[1000 Genomes Project Consortium et al. 2015]}. This haplotype resource at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels ^{[Baye, 2011]}.

Objectives of the Invention

Recent advances in NGS technologies allow for quick and cheap DNA and RNA sequencing, and as such have revolutionized the study of genomics and molecular biology. Genome sequencing projects for healthy and disease cohorts have identified numerous functional or disease-associated genomic variants, which can give clues about therapeutic targets or genomic markers for novel clinical applications.

Genetic variant calling is predominantly based on alignment of raw sequence reads against a reference genome (read mapping). This alignment-based approach has many limitations including incompleteness of genome assembly ^{[Meyer, L. R. et al., 2013]}, structural variations existing in the genomes of normal individuals ^{[Sudmant et al., 2015]}, sequencing errors in reads, and interference of single-nucleotide polymorphisms (SNP) on read mapping ^{[Iqbal, Z. et al., 2012]}.

Currently, at the time of filing the present application, read mapping against the linear HRG is the standard approach and is expected to remain the standard in clinical NGS analysis pipelines and resequencing human individuals, due to the relative effectiveness and ubiquity of the HRG as a coordinate system for the majority of the genome. In addition (and in contrast to the nascent state of genome inference using genome graphs), many successful methodologies have been published for calling variants using the linear reference genome ^{[Nielsen et al. 2011]}.

However, as described above, one major issue is bias in the HRG, ignoring prior information about genetic variation within the species. At present, the issue is typically solved by modifying the reference genome, such that variants called against the modified reference genome are the minor allele in the population.

The success of clinical genomics using NGS technologies requires the accurate and consistent identification of personal genome variants. A prerequisite for these objectives is accurate read mapping (alignment) and later variant calling.

One objective of the invention is the detection of new biomarkers, in particular genetic variants such as single-nucleotide variants (SNVs), insertions and deletions (inDels), copy number variations (CNV) and structural variants (SVs), e.g. chromosomal translocation, inversion, duplication, large inDels, for the usage of next-generation sequencing in human genome research.

Another objective is to increase the accuracy and confidence of the existing NGS based biomarkers e.g. as used for cancer treatment where the technique is used for analyzing the tumor cells and their damaged DNA.

DISCLOSURE OF THE INVENTION

In accordance with a first aspect of the invention, the present invention provides a method for genomic and/or genetic analysis of a human nucleic acid sample comprising the following steps:

• a) providing a group of human reference genomes;
• b) testing of the human nucleic acid sample for sex and/or ancestry;
• c) selecting one or more population-specific human reference genomes (PHREGs) from the group of human reference genomes on the basis of the results of the sex and/or ancestry test in step b); and
• d) aligning the human nucleic acid sample to the PHREGs selected in step c).

“Population-specific human reference genomes” (PHREGs) are understood in the following as ancestry-specific reference genomes and sex-specific reference genomes. PHREGs minimize the reference bias considerably and improve the alignment accuracy, and, if variant calling is performed subsequently, the variant calling accuracy. Advantageously, the invention does not only improve the precision of the alignment, but also improves calculation speed, the number of correctly aligned reads and the number of calculation steps of the alignment. The benefit of using PHREGs in the genomic and/or genetic analysis of a human nucleic acid sample can also result in an improved read coverage depth and can be assessed by an improved variant calling sensitivity.

In the context of the present invention, the term “human nucleic acid sample” generally means any nucleic acid sample which is isolated from a human sample. The human nucleic acid sample may in particular include NGS reads as defined in more detail below.

The human nucleic acid sample may generally comprise samples from all kind of standard biochemical, molecular and/or cell biological procedures which are suitable for the preparation of human nucleic acid. Such procedures comprise paracentesis, biopsy, liquid biopsy, cell free DNA isolation kits, or the like. The human nucleic acid sample may be or be derived from all kinds of suitable sources, including, but not limited to, body fluids, mucosa, tissues, tissue extracts or cells or any combination thereof. The human nucleic acid sample may also be a control sample derived from all kinds of suitable sources. The human nucleic acid sample may e.g. comprise blood samples, blood plasma samples, urine samples, tumor samples, possibly including undesired artefacts caused by the fixation in the tissue handling procedure FFPE (formalin-fixed paraffin-embedded tissue or formaldehyde-fixed paraffin-embedded tissue).

The human nucleic acid sample may in particular comprise DNA, RNA and/or size fractionated total DNA or RNA. Providing DNA from a sample of interest may include one or more biochemical purification steps such as, e.g., centrifugation, lysis and/or fractionation steps, cell lysis by means of mechanical or chemical disruption steps including, but not limited to, multiple freezing and/or thawing cycles, salt treatment(s), phenol-chloroform extraction, sodium dodecyl sulfate (SDS) treatment and proteinase K digestion. Optionally, providing DNA from a sample of interest may further include the removal of large RNA, such as abundant ribosomal rRNA, by precipitating in the presence of polyethylene or salt, or the removal of interfering sodium dodecyl sulfate (SDS) by precipitation in the presence of salt, preferably in the presence of potassium chloride solution. Methods of purifying total DNA or RNA from a cell and/or a tissue are well known to a person skilled in the art and include, e.g., standard procedures such as the use of guanidinium thiocyanate—acidic phenol-chloroform extraction (e.g. TRIzol®, Invitrogen, USA). Equally preferred, however, is that DNA from the sample of interest is provided without any of the herein described biochemical precipitation and/or purification steps.

In the context of the present invention, the term “nucleic acid” generally refers to any kind of single stranded or double stranded oligonucleotide molecule composed of either deoxyribonucleotides or ribonucleotides or both, including genomic DNA, nuclear DNA, somatic DNA, germline DNA, synthetically designed and/or manufactured DNA, including, but not limited to, in vitro generated DNA derived from messenger RNA profiles, preferably in form of cDNA. The term “nucleic acid” generally means single stranded or double stranded oligonucleotide molecules of identical or similar length, i.e. composed of either an identical or similar number of nucleotides.

The human nucleic acid sample may comprise genomic sequences which may serve for evaluating, analyzing, aligning, indexing and/or profiling of specific mutations on genomic, transcriptional or post-transcriptional level. As such, a human nucleic acid sample according to the present invention may refer and include, but not be limited to, any kind of coding regions, non coding regions, exons, introns, chromosomal and/or intra chromosomal regions, promoter regions, enhancer regions, regions encoding small and/or long regulatory RNAs, regions of active transcription and/or non transcribed regions, transposons, regions of hot spot mutations, regions of frame-shift mutations etc. and alike.

The “group of human reference genomes” comprises at least two human reference genomes, preferably a plurality of human reference genomes. The sex and/or ancestry test in step b) allows for the selection of one or more of the best suited human reference genomes from the group of human reference genomes in step c). In the preferred case, the sex and/or ancestry test in step b) leads to an auto-classification of the sex and/or ancestry and allows for the selection of one PHREG from the group of human reference genomes for the subsequent alignment step d), but the selection of one or more additional PHREGs for the subsequent analysis is also possible.

Preferably, the sex and/or ancestry test in step b) is based on an ancestry- and/or sex-specific subset of sequence variants related to sex and/or ancestry extracted from a curated database. Preferably, these sequence variants are single nucleotide polymorphisms (SNP)s and/or single nucleotide variants (SNV)s. The subset of sequence variants used for the sex and/or ancestry test is also referred to as Population dependent Human Ancestry and Sex Patterns (PHASPs). Preferably this curated database comprises all known sequence variants of all populations. The PHASP dataset is an excerpt of the curated database. It is a much smaller data set than the PHREG dataset and is the most discriminating set for the classification. Techniques used to generate PHASPs are computational methods from machine learning including feature reduction where features are genotypes. These learnings may be compared and tested with standard classification results.

Preferably, the sex and/or ancestry test includes a preliminary alignment step to detect the individual sequence variation pattern of the sample, wherein the human nucleic acid sample is aligned to a single human reference genome, for example GRCh37 or GRCh38. This single human reference genome used for the test in step b) is not ancestry or sex specific. By comparing the sequence variant pattern of the sample with the PHASP dataset, the patient's ancestry and sex is determined.

According to one embodiment, the testing may comprise a sex test. According to another embodiment, the testing may comprise an ancestry test. According to still another embodiment, the testing may comprise a sex test and an ancestry test.

In one exemplary embodiment, the group of human reference genomes comprises both male and female reference genomes. If the sex test in step b) determines that the human nucleic acid sample is a male or a female reference genome, then in step c), the respective male or female reference genome or genomes will be selected as the respective PHREGs for the subsequent alignment step d).

As sex chromosomes contain homologous sequences, using a sex-adjusted reference genome (with chromosomes X and Y for males, and without chromosome Y for females) will prevent misalignment of reads. Therefore, using sex-specific reference genomes reduces subsequent false positive and false negative variant calls.

In another exemplary embodiment, the group of human reference genomes comprises a number of ancestry-specific reference genomes. The ancestry test in step b) determines the best one or ones out of the number of ancestry-specific reference genomes. Then in step c), the closest one or ones will be selected as the PHREG or PHREGs for the subsequent alignment step d).

Choosing an incorrect ancestry can lead to large amounts of false positive and false negative variant calls. Using ancestry-specific reference genomes effectively increases the number of correctly aligned reads and reduces the false positives and false negatives.

Likewise, a combination of a sex and ancestry test is decisive in case that the group of human reference genomes comprises ancestry-specific male reference genomes and ancestry-specific female reference genomes.

The term “testing” in step b) is to be understood as encompassing at least one genetic and/or genomic test of the human nucleic acid sample. Genetic and/or genomic testing is more reliable than any information derived from “self-reporting”. Self-reported and investigator-assigned ancestry typically relies on the subjective interpretation of a complex combination of both genetic and non-genetic information including behavior, cultural, and societal norms, skin color, and other influences. It is rarely the case that a study participant or patient will report his/her ethnicity without errors. Self-reported ethnicity errors may occur for various reasons; some people may not be fully aware of their true ancestry or only know recent ancestry (or their geographic origin) while others may identify with one ethnic group despite their admixed background ^{[Mersha & Abebe 2015]}. Literature confirms that self-declared ancestry and sex are often incorrect ^{[Ainsworth, 2015; Mersha & Abebe, 2015]}. In fact, Ainsworth even explains that 1 person in 100 is affected by a disorder of sex development, leading to a physical appearance that does not match the person's genome.

Advantageously, the method can be also used as an additional quality check to identify sample swaps based on sex and ancestry. Mismatches between self-declared and predicted sex and ancestry in sequencing runs can reveal e.g. specimen transposition and other lab processing errors.

The term “alignment” generally means a computational step wherein a sequenced sample is compared with and fitted to a reference sequence. To this end, one needs to find the corresponding part of that sequence for each read in the generated sequencing data. In other words, alignment or read mapping is the process of determining the most likely source within the genome sequence for the observed nucleic acid sequencing read. In typical embodiments, the reads will be NGS reads, but it shall be understood that reads from other sequencing technologies are also encompassed by the teaching of the present invention.

The aligned reads derived from the human nucleic acid sample may be displayed, stored, printed, sent via a communication network, or otherwise processed further. Further applications or uses of the aligned human nucleic acid sample may in particular comprise one or more of the following:

1) Local realignment around insertions and deletions (inDels)

The term “inDels” means insertions or deletions of base pairs in the genome, typically including small genetic variations from 1 to 10000 bp in length. Realignment around inDels improves subsequent data analysis, in particular subsequent variant calls.

2) Base quality score recalibration (BQSR)

The term “base quality score” describes per-base estimates of error expressing how confident the base call made by the sequencing instrument is. The score may e.g. be used for weighing the evidence of subsequent variant calls. BQSR allows for adjusting the quality scores by taking into account systematic technical errors due to the physics or the chemistry of how the sequencing was performed.

3) Machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies

4) Variant discovery and genotyping to find all potential variants; herein also referred to as variant calling

Variant discovery may include the discovery of SNPs/SNVs, InDels, CNVs and SVs (chromosomal translocation, inversion, duplication, large inDels).

5) Evolutionary analysis studies

Evolutionary analysis studies may comprise tools measuring nucleotide diversity, population divergence, linkage disequilibrium, and the frequency spectrum of mutations from one or more populations. Evolutionary analysis may generally comprise computational tools for calculating evolutionary sequence statistics. The computational tools may be adapted to perform analyses in sliding windows across chromosomes or scaffolds. The computational tools may e.g. produce a phylogenetic tree of the sample.

Such evolutionary analysis may be performed e.g. by “POPBAM” software, described e.g. in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767577/.

6) Testing for wildtype biomarkers

Furthermore, the aligned human genome sample may be tested for the presence of wildtype biomarkers, i.e. biomarkers that will not be detected during variant calling because they are contained within the PHREG. The computation step after the alignment may thus comprise a test for each known biomarker, the test indicating whether the biomarker is present in the aligned human genome sample, irrespective of what the information of the PHREG at this position is.

According to one embodiment, the method comprises the additional step of performing variant calling of the aligned human nucleic acid sample with respect to the selected PHREGs. Advantageously, the invention improves the accuracy of variant calling by introducing the initial sex and/or ancestry test to determine the correct PHREGs for usage in the subsequent alignment and variant calling steps.

The aligned human nucleic acid sample, more specifically, the aligned NGS reads derived from the human nucleic acid sample may thus be further processed by one or more so-called variant callers which are computational modules, comprising different variant calling algorithms detecting any variant type (e.g. SNVs, InDels, Copy number alterations, structural variants). Subsequent method steps may comprise variant interpretation. The results of the variant calling and/or of the variant interpretation may be displayed, stored, printed, sent via a communication network, or otherwise processed further. Advantageously, the method will allow the detection of previously undiscovered biomarkers (e.g., in the context of cancer or other diseases) through the removal of bias from the used reference genome. In particular, the method according to the present invention allows for the discrimination of a variety of gene mutations, including, but not limited to SNVs, Multi-Nucleotide Variants (MNVs), complex events and large structural variants, in particular hot spot mutations, frame-shift mutations, non-silent mutations, stop-codon mutations, nucleotide insertions, nucleotide deletions, copy number variations, copy number alterations and/or splice sites.

The donor of the human nucleic acid sample can be a patient, i.e. a person having a disease or being suspected of having a disease. The application of the method, however, shall not be understood to be limited to patients only.

Variant calling and interpretation may comprise the analysis of genomic sequences indicative for the presence or absence of a certain disease. Based on the variant interpretation, the patient may be classified into a first group including patients where a certain treatment is not indicated, and into a second group including patients where a certain treatment is indicated. The invention may thus advantageously be used as a part of a disease screening procedure, evaluating the presence or absence of a disease in a patient.

Additionally or alternatively, the method may comprise a step of retrieving an indication of a disease related to, or associated with the human nucleic acid sample. The indication of a disease may be e.g. retrieved from an electronic health record or manually be entered via an input means of a computing device by the patient him/herself or by the attending physician. The indication may be identified according to disease ontologies, for instance ICD-10, MeSH, or MedDRA. For certain classes of indications there may also be specialized ontologies that may offer advantages like more precise categorization of the indication. In oncology it may be beneficial to use ICD-O-3 and/or the TNM staging system.

Based on the results of the variant calling and interpretation, and taking into account the disease of the patient, the method may involve providing a therapy plan for the patient. In the present context, the therapy plan may in particular be a personalized therapy plan for the patient, wherein the personalized therapy plan comprises treatment options tailored to the patient's genetic data, in particular to his/her clinical, molecular, and/or genetic condition.

In order to identify promising treatments for a patient, the method may comprise checking whether any of the variants, e.g. mutations found in the patient, e.g. in a patient's tumor or in the patient's normal control tissue, are indicative of the patient's outcome under any treatment. The method may further include identifying all treatments associated with any of the found variants. The method may include scoring the identified treatments and ranking the identified treatments according to the score to provide a treatment option or treatment contraindication prioritization for the patient.

In the context of the present invention, the term “treatment” includes the administration of a therapeutically effective drug or a pharmaceutically active compound in form of a pharmaceutical composition which prevents, ameliorates or treats the symptoms accompanying with the indication. The term “treatment” also includes any kind of surgery, radiotherapy and/or chemotherapy or any combination thereof.

For both alternatives, i.e. in the context of a screening method or a personalized therapy plan, the present invention may provide the physician with improved diagnostic capabilities, e.g. allowing for improved treatment decisions, because the precision of the alignment and the variant calling are improved.

According to one embodiment, the alignment is performed against the PHREG on a majority allele level. The majority allele level uses unique nucleotide codes (A,C,G,T) within the PHREG to adjust the reference sequence to a population. The single nucleotide is chosen which is most frequently observed at the given locus in the population. In case of ties in the allele frequency, the allele present in the underlying reference sequence (e.g. GRCh37 or GRCh38) may be used.

According to another embodiment, the alignment is performed against the PHREG on a non-rare alleles level. The non-rare alleles level uses ambiguity nucleotide codes according to the established IUPAC nomenclature ^{[Cornish-Bowden, 1985]}, e.g “R” for “A or G”. The non-rare alleles level may encode up to two or three, preferably two, alleles of substantial frequency in the population. Substantial frequency can be defined as being more than or equal to 30%, 20%, 15%, 10%, 5%, 3%, 1% or 0.1%, in particular more than or equal to 5%. As more than one variant allele per genomic position is incorporated into the PHREG, a more precise read alignment can be expected. In one embodiment, only single-nucleotide variations (SNVs) are considered in the non-rare alleles level. In other embodiments, inDels and other structural variations are considered as well.

According to one embodiment, the variant calling is performed against the PHREG on a majority allele level. In some embodiments, the alignment may be performed on a non-rare alleles level and the variant calling may be performed on a majority allele level. Alternatively, the variant calling is performed on a non-rare alleles level.

According to an embodiment, the human reference genomes provided in step a) are published human reference genomes. Published human reference genomes may in particular comprise the builds of the HRG, specifically the builds of GRCh37 and GRCh38. Additionally or alternatively, published human reference genomes may comprise the QTRG. Additionally or alternatively, published human reference genomes may comprise genomes derived from the 1000 Genomes (1 kG) project. For the 1 kG project, the VCF files for all chromosomes from the most current release on the 1 kG FTP site ftp[://]ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ may be downloaded and used. If more datasets with more individuals and ethnicities become publically available (e.g. the 1000 Arab genome project to study the Emirati population ^{[Al-Ali, M. et al., 2018]}), these could also be used in the method of the present invention.

Additionally or alternatively, the human reference genomes provided in step a) are derived from the published human reference genomes. The term “derived from” may in particular encompass error correction and/or adjusting the human reference genomes to a majority allele encoding level or to a non-rare alleles level.

Error correction may be performed such that reference nucleotides that are observed in zero individuals of a given population are replaced by the corresponding majority nucleotide.

In an embodiment, step a) comprises adjusting the human reference genomes to an encoding level, the encoding level comprising either unique nucleotide codes or ambiguous nucleotide codes. The encoding level comprising unique nucleotide codes may in particular be used to define the PHREGs on a majority allele level.

The encoding level comprising ambiguous nucleotide codes may in particular be used to define the PHREGs on a non-rare alleles level.

In one embodiment, for the adjustment to the encoding levels single-nucleotide variations are considered. For each population (or super-population) all reported SNVs together with their allele frequencies are used. In other embodiments, inDels, CNVs and/or SVs are also considered.

According to an embodiment, four different levels of adjusting the reference sequence to a population are proposed, wherein two of these are confined to unique nucleotide codes (A,C,G,T) and another two utilize ambiguous nucleotide encoding according to the IUPAC nomenclature ^{[Cornish-Bowden, 1985]}, e.g. “R” for “A or G”. These PHREG encoding levels are defined as follows:

1. Maximally conservative error correction: reference nucleotides that are observed in zero individuals of the population are replaced by the corresponding majority nucleotide, e.g. by the corresponding majority 1 kG nucleotide.

2. Majority allele: choose the single nucleotide which is most frequently observed at the given locus in the population (in case of ties in the allele frequency, the allele present in the underlying reference sequence, e.g. GRCh37 or GRCh38, is used).

3. Non-rare alleles: encode up to two alleles of substantial frequency (e.g. 5%) in the population, using IUPAC codes as necessary.

4. Complete modelling of observed alleles: encode at each position all (up to four) alleles that are reported in at least one individual of the population.

The complete representation of 1 kG variants in Level 4 PHREGs is, however, paid for by a disproportionately large number of genome modifications that introduce ambiguity and thereby may substantially impede the seed finding by read mappers. Therefore, in one embodiment, Level 3 is used for alignment using a IUPAC ambiguity-aware alignment algorithm. Since the currently best-performing variant callers are not designed to handle ambiguity codes, Level 2 PHREGs are used for subsequent variant calling unless better performing IUPAC ambiguity-aware alignment algorithms are available.

Advantageously, the method thus allows for user-defined levels of adjustments of the PHREG to population genetic variation, depending on the population(s) in focus and depending on the downstream analysis.

According to an embodiment, the human reference genomes provided in step a) are PHREGs. Step a) thus may comprise e.g. downloading the PHREGs from a public source.

As defined above, PHREGs are in a first place understood as ancestry-specific reference genomes and/or sex-specific reference genomes. In one embodiment, the human reference genomes provided in step a) are already population-specific because they comprise meta data indicating their ancestry and/or sex. For example, at the time of filing the present application, the current phase 3 analysis of the 1 kG project contains 2,504 individuals from 26 populations and from 5 so-called super-populations, which are formed as unions of 4 to 7 populations each. The 26 populations from the 1 kG study phase 3, and their associated 5 superpopulations (AFR, African; AMR, Ad Mixed American; EAS, East Asian; EUR, European; SAS, South Asian) can be found on http://www.internationalgenome.org/faq/which-populations-are-part-your-study.

In one embodiment, the data from the 1 kG project is used to build optimized population-specific human reference genomes for each of the 31 (super-) populations, and an additional super-population encompassing all other populations.

In case the human reference genomes provided in step a) are PHREGs, the public meta-data of the PHREG may as well be provided, e.g. via download from a public source. The meta-data may serve as a quality control for the method. If the meta-data and the sex- and ancestry classifier data coincide, then the quality control may be considered as successful. If not, the software may produce a warning or an alert which is displayed to the user, and, additionally or alternatively, the software may stop the procedure e.g. before the alignment step.

According to an embodiment, the sex test comprises at least one of the following: testing at least one position in a sex-specific gene on chromosome X and/or on chromosome Y; leveraging alignment differences of human genome samples on chromosome X and/or chromosome Y; cytogenetic tests; FISH analysis; CGH analysis, or any other experimental method allowing the determination of a human nucleic acid sample's sex, directly or indirectly.

The sex test may thus also be a result or a side product of a FISH analysis (fluorescence in situ hybridization analysis) ^{[Gall J. G. 1969]} of the human nucleic acid sample. The sex test may thus also be a result or a side product of a CGH analysis (comparative genomic hybridization) ^{[KallioniemiA. et al. 1992]} of the human nucleic acid sample.

The sex test enables efficient and reliable distinction of a male or female human nucleic acid sample.

As individuals from an ancestry or ethnicity share many SNPs that set them apart from other ancestries or ethnicities, the best-fitting PHREG for read alignment and variant calling can be identified by examining a range of ancestry-determining SNPs. The PHREGs may thus be selected from the group of human reference genomes on the basis of the results of an ancestry test.

Different experimental setups can be used in an upstream genomic analysis pipeline step to ascertain an individual's ancestry before proceeding with the alignment, to determine the best matching PHREG reference and to avoid errors.

1) The ancestry test may be based on a machine learning algorithm used on a human nucleic acid sample, or on another classification scheme that leverages ancestry-specific variants. The ancestry test method may in particular be based on machine learning that leverages the genotypes of exonic positions, e.g. more than 100, 500, 1000, 2000 or preferably more than 5000 exonic positions.

2) The determination of relevant genotypes can be based on NGS data or on an alternative experimental approach, for example a SNP array, as it is done in forensics research ^{[Fondevila et al. 2013]} Here, the use of non-coding SNPs can help determining ethnicity.

3) The same non-coding SNPs (plus flanking regions) as tested in the forensic SNP array from alternative 2) could be added to existing targeted NGS panels to determine relevant genotypes.

In particular, the ancestry test may comprise using the genotype of at least one genomic position.

In one particular embodiment, the ancestry test comprises testing at least one gene selected from the enclosed sequence protocol. The 249 genes from the enclosed sequence protocol were shown to yield exact results.

Additionally or alternatively, the ancestry test may comprise the testing of SNP arrays and/or SNP chips and/or testing of markers from Sanger sequencing or mass spectroscopy, or any other experimental method designed to determine relevant genotypes.

In one particular embodiment, the ancestry test comprises testing at least one gene selected from the group of genes consisting of ABL2, ATP1A3, CIC, CYP2C8, CYP2C9, EPHA3, EPHA7, ERBB3, ERG, ETV1, F2, FAS, HFE, IL11RA, IL2RA, ITGB6, KIF11, KIT, KLK3, LRP6, MDM4, NAT2, NTRK2, PDGFB, PIK3R1, PLA2G3, PLAU, PRKCB, RICTOR, SLC7A11, STAT3, T, TSC1, VCAM1, VDR, VEGFB, ACVRL1, AXL, CA9, CALCR, CASP9, ENG, EPHB1, ERBB4, ESR1, FGFR2, HPSE, HSP90AA1, ITK, MRE11A, PLK1, PTPRC, SERPINE1, SMC4, TERT, TLR3, WISP3, WT1, XRCC1, ANGPT2, ARID2, BARD1, CBR3, CDH2, CYP1B1, DDR2, DNMT3A, EPCAM, ERCC2, FANCG, FANCL, GSTP1, IRS2, ITGB1, JAK3, LHCGR, MSH6, NCF2, RNF43, SLC5A5, TMPRSS2, TNFRSF8, AKT1, CD248, CD4, ESR2, EZH2, IGF1R, ITGAV, ITGB2, KLHL6, MAP3K1, MET, MLL, MTHFR, NFKB1, NUP93, PARP8, RB1, RPE65, TSHR, ABL1, BLM, CYP19A1, DPP4, EPHA6, ERBB2, EWSR1, FOXP4, ITGAM, KDM5A, LPA, LTK, MLH1, PBRM1, PHLPP2, SF3B1, TNFRSF10A, ABCG2, ACPP, ADAM15, DPYD, EPHA5, EPHB6, FOLH1, KDR, MSH3, MST1R, NTRK1, ROCK2, SLC6A2, TET2, TGM2, TH, ABCB1, CD22, CD40, CD44, CDH20, CYP11B2, ERCC5, GPR124, IL7R, ITGB3, ITGB5, NCL, NOD2, NR4A1, PGR, PLCG1, PPP2R1A, PRAME, PTCH2, RET, SETD2, XPC, ASXL1, EPHB4, PLA2G6, SYK, TET1, EP300, FLT1, ITGA1, LOXL2, PDGFRB, PIK3CD, SSTR5, TEC, APC, ATR, CLU, CREBBP, CYP2D6, EML4, MMP2, PARP2, PDGFRA, TRPM8, CSF1R, DOT1L, FGFR3, FGFR4, GLP2R, IKBKE, JAK1, NOTCH2, SPEN, SPG7, BRCA1, CYP11B1, GNAS, ITGA5, LTF, NRP2, PTK2B, TNKS, ABCC1, CEACAM5, CYP4B1, EGFR, FLT3, INSR, PTCH1, SMARCA4, ZNF217, BCR, EEF2, SELP, SLCO1B1, ABCC2, FLT4, MTR, IL4R, MTOR, RPTOR, TEK, ATM, CARD11, FANCD2, MEFV, NF1, TP73, BRCA2, CD109, PTPRD, ABCC6, IGF2R, P2RX7, ROS1, ACE, PARP1, PRKDC, CENPE, TSC2, ALK, NOTCH1, TNC, NOTCH3, POLE, MLL2, MYH11, POLD1, GRIN3B, F5, FANCA, LRP1B, LRP2, VWF.

In a more particular embodiment, the ancestry test comprises testing at least one of the genomic coordinates selected from the group of genomic coordinates listed in Appendix 1. Appendix 1 describes the GRCh37-based genomic coordinates of the features used for the ancestry classifier. The first 3 columns are formatted according to the BED file standard (https[://]www.ensembl.org/info/website/upload/bed.html) and (from the left to the right) correspond to chromosome, 0-based start of the feature, and 0-based end of the feature (i.e., the first position after the end of the feature). Column 4 shows the bases that are relevant to the classifier at this position, and column 5 the corresponding gene name.

Gene names were approved by the HUGO Gene Nomenclature Committee (HGNC, https://www.genenames.org/). HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. The gene names used in the present application were retrieved in August 2013.

In another particular embodiment, the ancestry test comprises at least one of the SNPs listed in Appendix 2 ^{[Fondevila et al. 2013]} Appendix 2 indicates the number of the chromosome on which an SNP is positioned (left column), the exact chromosomal position (middle column) as well as the corresponding rs number (right column). The rs number is an accession number assigned by the NCBI (National Center for Biotechnology Information) in its SNP database (dbSNP, https://www.ncbi.nlm.nih.gov/projects/SNP/) and it is widely used to refer to specific SNPs across genomic databases. When researchers identify a SNP, they send a report (which includes the sequence immediately surrounding the SNP) to the dbSNP database. If overlapping reports are sent in, they are merged into the same, non-redundant Reference SNP cluster, which is assigned a unique rsid. More information is available in the following url http[://]www.ncbi.nlm.nih.gov/sites/books/NBK44406/.

Such an ancestry test may comprise genetic and/or genomic tests enabling a distinction of ancestry categories. Such ancestry categories may be defined as AFR, AMR, EAS, EUR, SAS, in accordance with the 1 kG project. The method is, however, not limited to the 1 kG project data, e.g. in case that more comprehensive datasets with more individuals/ethnicities were/became available, these could be used for the same purpose alternatively.

According to an embodiment, the human nucleic acid sample comprises a set of reads issued from a next-generation sequencing procedure, and the alignment comprises a step of mapping the reads to the selected PHREGs. Additionally or alternatively, the human nucleic acid sample comprises a set of reads issued from a targeted sequencing procedure, e.g. from panel sequencing.

Advantageously, the method can be seamlessly integrated into any existing NGS analysis workflow which is based on read mapping against a HRG.

Aligning the human nucleic acid sample to the selected PHREGs by mapping the reads to the selected PHREGs may presuppose the preparation of sequencing libraries by random fragmentation of the DNA or cDNA sample, followed by 5′- and 3′-adapter ligation in advance. In some embodiments, the fragmentation and ligation reaction is combined into a single step, followed by PCR amplification of the adapter-ligated fragments.

Aligning the human nucleic acid sample to the selected PHREGs by mapping the reads to the selected PHREGs may presuppose the sequencing of this set of DNA fragments, resulting in reads of approximately between 28 base pairs (bp) and 1000 base pairs (bp) in lengths ^{[Goodwin S. et al. 2016]}. The set encompasses enough reads to reach a pre-determined target region coverage suitable for the experimental questions asked (typically between a few x and several 1000x).

In one embodiment, the next-generation sequencing procedure involves whole exome sequencing. In another embodiment, the next-generation sequencing procedure involves whole genome sequencing. The term “whole exome sequencing” generally means a technique for sequencing all the protein-coding genes in a genome (known as the exome). It consists of first selecting only the subset of DNA that encodes proteins (known as exons) and then sequencing this DNA using any high-throughput DNA sequencing technology. Humans have about 180,000 exons, constituting about 1.5% of the human genome, or approximately million base pairs. In particular, the exome sequencing may be carried out by next-generation sequencing. “Whole genome sequencing” (also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria.

In accordance with another aspect of the invention, a computer system for gene analysis of a human genome sample comprises:

• • a) a first module comprising computer instructions for providing a group of human reference genomes;
  • b) a second module for testing of a human nucleic acid sample for sex and/or ancestry;
  • c) a third module comprising computer instructions for selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis of the results of the sex and/or ancestry test; and
  • d) a fourth module comprising computer instructions for aligning the human nucleic acid sample to the determined PHREGs

In particular, the computer system may be adapted for, or may be configured for performing any one of the methods disclosed above. Therefore, it is understood that features which have been described in the context of the methods are disclosed for the computer system, and, vice versa, that features which will be described in the context of the computer system are disclosed for the methods as well.

The modules may be software modules, software routines or software subroutines stored on a machine-readable storage medium such as a permanent or rewriteable storage means, or on a storage medium assigned to a computer means, for instance a mobile storage medium such as CD-ROM, DVD, Blu-ray disc, sticks or memory cards. Additionally or alternatively, the modules may be provided on a computer means such as a server or a cloud server for download, for example via a data network such as the internet or via a communication line such as a telephone line or a wireless line.

Any of the modules disclosed herein may be functional units which are not necessarily physically separated from each other. Several units of the modules may be realized in the form of one single physical unit, for instance if several functions are implemented in a software package.

The computer modules disclosed herein may not necessarily be part of an integral system, but may be distributed over several individual systems interacting with each other over a communication network.

According to one embodiment, the second module for testing of a human nucleic acid sample for sex and/or ancestry is a computer module comprising computer instructions. Additionally or alternatively, the second module may comprise a wet lab experiment, e.g. an experiment performing a FISH test. The results of the FISH test may be electronically or visually analyzed for determining the sex of the sample.

In accordance with yet another aspect of the invention, a computer program comprises instructions which, when the program is executed by a computer, cause the computer to carry out the steps a), b), c) and d) of any one of the methods described above.

In accordance with still another aspect of the invention, a computer-readable storage medium comprises instructions which, when executed by a computer, cause the computer to carry out the steps a), b), c) and d) of any one of the methods described above.

As already discussed above, the method of the present invention are especially suitable for identifying alterations in the genome of a patient which are indicative for a given disease or which are indicative for the susceptibility of the patient for a given treatment.

In this context, the term “disease” includes any disease which is characterized by one or more genomic alterations. This includes cancer, an autoimmune disease, a cardiovascular disease, and any inherited disease. The patient may be of any species but is preferably a mammal, more preferably a human.

Depending on the individual disease and treatment, the person skilled in the art will be able to select the individual treatment mode which is beneficial for the patient.

Consequently, in a further aspect of the invention, the invention relates to a method for diagnosing a disease in a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient, and

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein, thereby determining the disease status of the patient.

The identification of a disease indication may be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

In the context of this aspect of the invention, the term “disease status” means in one embodiment that the disease of the patient is confirmed. In a further embodiment, this term means that the disease is diagnosed more accurately, i.e. that the individual subtype of the disease is determined.

The invention further relates to a method for treating a disease in a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient, and

performing genomic and/or genetic analysis of the nucleic acid sample according to the claimed method, thereby determining the disease status of the patient, and treating the patient.

In a further aspect of the invention, the invention relates to a method for determining whether a patient is susceptible to a treatment by a given drug comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient,

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein,

retrieving possible treatments for the disease indication of the patient,

performing variant calling and interpretation, and

classification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patient.

By this method, it is possible to determine which treatment is available or advantageous for the patient. For example, it is possible to determine whether the patient is susceptible to a given treatment or whether a given treatment is expected to have only acceptable side effects.

The identification of a disease indication may again be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

The possible treatments for the disease indication of the patient may be retrieved by any method known in the art, e.g. from a data base.

The invention also relates to a method of treating a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient,

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein,

retrieving possible treatments for the disease indication of the patient,

performing variant calling and interpretation,

classification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patient,

selecting one of the indicated treatments, and

treating of the patient according to the selected treatment.

The identification of a disease indication may again be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

The possible treatments for the disease indication of the patient may again be retrieved by any method known in the art, eg from a data base.

BRIEF DESCRIPTION OF THE FIGURES

The foregoing and other objects, aspects, features, and advantages of the disclosure will become more apparent and better understood by referring to the following description taken in conjunction with the accompanying drawings, in which:

FIG. 1 is a flow diagram depicting a method for genomic and/or genetic analysis of a human nucleic acid sample in accordance with the present invention;

FIG. 2 is a flow diagram depicting methods for data analysis in accordance with the present invention;

FIG. 3 is a representation of read mapping steps;

FIG. 4 is a flow diagram depicting a method for genomic and/or genetic analysis of a human nucleic acid sample in accordance with the present invention;

FIG. 5 is a diagram representing the distribution of chosen features for the sex classifier by class computed on the MH Panel data; and

FIG. 6 are boxplots of memory usage and runtime of the two Ansextry classifiers (classifiers for sex and ancestry) and EthSEQ.

DETAILED DESCRIPTION OF THE FIGURES

FIG. 1 illustrates the general workflow for genomic and/or genetic analysis of a human nucleic acid sample, which comprises the process of extraction of the human nucleic acid sample, the preparation of a sequencing library, the sequencing and the subsequent data analysis. In the context of the present invention, the processes of extraction of the human nucleic acid sample, the preparation of a sequencing library and the sequencing may involve well-known standard processes and will not be explained in more detail. The inventive data analysis part is shown in FIG. 2 in more detail.

FIG. 2 shows the data analysis step of FIG. 1 comprising a first sex and ancestry test step, followed by an alignment (or read mapping) step, a variant calling step and an annotation step. The input file for the read mapping computational module is raw sequence data, e.g., in the form of a FASTQ file. The output file of the read mapping computational module is, e.g., a BAM file, being the input file for the variant calling computational module. The output file of the variant calling computational module is, e.g., a VCF file. The subsequent annotating computational module may annotate the data from the VCF file and export it in the required format, such as PDF, HTML, or the like. The file formats are merely exemplary and may be different, e.g. instead of BAM, there may be SAM or CRAM files, and the like. The data analysis pipeline in FIG. 2 may also comprise computer modules which transform the input or output files from one file format into another file format.

FIG. 2 also compares the prior art scenario with the scenario of the present invention. Prior art methods (referred to under “A” in FIG. 2) do not provide for a sex and ancestry test. Alignment and variant calling is thus performed against the standard HRG. The method according to the present invention (referred to under “B” in FIG. 2) provides a sex and ancestry test, which allows for the selection of one or more determined PHREGs. Subsequent alignment and variant calling is then performed against the determined PHREGs.

FIG. 3 is a schematic representation of an exemplary read mapping step. In the example, NGS reads carry an ancestry-specific SNP “A”. Ancestry-specific SNP “A” is located within the close vicinity of a previously undiscovered biomarker variant “G”. The vicinity can be up to the read length.

During alignment, the NGS reads will produce 2 mismatches when they are compared against the standard HRG, namely the ancestry-specific SNP and the biomarker variant. During alignment, the NGS reads will, however, produce only one mismatch, namely the biomarker variant, when they are compared against the corresponding PHREG, as the PHREG has been modified at the ancestry-specific position, such that the PHREG is identical to the ancestry-specific SNP.

The alignment algorithm uses a scoring system that involves penalties for every mismatch and/or gap between a sequenced read and the chosen reference genome. Reads are then aligned to the best-scoring position, or may not be aligned at all due to a low overall score, or too many genomic positions with equal alignment score. Because of mismatch penalties in the alignment algorithm, reads are less likely to be aligned against the HRG than against the PHREG, especially if further variants are within read length. The reads will thus be discarded or, in the worst case, even be aligned in a wrong position of the HRG.

Thus, PHREGs have the effect that reads originating from regions of ancestry-specific variation can be rescued, especially if they carry additional variants (e.g. disease causing variants) besides the ancestry-specific variation. This allows the detection of previously undiscovered biomarkers.

FIG. 4 shows a flow chart depicting a method for genomic and/or genetic analysis of a human nucleic acid sample according to the present invention.

In a first step, a group of human reference genomes is provided to a system comprising a processing unit. To this end, a first computer module of the system may download reference genomes from a remote facility, such as an internet database. The processing unit can be any programmable computer means which substantially includes at least a processor with an internal memory such as RAM (Random Access Memory), which allows for storing and executing instructions.

The processing unit has access to a non-volatile storage means in which data sets and computer files may be stored, e.g. human reference genomes, as well as clinical data and the genetic profiles of patients. The system has access to a communication network such as LAN or the internet.

In a second step, a computer module of the system adjusts the human reference genomes to an encoding level, preferably set by a user of the system. The encoding level may comprise unique nucleotide codes or ambiguous nucleotide codes. In some embodiments, four different levels of adjusting the human reference genomes to a population are proposed, wherein two of these are confined to unique nucleotide codes (A,C,G,T) and another two utilize ambiguous nucleotide encoding according to the IUPAC nomenclature, in particular maximally conservative error correction, majority allele level, non-rare alleles level and complete modelling of all observed alleles.

In a third step, a human nucleic acid sample of a patient is provided. To this end, another computer module of the system may download the raw sequence data, e.g. in the form of a FASTQ file, from a sequencing laboratory which performs the sequencing of a sample of interest on a remote platform. In an alternative embodiment, the sequencing is performed locally and the results are internally transferred. In the context of the third step, the system may also receive further clinical data of the patient from further input sources, e.g. the information about a disease the patient suffers from, information about current treatments, or the like. The clinical patient data may e.g. be directly received from the patient, e.g. may be typed on a keyboard or may be deduced from a free text typed on a keyboard, or may also be received from a multiple-choice element in a GUI. The clinical patient data may also be retrieved from an electronic health record (EHR) or from electronic medical record (EMR), possibly on a chip-card or in a database retrievable over a communication network.

In a fourth step, the human nucleic acid sample is tested for sex and/or ancestry. Again, the tests may be performed locally, or another computer module of the system may retrieve the results of the tests from an external service provider via a communication network. The sex and/or ancestry test may be performed by a second computation module or another wet lab experiment.

In a fifth step, one or more PHREGs are selected from the group of human reference genomes on the basis on the results of the sex and/or ancestry test in step. The selection may be performed by a third computation module.

In a sixth step, the human nucleic acid sample is aligned to the selected PHREGs. The alignment comprises mapping the set of reads issued from an NGS procedure to the selected PHREGs. The alignment may be performed by a fourth computation module, and the output file may be a BAM file.

In a seventh step, variant calling of the aligned human nucleic acid sample is performed with respect to the selected PHREGs. Before the variant calling takes place, a computer module of the system may re-adjust the human reference genomes to an encoding level, preferably set by a user of the system. The encoding level may comprise unique nucleotide codes or ambiguous nucleotide codes and be different from the encoding level used at the alignment step. Variants may be identified using best suited state-of-the-art algorithms. The variant calling may be performed by a fifth computation module, and the output may comprise sequence data in the form of variants with respect to the PHREG in variant call format (VCF file).

In an eighth step, variant interpretation is performed. The system may thus comprise a further post-processing computation module adapted for performing an analysis of the identified variants. In one embodiment, the post-processing module may analyze a set of genes and/or variants indicative for the presence or absence of a disease in the patient. Additionally or alternatively, the post-processing module may determine a set of treatments for the disease of the patient, taking the further clinical patient data into account, and may determine the best fitted personal treatment for the patient based on the patient's genetic data, in particular based on the identified genetic variants. In yet another embodiment, the post-processing module may perform statistics and determine mutational load, nucleotide substitution rates and hotspot mutations from the identified variations.

The variants found can also be used as an input for classifier predicting treatment efficacy or treatment safety or for classifier for diagnostic and/or therapeutic purposes.

In a ninth step, diagnostic and/or therapeutic implications may be generated and provided. To this end, the system may include an output interface in functional connection with any one of the third, fourth, fifth and the post-processing module, such that their results can be outputted. The output interface may be coupled to any display means or printers such that information calculated by the processing unit may be presented. Furthermore, there can be links to communication systems for an intranet and/or the internet such as a program for the sending and receiving of e-mails realized via an output interface.

FIG. 5 shows a diagram representing the distribution of chosen features for the sex classifier by class (F: female; M: male), computed on the MH Panel data. Colored vertical lines represent the class median. Top: chrX/chrY aligned read ratio; middle: for 500 common SNP positions on chrX, fraction of the major allele frequencies in bin 0.8-1.0; bottom: percentage of properly paired reads on chrY. FIG. 5 should be viewed in the context of the example described below.

FIG. 6 shows boxplots of memory usage (top, in GB) and runtime (bottom, in minutes) of the two Ansextry classifiers and EthSEQ on the 300 TCGA whole-exome samples. FIG. 6 should be viewed in the context of the example described below.

Example 1

AnSextry, a machine-learning based tool that derives sex and ancestry of a sample using read alignments from whole-exome sequencing data is presented. Self-declaration of both traits is known to be unreliable, and AnSextry predictions are useful both in the context of sample-swap detection and for unbiased genomic variant interpretation, especially in large cohort studies. A benchmark of AnSextry on over 1,300 samples showed high precision and low time and memory requirements.

1 INTRODUCTION

With the sharp drop in cost observed over the last decade, next-generation sequencing of large cohorts is becoming commonplace ^{[Cancer Genome Atlas Research Network et al., 2013; Rand et al., 2016]}, and whole-exome approaches play a major role in large studies, especially in the area of precision medicine or the comprehensive characterization of disease. In this context, reliable knowledge of a sample's ancestry and sex comes with multiple benefits. First, it can be used as an easy quality control to help identifying sample swaps arising from the complex protocols and manual work involved in sample processing. Second, ancestry is crucial for the interpretation of variant impact, to circumvent the strong European bias present in most genomic studies and in the human reference genome, and to improve clinical care for people with diverse ancestries ^{[Petrovski et al., 2016; Mersha et al., 2015; Fakhro et al., 2016]}. Finally, ancestry is widely used in genetic association studies to avoid false associations with disease due to population stratification ^{[Wu et al., 2011]}. Self-declaration of sex and ancestry is often unreliable ^{[Mersha et al., 2015; Ainsworth, 2015]}, calling for an identification using genomic information.

AnSextry, a machine-learning method based on logistic regression, was developed to quickly and reliably characterize sex and ancestry from whole-exome sequencing paired-end read alignments. The algorithm relies on standard file formats and can be readily integrated in an existing next-generation sequencing analysis workflow. It provides a ready-to-use model and only requires a simple BAM file as an input. In addition, its low memory requirements allow it to be run on a desktop computer. A benchmark against EthSEQ ^{[Romanel et al., 2017]}, the only other whole-exome, BAM-file-based ancestry inference tool known, shows that AnSextry compares favorably in terms of precision, runtime and memory usage. No other published method for sex prediction is known to date.

2 METHODS

2.1 Algorithm

A set of two classifiers was prepared, which infer the most probable sex and ancestry of an individual, based on whole-exome sequencing paired-end read alignments. This tool leveraged differences in read mapping and individual genotypes for its predictions.

The sex and the ancestry classifier were based on logistic regression using Python and the scikit-learn machine learning library. Features for both were derived from an input BAM file. Paired-end reads were aligned with BWA 0.7.15 with default settings for alignment and without post-processing steps like local realignment or duplicate removal. The GRCh37 reference genome was used without the non-chromosomal supercontigs and with masked pseudo-autosomal regions PAR1 and PAR2 to avoid alignment distortions on chromosomes X and Y. In the context of the present invention, the term “supercontigs” is generally to be understood as an ordered set of contigs, i.e. contiguous lengths of genomic sequence in which the order of bases is known to a high confidence level.

The sex classifier worked with two-class logistic regression using L1-regularization and returned a probability for each class. 5-fold cross-validation was used to determine a suitable regularization strength. The model yielding the highest area under the precision-recall curve for the training data was chosen as best model and evaluated on test data sets.

The ancestry classifier was based on multinomial logistic regression using L2-regularization and Principal Component Analysis, and returned a probability for each of the 5 continental ancestries defined in the 1000 Genomes Project: African (AFR), Ad Mixed American (AMR), East Asian (EAS), European (EUR), South Asian (SAS) (The 1000 Genomes Project Consortium et al., 2015). 5-fold cross-validation was used to determine suitable parameters. The model yielding the highest F1 score for the training data was chosen as best model and evaluated on test data sets.

2.2 Features

Features for the sex classifier were based on alignment differences between chromosome X and Y (FIG. 5). The chrX to chrY reads ratio as well as the percentage of properly paired reads on chrY were used. In addition, the major allele frequencies at 500 common exonic SNP positions on chrX were compounded. To avoid population bias, SNPs frequent across major ancestries were chosen.

For the ancestry classifier, the genotypes of all autosomal SNPs with a genomic position within the intersection of target regions of common Agilent All Exon kits (V5, V6, V6+COSMIC) and the Molecular Health Pan-Cancer gene panel (target size 2.9 Mbp) were determined from the 1000 Genomes data described in section 2.3. Feature selection was used to retain meaningful SNPs showing variance across ancestries, resulting in 10,000 genotypes corresponding to 5,040 genomic positions used as features for the classifier. A corresponding BED file can be found in Appendix 1 and could be used to determine overlap with any targeted sequencing kit.

2.3 Data

In order to obtain data from diverse ancestries, genotype data from 1735 individuals from the 1000 Genomes Project phase 3 was used to train and test the ancestry classifier. Continental ancestries (AFR, AMR, EAS, EUR, SAS) were used for classification and individuals were randomly chosen to achieve balanced classes. 694 individuals were part of the test set.

Primary whole-exome control data from 300 individuals with self-reported race and sex was downloaded from TCGA (cancergenome.nih.gov) as a test set, corresponding to 3 cancer types (urothelial bladder carcinoma, lung adenocarcinoma/squamous cell lung cancer, gastric adenocarcinoma). All samples were sequenced using the Agilent SureSelect Human All Exon 50 Mb kit. Records were chosen randomly to achieve balanced class sizes corresponding to TCGA categories: 150 male and 150 female individuals, as well as 100 white, 100 asian, and 100 black or African American individuals.

Targeted sequencing data from 988 cancer patients with self-reported sex, sequenced using the Molecular Health Pan-Cancer gene panel was used to train and test the sex classifier. Individuals were chosen randomly to achieve female/male class balance. 396 cases were randomly chosen as test data for the sex classifier. The 300 TCGA cases described above were used as an additional test set.

3 RESULTS

3.1 Sex classifier

The sex classifier was trained using 592 datasets sequenced with the Molecular Health Pan-Cancer gene panel. Paired-end reads were aligned and features computed as described in the Methods section. After tuning the method with cross-validation, performance was evaluated on two test datasets: 396 individuals sequenced with the abovementioned gene panel, and 300 TCGA individuals with whole-exome data available.

On the panel test data, the sex classifier reached an average precision of 97.5%, with 10 individuals (5 male, 5 female) being misclassified (see Table 1). Misclassification was not associated with lower coverage.

TABLE 1
Details on individuals sequenced with MH Panel where predicted sex
did not match self-declared sex. Median coverage over all samples
used was 2116x. The mean coverage of all misclassified samples
was either close or above this median, showing that misprediction
did not seem to be linked to lower-than-median coverage.
		Predicted probability for	Mean coverage (with
Sex	Predicted sex	true sex [%]	duplicates)
F	M	39.0	2579
F	M	15.3	2099
F	M	33.8	1656
F	M	17.1	1787
F	M	0.8	1797
M	F	0.0	6016
M	F	28.0	2401
M	F	0.3	3603
M	F	0.0	1606
M	F	0.0	1705

Since disorders of sex development are thought to occur with a frequency of 1% in the general population ^{[Ainsworth, 2015]}, it is possible that some of the misclassified cases were actually correctly classified, but had incorrect self-declared sex.

On the TCGA test data, the sex classifier reached a precision of 100%. All 300 individuals were correctly classified. In terms of runtime and memory usage, sex prediction took less than a minute in all cases with an average memory usage of 526 MB (FIG. 6).

3.2 Ancestry classifier

The ancestry classifier was trained on 1041 datasets from the 1000 Genomes Project. Individual genotypes were used as features, as described in 2.2. The best-performing model was evaluated on two test datasets: a remaining 694 individuals from the 1000 Genomes Project, as well as 300 TCGA individuals with sequenced whole-exomes.

The ancestry classifier reached a high average precision of 99% on the 1000 Genomes test data, performing best for Asian ancestries (100% precision both for South and East Asian), followed by African and South American ancestry (99% precision), and European ancestry (98%). In total, only 5 individuals out of 694 were misclassified.

On the 300 TCGA exome test datasets, the ancestry classifier reached a slightly lower precision of 96.33%, with a total of 11 individuals misclassified. These results were compared to EthSEQ ^{[Romanel et al., 2017]}, which is currently the only other ancestry prediction method known that provides a suitable pre-computed model and is designed to work out of the box on single whole-exome BAM files. Results were highly concordant between the two methods, however, the precision reached by EthSEQ was a bit lower (94%) with a total of 18 individuals misclassified. In addition, runtime and memory required by EthSEQ were much higher: while the ancestry classifier had an average runtime of 28 seconds with 540 MB average memory usage, EthSEQ, even with the use of multithreading (4 cores), took 4.8 minutes and 14.7 GB on average (FIG. 6).

As an important observation, the concordance between the two algorithms was also high for misclassified datasets: 10 out of 11 individuals whose ancestry prediction did not match the race provided by TCGA were also differently classified by EthSEQ, and in 8 out of 10 cases, both methods predicted the same ancestry. This suggests that at least a part of these individuals may have been wrongly categorized by TCGA, whose race information is based on self-declaration. 6 out of the 10 concordant cases were predicted as AFR or AMR, which is in accordance with Mersha et al. who claim that errors in self-declaration are most prevalent in African American and Latino populations. Table 2 shows misclassified individuals.

TABLE 2
Details on TCGA individuals where predicted ancestry (either by Ansextry, EthSEQ, or
both) did not match TCGA self-declared race. TCGA race categories include “black
or african american” (black/afr.am.), “white”, and “asian”. Unmarked
rows corresponded to samples where neither Ansextry nor EthSEQ match TCGA race; rows
marked with “*” were samples where only EthSEQ prediction did not match TCGA;
and samples marked with “!” where only Ansextry prediction did not match
TCGA. Genotypes were imputed from reference for Ansextry prediction when the corresponding
locus had insufficient coverage. The median coverage across all samples was 91x, showing
that most mispredicted samples had a median or above-median coverage, therefore, misprediction
did not seem to be linked to lower-than-median coverage. Also, the median number of
imputed genotypes for Ansextry classification across all samples was 390, which was
close to the median of mispredicted Ansextry samples (393). Number of imputed genotypes
across all 300 TCGA samples varied between 227 (min) and 690 (max), showing that 10-
15% imputed genotypes did not seem to have a negative impact on Ansextry prediction.
TCGA
self-
declared	Ansextry	EthSEQ
race	prediction	prediction	Ansextry detailed prediction [%]
black/afr.	AMR	AMR	AFR(0.21)|AMR(90.53)|EAS(0.04)|EUR(7.75)|SAS(1.48)
am.
white	AFR	AFR	AFR(99.94)|AMR(0.06)|EAS(0.0)|EUR(0.0)|SAS(0.0)
black/afr.	EUR	AMR	AFR(0.02)|AMR(17.04)|EAS(0.0)|EUR(82.76)|SAS(0.17)
am.
black/afr.	AFR	AMR	AFR(68.03)|AMR(21.63)|EAS(0.2)|EUR(9.41)|SAS(0.73)
am.
white	AMR	EUR	AFR(0.0)|AMR(54.79)|EAS(0.0)|EUR(45.1)|SAS(0.1)
white	AMR	AMR	AFR(0.01)|AMR(98.88)|EAS(0.01)|EUR(1.01)|SAS(0.08)
white	AFR	AFR	AFR(99.99)|AMR(0.0)|EAS(0.0)|EUR(0.0)|SAS(0.0)
white	AMR	AMR	AFR(0.01)|AMR(97.87)|EAS(0.11)|EUR(1.73)|SAS(0.27)
white	EUR	AMR	AFR(0.0)|AMR(0.84)|EAS(0.01)|EUR(98.92)|SAS(0.22)
white	EUR	AMR	AFR(0.0)|AMR(2.1)|EAS(0.0)|EUR(97.73)|SAS(0.15)
white	EUR	AMR	AFR(0.03)|AMR(31.14)|EAS(0.09)|EUR(65.73)|SAS(3.01)
white	EUR	AMR	AFR(0.01)|AMR(16.3)|EAS(0.01)|EUR(83.36)|SAS(0.33)
white	EUR	AMR	AFR(0.0)|AMR(0.44)|EAS(0.0)|EUR(99.38)|SAS(0.17)
asian	EUR	EUR	AFR(0.01)|AMR(3.12)|EAS(0.03)|EUR(95.6)|SAS(1.24)
black/afr.	EUR	AMR	AFR(28.14)|AMR(30.99)|EAS(0.36)|EUR(40.32)|SAS(0.18)
am.
black/afr.	EUR	EUR	AFR(0.0)|AMR(0.01)|EAS(0.0)|EUR(99.93)|SAS(0.06)
am.
black/afr.	EUR	EUR	AFR(0.0)|AMR(17.35)|EAS(0.0)|EUR(82.6)|SAS(0.05)
am.
black/afr.	AFR	AMR	AFR(84.43)|AMR(15.38)|EAS(0.08)|EUR(0.09)|SAS(0.02)
am.
black/afr.	AFR	AMR	AFR(60.73)|AMR(34.86)|EAS(0.25)|EUR(3.97)|SAS(0.19)
am.
	TCGA		Number of
	self-		imputed
	declared	EthSEQ detailed	genotypes	Mean
	race	prediction [%]	(Ansextry)	coverage
	black/afr.	n/a	410	81
	am.
	white	EUR(16.24)|AMR	295	121
		(19.97)|SAS(17.76)|AFR(46.02)
	black/afr.	n/a	393	97
	am.
	black/afr.	EUR(21.73)|EAS(9.16)|AMR(27.11)|	392	90	*
	am.	SAS(23.21)|AFR(18.78)
	white	n/a	330	156	!
	white	n/a	462	63
	white	n/a	322	124
	white	n/a	444	64
	white	n/a	263	181	*
	white	n/a	412	132	*
	white	n/a	325	121	*
	white	n/a	410	109	*
	white	n/a	302	113	*
	asian	n/a	275	242
	black/afr.	EUR(21.12)|EAS(9.6)|AMR(25.78)|	479	59
	am.	SAS(22.41)|AFR(21.1)
	black/afr.	n/a	319	122
	am.
	black/afr.	n/a	417	77
	am.
	black/afr.	EUR(19.18)|EAS(9.78)|AMR(25.38)|	333	114	*
	am.	SAS(20.9)|AFR(24.77)
	black/afr.	EUR(21.8)|EAS(9.45)|AMR(25.68)|	351	133	*
	am.	SAS(22.5)|AFR(20.57)

Interestingly, the only individual misclassified by AnSextry and not by EthSEQ, which was categorized as white by TCGA, but predicted as AMR by the ancestry classifier, was actually predicted to be of admixed ancestry with a probability of 54.7% AMR and 45.1% EUR.

4 CONCLUSIONS

AnSextry, a novel method to reliably and easily determine the sex and ancestry of an individual based on aligned paired-end reads from whole-exome or, if target size permits, targeted sequencing experiments is presented. The tool provides a set of two Python-based classifiers relying on logistic regression, and the ancestry prediction represents an alternative approach to the mainly PCA-based methods used in the field of population genetics. AnSextry provides a ready-to-use reference model and requires minimal user input. It is fast, precise, and straightforward to use.

Disclaimer

Throughout this document the terms “ancestry-specifc”/“ethnicity-specific”/“population-specific” have been used interchangably, as different authors use different terms for the same purpose.

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Example 2

Using PHREGs as a Reference for NGS Read Mapping Increases Coverage of Clinically Relevant Biomarkers

We used 741 germline samples from GDC/TCGA [1] that were sequenced with whole-exome capture Illumina sequencing. This data set had 155 samples of African (AFR), 33 samples of Latino/admixed American (AMR), 179 samples of East Asian (EAS), 354 samples of European (EUR), and 20 samples of South Asian (SAS) ancestry. Each sample was aligned with Novoalign 4.00.01 to the standard human reference genome (HRG) GRCh37 [3], to the PHREG that was assigned by our ancestry classifier and to the HSA PHREG. The HSA PHREG was generated by aggregating the variant data over all GnomAD v2.1 ancestries [4], including AFR, AMR, EAS, EUR, and SAS.

For these read mapping strategies, we compared the coverage of 15,483 pathogenic ClinVar biomarkers version 2019-12 [5] in Gencode v31 CDS exons covering 1,288 genes [6]. We found increased coverage for 211 (AFR), 147 (AMR), 121 (EAS), 173 (EUR), 105 (SAS), and 162 (HSA) ClinVar biomarkers when aligning to the PHREG instead of the HRG (see Table 1). The majority of the variants with increased coverage were in vicinity of sites where the population-specific nucleotide was implanted in the PHREG. When mapping reads of a sample to its closest PHREG, the number of mismatches during alignment are reduced and thus coverage is increased, resulting in an elimination of the coverage drops when aligning to HRG.

In summary, our analysis indicates that the usage of the correct PHREG can increase the coverage and thus improve the detection of clinically relevant biomarkers.

TABLE 1
Caption Table 1 (ClinVar_PHREG_coverage_diff_relative.xlsx): List
of ClinVar biomarkers (gene name|contig|start|end) in Gencode CDS
exons that showed coverage differences when aligning to the PHREG compared
to HRG. The difference is given relative to the coverage computed based on
HRG alignments for each PHREG (AFR, AMR, EAS, EUR, SAS, HSA) as the median
over the cases by ancestry and over all 741 cases (HSA). A positive number
means increase in coverage, a negative number decrease in coverage.
variant	AFR	AMR	EAS	EUR	SAS	HSA
ABCD1|chrX|153006054|153006054	0.015	0	0	0	0	0
ABCD1|chrX|153006072|153006072	0.015	0	0	0	0	0
ABCD1|chrX|153006164|153006164	0.015	0	0	0	0	0
ABCD1|chrX|153006165|153006165	0.015	0	0	0	0	0
ABCD1|chrX|153008477|153008477	0	0.074	0	0.074	0	0.077
ABCD1|chrX|153008485|153008485	0	0.074	0	0.074	0	0.077
ABCD1|chrX|153008510|153008510	0	0.074	0	0.074	0	0.077
ALG1|chr16|5132566|5132566	0	0.025	0.016	0.013	0.018	0.021
ANKRD11|chr16|89345975|89345982	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89346103|89346103	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89349179|89349180	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89349245|89349248	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89349723|89349726	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89349751|89349752	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89349866|89349866	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350538|89350541	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350538|89350542	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350549|89350552	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350753|89350753	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350772|89350775	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89350973|89350973	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89351043|89351047	0.01	0.008	0.009	0.008	0	0.01
ANKRD11|chr16|89351487|89351488	0.01	0.008	0.009	0.008	0	0.01
ATAD3A|chr1|1464679|1464679	0.455	0.727	0.561	0.133	0	0.958
ATM|chr11|108159703|108159703	0	0.01	0	0	0	0
ATM|chr11|108159705|108159705	0	0.01	0	0	0	0
ATM|chr11|108159737|108159737	0	0.01	0	0	0	0
ATM|chr11|108159792|108159792	0	0.01	0	0	0	0
ATM|chr11|108159821|108159821	0	0.01	0	0	0	0
BMPR1A|chr10|88635776|88635776	0.053	0.009	0.055	0	0.018	0.032
BMPR1A|chr10|88676897|88676897	0.102	0.124	0.108	0.113	0	0.11
BMPR1A|chr10|88676945|88676945	0.102	0.124	0.108	0.113	0	0.11
BMPR1A|chr10|88677032|88677032	0.102	0.124	0.108	0.113	0	0.11
BMPR1A|chr10|88677041|88677042	0.102	0.124	0.108	0.113	0	0.11
BMPR1A|chr10|88679141|88679141	0.067	−0.002	−0.002	−0.003	0	0.066
BMPR1A|chr10|88681331|88681331	0.018	0.012	0.014	0.014	0	0.015
BMPR1A|chr10|88683150|88683150	0.017	0.015	0.016	0	0	0
BMPR1A|chr10|88683357|88683357	0.042	0.054	0	0.065	0	0.064
BMPR1A|chr10|88683388|88683388	0.042	0.054	0	0.065	0	0.064
CFTR|chr7|117188696|117188696	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188719|117188723	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188725|117188725	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188786|117188792	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188815|117188815	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188825|117188825	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188843|117188843	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188849|117188849	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188850|117188851	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188852|117188852	0.133	0.133	0	0.165	0.18	0.162
CFTR|chr7|117188858|117188858	0.133	0.133	0	0.165	0.18	0.162
CYP11B1|chr8|143956669|143956669	0.145	0.098	0.386	0.059	0.013	0.127
CYP11B1|chr8|143957183|143957183	0.003	0.015	0.014	0	0	0.001
CYP11B1|chr8|143958438|143958438	0.194	0.088	0.225	0.134	0.158	0.184
CYP21A2|chr6|32006291|32006291	0.636	0.594	0.407	0.375	0.442	0.396
CYP21A2|chr6|32006858|32006858	0.027	0.155	0.048	0.146	0	0.146
CYP21A2|chr6|32006910|32006917	0.027	0.155	0.048	0.146	0	0.146
CYP21A2|chr6|32007203|32007203	0.024	0.145	0.027	0.128	−0.547	0.137
CYP21A2|chr6|32007887|32007887	−0.044	−0.218	0.022	−0.026	−0.032	−0.019
CYP21A2|chr6|32008500|32008500	−0.919	−0.538	−0.93	−0.928	0.418	−0.928
CYP21A2|chr6|32008783|32008783	−0.175	0.041	0.086	0.069	0.037	0.045
CYP21A2|chr6|32008870|32008870	−0.175	0.041	0.086	0.069	0.037	0.045
DCLRE1C|chr10|14976460|14976460	0.041	0.024	0.029	0.024	0.027	0.03
DUOX2|chr15|45403694|45403694	0.467	0	0	0.16	0	0
FLG|chr1|152277475|152277475	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152280023|152280023	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152280331|152280331	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152281123|152281123	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152283457|152283457	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152285861|152285861	0.069	−0.01	0.027	0.013	−0.012	0.027
FLG|chr1|152286875|152286875	0.069	−0.01	0.027	0.013	−0.012	0.027
GBA|chr1|155205518|155205518	0.056	0.051	0.054	0.048	0.056	0.05
GBA|chr1|155205541|155205595	0.056	0.051	0.054	0.048	0.056	0.05
GBA|chr1|155205563|155205563	0.056	0.051	0.054	0.048	0.056	0.05
GBA|chr1|155205614|155205614	0.056	0.051	0.054	0.048	0.056	0.05
GBA|chr1|155208421|155208421	−0.683	0.003	−0.686	0	0	0
GLDC|chr9|6589230|6589230	0.017	0	0	0	0	0
GLUD1|chr10|88820766|88820766	0	0	0.027	0	0	0
HSPB1|chr7|75933395|75933395	0.047	0.033	0.027	0.037	0	0.041
HSPB1|chr7|75933411|75933411	0.047	0.033	0.027	0.037	0	0.041
KRT14|chr17|39742714|39742714	0.068	0.084	0.133	0.089	0.093	0.1
KRT16|chr17|39768562|39768562	0.076	0.06	0.055	0.072	0.071	0.069
KRT16|chr17|39768567|39768567	0.076	0.06	0.055	0.072	0.071	0.069
KRT17|chr17|39780487|39780487	0.007	−0.001	0	−0.002	−0.001	0.006
MT-ND1|chrM|3460|3460	0.013	0	0	0	0	0
MYH7|chr14|23889434|23889434	2.198	0.038	0.041	0.037	0.038	0.038
MYH7|chr14|23894969|23894969	0.019	0	0	0	0	0
MYH7|chr14|23894983|23894983	0.019	0	0	0	0	0
MYH7|chr14|23894999|23894999	0.019	0	0	0	0	0
MYH7|chr14|23895023|23895023	0.019	0	0	0	0	0
MYH7|chr14|23895027|23895027	0.019	0	0	0	0	0
OFD1|chrX|13767594|13767595	0	0	0	0.01	0	0.01
PIK3CA|chr3|178938934|178938934	0.026	0.02	0.032	0.02	0	0.02
PKD1|chr16|2153513|2153513	0.004	−0.006	−0.005	−0.005	0	−0.005
PKD1|chr16|2153747|2153747	0.004	−0.006	−0.005	−0.005	0	−0.005
PKD1|chr16|2156811|2156811	0.059	0	0	0	0	0.008
PKD1|chr16|2158440|2158441	0.002	0	0	0	0	0
PKD1|chr16|2158681|2158681	0.002	0	0	0	0	0
PKD1|chr16|2158969|2158969	0.002	0	0	0	0	0
PKD1|chr16|2159137|2159137	0.002	0	0	0	0	0
PKD1|chr16|2160153|2160154	0.002	0	0	0	0	0
PKD1|chr16|2164490|2164490	0.021	0.016	0.026	0.011	0.009	0.011
PKD1|chr16|2164809|2164809	0.021	0.016	0.026	0.011	0.009	0.011
PLEC|chr8|144994988|144994989	0.001	0	0	0	0	0
PMS2|chr7|6013113|6013113	3.649	0.4	3.567	0.5	4.198	2.771
PMS2|chr7|6017218|6017218	0.019	0	0	0	0	0
PMS2|chr7|6017251|6017251	0.019	0	0	0	0	0
PMS2|chr7|6017260|6017260	0.019	0	0	0	0	0
PMS2|chr7|6017300|6017303	0.019	0	0	0	0	0
PMS2|chr7|6022454|6022454	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022473|6022473	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022474|6022474	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022489|6022489	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022492|6022492	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022512|6022512	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6022516|6022516	0.233	−0.253	0.514	−0.242	0	−0.154
PMS2|chr7|6026409|6026409	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026425|6026425	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026426|6026426	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026457|6026457	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026469|6026469	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026484|6026484	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026505|6026505	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026514|6026514	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026522|6026522	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026531|6026532	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026556|6026556	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026564|6026564	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026618|6026618	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026628|6026628	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026653|6026653	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026658|6026658	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026665|6026665	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026709|6026709	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026743|6026743	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026757|6026758	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026816|6026817	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026820|6026820	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026864|6026864	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026894|6026904	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026896|6026896	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026925|6026925	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6026968|6026971	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027020|6027020	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027064|6027064	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027089|6027089	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027099|6027099	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027117|6027121	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027135|6027135	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027156|6027156	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027175|6027175	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027190|6027190	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027215|6027215	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6027232|6027232	0.111	0.017	0.023	0.018	0.075	0.021
PMS2|chr7|6031643|6031643	0.024	−0.023	−0.018	0.03	0	0.029
PMS2|chr7|6031649|6031649	0.024	−0.023	−0.018	0.03	0	0.029
PRSS1|chr7|142458451|142458451	0.052	−0.023	−0.041	−0.042	−0.002	−0.021
PTEN|chr10|89720671|89720671	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720676|89720676	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720709|89720709	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720714|89720714	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720719|89720719	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720733|89720733	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720741|89720741	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720749|89720749	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720804|89720804	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720804|89720807	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720805|89720808	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720808|89720808	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720817|89720817	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720836|89720839	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720852|89720852	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720857|89720857	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720876|89720876	0	0.019	0	0.019	0.016	0.019
PTEN|chr10|89720877|89720877	0	0.019	0	0.019	0.016	0.019
PTPN11|chr12|112910758|112910758	0.006	0	0	0	0	0.006
PTPN11|chr12|112910765|112910765	0.006	0	0	0	0	0.006
PTPN11|chr12|112910772|112910772	0.006	0	0	0	0	0.006
PTPN11|chr12|112910776|112910776	0.006	0	0	0	0	0.006
PTPN11|chr12|112910785|112910785	0.006	0	0	0	0	0.006
PTPN11|chr12|112910793|112910793	0.006	0	0	0	0	0.006
PTPN11|chr12|112910827|112910827	0.006	0	0	0	0	0.006
PTPN11|chr12|112910835|112910835	0.006	0	0	0	0	0.006
PTPN11|chr12|112910837|112910837	0.006	0	0	0	0	0.006
PTPN11|chr12|112910844|112910844	0.006	0	0	0	0	0.006
SCN1A|chr2|166848059|166848059	0.013	0	0	0	0	0
SCN1A|chr2|166848111|166848111	0.013	0	0	0	0	0
SCN1A|chr2|166848129|166848129	0.013	0	0	0	0	0
SCN1A|chr2|166848230|166848230	0.013	0	0	0	0	0
SCN1A|chr2|166848246|166848249	0.013	0	0	0	0	0
SCN1A|chr2|166848437|166848437	0.013	0	0	0	0	0
SCN1A|chr2|166848438|166848438	0.013	0	0	0	0	0
SCN1A|chr2|166848563|166848563	0.013	0	0	0	0	0
SCN1A|chr2|166848772|166848775	0.013	0	0	0	0	0
SCN1A|chr2|166848788|166848788	0.013	0	0	0	0	0
SCN1A|chr2|166848800|166848800	0.013	0	0	0	0	0
SCN1A|chr2|166848851|166848851	0.013	0	0	0	0	0
SCN1A|chr2|166848878|166848878	0.013	0	0	0	0	0
SCN1A|chr2|166848879|166848879	0.013	0	0	0	0	0
SDHA|chr5|224547|224547	0.052	0.023	0	0	0	0
SDHA|chr5|226094|226094	0.024	0.079	0.019	0.078	0	0.081
SDHA|chr5|226156|226156	0.024	0.079	0.019	0.078	0	0.081
SDHA|chr5|235345|235345	0.007	0.004	0	0.006	0.002	0.005
SDHA|chr5|236714|236715	0.082	0	−0.013	−0.02	−0.016	−0.015
SDHA|chr5|240566|240567	0.026	0	0	0	0	0
SDHA|chr5|240574|240574	0.026	0	0	0	0	0
SDHA|chr5|251554|251554	0.172	0	0	0	0	0
SDHD|chr11|111965539|111965539	0	0	0	0.003	0	0
SDHD|chr11|111965551|111965554	0	0	0	0.003	0	0
SDHD|chr11|111965555|111965555	0	0	0	0.003	0	0
STRC|chr15|43896918|43896918	0.1	0	0	0	0	0
STRC|chr15|43896948|43896948	0.1	0	0	0	0	0
SUZ12|chr17|30267467|30267470	0.638	0	0	0	0	−0.457
TUBA1A|chr12|49578875|49578875	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578884|49578884	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578885|49578885	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578923|49578923	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578944|49578944	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578945|49578945	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578980|49578980	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49578981|49578981	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579001|49579001	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579044|49579044	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579053|49579053	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579163|49579163	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579190|49579190	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579229|49579229	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579341|49579341	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579359|49579359	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579508|49579508	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579668|49579668	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49579725|49579725	0.006	−0.03	−0.021	0.003	−0.016	−0.03
TUBA1A|chr12|49580100|49580100	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580101|49580101	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580116|49580116	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580185|49580185	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580430|49580430	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580453|49580453	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580541|49580541	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580603|49580603	0.006	0.013	0.024	0.009	0.014	0.014
TUBA1A|chr12|49580615|49580615	0.006	0.013	0.024	0.009	0.014	0.014
TUBB2A|chr6|3154402|3154402	−0.054	−0.053	−0.088	0.109	−0.032	−0.022
TUBB2A|chr6|3154707|3154707	−0.054	−0.053	−0.088	0.109	−0.032	−0.022
TUBB2A|chr6|3155143|3155143	−0.054	−0.053	−0.088	0.109	−0.032	−0.022
VWF|chr12|6127701|6127701	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6127795|6127795	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128449|6128449	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128463|6128463	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128464|6128464	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128638|6128638	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128662|6128662	0.014	0.004	0.027	0.023	0.029	0.006
VWF|chr12|6128668|6128668	0.014	0.004	0.027	0.023	0.029	0.006

REFERENCES FOR EXAMPLE 2

• [1] https[://]portal.gdc.cancer.gov
• [2] http[://]www.novocraft.com/products/novoalign
• [3] https[://]www.ncbi.nlm.nih.gov/grc/human
• [4] https[://]gnomad.broadinstitute.org/faq
• [5] https[://]www.ncbi.nlm.nih.gov/clinvar
• [6] https[://]www.gencodegenes.org/human/release_31lift37.html

APPENDIX 1
chr1	1146964	1146965	A, G	TNFRSF4
chr1	1147421	1147422	C, T	TNFRSF4
chr1	1148099	1148100	C, G	TNFRSF4
chr1	1148724	1148725	A, G	TNFRSF4
chr1	1148820	1148821	A, G	TNFRSF4
chr1	2488152	2488153	A, G	TNFRSF14
chr1	2490512	2490513	C, G	TNFRSF14
chr1	2491204	2491205	C, T	TNFRSF14
chr1	2494329	2494330	A, G	TNFRSF14
chr1	3598899	3598900	A, G	TP73
chr1	3598909	3598910	C, T	TP73
chr1	3599592	3599593	C, T	TP73
chr1	3607519	3607520	A, G	TP73
chr1	3607531	3607532	A, G	TP73
chr1	3607605	3607606	A, C	TP73
chr1	3638566	3638567	C, T	TP73
chr1	3638592	3638593	A, G	TP73
chr1	3638673	3638674	C, T	TP73
chr1	3643680	3643681	A, G	TP73
chr1	3643710	3643711	C, T	TP73
chr1	3644290	3644291	A, C	TP73
chr1	3644305	3644306	C, T	TP73
chr1	3644321	3644322	A, G	TP73
chr1	3644714	3644715	C, T	TP73
chr1	3644753	3644754	C, T	TP73
chr1	3644804	3644805	A, G	TP73
chr1	3644857	3644858	C, G	TP73
chr1	3645988	3645989	A, G	TP73
chr1	3646517	3646518	A, G	TP73
chr1	3647961	3647962	C, T	TP73
chr1	3647972	3647973	A, G	TP73
chr1	3649402	3649403	A, G	TP73
chr1	3649420	3649421	C, T	TP73
chr1	3649561	3649562	A, G	TP73
chr1	7995089	7995090	G, T	TNFRSF9
chr1	7999970	7999971	A, G	TNFRSF9
chr1	8000024	8000025	A, G	TNFRSF9
chr1	9775903	9775904	C, T	PIK3CD
chr1	9776574	9776575	A, G	PIK3CD
chr1	9776604	9776605	A, G	PIK3CD
chr1	9776714	9776715	A, C	PIK3CD
chr1	9777121	9777122	A, G	PIK3CD
chr1	9777665	9777666	C, T	PIK3CD
chr1	9777668	9777669	C, T	PIK3CD
chr1	9778765	9778766	C, T	PIK3CD
chr1	9780103	9780104	C, T	PIK3CD
chr1	9780195	9780196	A, G	PIK3CD
chr1	9780597	9780598	C, T	PIK3CD
chr1	9780761	9780762	A, G	PIK3CD
chr1	9780780	9780781	C, T	PIK3CD
chr1	9782260	9782261	C, T	PIK3CD
chr1	9782555	9782556	C, T	PIK3CD
chr1	9784422	9784423	C, T	PIK3CD
chr1	11167145	11167146	A, G	MTOR
chr1	11169271	11169272	A, G	MTOR
chr1	11169272	11169273	C, G	MTOR
chr1	11169675	11169676	C, T	MTOR
chr1	11172996	11172997	C, T	MTOR
chr1	11174849	11174850	C, T	MTOR
chr1	11174858	11174859	C, T	MTOR
chr1	11181326	11181327	C, T	MTOR
chr1	11181456	11181457	G, T	MTOR
chr1	11182062	11182063	A, G	MTOR
chr1	11190645	11190646	A, G	MTOR
chr1	11199447	11199448	C, T	MTOR
chr1	11205057	11205058	C, T	MTOR
chr1	11206689	11206690	A, T	MTOR
chr1	11272318	11272319	C, T	MTOR
chr1	11272467	11272468	C, G	MTOR
chr1	11288757	11288758	A, G	MTOR
chr1	11291511	11291512	A, G	MTOR
chr1	11293463	11293464	C, T	MTOR
chr1	11298582	11298583	A, G	MTOR
chr1	11300337	11300338	A, G	MTOR
chr1	11301713	11301714	A, G	MTOR
chr1	11308073	11308074	A, G	MTOR
chr1	11850926	11850927	C, T	MTHFR
chr1	11852299	11852300	C, T	MTHFR
chr1	11852302	11852303	A, G	MTHFR
chr1	11854017	11854018	C, T	MTHFR
chr1	11854456	11854457	A, G	MTHFR
chr1	11854475	11854476	G, T	MTHFR
chr1	11854754	11854755	A, G	MTHFR
chr1	11854895	11854896	A, G	MTHFR
chr1	11856377	11856378	A, G	MTHFR
chr1	11863056	11863057	A, G	MTHFR
chr1	11863565	11863566	G, T	MTHFR
chr1	12144433	12144434	A, G	TNFRSF8
chr1	12157287	12157288	C, T	TNFRSF8
chr1	12157320	12157321	C, G	TNFRSF8
chr1	12169534	12169535	A, G	TNFRSF8
chr1	12170286	12170287	C, T	TNFRSF8
chr1	12172048	12172049	A, G	TNFRSF8
chr1	12172124	12172125	C, T	TNFRSF8
chr1	12186057	12186058	A, G	TNFRSF8
chr1	12195660	12195661	A, G	TNFRSF8
chr1	12195728	12195729	C, T	TNFRSF8
chr1	15820447	15820448	G, T	CASP9
chr1	15821958	15821959	A, G	CASP9
chr1	15831271	15831272	C, T	CASP9
chr1	15832542	15832543	C, T	CASP9
chr1	15834359	15834360	A, G	CASP9
chr1	15834490	15834491	A, G	CASP9
chr1	15844925	15844926	C, T	CASP9
chr1	15850602	15850603	A, G	CASP9
chr1	15850612	15850613	A, G	CASP9
chr1	16237806	16237807	A, G	SPEN
chr1	16242619	16242620	A, C	SPEN
chr1	16255643	16255644	C, T	SPEN
chr1	16256005	16256006	C, G	SPEN
chr1	16256006	16256007	C, T	SPEN
chr1	16257255	16257256	A, G	SPEN
chr1	16257644	16257645	C, T	SPEN
chr1	16259142	16259143	A, G	SPEN
chr1	16259812	16259813	A, G	SPEN
chr1	16260381	16260382	C, T	SPEN
chr1	16260391	16260392	A, G	SPEN
chr1	16260512	16260513	A, G	SPEN
chr1	16260915	16260916	C, T	SPEN
chr1	16262236	16262237	C, G	SPEN
chr1	16262355	16262356	C, T	SPEN
chr1	16262403	16262404	C, T	SPEN
chr1	16262718	16262719	C, T	SPEN
chr1	16264115	16264116	C, T	SPEN
chr1	20246986	20246987	C, T	PLA2G2E
chr1	20249252	20249253	A, G	PLA2G2E
chr1	20304925	20304926	A, G	PLA2G2A
chr1	20304961	20304962	C, G	PLA2G2A
chr1	20411331	20411332	C, T	PLA2G5
chr1	20412722	20412723	A, G	PLA2G5
chr1	20440782	20440783	C, T	PLA2G2D
chr1	20442053	20442054	C, T	PLA2G2D
chr1	20442073	20442074	C, T	PLA2G2D
chr1	20470147	20470148	C, T	PLA2G2F
chr1	20915700	20915701	A, C	CDA
chr1	20931448	20931449	A, G	CDA
chr1	20940257	20940258	A, T	CDA
chr1	25256048	25256049	C, T	RUNX3
chr1	25291009	25291010	A, T	RUNX3
chr1	26644536	26644537	A, C	CD52
chr1	26646725	26646726	A, G	CD52
chr1	26646729	26646730	A, G	CD52
chr1	27057620	27057621	A, C	ARID1A
chr1	27100242	27100243	C, T	ARID1A
chr1	27102187	27102188	A, G	ARID1A
chr1	29138974	29138975	G, T	OPRD1
chr1	29139048	29139049	A, G	OPRD1
chr1	29139139	29139140	C, G	OPRD1
chr1	29189482	29189483	C, T	OPRD1
chr1	29189596	29189597	C, T	OPRD1
chr1	29189600	29189601	A, G	OPRD1
chr1	32790045	32790046	G, T	HDAC1
chr1	32797240	32797241	C, G	HDAC1
chr1	38289382	38289383	C, T	MTF1
chr1	40363053	40363054	C, G	MYCL1
chr1	40366647	40366648	A, G	MYCL1
chr1	40367494	40367495	C, G	MYCL1
chr1	43803669	43803670	A, G	MPL
chr1	43803806	43803807	G, T	MPL
chr1	43804339	43804340	A, G	MPL
chr1	43805239	43805240	A, G	MPL
chr1	45291907	45291908	A, G	PTCH2
chr1	45292172	45292173	A, G	PTCH2
chr1	45292482	45292483	C, T	PTCH2
chr1	45292703	45292704	A, G	PTCH2
chr1	45292865	45292866	A, G	PTCH2
chr1	45293056	45293057	A, G	PTCH2
chr1	45293089	45293090	A, G	PTCH2
chr1	45293517	45293518	A, G	PTCH2
chr1	45294143	45294144	C, T	PTCH2
chr1	45294155	45294156	C, T	PTCH2
chr1	45296645	45296646	A, G	PTCH2
chr1	45297752	45297753	A, C, G	PTCH2
chr1	45307505	45307506	A, G	PTCH2
chr1	45308616	45308617	C, G	PTCH2
chr1	45795026	45795027	C, T	MUTYH
chr1	45796114	45796115	A, G	MUTYH
chr1	45796898	45796899	C, G	MUTYH
chr1	45798509	45798510	C, T	MUTYH
chr1	45800032	45800033	C, T	MUTYH
chr1	45800155	45800156	C, T	MUTYH
chr1	45805623	45805624	A, G	MUTYH
chr1	47264946	47264947	A, G	CYP4B1
chr1	47276727	47276728	C, G	CYP4B1
chr1	47276818	47276819	A, G	CYP4B1
chr1	47276839	47276840	C, T	CYP4B1
chr1	47276883	47276884	G, T	CYP4B1
chr1	47276938	47276939	A, G	CYP4B1
chr1	47278168	47278169	A, G	CYP4B1
chr1	47279099	47279100	C, G	CYP4B1
chr1	47279175	47279176	A, G	CYP4B1
chr1	47279836	47279837	A, G	CYP4B1
chr1	47279897	47279898	C, T	CYP4B1
chr1	47280851	47280852	A, C	CYP4B1
chr1	47280858	47280859	A, G	CYP4B1
chr1	47280883	47280884	C, T	CYP4B1
chr1	47282702	47282703	G, T	CYP4B1
chr1	47282754	47282755	C, G	CYP4B1
chr1	47282771	47282772	C, T	CYP4B1
chr1	47283626	47283627	C, T	CYP4B1
chr1	47284242	47284243	C, T	CYP4B1
chr1	47284394	47284395	A, G	CYP4B1
chr1	59247992	59247993	C, T	JUN
chr1	59248220	59248221	A, G	JUN
chr1	65301764	65301765	G, T	JAK1
chr1	65303646	65303647	A, G	JAK1
chr1	65303658	65303659	C, T	JAK1
chr1	65303661	65303662	A, G	JAK1
chr1	65310488	65310489	C, T	JAK1
chr1	65311213	65311214	C, G	JAK1
chr1	65311261	65311262	A, G	JAK1
chr1	65312341	65312342	A, G	JAK1
chr1	65321249	65321250	A, G	JAK1
chr1	65321387	65321388	A, G	JAK1
chr1	65321408	65321409	C, T	JAK1
chr1	65321418	65321419	A, G	JAK1
chr1	65325969	65325970	C, T	JAK1
chr1	65332626	65332627	C, T	JAK1
chr1	65335061	65335062	A, G	JAK1
chr1	65335094	65335095	C, T	JAK1
chr1	65339121	65339122	G	JAK1
chr1	65351895	65351896	C, T	JAK1
chr1	68896897	68896898	A, G	RPE65
chr1	68896944	68896945	G, T	RPE65
chr1	68897000	68897001	C, G, T	RPE65
chr1	68897001	68897002	A, G	RPE65
chr1	68903941	68903942	C, T	RPE65
chr1	68904659	68904660	A, C	RPE65
chr1	68904741	68904742	G, T	RPE65
chr1	68904786	68904787	C, T	RPE65
chr1	68905357	68905358	C, G	RPE65
chr1	68910309	68910310	A, G	RPE65
chr1	68910314	68910315	C, T	RPE65
chr1	91973799	91973800	G, T	CDC7
chr1	91977393	91977394	C, G	CDC7
chr1	91981483	91981484	A, G	CDC7
chr1	91989706	91989707	A, G	CDC7
chr1	95001599	95001600	A, C	F3
chr1	95001654	95001655	C, T	F3
chr1	95005757	95005758	A, G	F3
chr1	95007260	95007261	G, T	F3
chr1	97544542	97544543	G, T	DPYD
chr1	97770919	97770920	C, T	DPYD
chr1	97848040	97848041	G, T	DPYD
chr1	97915623	97915624	A, G	DPYD
chr1	97981394	97981395	C, T	DPYD
chr1	97981420	97981421	C, T	DPYD
chr1	97981507	97981508	C, T	DPYD
chr1	98015145	98015146	C, T	DPYD
chr1	98039436	98039437	C, T	DPYD
chr1	98060752	98060753	A, G	DPYD
chr1	98157361	98157362	A, G	DPYD
chr1	98165090	98165091	C, T	DPYD
chr1	98348884	98348885	A, G	DPYD
chr1	101185362	101185363	A, G	VCAM1
chr1	101190172	101190173	C, T	VCAM1
chr1	101194686	101194687	C, T	VCAM1
chr1	101194883	101194884	A, G	VCAM1
chr1	101196786	101196787	C, G	VCAM1
chr1	101197011	101197012	A, G	VCAM1
chr1	101203764	101203765	A, T	VCAM1
chr1	101203826	101203827	A, G	VCAM1
chr1	101704571	101704572	A, C	S1PR1
chr1	113456545	113456546	A, T	SLC16A1
chr1	115829202	115829203	C, T	NGF
chr1	115829243	115829244	A, G	NGF
chr1	115829312	115829313	A, G	NGF
chr1	115829362	115829363	C, T	NGF
chr1	118165576	118165577	C, G	FAM46C
chr1	118165690	118165691	C, G, T	FAM46C
chr1	118165972	118165973	C, T	FAM46C
chr1	118166095	118166096	C, T	FAM46C
chr1	118166194	118166195	C, T	FAM46C
chr1	120458003	120458004	A, T	NOTCH2
chr1	120458923	120458924	A, G	NOTCH2
chr1	120463043	120463044	C, T	NOTCH2
chr1	120465006	120465007	A, T	NOTCH2
chr1	120468127	120468128	A, G	NOTCH2
chr1	120468133	120468134	C, T	NOTCH2
chr1	120468424	120468425	A, G	NOTCH2
chr1	120468486	120468487	C, T	NOTCH2
chr1	120469146	120469147	C, T	NOTCH2
chr1	120471856	120471857	C, T	NOTCH2
chr1	120480582	120480583	A, G	NOTCH2
chr1	120483243	120483244	C, T	NOTCH2
chr1	120484420	120484421	A, G	NOTCH2
chr1	120491617	120491618	C, G	NOTCH2
chr1	120512302	120512303	A, G	NOTCH2
chr1	120548151	120548152	C, T	NOTCH2
chr1	120611559	120611560	C, T	NOTCH2
chr1	120612005	120612006	A, G	NOTCH2
chr1	150551294	150551295	C, T	MCL1
chr1	150551418	150551419	C, T	MCL1
chr1	155023997	155023998	G, T	ADAM15
chr1	155026374	155026375	C, T	ADAM15
chr1	155026870	155026871	G, T	ADAM15
chr1	155026941	155026942	A, C	ADAM15
chr1	155028449	155028450	A, C	ADAM15
chr1	155028521	155028522	A, G	ADAM15
chr1	155029747	155029748	C, T	ADAM15
chr1	155030556	155030557	A, C	ADAM15
chr1	155030970	155030971	A, G	ADAM15
chr1	155032751	155032752	A, G	ADAM15
chr1	155033307	155033308	A, G	ADAM15
chr1	155033316	155033317	C, T	ADAM15
chr1	155033917	155033918	C, T	ADAM15
chr1	156212566	156212567	A, C	BGLAP
chr1	156212925	156212926	C, G	BGLAP
chr1	156212930	156212931	A, G	BGLAP
chr1	156785616	156785617	A, G	NTRK1
chr1	156834511	156834512	C, T	NTRK1
chr1	156837846	156837847	C, T	NTRK1
chr1	156838431	156838432	C, T	NTRK1
chr1	156843653	156843654	A, G	NTRK1
chr1	156844776	156844777	A, G	NTRK1
chr1	156846232	156846233	A, G	NTRK1
chr1	156848917	156848918	C, T	NTRK1
chr1	156848945	156848946	G, T	NTRK1
chr1	156848967	156848968	C, T	NTRK1
chr1	156848994	156848995	C, T	NTRK1
chr1	156849795	156849796	A, G	NTRK1
chr1	156849945	156849946	A, G	NTRK1
chr1	162688808	162688809	A, G	DDR2
chr1	162722845	162722846	C, G	DDR2
chr1	162722880	162722881	C, T	DDR2
chr1	162725037	162725038	C, T	DDR2
chr1	162731255	162731256	A, C	DDR2
chr1	162737115	162737116	C, G	DDR2
chr1	162740312	162740313	C, T	DDR2
chr1	162740326	162740327	C, T	DDR2
chr1	162743417	162743418	G, T	DDR2
chr1	162749948	162749949	G, T	DDR2
chr1	169483560	169483561	C, T	F5
chr1	169484766	169484767	A, G	F5
chr1	169487820	169487821	G, T	F5
chr1	169489721	169489722	A, G	F5
chr1	169492614	169492615	C, T	F5
chr1	169497291	169497292	C, T	F5
chr1	169498974	169498975	C, T	F5
chr1	169500209	169500210	C, T	F5
chr1	169510117	169510118	A, G	F5
chr1	169510138	169510139	A, G	F5
chr1	169510347	169510348	C, T	F5
chr1	169510375	169510376	G, T	F5
chr1	169510379	169510380	A, G	F5
chr1	169510823	169510824	G, T	F5
chr1	169510889	169510890	C, G	F5
chr1	169511554	169511555	C, T	F5
chr1	169511733	169511734	C, T	F5
chr1	169511754	169511755	C, T	F5
chr1	169511877	169511878	G, T	F5
chr1	169511902	169511903	A, G	F5
chr1	169512026	169512027	C, T	F5
chr1	169512038	169512039	C, T	F5
chr1	169512092	169512093	A, G	F5
chr1	169512119	169512120	A, G	F5
chr1	169512222	169512223	A, G	F5
chr1	169513582	169513583	G, T	F5
chr1	169515725	169515726	C, T	F5
chr1	169519111	169519112	C, T	F5
chr1	169519893	169519894	A, G	F5
chr1	169521852	169521853	A, G	F5
chr1	169526019	169526020	A, G	F5
chr1	169528579	169528580	C, T	F5
chr1	169529754	169529755	A, G	F5
chr1	169529813	169529814	C, G	F5
chr1	169529825	169529826	A, C	F5
chr1	169541512	169541513	C, G	F5
chr1	169541619	169541620	A, G	F5
chr1	169551681	169551682	C, T	F5
chr1	169555453	169555454	A, G	F5
chr1	169555581	169555582	C, T	F5
chr1	169560612	169560613	A, T	SELP
chr1	169562903	169562904	C, T	SELP
chr1	169562948	169562949	A, G	SELP
chr1	169563950	169563951	G, T	SELP
chr1	169565245	169565246	C, T	SELP
chr1	169565283	169565284	C, T	SELP
chr1	169565345	169565346	A, C	SELP
chr1	169565392	169565393	A, C	SELP
chr1	169566241	169566242	C, T	SELP
chr1	169566264	169566265	A, C	SELP
chr1	169566307	169566308	A, G	SELP
chr1	169566312	169566313	C, T	SELP
chr1	169566325	169566326	A, G	SELP
chr1	169566328	169566329	A, G	SELP
chr1	169576374	169576375	A, G	SELP
chr1	169580884	169580885	C, T	SELP
chr1	169581594	169581595	A, G	SELP
chr1	169582316	169582317	C, T	SELP
chr1	169586668	169586669	G, T	SELP
chr1	169588353	169588354	A, G	SELP
chr1	169599253	169599254	C, T	SELP
chr1	169660938	169660939	C, T	SELL
chr1	169665631	169665632	C, T	SELL
chr1	169676485	169676486	A, G	SELL
chr1	169677678	169677679	A, G	SELL
chr1	169677981	169677982	A, T	SELL
chr1	169679552	169679553	C, T	SELL
chr1	172628487	172628488	A, G	FASLG
chr1	172628620	172628621	G, T	FASLG
chr1	172633610	172633611	C, G	FASLG
chr1	179077557	179077558	A, G	ABL2
chr1	179078196	179078197	A, C	ABL2
chr1	179078590	179078591	C, T	ABL2
chr1	179084079	179084080	G, T	ABL2
chr1	179090750	179090751	C, T	ABL2
chr1	179095547	179095548	C, T	ABL2
chr1	179112109	179112110	G, T	ABL2
chr1	179112144	179112145	C, G	ABL2
chr1	183532436	183532437	A, G	NCF2
chr1	183532444	183532445	C, G	NCF2
chr1	183532471	183532472	C	NCF2
chr1	183532579	183532580	G, T	NCF2
chr1	183533216	183533217	C	NCF2
chr1	183534934	183534935	C, T	NCF2
chr1	183534944	183534945	C, T	NCF2
chr1	183536088	183536089	A, G	NCF2
chr1	183542386	183542387	C, T	NCF2
chr1	183555962	183555963	C, T	NCF2
chr1	186643540	186643541	C, T	PTGS2
chr1	186643767	186643768	A, G	PTGS2
chr1	186645077	186645078	A, G	PTGS2
chr1	186645668	186645669	A, G	PTGS2
chr1	186645926	186645927	C, T	PTGS2
chr1	186648354	186648355	C, G	PTGS2
chr1	193117123	193117124	A, T	CDC73
chr1	193173025	193173026	A, G	CDC73
chr1	193202152	193202153	A, G	CDC73
chr1	197008596	197008597	A, C	F13B
chr1	197009797	197009798	A, G	F13B
chr1	197019857	197019858	A, C	F13B
chr1	197019978	197019979	A, G	F13B
chr1	197026264	197026265	C, T	F13B
chr1	197031020	197031021	C, T	F13B
chr1	198661414	198661415	A, G	PTPRC
chr1	198671652	198671653	A, G	PTPRC
chr1	198672538	198672539	A, G	PTPRC
chr1	198678833	198678834	A, G	PTPRC
chr1	198682057	198682058	A, G	PTPRC
chr1	198704293	198704294	C, T	PTPRC
chr1	198711166	198711167	A, G	PTPRC
chr1	198718691	198718692	C, T	PTPRC
chr1	198725168	198725169	C, T	PTPRC
chr1	204494737	204494738	A, G	MDM4
chr1	204501382	204501383	C, T	MDM4
chr1	204506106	204506107	C, T	MDM4
chr1	204511923	204511924	C, T	MDM4
chr1	204515941	204515942	A	MDM4
chr1	204516024	204516025	A, G	MDM4
chr1	204518245	204518246	A, G	MDM4
chr1	204518740	204518741	A, G	MDM4
chr1	206647786	206647787	C, T	IKBKE
chr1	206647843	206647844	C, T	IKBKE
chr1	206649680	206649681	A, G	IKBKE
chr1	206650064	206650065	A, G	IKBKE
chr1	206651106	206651107	A, G	IKBKE
chr1	206651595	206651596	C, T	IKBKE
chr1	206651724	206651725	C, T	IKBKE
chr1	206652403	206652404	A, G	IKBKE
chr1	206652499	206652500	A, G	IKBKE
chr1	206652523	206652524	C, T	IKBKE
chr1	206661262	206661263	T	IKBKE
chr1	206665051	206665052	C, T	IKBKE
chr1	206666280	206666281	C, T	IKBKE
chr1	206666583	206666584	A, G	IKBKE
chr1	206666733	206666734	G, T	IKBKE
chr1	206669398	206669399	C, G	IKBKE
chr1	206669441	206669442	C, T	IKBKE
chr1	206669464	206669465	C, T	IKBKE
chr1	223284527	223284528	A, G	TLR5
chr1	223284598	223284599	C, T	TLR5
chr1	223285041	223285042	A, G	TLR5
chr1	223285506	223285507	G, T	TLR5
chr1	223285945	223285946	G, T	TLR5
chr1	223286039	223286040	C, G	TLR5
chr1	226550740	226550741	C, T	PARP1
chr1	226550828	226550829	C, T	PARP1
chr1	226550923	226550924	C, G	PARP1
chr1	226553579	226553580	A, G	PARP1
chr1	226555301	226555302	A, G	PARP1
chr1	226555347	226555348	A, G	PARP1
chr1	226564835	226564836	A, G	PARP1
chr1	226565048	226565049	G, T	PARP1
chr1	226566958	226566959	C	PARP1
chr1	226567007	226567008	C, G	PARP1
chr1	226567026	226567027	A, G	PARP1
chr1	226567171	226567172	A, C	PARP1
chr1	226567191	226567192	C, T	PARP1
chr1	226567240	226567241	C, T	PARP1
chr1	226570839	226570840	C, T	PARP1
chr1	226573363	226573364	A, G	PARP1
chr1	226573401	226573402	C, T	PARP1
chr1	226573984	226573985	C, T	PARP1
chr1	226576269	226576270	A, G	PARP1
chr1	226576295	226576296	A, G	PARP1
chr1	226576334	226576335	A, G	PARP1
chr1	226576335	226576336	A, G	PARP1
chr1	226580020	226580021	G, T	PARP1
chr1	226580052	226580053	G, T	PARP1
chr1	226589708	226589709	C, T	PARP1
chr1	226589832	226589833	C, T	PARP1
chr1	226589857	226589858	C	PARP1
chr1	226595646	226595647	C, G	PARP1
chr1	236958682	236958683	C, G	MTR
chr1	236958936	236958937	C, T	MTR
chr1	236971982	236971983	C, T	MTR
chr1	236971997	236971998	C, T	MTR
chr1	236975053	236975054	C, G	MTR
chr1	236990140	236990141	A, G	MTR
chr1	237038160	237038161	C, T	MTR
chr1	237038220	237038221	C, G	MTR
chr1	237048499	237048500	A, G	MTR
chr1	237048515	237048516	C, G	MTR
chr1	237054565	237054566	C, T	MTR
chr1	237054568	237054569	A, G	MTR
chr1	237058728	237058729	C, T	MTR
chr1	237058742	237058743	A, G	MTR
chr1	237058743	237058744	A, C	MTR
chr1	237058747	237058748	C, T	MTR
chr1	237060294	237060295	A, G	MTR
chr1	237060295	237060296	A, C	MTR
chr1	237060371	237060372	A, G	MTR
chr1	237060432	237060433	G, T	MTR
chr1	237060849	237060850	C, T	MTR
chr1	237060996	237060997	A, G	MTR
chr2	10262858	10262859	A, G	RRM2
chr2	10262864	10262865	C, G	RRM2
chr2	10262891	10262892	C, T	RRM2
chr2	10262919	10262920	G, T	RRM2
chr2	10267210	10267211	C, T	RRM2
chr2	11323530	11323531	A, C	ROCK2
chr2	11323540	11323541	C, T	ROCK2
chr2	11334383	11334384	G, T	ROCK2
chr2	11347940	11347941	G, T	ROCK2
chr2	11351864	11351865	C, T	ROCK2
chr2	11355232	11355233	A, G	ROCK2
chr2	11359119	11359120	G, T	ROCK2
chr2	11389813	11389814	A, G	ROCK2
chr2	11389906	11389907	C, T	ROCK2
chr2	11426622	11426623	C, T	ROCK2
chr2	11426733	11426734	C, T	ROCK2
chr2	11427886	11427887	A, T	ROCK2
chr2	11484095	11484096	C, G	ROCK2
chr2	25457198	25457199	C, T	DNMT3A
chr2	25457350	25457351	C, T	DNMT3A
chr2	25458545	25458546	C, T	DNMT3A
chr2	25462326	25462327	C, G	DNMT3A
chr2	25469184	25469185	G	DNMT3A
chr2	25469501	25469502	C, T	DNMT3A
chr2	25469627	25469628	C, T	DNMT3A
chr2	25471001	25471002	A, G	DNMT3A
chr2	25475036	25475037	A, C	DNMT3A
chr2	25523064	25523065	C, T	DNMT3A
chr2	29416356	29416357	A, G	ALK
chr2	29416365	29416366	C, G	ALK
chr2	29416480	29416481	C, T	ALK
chr2	29416571	29416572	C, T	ALK
chr2	29416614	29416615	A, G	ALK
chr2	29416749	29416750	A, G	ALK
chr2	29416793	29416794	A, G	ALK
chr2	29420549	29420550	C, T	ALK
chr2	29430757	29430758	A, G	ALK
chr2	29432775	29432776	C, T	ALK
chr2	29443616	29443617	C, G	ALK
chr2	29443748	29443749	G, T	ALK
chr2	29444075	29444076	G, T	ALK
chr2	29444094	29444095	C, T	ALK
chr2	29445156	29445157	C, G	ALK
chr2	29445424	29445425	A, G	ALK
chr2	29446201	29446202	A, G	ALK
chr2	29450372	29450373	A, T	ALK
chr2	29455266	29455267	A, G	ALK
chr2	29473999	29474000	A, G	ALK
chr2	29474041	29474042	A, G	ALK
chr2	29497920	29497921	A, C	ALK
chr2	29497994	29497995	A, G	ALK
chr2	29519714	29519715	C, T	ALK
chr2	29519851	29519852	A, G	ALK
chr2	29541103	29541104	C, T	ALK
chr2	29543662	29543663	C, T	ALK
chr2	29543735	29543736	A, G	ALK
chr2	29543773	29543774	C, T	ALK
chr2	29754824	29754825	C	ALK
chr2	29940528	29940529	A, T	ALK
chr2	30142880	30142881	A, G	ALK
chr2	38298138	38298139	C, T	CYP1B1
chr2	38298149	38298150	A, G	CYP1B1
chr2	38298168	38298169	C, G	CYP1B1
chr2	38298202	38298203	C, G	CYP1B1
chr2	38298393	38298394	C, T	CYP1B1
chr2	38301802	38301803	C, G	CYP1B1
chr2	38301846	38301847	C, T	CYP1B1
chr2	38301937	38301938	A, G	CYP1B1
chr2	38302176	38302177	A, C	CYP1B1
chr2	38302389	38302390	C, G	CYP1B1
chr2	42396721	42396722	A, G	EML4
chr2	42491940	42491941	C, T	EML4
chr2	42491950	42491951	C, T	EML4
chr2	42491996	42491997	A, G	EML4
chr2	42508047	42508048	C, T	EML4
chr2	42508151	42508152	C, G	EML4
chr2	42510177	42510178	C, T	EML4
chr2	42511902	42511903	A, G	EML4
chr2	42515387	42515388	A, G	EML4
chr2	42515436	42515437	A, G	EML4
chr2	42515500	42515501	C, T	EML4
chr2	42531706	42531707	C, G	EML4
chr2	42531716	42531717	A, G	EML4
chr2	42552283	42552284	C, G	EML4
chr2	42552407	42552408	A, G	EML4
chr2	42556021	42556022	A, T	EML4
chr2	42557333	42557334	C, T	EML4
chr2	47380144	47380145	C, T	CALM2
chr2	47380202	47380203	C, T	CALM2
chr2	47399600	47399601	A, G	CALM2
chr2	47596199	47596200	A, G	EPCAM
chr2	47600765	47600766	C, T	EPCAM
chr2	47601105	47601106	C, T	EPCAM
chr2	47604175	47604176	C, T	EPCAM
chr2	47604277	47604278	A, G	EPCAM
chr2	47612223	47612224	C, T	EPCAM
chr2	47612297	47612298	C, T	EPCAM
chr2	47612298	47612299	A, G	EPCAM
chr2	47613698	47613699	C, T	EPCAM
chr2	47613787	47613788	A, G	EPCAM
chr2	47637245	47637246	A, G	MSH2
chr2	47637438	47637439	C, T	MSH2
chr2	47643475	47643476	C, T	MSH2
chr2	47693787	47693788	A, T	MSH2
chr2	47698094	47698095	A, G	MSH2
chr2	47710048	47710049	C, T	MSH2
chr2	47739550	47739551	A, G	MSH2
chr2	48010487	48010488	A, G	MSH6
chr2	48010557	48010558	A, C	MSH6
chr2	48018080	48018081	A, G	MSH6
chr2	48023114	48023115	C, T	MSH6
chr2	48025763	48025764	C, T	MSH6
chr2	48026285	48026286	C, T	MSH6
chr2	48027374	48027375	C, T	MSH6
chr2	48027393	48027394	C, T	MSH6
chr2	48030691	48030692	A, T	MSH6
chr2	48033550	48033551	C, G	MSH6
chr2	48915266	48915267	C, T	LHCGR
chr2	48915870	48915871	A, G	LHCGR
chr2	48921374	48921375	C, T	LHCGR
chr2	48921437	48921438	C, T	LHCGR
chr2	48925745	48925746	C, T	LHCGR
chr2	48948855	48948856	A, G	LHCGR
chr2	48948977	48948978	A, G	LHCGR
chr2	48956416	48956417	C, T	LHCGR
chr2	48956430	48956431	A, T	LHCGR
chr2	48982621	48982622	C, G	LHCGR
chr2	55460086	55460087	A, G	RPS27A
chr2	58388695	58388696	A, G	FANCL
chr2	58390513	58390514	C, G	FANCL
chr2	58390537	58390538	C, T	FANCL
chr2	58390546	58390547	A, G	FANCL
chr2	58390588	58390589	A, C	FANCL
chr2	58421265	58421266	C, T	FANCL
chr2	58431409	58431410	C, G	FANCL
chr2	58431445	58431446	C, T	FANCL
chr2	58453929	58453930	A, G	FANCL
chr2	58453962	58453963	A, T	FANCL
chr2	61709488	61709489	C, G	XPO1
chr2	61710076	61710077	A, G	XPO1
chr2	61711210	61711211	C, T	XPO1
chr2	61715323	61715324	C, T	XPO1
chr2	61722723	61722724	G, T	XPO1
chr2	61729229	61729230	C, T	XPO1
chr2	61749721	61749722	A, C	XPO1
chr2	69093287	69093288	G, T	BMP10
chr2	69093311	69093312	A, G	BMP10
chr2	75276648	75276649	C, T	TACR1
chr2	75276858	75276859	C, T	TACR1
chr2	75425727	75425728	A, G	TACR1
chr2	75426070	75426071	G	TACR1
chr2	108994807	108994808	C, G	SULT1C4
chr2	108998211	108998212	C, T	SULT1C4
chr2	108998797	108998798	A, G, T	SULT1C4
chr2	108999785	108999786	C, T	SULT1C4
chr2	109003716	109003717	G, T	SULT1C4
chr2	109003760	109003761	A, G	SULT1C4
chr2	111397344	111397345	C, T	BUB1
chr2	111419352	111419353	C, T	BUB1
chr2	111419425	111419426	A, G	BUB1
chr2	111423829	111423830	C, T	BUB1
chr2	111430380	111430381	A, C	BUB1
chr2	111431950	111431951	C, G	BUB1
chr2	113532884	113532885	G, T	IL1A
chr2	113537150	113537151	C, T	IL1A
chr2	113539223	113539224	A, G	IL1A
chr2	113540412	113540413	A, G	IL1A
chr2	113541381	113541382	C, T	IL1A
chr2	140992322	140992323	C, T	LRP1B
chr2	140992336	140992337	A, C	LRP1B
chr2	140992346	140992347	C, T	LRP1B
chr2	141027925	141027926	A, G	LRP1B
chr2	141032087	141032088	C, T	LRP1B
chr2	141079616	141079617	A, G	LRP1B
chr2	141108530	141108531	A, G	LRP1B
chr2	141110676	141110677	A, C	LRP1B
chr2	141130694	141130695	C, T	LRP1B
chr2	141242917	141242918	C, T	LRP1B
chr2	141245160	141245161	C, T	LRP1B
chr2	141259375	141259376	A, G	LRP1B
chr2	141260667	141260668	A, G	LRP1B
chr2	141267572	141267573	A, G	LRP1B
chr2	141272252	141272253	C, T	LRP1B
chr2	141274563	141274564	C, T	LRP1B
chr2	141274575	141274576	C, T	LRP1B
chr2	141283400	141283401	A, T	LRP1B
chr2	141283424	141283425	A, G	LRP1B
chr2	141294249	141294250	C, T	LRP1B
chr2	141298673	141298674	C, T	LRP1B
chr2	141298681	141298682	C, G	LRP1B
chr2	141457961	141457962	C, T	LRP1B
chr2	141457984	141457985	A, T	LRP1B
chr2	141459963	141459964	C, T	LRP1B
chr2	141473504	141473505	A, T	LRP1B
chr2	141526813	141526814	C, G	LRP1B
chr2	141528434	141528435	C, T	LRP1B
chr2	141528442	141528443	C, T	LRP1B
chr2	141533661	141533662	C, T	LRP1B
chr2	141571328	141571329	C, T	LRP1B
chr2	141625345	141625346	C, T	LRP1B
chr2	141680637	141680638	C, T	LRP1B
chr2	141707867	141707868	G, T	LRP1B
chr2	141707982	141707983	C, T	LRP1B
chr2	141708020	141708021	A, T	LRP1B
chr2	141709405	141709406	G, T	LRP1B
chr2	141709418	141709419	G, T	LRP1B
chr2	141747248	141747249	A, T	LRP1B
chr2	141751591	141751592	A, G	LRP1B
chr2	141751675	141751676	C, T	LRP1B
chr2	141763011	141763012	G, T	LRP1B
chr2	141763070	141763071	A, G	LRP1B
chr2	141771115	141771116	C, T	LRP1B
chr2	141773396	141773397	A, C	LRP1B
chr2	141816494	141816495	A, G	LRP1B
chr2	141946093	141946094	A, G	LRP1B
chr2	141946168	141946169	A, C	LRP1B
chr2	141946176	141946177	G, T	LRP1B
chr2	142012035	142012036	G, T	LRP1B
chr2	142567909	142567910	C, T	LRP1B
chr2	145147191	145147192	G	ZEB2
chr2	145156550	145156551	A, G	ZEB2
chr2	145157823	145157824	A, G	ZEB2
chr2	145161479	145161480	C	ZEB2
chr2	145255209	145255210	C, T	ZEB2
chr2	160958342	160958343	C, T	ITGB6
chr2	160968627	160968628	A, G	ITGB6
chr2	160994292	160994293	C, T	ITGB6
chr2	160994347	160994348	C, T	ITGB6
chr2	160994408	160994409	C, T	ITGB6
chr2	161029217	161029218	A, G	ITGB6
chr2	161030526	161030527	C, G	ITGB6
chr2	161051852	161051853	A, G	ITGB6
chr2	162862391	162862392	G, T	DPP4
chr2	162865067	162865068	A, G	DPP4
chr2	162865132	162865133	C, T	DPP4
chr2	162865822	162865823	A, T	DPP4
chr2	162875348	162875349	C, G	DPP4
chr2	162875842	162875843	A, C	DPP4
chr2	162876767	162876768	A, G	DPP4
chr2	162881474	162881475	C, G	DPP4
chr2	162903311	162903312	C, T	DPP4
chr2	162903409	162903410	C, T	DPP4
chr2	162929921	162929922	C, T	DPP4
chr2	162929978	162929979	A, G	DPP4
chr2	169985619	169985620	A, C	LRP2
chr2	169993976	169993977	C	LRP2
chr2	169996936	169996937	C, T	LRP2
chr2	169997008	169997009	A, G	LRP2
chr2	169997029	169997030	C, G	LRP2
chr2	169997050	169997051	A, G	LRP2
chr2	170003431	170003432	G, T	LRP2
chr2	170003507	170003508	A, G	LRP2
chr2	170010984	170010985	C, T	LRP2
chr2	170012779	170012780	A, G	LRP2
chr2	170019114	170019115	A, C	LRP2
chr2	170019120	170019121	A, C	LRP2
chr2	170025082	170025083	A, G	LRP2
chr2	170027094	170027095	A, G	LRP2
chr2	170031823	170031824	C, T	LRP2
chr2	170032988	170032989	C, T	LRP2
chr2	170033088	170033089	A, G	LRP2
chr2	170038760	170038761	C, T	LRP2
chr2	170048555	170048556	C	LRP2
chr2	170053504	170053505	C, T	LRP2
chr2	170055254	170055255	C, T	LRP2
chr2	170062077	170062078	C, G	LRP2
chr2	170063419	170063420	C, T	LRP2
chr2	170063470	170063471	A, G	LRP2
chr2	170068490	170068491	C, T	LRP2
chr2	170068712	170068713	A, G	LRP2
chr2	170070347	170070348	C, T	LRP2
chr2	170072886	170072887	C, G	LRP2
chr2	170082012	170082013	A, G	LRP2
chr2	170083032	170083033	C, T	LRP2
chr2	170088350	170088351	A, G	LRP2
chr2	170092394	170092395	A, G	LRP2
chr2	170092601	170092602	A, G	LRP2
chr2	170092612	170092613	C, G	LRP2
chr2	170094762	170094763	C, G	LRP2
chr2	170096017	170096018	A, G	LRP2
chr2	170096094	170096095	C, G	LRP2
chr2	170096290	170096291	A, G	LRP2
chr2	170097706	170097707	G, T	LRP2
chr2	170099445	170099446	G, T	LRP2
chr2	170099452	170099453	A, T	LRP2
chr2	170099472	170099473	C, T	LRP2
chr2	170099473	170099474	A, G	LRP2
chr2	170103335	170103336	C, T	LRP2
chr2	170103350	170103351	G, T	LRP2
chr2	170112659	170112660	C, T	LRP2
chr2	170115587	170115588	C, T	LRP2
chr2	170115671	170115672	A, G	LRP2
chr2	170129527	170129528	A, G	LRP2
chr2	170129528	170129529	A, G	LRP2
chr2	170139345	170139346	C, T	LRP2
chr2	170139386	170139387	A, C	LRP2
chr2	170145660	170145661	C, T	LRP2
chr2	170147501	170147502	C, G	LRP2
chr2	170148744	170148745	A, G	LRP2
chr2	170150670	170150671	A, G	LRP2
chr2	170163767	170163768	C, T	LRP2
chr2	170163815	170163816	G, T	LRP2
chr2	170175333	170175334	C, T	LRP2
chr2	170177381	170177382	A, G	LRP2
chr2	170218815	170218816	C, T	LRP2
chr2	170218846	170218847	C, G	LRP2
chr2	173427052	173427053	G, T	PDK1
chr2	173427079	173427080	A, G	PDK1
chr2	173428873	173428874	C, T	PDK1
chr2	178098678	178098679	C, T	NFE2L2
chr2	178098721	178098722	A, G	NFE2L2
chr2	187455277	187455278	C, T	ITGAV
chr2	187490231	187490232	A, G	ITGAV
chr2	187498106	187498107	C, T	ITGAV
chr2	187501741	187501742	A, G	ITGAV
chr2	187505701	187505702	A, T	ITGAV
chr2	187511465	187511466	A, G	ITGAV
chr2	187519337	187519338	G, T	ITGAV
chr2	187532009	187532010	G, T	ITGAV
chr2	187532372	187532373	G, T	ITGAV
chr2	187532416	187532417	A, G	ITGAV
chr2	187543373	187543374	C, T	ITGAV
chr2	190925076	190925077	C, T	MSTN
chr2	190927142	190927143	A, G	MSTN
chr2	190927159	190927160	C, T	MSTN
chr2	191899345	191899346	A, C	STAT4
chr2	191905713	191905714	C, T	STAT4
chr2	191922840	191922841	A, G	STAT4
chr2	191927472	191927473	A, T	STAT4
chr2	191996517	191996518	C, T	STAT4
chr2	191996588	191996589	A, C	STAT4
chr2	198257200	198257201	A, G	SF3B1
chr2	198257794	198257795	C, T	SF3B1
chr2	198257919	198257920	A, G	SF3B1
chr2	198263721	198263722	A, G	SF3B1
chr2	198265525	198265526	A, G	SF3B1
chr2	198266660	198266661	C, T	SF3B1
chr2	198266827	198266828	G, T	SF3B1
chr2	198266861	198266862	A, T	SF3B1
chr2	198270016	198270017	C, T	SF3B1
chr2	198281458	198281459	A, T	SF3B1
chr2	198281488	198281489	C, T	SF3B1
chr2	198283304	198283305	C, T	SF3B1
chr2	202122955	202122956	C, T	CASP8
chr2	202134320	202134321	T	CASP8
chr2	202141677	202141678	A, G	CASP8
chr2	202149588	202149589	C, G	CASP8
chr2	202149695	202149696	A, G	CASP8
chr2	204732713	204732714	A, G	CTLA4
chr2	204732739	204732740	C, G	CTLA4
chr2	206562222	206562223	C, T	NRP2
chr2	206562249	206562250	C, T	NRP2
chr2	206562316	206562317	C, T	NRP2
chr2	206565450	206565451	C, T	NRP2
chr2	206581032	206581033	A, G	NRP2
chr2	206588569	206588570	A, G	NRP2
chr2	206590685	206590686	C, T	NRP2
chr2	206592694	206592695	C, T	NRP2
chr2	206605179	206605180	G, T	NRP2
chr2	206605222	206605223	C, T	NRP2
chr2	206605244	206605245	A, G	NRP2
chr2	206608038	206608039	C, T	NRP2
chr2	206610501	206610502	G, T	NRP2
chr2	206630360	206630361	G	NRP2
chr2	206631617	206631618	A, C	NRP2
chr2	206656915	206656916	C, T	NRP2
chr2	206656918	206656919	A, T	NRP2
chr2	206659462	206659463	C, T	NRP2
chr2	206659473	206659474	A, G	NRP2
chr2	208631703	208631704	A, T	FZD5
chr2	208631747	208631748	A, G	FZD5
chr2	208631783	208631784	A, G	FZD5
chr2	208632092	208632093	A, G	FZD5
chr2	208632816	208632817	A, G	FZD5
chr2	208633373	208633374	A, G	FZD5
chr2	208633412	208633413	C, T	FZD5
chr2	209106874	209106875	A, G	IDH1
chr2	209108316	209108317	C, T	IDH1
chr2	209113191	209113192	A, G	IDH1
chr2	209113295	209113296	C, T	IDH1
chr2	209113387	209113388	A, G	IDH1
chr2	212251863	212251864	C, T	ERBB4
chr2	212286681	212286682	C, G	ERBB4
chr2	212488646	212488647	C, T	ERBB4
chr2	212530216	212530217	C, T	ERBB4
chr2	212537986	212537987	A, G	ERBB4
chr2	212537993	212537994	A, T	ERBB4
chr2	212543923	212543924	A, G	ERBB4
chr2	212543929	212543930	A, G	ERBB4
chr2	212615341	212615342	A, G	ERBB4
chr2	215595068	215595069	G, T	BARD1
chr2	215595202	215595203	A, G	BARD1
chr2	215595644	215595645	C, T	BARD1
chr2	215632255	215632256	A, G	BARD1
chr2	215645463	215645464	C, G	BARD1
chr2	215645977	215645978	T	BARD1
chr2	215661882	215661883	G, T	BARD1
chr2	215661910	215661911	A, C	BARD1
chr2	215674089	215674090	G, T	BARD1
chr2	215674223	215674224	A, G	BARD1
chr2	219000192	219000193	A, G	CXCR2
chr2	219000279	219000280	C, T	CXCR2
chr2	219000459	219000460	C, T	CXCR2
chr2	219028909	219028910	A, G	CXCR1
chr2	219029301	219029302	G, T	CXCR1
chr2	232320101	232320102	C, T	NCL
chr2	232320280	232320281	G	NCL
chr2	232320797	232320798	C, T	NCL
chr2	232321306	232321307	C, T	NCL
chr2	232321497	232321498	G, T	NCL
chr2	232322332	232322333	G, T	NCL
chr2	232323799	232323800	A, G	NCL
chr2	232323874	232323875	A, G	NCL
chr2	232325038	232325039	C, G	NCL
chr2	232325152	232325153	T	NCL
chr2	232325622	232325623	A, C	NCL
chr2	232326662	232326663	A, G	NCL
chr2	232326800	232326801	A, T	NCL
chr2	232327361	232327362	A, G	NCL
chr2	234590615	234590616	A, C	UGT1A7
chr2	234590925	234590926	A, G	UGT1A7
chr2	234591204	234591205	C, T	UGT1A7
chr2	234599088	234599089	C, G	UGT1A7
chr2	234669143	234669144	A, G	UGT1A1
chr2	234669618	234669619	A, C	UGT1A1
chr2	234675825	234675826	C, T	UGT1A1
chr2	234675828	234675829	C, T	UGT1A1
chr2	234676457	234676458	C, T	UGT1A1
chr2	234835169	234835170	C, T	TRPM8
chr2	234839403	234839404	C, T	TRPM8
chr2	234854539	234854540	C, G	TRPM8
chr2	234854546	234854547	A, T	TRPM8
chr2	234854549	234854550	C, G	TRPM8
chr2	234854551	234854552	A, G	TRPM8
chr2	234856211	234856212	C, T	TRPM8
chr2	234863787	234863788	A, G	TRPM8
chr2	234878472	234878473	C, T	TRPM8
chr2	234890618	234890619	A, T	TRPM8
chr2	234891854	234891855	A, C	TRPM8
chr2	234905077	234905078	C, T	TRPM8
chr2	234915539	234915540	C, G	TRPM8
chr2	234916793	234916794	A, G	TRPM8
chr2	234916804	234916805	C, T	TRPM8
chr2	234923123	234923124	A, C	TRPM8
chr2	234926007	234926008	C, T	TRPM8
chr2	242793272	242793273	A, G	PDCD1
chr2	242793432	242793433	A, G	PDCD1
chr2	242794812	242794813	C	PDCD1
chr2	242800899	242800900	A, G	PDCD1
chr3	10070335	10070336	C, G	FANCD2
chr3	10070416	10070417	C, G	FANCD2
chr3	10074645	10074646	C, G	FANCD2
chr3	10076974	10076975	A, C	FANCD2
chr3	10077954	10077955	A, G	FANCD2
chr3	10080986	10080987	A, G	FANCD2
chr3	10081410	10081411	A, G	FANCD2
chr3	10081544	10081545	C, G	FANCD2
chr3	10084395	10084396	A, G	FANCD2
chr3	10085129	10085130	C, G	FANCD2
chr3	10089688	10089689	G, T	FANCD2
chr3	10089772	10089773	A, C	FANCD2
chr3	10091034	10091035	C, T	FANCD2
chr3	10094012	10094013	A, T	FANCD2
chr3	10106514	10106515	C, T	FANCD2
chr3	10108990	10108991	A, G	FANCD2
chr3	10115042	10115043	C, T	FANCD2
chr3	10119916	10119917	C, T	FANCD2
chr3	10133948	10133949	A, G	FANCD2
chr3	10136072	10136073	A, G	FANCD2
chr3	10136102	10136103	C, T	FANCD2
chr3	10138068	10138069	G, T	FANCD2
chr3	10138188	10138189	C, T	FANCD2
chr3	10142948	10142949	C, T	FANCD2
chr3	12393124	12393125	C, G	PPARG
chr3	12413338	12413339	G, T	PPARG
chr3	12413589	12413590	A, G	PPARG
chr3	12434069	12434070	C, G	PPARG
chr3	12434090	12434091	A, C	PPARG
chr3	12458273	12458274	C, G	PPARG
chr3	12475556	12475557	C, T	PPARG
chr3	12626393	12626394	C, T	RAF1
chr3	12626515	12626516	A, G	RAF1
chr3	12629180	12629181	A, G	RAF1
chr3	12645006	12645007	C, T	RAF1
chr3	13539983	13539984	A, G	HDAC11
chr3	13545696	13545697	C, T	HDAC11
chr3	14188761	14188762	C, G	XPC
chr3	14189511	14189512	A, G	XPC
chr3	14190267	14190268	C, G	XPC
chr3	14193888	14193889	C, T	XPC
chr3	14199541	14199542	A, G	XPC
chr3	14199886	14199887	A, G	XPC
chr3	14199907	14199908	C, T	XPC
chr3	14200020	14200021	A, G	XPC
chr3	14201351	14201352	C, T	XPC
chr3	14207100	14207101	C, G	XPC
chr3	14212049	14212050	C, T	XPC
chr3	14220022	14220023	C, G	XPC
chr3	14220089	14220090	C, T	XPC
chr3	14220094	14220095	C, G	XPC
chr3	30686413	30686414	A, G	TGFBR2
chr3	30713125	30713126	A, T	TGFBR2
chr3	30713245	30713246	A, G	TGFBR2
chr3	30713673	30713674	A, G	TGFBR2
chr3	30713841	30713842	C, T	TGFBR2
chr3	30715607	30715608	A, G	TGFBR2
chr3	32995927	32995928	C, T	CCR4
chr3	37042540	37042541	G, T	MLH1
chr3	37048440	37048441	A, G	MLH1
chr3	37050324	37050325	C, T	MLH1
chr3	37050415	37050416	A	MLH1
chr3	37053363	37053364	C, G	MLH1
chr3	37053486	37053487	C, T	MLH1
chr3	37053549	37053550	A, G	MLH1
chr3	37053567	37053568	A, G	MLH1
chr3	37067239	37067240	A, T	MLH1
chr3	37083739	37083740	A, G	MLH1
chr3	37092024	37092025	C, T	MLH1
chr3	37107129	37107130	A, C	MLH1
chr3	38180226	38180227	C, G	MYD88
chr3	41266012	41266013	A, G	CTNNB1
chr3	41266622	41266623	C, T	CTNNB1
chr3	41275349	41275350	C, T	CTNNB1
chr3	41275804	41275805	A, G	CTNNB1
chr3	41280826	41280827	C, T	CTNNB1
chr3	46414556	46414557	A, T	CCR5
chr3	46415060	46415061	A, G	CCR5
chr3	46415396	46415397	C, T	CCR5
chr3	46480800	46480801	A, G	LTF
chr3	46480957	46480958	C, G	LTF
chr3	46482860	46482861	A, G	LTF
chr3	46482979	46482980	A, T	LTF
chr3	46484963	46484964	A, G	LTF
chr3	46488853	46488854	C, T	LTF
chr3	46488935	46488936	C, T	LTF
chr3	46490365	46490366	A, G	LTF
chr3	46490455	46490456	A, G	LTF
chr3	46495715	46495716	C, T	LTF
chr3	46496853	46496854	A, G	LTF
chr3	46497367	46497368	G, T	LTF
chr3	46497490	46497491	A, G	LTF
chr3	46501099	46501100	A, C	LTF
chr3	46501123	46501124	C, T	LTF
chr3	46501167	46501168	A, T	LTF
chr3	46501212	46501213	C, T	LTF
chr3	46501267	46501268	C, T	LTF
chr3	46509711	46509712	A, G	LTF
chr3	47098587	47098588	A, C	SETD2
chr3	47103866	47103867	G, T	SETD2
chr3	47108653	47108654	C, T	SETD2
chr3	47125384	47125385	A, G	SETD2
chr3	47144880	47144881	A, T	SETD2
chr3	47161805	47161806	A, T	SETD2
chr3	47162660	47162661	A, G	SETD2
chr3	47162876	47162877	G, T	SETD2
chr3	47162885	47162886	C, T	SETD2
chr3	47163421	47163422	C, G	SETD2
chr3	47163522	47163523	C, T	SETD2
chr3	47163582	47163583	A, G	SETD2
chr3	47165547	47165548	A, G	SETD2
chr3	47165568	47165569	A, G	SETD2
chr3	49924939	49924940	C, T	MST1R
chr3	49928034	49928035	A, G	MST1R
chr3	49928613	49928614	A, T	MST1R
chr3	49933239	49933240	A, G	MST1R
chr3	49933460	49933461	C, T	MST1R
chr3	49933615	49933616	C, T	MST1R
chr3	49935502	49935503	A, T	MST1R
chr3	49935525	49935526	G, T	MST1R
chr3	49936101	49936102	C, T	MST1R
chr3	49936607	49936608	C, T	MST1R
chr3	49940077	49940078	C, T	MST1R
chr3	49940498	49940499	A, G	MST1R
chr3	49940811	49940812	G, T	MST1R
chr3	52255919	52255920	C, T	TLR9
chr3	52256696	52256697	C, T	TLR9
chr3	52257890	52257891	G, T	TLR9
chr3	52436258	52436259	C, G	BAP1
chr3	52436266	52436267	C, T	BAP1
chr3	52437205	52437206	A, G	BAP1
chr3	52437257	52437258	C, T	BAP1
chr3	52437747	52437748	A, C	BAP1
chr3	52440268	52440269	C, T	BAP1
chr3	52584714	52584715	A, G	PBRM1
chr3	52584786	52584787	C, T	PBRM1
chr3	52610650	52610651	A, T	PBRM1
chr3	52620713	52620714	G, T	PBRM1
chr3	52620744	52620745	A, G	PBRM1
chr3	52643306	52643307	A, G	PBRM1
chr3	52643684	52643685	C, T	PBRM1
chr3	52658996	52658997	A, C	PBRM1
chr3	52668637	52668638	A, G	PBRM1
chr3	52668775	52668776	A, G	PBRM1
chr3	52702505	52702506	C, T	PBRM1
chr3	52712458	52712459	C, T	PBRM1
chr3	69928509	69928510	A, G	MITF
chr3	69985837	69985838	A, G	MITF
chr3	70014383	70014384	A, G	MITF
chr3	70014386	70014387	A, G	MITF
chr3	70014446	70014447	C, T	MITF
chr3	89156883	89156884	C, G	EPHA3
chr3	89456513	89456514	A, G	EPHA3
chr3	89456554	89456555	A, T	EPHA3
chr3	89480264	89480265	A, G	EPHA3
chr3	89498427	89498428	A, G	EPHA3
chr3	89521643	89521644	C, T	EPHA3
chr3	89521692	89521693	C, T	EPHA3
chr3	89521724	89521725	C, T	EPHA3
chr3	96533682	96533683	C, T	EPHA6
chr3	96533867	96533868	C, G	EPHA6
chr3	96533873	96533874	C, T	EPHA6
chr3	96963003	96963004	C, T	EPHA6
chr3	97185265	97185266	G, T	EPHA6
chr3	97194241	97194242	C, T	EPHA6
chr3	97194316	97194317	G, T	EPHA6
chr3	97202934	97202935	C, G	EPHA6
chr3	97311482	97311483	C, T	EPHA6
chr3	97331268	97331269	A, C	EPHA6
chr3	97365073	97365074	A, G	EPHA6
chr3	97365123	97365124	A, G	EPHA6
chr3	119582290	119582291	A, G	GSK3B
chr3	119720979	119720980	A, T	GSK3B
chr3	124456741	124456742	C, G	UMPS
chr3	124458925	124458926	A, G	UMPS
chr3	124458937	124458938	A, T	UMPS
chr3	124462777	124462778	A, G	UMPS
chr3	124462807	124462808	C, T	UMPS
chr3	124462823	124462824	A, G	UMPS
chr3	124462958	124462959	A, G	UMPS
chr3	124483189	124483190	A, G	ITGB5
chr3	124485234	124485235	A, G	ITGB5
chr3	124492733	124492734	C, T	ITGB5
chr3	124515307	124515308	A, G	ITGB5
chr3	124515313	124515314	A, G	ITGB5
chr3	124515394	124515395	A, G	ITGB5
chr3	124515495	124515496	C, T	ITGB5
chr3	124515508	124515509	A, G	ITGB5
chr3	124515635	124515636	C, T	ITGB5
chr3	124540192	124540193	A, G	ITGB5
chr3	124605735	124605736	C, T	ITGB5
chr3	124606473	124606474	A, G	ITGB5
chr3	124606508	124606509	A, G	ITGB5
chr3	124606535	124606536	C, T	ITGB5
chr3	128200805	128200806	A, G	GATA2
chr3	128204692	128204693	C, G	GATA2
chr3	128204876	128204877	C, G	GATA2
chr3	128204950	128204951	C, T	GATA2
chr3	128205859	128205860	C, G	GATA2
chr3	132050616	132050617	A, T	ACPP
chr3	132050623	132050624	A, G	ACPP
chr3	132063913	132063914	A, T	ACPP
chr3	132068830	132068831	C, T	ACPP
chr3	132068844	132068845	C, T	ACPP
chr3	132068875	132068876	A, G	ACPP
chr3	132068924	132068925	A, T	ACPP
chr3	132071536	132071537	A, C	ACPP
chr3	132071601	132071602	T	ACPP
chr3	132075706	132075707	A, G	ACPP
chr3	132075742	132075743	C, G	ACPP
chr3	132075745	132075746	A, G	ACPP
chr3	132075758	132075759	C, T	ACPP
chr3	134514578	134514579	C, T	EPHB1
chr3	134644634	134644635	C, T	EPHB1
chr3	134644635	134644636	G, T	EPHB1
chr3	134670523	134670524	C, T	EPHB1
chr3	134851604	134851605	C, T	EPHB1
chr3	134851715	134851716	C, T	EPHB1
chr3	134898741	134898742	C, T	EPHB1
chr3	134920305	134920306	C, T	EPHB1
chr3	134960158	134960159	C, G	EPHB1
chr3	137743507	137743508	A, T	CLDN18
chr3	138374238	138374239	G, T	PIK3CB
chr3	138384072	138384073	C, T	PIK3CB
chr3	138403666	138403667	C, T	PIK3CB
chr3	138413665	138413666	A, G	PIK3CB
chr3	138433567	138433568	C, T	PIK3CB
chr3	138456725	138456726	A, G	PIK3CB
chr3	138665028	138665029	C, G	FOXL2
chr3	138665042	138665043	A, G	FOXL2
chr3	138665063	138665064	A, G	FOXL2
chr3	142168330	142168331	C, T	ATR
chr3	142178117	142178118	C, G	ATR
chr3	142178143	142178144	C, T	ATR
chr3	142188391	142188392	C, T	ATR
chr3	142217536	142217537	A, G	ATR
chr3	142217656	142217657	A, G	ATR
chr3	142222283	142222284	A, G	ATR
chr3	142231118	142231119	C, T	ATR
chr3	142242984	142242985	C, T	ATR
chr3	142272631	142272632	C, T	ATR
chr3	142272756	142272757	C, T	ATR
chr3	142277535	142277536	A, G	ATR
chr3	142277574	142277575	A, T	ATR
chr3	142280105	142280106	C, G	ATR
chr3	142281611	142281612	A, G	ATR
chr3	142286938	142286939	C, T	ATR
chr3	142287046	142287047	A, T	ATR
chr3	160118659	160118660	C, G	SMC4
chr3	160119820	160119821	C, T	SMC4
chr3	160120451	160120452	C, T	SMC4
chr3	160130109	160130110	A, G	SMC4
chr3	160132135	160132136	A, G	SMC4
chr3	160143938	160143939	C, T	SMC4
chr3	160143942	160143943	A, G	SMC4
chr3	160144028	160144029	A, C	SMC4
chr3	160144031	160144032	A, G	SMC4
chr3	172224725	172224726	C, G	TNFSF10
chr3	172232779	172232780	G, T	TNFSF10
chr3	172241077	172241078	C, T	TNFSF10
chr3	178921311	178921312	C, G	PIK3CA
chr3	178922272	178922273	A, C	PIK3CA
chr3	178922273	178922274	A, C	PIK3CA
chr3	178927409	178927410	A, G	PIK3CA
chr3	178938746	178938747	A, T	PIK3CA
chr3	178952019	178952020	C, T	PIK3CA
chr3	183210264	183210265	A, G	KLHL6
chr3	183210293	183210294	C, T	KLHL6
chr3	183211905	183211906	A, G	KLHL6
chr3	183212025	183212026	C, T	KLHL6
chr3	183217606	183217607	C, T	KLHL6
chr3	183225809	183225810	C, T	KLHL6
chr3	183226024	183226025	C, T	KLHL6
chr3	183226071	183226072	A, G	KLHL6
chr3	183226113	183226114	G, T	KLHL6
chr3	183226185	183226186	C, T	KLHL6
chr3	183226212	183226213	A, G	KLHL6
chr3	185766561	185766562	A, G	ETV5
chr3	185766565	185766566	C, T	ETV5
chr3	185769791	185769792	G, T	ETV5
chr3	185774812	185774813	A, C	ETV5
chr3	185797810	185797811	C, G	ETV5
chr3	187446210	187446211	C, T	BCL6
chr3	187447031	187447032	A, G	BCL6
chr3	187447700	187447701	A, C	BCL6
chr3	189455680	189455681	C, T	TP63
chr3	189587090	189587091	A, G	TP63
chr3	189604148	189604149	G, T	TP63
chr3	189604159	189604160	C, T	TP63
chr3	189607099	189607100	A, C	TP63
chr4	1801510	1801511	C, T	FGFR3
chr4	1801541	1801542	A, G	FGFR3
chr4	1803235	1803236	C, T	FGFR3
chr4	1803250	1803251	C, T	FGFR3
chr4	1803270	1803271	C, G	FGFR3
chr4	1803306	1803307	C, T	FGFR3
chr4	1803384	1803385	C, G	FGFR3
chr4	1803703	1803704	C, T	FGFR3
chr4	1805477	1805478	C, T	FGFR3
chr4	1806039	1806040	C, T	FGFR3
chr4	1806632	1806633	C, T	FGFR3
chr4	1807410	1807411	A, G	FGFR3
chr4	1807477	1807478	G, T	FGFR3
chr4	1807710	1807711	C, T	FGFR3
chr4	1807893	1807894	A, G	FGFR3
chr4	1807921	1807922	A, G	FGFR3
chr4	1809275	1809276	C, T	FGFR3
chr4	1809348	1809349	A, G	FGFR3
chr4	15835843	15835844	A, C	CD38
chr4	15835982	15835983	C, T	CD38
chr4	15839792	15839793	A, G	CD38
chr4	15850109	15850110	A, G	CD38
chr4	48139564	48139565	A, C	TEC
chr4	48147308	48147309	C, T	TEC
chr4	48148408	48148409	A, G	TEC
chr4	48148434	48148435	A, G	TEC
chr4	48152861	48152862	A, C	TEC
chr4	48152920	48152921	C, T	TEC
chr4	48165756	48165757	A, G	TEC
chr4	48165833	48165834	C, T	TEC
chr4	48169768	48169769	A, G	TEC
chr4	48169774	48169775	C, T	TEC
chr4	48170652	48170653	C, T	TEC
chr4	48170668	48170669	A, G	TEC
chr4	48172217	48172218	C, T	TEC
chr4	48172265	48172266	A, G	TEC
chr4	48173546	48173547	A, G	TEC
chr4	48178063	48178064	A, C	TEC
chr4	55124869	55124870	C, T	PDGFRA
chr4	55125057	55125058	A, T	PDGFRA
chr4	55129830	55129831	C, T	PDGFRA
chr4	55130077	55130078	C, T	PDGFRA
chr4	55133714	55133715	A, G	PDGFRA
chr4	55133725	55133726	G, T	PDGFRA
chr4	55133805	55133806	A, G	PDGFRA
chr4	55138642	55138643	A, G	PDGFRA
chr4	55139770	55139771	C, T	PDGFRA
chr4	55141054	55141055	A, G	PDGFRA
chr4	55143576	55143577	A, G	PDGFRA
chr4	55145112	55145113	A, G	PDGFRA
chr4	55151507	55151508	G, T	PDGFRA
chr4	55151508	55151509	C, T	PDGFRA
chr4	55151710	55151711	A, C	PDGFRA
chr4	55152039	55152040	C, T	PDGFRA
chr4	55161253	55161254	C, T	PDGFRA
chr4	55524303	55524304	C, T	KIT
chr4	55561861	55561862	G, T	KIT
chr4	55564643	55564644	G	KIT
chr4	55575592	55575593	C, T	KIT
chr4	55597457	55597458	A, G	KIT
chr4	55599267	55599268	C, T	KIT
chr4	55602764	55602765	C, G	KIT
chr4	55604638	55604639	C, T	KIT
chr4	55946170	55946171	A, G	KDR
chr4	55956224	55956225	C, T	KDR
chr4	55961158	55961159	C, T	KDR
chr4	55961872	55961873	C, T	KDR
chr4	55964834	55964835	C, T	KDR
chr4	55968052	55968053	A, C	KDR
chr4	55970781	55970782	A, G	KDR
chr4	55970962	55970963	A, G	KDR
chr4	55972973	55972974	A, T	KDR
chr4	55973931	55973932	A, C	KDR
chr4	55979557	55979558	C, T	KDR
chr4	55987392	55987393	C, G	KDR
chr4	55991460	55991461	A, C	KDR
chr4	66197803	66197804	C, T	EPHA5
chr4	66201633	66201634	A, G	EPHA5
chr4	66217077	66217078	A, G	EPHA5
chr4	66218755	66218756	C, T	EPHA5
chr4	66230726	66230727	A, T	EPHA5
chr4	66231698	66231699	A, G	EPHA5
chr4	66242660	66242661	A, G	EPHA5
chr4	66280106	66280107	C, G	EPHA5
chr4	66286313	66286314	G	EPHA5
chr4	66467731	66467732	A, G	EPHA5
chr4	66509039	66509040	G, T	EPHA5
chr4	66509084	66509085	G, T	EPHA5
chr4	66535283	66535284	A, G	EPHA5
chr4	68619909	68619910	C, G	GNRHR
chr4	74302799	74302800	A, C	AFP
chr4	74302869	74302870	C, T	AFP
chr4	74309178	74309179	C	AFP
chr4	74310843	74310844	A, G	AFP
chr4	74316376	74316377	A, G	AFP
chr4	74318176	74318177	C, T	AFP
chr4	74319537	74319538	C, G	AFP
chr4	84222207	84222208	A, G	HPSE
chr4	84223454	84223455	A, G	HPSE
chr4	84223460	84223461	C, G	HPSE
chr4	84230032	84230033	C, T	HPSE
chr4	84230618	84230619	C, T	HPSE
chr4	84234228	84234229	A, G	HPSE
chr4	84240460	84240461	G, T	HPSE
chr4	84240653	84240654	A, G	HPSE
chr4	84243548	84243549	A, G	HPSE
chr4	88898940	88898941	C, T	SPP1
chr4	88902691	88902692	C, T	SPP1
chr4	88902724	88902725	A, G	SPP1
chr4	88902850	88902851	C, T	SPP1
chr4	88903773	88903774	A, G	SPP1
chr4	88903852	88903853	C, T	SPP1
chr4	88904004	88904005	A, G	SPP1
chr4	89018564	89018565	A, G	ABCG2
chr4	89020426	89020427	A, C	ABCG2
chr4	89020437	89020438	C, T	ABCG2
chr4	89028283	89028284	A, G	ABCG2
chr4	89034550	89034551	C, T	ABCG2
chr4	89039242	89039243	C, T	ABCG2
chr4	89052322	89052323	G, T	ABCG2
chr4	89053717	89053718	C, T	ABCG2
chr4	89053789	89053790	A, G	ABCG2
chr4	89060908	89060909	C, T	ABCG2
chr4	89080350	89080351	C, G	ABCG2
chr4	89080400	89080401	G, T	ABCG2
chr4	89080413	89080414	G, T	ABCG2
chr4	103446730	103446731	C	NFKB1
chr4	103446736	103446737	A, T	NFKB1
chr4	103514657	103514658	C, T	NFKB1
chr4	103514736	103514737	C, T	NFKB1
chr4	103514740	103514741	C, T	NFKB1
chr4	103518699	103518700	A, G	NFKB1
chr4	103518840	103518841	A, T	NFKB1
chr4	103528816	103528817	G, T	NFKB1
chr4	103533630	103533631	C, G	NFKB1
chr4	103534559	103534560	C, G	NFKB1
chr4	103534577	103534578	A, G	NFKB1
chr4	104027497	104027498	G, T	CENPE
chr4	104030206	104030207	C, T	CENPE
chr4	104059440	104059441	C, T	CENPE
chr4	104059449	104059450	C, T	CENPE
chr4	104059541	104059542	A, G	CENPE
chr4	104061550	104061551	G, T	CENPE
chr4	104061992	104061993	C, G	CENPE
chr4	104063070	104063071	C, T	CENPE
chr4	104066322	104066323	G, T	CENPE
chr4	104066347	104066348	A, G	CENPE
chr4	104066460	104066461	A, G	CENPE
chr4	104067126	104067127	A, G	CENPE
chr4	104067194	104067195	C, T	CENPE
chr4	104068552	104068553	A, T	CENPE
chr4	104070040	104070041	A, G	CENPE
chr4	104070432	104070433	A, T	CENPE
chr4	104079423	104079424	C, T	CENPE
chr4	104080216	104080217	A, C	CENPE
chr4	104081919	104081920	C, T	CENPE
chr4	104082348	104082349	C, T	CENPE
chr4	104096062	104096063	A, G	CENPE
chr4	104102562	104102563	C, T	CENPE
chr4	104104005	104104006	A, G	CENPE
chr4	104107042	104107043	C, T	CENPE
chr4	104107057	104107058	G, T	CENPE
chr4	104115716	104115717	A, G	CENPE
chr4	104116431	104116432	A, G	CENPE
chr4	104117190	104117191	A, G	CENPE
chr4	104117218	104117219	C, T	CENPE
chr4	104117303	104117304	C, T	CENPE
chr4	104118026	104118027	G, T	CENPE
chr4	106111580	106111581	A, G	TET2
chr4	106155184	106155185	C, G	TET2
chr4	106155704	106155705	C, T	TET2
chr4	106155750	106155751	A, G	TET2
chr4	106156162	106156163	A, G	TET2
chr4	106156186	106156187	C, T	TET2
chr4	106156982	106156983	A, G	TET2
chr4	106158188	106158189	A, G	TET2
chr4	106158214	106158215	C, T	TET2
chr4	106158215	106158216	A, G	TET2
chr4	106190731	106190732	A, C	TET2
chr4	106196950	106196951	A, G	TET2
chr4	106196999	106197000	A, G	TET2
chr4	110638809	110638810	C, T	PLA2G12A
chr4	123377481	123377482	A, C	IL2
chr4	123747941	123747942	C, G	FGF2
chr4	123747946	123747947	A, G	FGF2
chr4	123748085	123748086	C, T	FGF2
chr4	123748523	123748524	C, T	FGF2
chr4	123797427	123797428	G, T	FGF2
chr4	128802344	128802345	A, G	PLK4
chr4	128814491	128814492	A, G	PLK4
chr4	128819617	128819618	A, G	PLK4
chr4	139104413	139104414	C, T	SLC7A11
chr4	139104414	139104415	C, T	SLC7A11
chr4	139106248	139106249	C, T	SLC7A11
chr4	139135798	139135799	C, T	SLC7A11
chr4	139140387	139140388	A, G	SLC7A11
chr4	139140493	139140494	C, G	SLC7A11
chr4	139153505	139153506	G, T	SLC7A11
chr4	139153538	139153539	A, T	SLC7A11
chr4	148441138	148441139	A, G	EDNRA
chr4	148461036	148461037	C, T	EDNRA
chr4	148461072	148461073	A, G	EDNRA
chr4	153303353	153303354	A, C	FBXW7
chr4	153332558	153332559	C, T	FBXW7
chr4	154624655	154624656	C, T	TLR2
chr4	154625408	154625409	C, T	TLR2
chr4	154626401	154626402	A, G	TLR2
chr4	177605222	177605223	A, G	VEGFC
chr4	177608706	177608707	C, T	VEGFC
chr4	177649119	177649120	C, T	VEGFC
chr4	177713287	177713288	A, G	VEGFC
chr4	185552134	185552135	C, T	CASP3
chr4	185553097	185553098	G, T	CASP3
chr4	185556617	185556618	C, T	CASP3
chr4	185559486	185559487	C, G	CASP3
chr4	185565619	185565620	G, T	CASP3
chr4	185565620	185565621	C, T	CASP3
chr4	187003677	187003678	A, G	TLR3
chr4	187003758	187003759	G, T	TLR3
chr4	187004073	187004074	C, T	TLR3
chr4	187004516	187004517	A, G	TLR3
chr4	187004543	187004544	C, T	TLR3
chr4	187004766	187004767	A, C	TLR3
chr4	187005048	187005049	A, T	TLR3
chr4	187005864	187005865	C, T	TLR3
chr4	187005867	187005868	G, T	TLR3
chr5	1254450	1254451	C, T	TERT
chr5	1255519	1255520	A, G	TERT
chr5	1268579	1268580	C, T	TERT
chr5	1279504	1279505	A, G	TERT
chr5	1279626	1279627	A, G	TERT
chr5	1280251	1280252	A, G	TERT
chr5	1282653	1282654	A, G	TERT
chr5	1294085	1294086	C, T	TERT
chr5	1294165	1294166	C, T	TERT
chr5	35068247	35068248	C, G	PRLR
chr5	35072711	35072712	G, T	PRLR
chr5	35084646	35084647	C, T	PRLR
chr5	35089576	35089577	A, G	PRLR
chr5	35857176	35857177	C, G	IL7R
chr5	35857206	35857207	C, T	IL7R
chr5	35857234	35857235	C, G	IL7R
chr5	35861023	35861024	A, G	IL7R
chr5	35861067	35861068	C, T	IL7R
chr5	35871189	35871190	A, G	IL7R
chr5	35871272	35871273	C, T	IL7R
chr5	35873567	35873568	A, C	IL7R
chr5	35873604	35873605	A, G	IL7R
chr5	35874574	35874575	C, T	IL7R
chr5	35875592	35875593	A, T	IL7R
chr5	35876273	35876274	A, G	IL7R
chr5	35876438	35876439	A, G	IL7R
chr5	35876448	35876449	C, T	IL7R
chr5	38942448	38942449	A, G	RICTOR
chr5	38950775	38950776	A, G	RICTOR
chr5	38954993	38954994	C, T	RICTOR
chr5	38955795	38955796	A, G	RICTOR
chr5	38958876	38958877	C, T	RICTOR
chr5	38959419	38959420	A, G	RICTOR
chr5	38962542	38962543	A, G	RICTOR
chr5	38967376	38967377	C, T	RICTOR
chr5	44305091	44305092	A, T	FGF10
chr5	44305132	44305133	A, G	FGF10
chr5	44388816	44388817	C, T	FGF10
chr5	50040669	50040670	C	PARP8
chr5	50045966	50045967	G, T	PARP8
chr5	50057728	50057729	A, G, T	PARP8
chr5	50074530	50074531	A, G	PARP8
chr5	50091151	50091152	A, G	PARP8
chr5	50091161	50091162	A, G	PARP8
chr5	50091169	50091170	C, T	PARP8
chr5	50118249	50118250	A, G	PARP8
chr5	50122644	50122645	G, T	PARP8
chr5	50128569	50128570	A, T	PARP8
chr5	50129160	50129161	C, T	PARP8
chr5	52084299	52084300	A, G	ITGA1
chr5	52157373	52157374	C, T	ITGA1
chr5	52177742	52177743	A, G	ITGA1
chr5	52193286	52193287	C, T	ITGA1
chr5	52193390	52193391	C, T	ITGA1
chr5	52201721	52201722	C, T	ITGA1
chr5	52201744	52201745	C, T	ITGA1
chr5	52214580	52214581	A, G	ITGA1
chr5	52216216	52216217	C, T	ITGA1
chr5	52218693	52218694	C, T	ITGA1
chr5	52223349	52223350	A, G	ITGA1
chr5	52228024	52228025	A, G	ITGA1
chr5	52229744	52229745	G, T	ITGA1
chr5	52235644	52235645	C, T	ITGA1
chr5	52235801	52235802	G, T	ITGA1
chr5	52240809	52240810	A, G	ITGA1
chr5	56111444	56111445	A, G	MAP3K1
chr5	56111480	56111481	C, T	MAP3K1
chr5	56111564	56111565	A, G	MAP3K1
chr5	56111750	56111751	C, G	MAP3K1
chr5	56161786	56161787	A, G	MAP3K1
chr5	56168789	56168790	A, G	MAP3K1
chr5	56171088	56171089	A, G	MAP3K1
chr5	56177442	56177443	A, G	MAP3K1
chr5	56177742	56177743	A, G	MAP3K1
chr5	56178216	56178217	A, C	MAP3K1
chr5	56179340	56179341	A, G	MAP3K1
chr5	67522721	67522722	C, T	PIK3R1
chr5	67535721	67535722	C, T	PIK3R1
chr5	67535788	67535789	C, T	PIK3R1
chr5	67535809	67535810	A, C	PIK3R1
chr5	67575547	67575548	C, T	PIK3R1
chr5	67588147	67588148	A, G	PIK3R1
chr5	67589037	67589038	A, G	PIK3R1
chr5	67593362	67593363	C, T	PIK3R1
chr5	68530702	68530703	A, G	CDK7
chr5	68531252	68531253	C, T	CDK7
chr5	79950402	79950403	C, T	DHFR
chr5	79950496	79950497	C, T	MSH3
chr5	79950507	79950508	C, T	MSH3
chr5	79950511	79950512	A, G	MSH3
chr5	79950716	79950717	C, T	MSH3
chr5	79950723	79950724	C, G	MSH3
chr5	79950726	79950727	C, G	MSH3
chr5	79952389	79952390	C, T	MSH3
chr5	79960954	79960955	A, G	MSH3
chr5	79966028	79966029	A, G	MSH3
chr5	79968257	79968258	A, T	MSH3
chr5	79968270	79968271	A, G	MSH3
chr5	80024782	80024783	A, G	MSH3
chr5	80149980	80149981	A, G	MSH3
chr5	112043383	112043384	G, T	APC
chr5	112043491	112043492	A, C	APC
chr5	112111309	112111310	A, T	APC
chr5	112116631	112116632	C, T	APC
chr5	112136946	112136947	A, T	APC
chr5	112162853	112162854	C, T	APC
chr5	112164560	112164561	A, G	APC
chr5	112164620	112164621	A, G	APC
chr5	112173898	112173899	C, T	APC
chr5	112175022	112175023	A, G	APC
chr5	112175769	112175770	A, G	APC
chr5	112176324	112176325	A, G	APC
chr5	112176558	112176559	G, T	APC
chr5	112176755	112176756	A, T	APC
chr5	112177170	112177171	A, G	APC
chr5	112178994	112178995	A, G	APC
chr5	112198127	112198128	C, T	APC
chr5	131409581	131409582	A, G	CSF2
chr5	131409596	131409597	A, G	CSF2
chr5	131411459	131411460	C, T	CSF2
chr5	131994030	131994031	A, C	IL13
chr5	131995078	131995079	C, T	IL13
chr5	131995963	131995964	A, G	IL13
chr5	132009709	132009710	C, T	IL4
chr5	132009786	132009787	A, G	IL4
chr5	132018131	132018132	A, G	IL4
chr5	132018168	132018169	A, C	IL4
chr5	138117937	138117938	A, G	CTNNA1
chr5	138147948	138147949	G, T	CTNNA1
chr5	138148035	138148036	A, G	CTNNA1
chr5	138221988	138221989	C, G	CTNNA1
chr5	138266545	138266546	A, G	CTNNA1
chr5	138268310	138268311	A, G	CTNNA1
chr5	139722344	139722345	A, G	HBEGF
chr5	139725960	139725961	A, G	HBEGF
chr5	141975066	141975067	A, C	FGF1
chr5	149433856	149433857	C, G	CSF1R
chr5	149435607	149435608	C, G	CSF1R
chr5	149435758	149435759	A, G	CSF1R
chr5	149439257	149439258	A, G	CSF1R
chr5	149447765	149447766	A, G	CSF1R
chr5	149447770	149447771	A, G	CSF1R
chr5	149450131	149450132	C, T	CSF1R
chr5	149456810	149456811	A, G	CSF1R
chr5	149456892	149456893	C, T	CSF1R
chr5	149456994	149456995	A, C	CSF1R
chr5	149457677	149457678	A, G	CSF1R
chr5	149457682	149457683	C, T	CSF1R
chr5	149459789	149459790	C	CSF1R
chr5	149460342	149460343	A, G	CSF1R
chr5	149460444	149460445	A, G	CSF1R
chr5	149460552	149460553	A, G	CSF1R
chr5	149465862	149465863	A, G	CSF1R
chr5	149465890	149465891	C, T	CSF1R
chr5	149495394	149495395	C, T	PDGFRB
chr5	149495536	149495537	A, G	PDGFRB
chr5	149497176	149497177	C, T	PDGFRB
chr5	149497198	149497199	A, C	PDGFRB
chr5	149497227	149497228	A, G	PDGFRB
chr5	149499671	149499672	C, T	PDGFRB
chr5	149499725	149499726	A, T	PDGFRB
chr5	149500401	149500402	C, T	PDGFRB
chr5	149504257	149504258	C, T	PDGFRB
chr5	149505053	149505054	C, T	PDGFRB
chr5	149509445	149509446	C, T	PDGFRB
chr5	149509507	149509508	A, G	PDGFRB
chr5	149510045	149510046	A, C	PDGFRB
chr5	149513402	149513403	C, T	PDGFRB
chr5	149515379	149515380	A, G	PDGFRB
chr5	149515396	149515397	A, T	PDGFRB
chr5	149781564	149781565	C, T	CD74
chr5	149781626	149781627	C, T	CD74
chr5	149781994	149781995	A, G	CD74
chr5	149785923	149785924	C, T	CD74
chr5	149785933	149785934	C, G	CD74
chr5	149792336	149792337	C, T	CD74
chr5	156607956	156607957	A, C	ITK
chr5	156636026	156636027	G, T	ITK
chr5	156644938	156644939	A, G	ITK
chr5	156649816	156649817	A, G	ITK
chr5	156665280	156665281	C, T	ITK
chr5	156670822	156670823	A, G	ITK
chr5	156675843	156675844	C, T	ITK
chr5	156679572	156679573	A, G	ITK
chr5	156679575	156679576	C, T	ITK
chr5	162866547	162866548	C, T	CCNG1
chr5	162870635	162870636	C, G	CCNG1
chr5	162870725	162870726	C, G	CCNG1
chr5	170819886	170819887	A, G	NPM1
chr5	170837456	170837457	A, G	NPM1
chr5	175110280	175110281	C, T	HRH2
chr5	175110778	175110779	A, G	HRH2
chr5	175112619	175112620	C, T	HRH2
chr5	176516541	176516542	C, T	FGFR4
chr5	176516630	176516631	A, G	FGFR4
chr5	176516952	176516953	A, G	FGFR4
chr5	176516953	176516954	C, T	FGFR4
chr5	176517291	176517292	A, G	FGFR4
chr5	176517325	176517326	C, T	FGFR4
chr5	176517460	176517461	G, T	FGFR4
chr5	176517796	176517797	C, T	FGFR4
chr5	176518036	176518037	A, G	FGFR4
chr5	176518765	176518766	C, T	FGFR4
chr5	176518783	176518784	C, T	FGFR4
chr5	176519515	176519516	A, G	FGFR4
chr5	176520242	176520243	A, G	FGFR4
chr5	176522561	176522562	C, T	FGFR4
chr5	176523185	176523186	A, G	FGFR4
chr5	176523561	176523562	A, C	FGFR4
chr5	176523596	176523597	A, G	FGFR4
chr5	176524702	176524703	A, T	FGFR4
chr5	180030324	180030325	C, T	FLT4
chr5	180035993	180035994	A, G	FLT4
chr5	180039605	180039606	C, T	FLT4
chr5	180039638	180039639	A, G	FLT4
chr5	180043387	180043388	A, G	FLT4
chr5	180043438	180043439	A, G	FLT4
chr5	180046343	180046344	C, G	FLT4
chr5	180046635	180046636	C, G	FLT4
chr5	180048034	180048035	C, T	FLT4
chr5	180049807	180049808	C, T	FLT4
chr5	180051002	180051003	C, T	FLT4
chr5	180052945	180052946	A, G	FLT4
chr5	180053089	180053090	A, G	FLT4
chr5	180053096	180053097	C, T	FLT4
chr5	180056043	180056044	A, G	FLT4
chr5	180056862	180056863	C, T	FLT4
chr5	180056985	180056986	C, T	FLT4
chr5	180057230	180057231	A, C	FLT4
chr5	180057248	180057249	A, G	FLT4
chr5	180057292	180057293	C, T	FLT4
chr5	180058760	180058761	A, C	FLT4
chr5	180076459	180076460	C, G	FLT4
chr6	393358	393359	C, G	IRF4
chr6	395888	395889	A, G	IRF4
chr6	398774	398775	A, G	IRF4
chr6	405145	405146	C, G	IRF4
chr6	18130992	18130993	C, T	TPMT
chr6	18134020	18134021	A, C	TPMT
chr6	18134077	18134078	A, C	TPMT
chr6	18139227	18139228	C, T	TPMT
chr6	18139801	18139802	A, T	TPMT
chr6	26087778	26087779	G	HFE
chr6	26091178	26091179	C, G	HFE
chr6	26091335	26091336	C, T	HFE
chr6	26092864	26092865	C, G	HFE
chr6	26094366	26094367	A, G	HFE
chr6	26094432	26094433	C, T	HFE
chr6	26094514	26094515	C, T	HFE
chr6	26096747	26096748	C, G	HFE
chr6	31540555	31540556	C, T	LTA
chr6	31540756	31540757	A, C	LTA
chr6	31543604	31543605	G, T	TNF
chr6	33288074	33288075	A, C	DAXX
chr6	33288270	33288271	A, G	DAXX
chr6	33288505	33288506	A, C	DAXX
chr6	35391786	35391787	C, T	PPARD
chr6	35420266	35420267	C, T	FANCE
chr6	35423661	35423662	A, C	FANCE
chr6	35423885	35423886	C, T	FANCE
chr6	35425415	35425416	A, G	FANCE
chr6	35426131	35426132	A, G	FANCE
chr6	35426174	35426175	C, T	FANCE
chr6	35430685	35430686	A, G	FANCE
chr6	37138304	37138305	G	PIM1
chr6	37138443	37138444	C, T	PIM1
chr6	37139321	37139322	C, T	PIM1
chr6	37141695	37141696	C	PIM1
chr6	41533572	41533573	A, G	FOXP4
chr6	41533578	41533579	A, C	FOXP4
chr6	41554992	41554993	C, G	FOXP4
chr6	41555211	41555212	C, T	FOXP4
chr6	41557566	41557567	C, T	FOXP4
chr6	41557646	41557647	A, C	FOXP4
chr6	41557944	41557945	A, G	FOXP4
chr6	41558042	41558043	C, T	FOXP4
chr6	41558951	41558952	C, T	FOXP4
chr6	41565471	41565472	C, T	FOXP4
chr6	41565580	41565581	C, T	FOXP4
chr6	41566508	41566509	A, G	FOXP4
chr6	41903781	41903782	A, C	CCND3
chr6	41903782	41903783	A, G	CCND3
chr6	41904482	41904483	C, T	CCND3
chr6	41904955	41904956	A, G	CCND3
chr6	44187385	44187386	C, T	SLC29A1
chr6	44197801	44197802	A, G	SLC29A1
chr6	44198311	44198312	A, G	SLC29A1
chr6	44199201	44199202	C, T	SLC29A1
chr6	44217373	44217374	G, T	HSP90AB1
chr6	44219098	44219099	G, T	HSP90AB1
chr6	44219709	44219710	A, C	HSP90AB1
chr6	44219925	44219926	A, G	HSP90AB1
chr6	44221068	44221069	C	HSP90AB1
chr6	44221141	44221142	C, T	HSP90AB1
chr6	44221166	44221167	G, T	HSP90AB1
chr6	74405948	74405949	C, G	CD109
chr6	74405973	74405974	C, G	CD109
chr6	74407181	74407182	G, T	CD109
chr6	74432922	74432923	C, T	CD109
chr6	74440271	74440272	A, C	CD109
chr6	74466376	74466377	C, T	CD109
chr6	74491001	74491002	G, T	CD109
chr6	74493431	74493432	A, C	CD109
chr6	74493597	74493598	A, G	CD109
chr6	74495202	74495203	A, G	CD109
chr6	74495256	74495257	A, G	CD109
chr6	74496993	74496994	G, T	CD109
chr6	74497008	74497009	A, G	CD109
chr6	74497101	74497102	A, G	CD109
chr6	74497151	74497152	A, G	CD109
chr6	74513053	74513054	A, G	CD109
chr6	74517983	74517984	A, G	CD109
chr6	74519701	74519702	G, T	CD109
chr6	74520862	74520863	C, T	CD109
chr6	74521946	74521947	C, T	CD109
chr6	74521947	74521948	G, T	CD109
chr6	74521998	74521999	A, T	CD109
chr6	74524723	74524724	A, G	CD109
chr6	74524756	74524757	G, T	CD109
chr6	74530289	74530290	A, G	CD109
chr6	74533191	74533192	G, T	CD109
chr6	93967850	93967851	C, T	EPHA7
chr6	93982099	93982100	C, T	EPHA7
chr6	93982123	93982124	A, G	EPHA7
chr6	94067980	94067981	C, T	EPHA7
chr6	94120218	94120219	A, G	EPHA7
chr6	94120638	94120639	C, T	EPHA7
chr6	94124352	94124353	A, C	EPHA7
chr6	94124529	94124530	A, C	EPHA7
chr6	106547371	106547372	C, G	PRDM1
chr6	106552891	106552892	C, G	PRDM1
chr6	106555024	106555025	A, G	PRDM1
chr6	106555194	106555195	A, G	PRDM1
chr6	111995665	111995666	A, G	FYN
chr6	112015558	112015559	C, T	FYN
chr6	112015740	112015741	C, T	FYN
chr6	112015822	112015823	G, T	FYN
chr6	112375643	112375644	A, G	WISP3
chr6	112381262	112381263	C, T	WISP3
chr6	112382222	112382223	A, T	WISP3
chr6	112382312	112382313	G, T	WISP3
chr6	112382322	112382323	C, T	WISP3
chr6	112382381	112382382	C, T	WISP3
chr6	112388226	112388227	A, G	WISP3
chr6	112390564	112390565	A, G	WISP3
chr6	112390649	112390650	A, C	WISP3
chr6	114265586	114265587	C, T	HDAC2
chr6	114279976	114279977	C, T	HDAC2
chr6	114281188	114281189	C, T	HDAC2
chr6	114281235	114281236	C, T	HDAC2
chr6	114292184	114292185	C, T	HDAC2
chr6	114292361	114292362	C, G	HDAC2
chr6	117622183	117622184	C, G	ROS1
chr6	117622187	117622188	G, T	ROS1
chr6	117622232	117622233	C, T	ROS1
chr6	117632150	117632151	A, G	ROS1
chr6	117638254	117638255	G, T	ROS1
chr6	117639300	117639301	C, T	ROS1
chr6	117639418	117639419	C, T	ROS1
chr6	117642456	117642457	A, G	ROS1
chr6	117645661	117645662	C, T	ROS1
chr6	117650531	117650532	C, G	ROS1
chr6	117665327	117665328	G, T	ROS1
chr6	117678082	117678083	A, G	ROS1
chr6	117681088	117681089	C, T	ROS1
chr6	117683820	117683821	A, G	ROS1
chr6	117686839	117686840	C, T	ROS1
chr6	117704606	117704607	C, T	ROS1
chr6	117710572	117710573	C, G	ROS1
chr6	117710660	117710661	C, T	ROS1
chr6	117714345	117714346	C, G	ROS1
chr6	117717347	117717348	C, T	ROS1
chr6	117718217	117718218	A, G	ROS1
chr6	117718302	117718303	A, G	ROS1
chr6	117724378	117724379	C, T	ROS1
chr6	117724461	117724462	A, C	ROS1
chr6	117725577	117725578	A, T	ROS1
chr6	117730818	117730819	A, G	ROS1
chr6	117730898	117730899	G, T	ROS1
chr6	138196065	138196066	G, T	TNFAIP3
chr6	138196816	138196817	C, G	TNFAIP3
chr6	138197328	138197329	C, T	TNFAIP3
chr6	138197330	138197331	A, C	TNFAIP3
chr6	138202377	138202378	C, T	TNFAIP3
chr6	152129275	152129276	A, G	ESR1
chr6	152129307	152129308	C, G	ESR1
chr6	152130313	152130314	C, T	ESR1
chr6	152201874	152201875	C, T	ESR1
chr6	152265521	152265522	C, G	ESR1
chr6	152419986	152419987	A, G	ESR1
chr6	152446315	152446316	C, T	ESR1
chr6	152446319	152446320	C, T	ESR1
chr6	152446486	152446487	C, T	ESR1
chr6	160106087	160106088	A, C	SOD2
chr6	160113598	160113599	G, T	SOD2
chr6	160113871	160113872	A, G	SOD2
chr6	160114167	160114168	C, T	SOD2
chr6	160114260	160114261	C, G	SOD2
chr6	160430209	160430210	A, T	IGF2R
chr6	160448263	160448264	A, G	IGF2R
chr6	160448314	160448315	C, T	IGF2R
chr6	160448323	160448324	C, G	IGF2R
chr6	160453560	160453561	G, T	IGF2R
chr6	160453568	160453569	A, G	IGF2R
chr6	160464288	160464289	A, G	IGF2R
chr6	160468179	160468180	A, G	IGF2R
chr6	160468277	160468278	A, G	IGF2R
chr6	160468308	160468309	A, G	IGF2R
chr6	160469541	160469542	A, G	IGF2R
chr6	160479881	160479882	A, G	IGF2R
chr6	160479923	160479924	C, T	IGF2R
chr6	160482591	160482592	C, T	IGF2R
chr6	160482928	160482929	C, G	IGF2R
chr6	160483732	160483733	A, G	IGF2R
chr6	160485495	160485496	A, G	IGF2R
chr6	160493833	160493834	A, G	IGF2R
chr6	160494408	160494409	A, G	IGF2R
chr6	160499212	160499213	C, T	IGF2R
chr6	160499380	160499381	C, T	IGF2R
chr6	160500811	160500812	C, T	IGF2R
chr6	160510101	160510102	A, G	IGF2R
chr6	160524772	160524773	A, T	IGF2R
chr6	160524810	160524811	C, T	IGF2R
chr6	160524824	160524825	A, G	IGF2R
chr6	160524875	160524876	A, G	IGF2R
chr6	160953641	160953642	A, G	LPA
chr6	160961136	160961137	C, T	LPA
chr6	160962234	160962235	A, G	LPA
chr6	160969628	160969629	A, G	LPA
chr6	160969737	160969738	C, G	LPA
chr6	161007495	161007496	C, G	LPA
chr6	161007537	161007538	C, G	LPA
chr6	161010765	161010766	A, T	LPA
chr6	161015171	161015172	A, C	LPA
chr6	161016373	161016374	C, T	LPA
chr6	161022168	161022169	C, T	LPA
chr6	161026196	161026197	A, G	LPA
chr6	166571934	166571935	C, T	T
chr6	166572004	166572005	C, T	T
chr6	166572011	166572012	C, T	T
chr6	166574307	166574308	C, T	T
chr6	166574461	166574462	A, G	T
chr6	166579269	166579270	C, T	T
chr6	166580187	166580188	A, G	T
chr6	166580256	166580257	A, G	T
chr7	2946337	2946338	A, G	CARD11
chr7	2951823	2951824	A, G	CARD11
chr7	2954961	2954962	A, G	CARD11
chr7	2956917	2956918	A, C	CARD11
chr7	2957004	2957005	C, T	CARD11
chr7	2959171	2959172	A, G	CARD11
chr7	2962292	2962293	C, G	CARD11
chr7	2962418	2962419	C, T	CARD11
chr7	2963838	2963839	A, G	CARD11
chr7	2963883	2963884	C, T	CARD11
chr7	2966333	2966334	A, G	CARD11
chr7	2966444	2966445	G, T	CARD11
chr7	2966473	2966474	C, G	CARD11
chr7	2968244	2968245	C, T	CARD11
chr7	2968290	2968291	A, G	CARD11
chr7	2968354	2968355	A, G	CARD11
chr7	2968358	2968359	C, T	CARD11
chr7	2969679	2969680	A, G	CARD11
chr7	2969688	2969689	G, T	CARD11
chr7	2974164	2974165	C, T	CARD11
chr7	2976751	2976752	C, T	CARD11
chr7	2976766	2976767	A, G	CARD11
chr7	2976799	2976800	C, T	CARD11
chr7	2985585	2985586	C, G	CARD11
chr7	13950837	13950838	C, T	ETV1
chr7	13971422	13971423	C, T	ETV1
chr7	13975299	13975300	A, G	ETV1
chr7	13978808	13978809	C, T	ETV1
chr7	14017006	14017007	C, T	ETV1
chr7	14017007	14017008	C, G	ETV1
chr7	14025726	14025727	C, T	ETV1
chr7	14025765	14025766	A, T	ETV1
chr7	50367291	50367292	A, C	IKZF1
chr7	50435776	50435777	G, T	IKZF1
chr7	50435902	50435903	A, C	IKZF1
chr7	50436032	50436033	A, G	IKZF1
chr7	50467766	50467767	A, C	IKZF1
chr7	50467773	50467774	A, G	IKZF1
chr7	50467940	50467941	C, T	IKZF1
chr7	55214347	55214348	C, T	EGFR
chr7	55214404	55214405	A, G	EGFR
chr7	55214442	55214443	A, G	EGFR
chr7	55218902	55218903	C, T	EGFR
chr7	55227824	55227825	A, G	EGFR
chr7	55227849	55227850	A, G	EGFR
chr7	55229254	55229255	A, G	EGFR
chr7	55231425	55231426	C, T	EGFR
chr7	55233037	55233038	A, G	EGFR
chr7	55233088	55233089	C, T	EGFR
chr7	55236256	55236257	A, C	EGFR
chr7	55237976	55237977	C, T	EGFR
chr7	55238036	55238037	A, C	EGFR
chr7	55238086	55238087	C, T	EGFR
chr7	55238873	55238874	A, T	EGFR
chr7	55241754	55241755	A, G	EGFR
chr7	55249062	55249063	A, G	EGFR
chr7	55260439	55260440	C, T	EGFR
chr7	55268896	55268897	A, C	EGFR
chr7	55268915	55268916	C, T	EGFR
chr7	65425893	65425894	A, G	GUSB
chr7	81346684	81346685	C, T	HGF
chr7	81359050	81359051	C, T	HGF
chr7	81372323	81372324	C, G	HGF
chr7	81374350	81374351	A, G	HGF
chr7	81386482	81386483	C, T	HGF
chr7	81388041	81388042	C, T	HGF
chr7	86394592	86394593	A, G	GRM3
chr7	86415986	86415987	C, T	GRM3
chr7	86468515	86468516	C, T	GRM3
chr7	87133537	87133538	A, G	ABCB1
chr7	87133803	87133804	A, C	ABCB1
chr7	87138644	87138645	A, G	ABCB1
chr7	87138658	87138659	A, T	ABCB1
chr7	87145808	87145809	A, G	ABCB1
chr7	87160617	87160618	A, C, T	ABCB1
chr7	87168748	87168749	C, T	ABCB1
chr7	87179142	87179143	A, G	ABCB1
chr7	87179442	87179443	A, G	ABCB1
chr7	87193596	87193597	A, G	ABCB1
chr7	87193601	87193602	A, G	ABCB1
chr7	87199563	87199564	A, C	ABCB1
chr7	87229439	87229440	C, T	ABCB1
chr7	87229500	87229501	C, T	ABCB1
chr7	90894384	90894385	A, G	FZD1
chr7	90895943	90895944	C, T	FZD1
chr7	92355032	92355033	A, T	CDK6
chr7	93055752	93055753	A, G	CALCR
chr7	93067398	93067399	G, T	CALCR
chr7	93070810	93070811	C, T	CALCR
chr7	93070949	93070950	C, T	CALCR
chr7	93072952	93072953	C, T	CALCR
chr7	93097973	93097974	A, G	CALCR
chr7	93101649	93101650	A, G	CALCR
chr7	93116298	93116299	A, G	CALCR
chr7	93125109	93125110	C, T	CALCR
chr7	99358614	99358615	A, G	CYP3A4
chr7	99365942	99365943	A, C	CYP3A4
chr7	99367866	99367867	C, G	CYP3A4
chr7	100401097	100401098	A, C	EPHB4
chr7	100403142	100403143	A, G	EPHB4
chr7	100410596	100410597	A, G	EPHB4
chr7	100410655	100410656	C, T	EPHB4
chr7	100410656	100410657	A, G	EPHB4
chr7	100411277	100411278	C, T	EPHB4
chr7	100411286	100411287	A, G	EPHB4
chr7	100411371	100411372	C, T	EPHB4
chr7	100411687	100411688	C, T	EPHB4
chr7	100414786	100414787	C, T	EPHB4
chr7	100416138	100416139	C, T	EPHB4
chr7	100416249	100416250	A, G	EPHB4
chr7	100417363	100417364	A, G	EPHB4
chr7	100420154	100420155	A, G	EPHB4
chr7	100420211	100420212	C, T	EPHB4
chr7	100771716	100771717	A, G	SERPINE1
chr7	100775204	100775205	C, G	SERPINE1
chr7	100775297	100775298	C, T	SERPINE1
chr7	100780384	100780385	C, T	SERPINE1
chr7	100781407	100781408	C, T	SERPINE1
chr7	100781412	100781413	C, T	SERPINE1
chr7	100781444	100781445	G, T	SERPINE1
chr7	100781467	100781468	A, C	SERPINE1
chr7	100781474	100781475	A, C	SERPINE1
chr7	105891671	105891672	A, C	NAMPT
chr7	105903903	105903904	C, T	NAMPT
chr7	106508977	106508978	A, G	PIK3CG
chr7	106508986	106508987	C, T	PIK3CG
chr7	106509330	106509331	A, C	PIK3CG
chr7	106509932	106509933	A, G	PIK3CG
chr7	106513010	106513011	C, T	PIK3CG
chr7	106519942	106519943	C, T	PIK3CG
chr7	106524688	106524689	C, T	PIK3CG
chr7	116339281	116339282	A, G	MET
chr7	116339671	116339672	C, T	MET
chr7	116340261	116340262	A, G	MET
chr7	116340268	116340269	C, T	MET
chr7	116381103	116381104	A, G	MET
chr7	116397571	116397572	A, G	MET
chr7	116411866	116411867	A, G	MET
chr7	116422213	116422214	C, T	MET
chr7	116435767	116435768	C, T	MET
chr7	116436021	116436022	A, G	MET
chr7	116436096	116436097	A, G	MET
chr7	128828957	128828958	G, T	SMO
chr7	128843395	128843396	A, G	SMO
chr7	128845087	128845088	A, G	SMO
chr7	128846222	128846223	A, G	SMO
chr7	128851794	128851795	A, C	SMO
chr7	128851805	128851806	C, G	SMO
chr7	128851979	128851980	A, G	SMO
chr7	140426256	140426257	A, G	BRAF
chr7	140447158	140447159	G, T	BRAF
chr7	140476935	140476936	A, G	BRAF
chr7	140477726	140477727	C, T	BRAF
chr7	140481510	140481511	A, C	BRAF
chr7	140500334	140500335	C, T	BRAF
chr7	140624425	140624426	A, C	BRAF
chr7	142457429	142457430	A, C	PRSS1
chr7	142459702	142459703	C	PRSS1
chr7	142460393	142460394	T	PRSS1
chr7	142460864	142460865	C, T	PRSS1
chr7	142561535	142561536	C, T	EPHB6
chr7	142562010	142562011	C, T	EPHB6
chr7	142562079	142562080	C, T	EPHB6
chr7	142562403	142562404	C, T	EPHB6
chr7	142563252	142563253	G, T	EPHB6
chr7	142563299	142563300	C, T	EPHB6
chr7	142564109	142564110	C, T	EPHB6
chr7	142565384	142565385	A, G	EPHB6
chr7	142565775	142565776	A, G	EPHB6
chr7	142566162	142566163	C, G	EPHB6
chr7	142566370	142566371	C, T	EPHB6
chr7	142567941	142567942	A, G	EPHB6
chr7	142568517	142568518	A, G	EPHB6
chr7	148504817	148504818	A, G	EZH2
chr7	148506362	148506363	G, T	EZH2
chr7	148506395	148506396	A, C	EZH2
chr7	148508832	148508833	A, G	EZH2
chr7	148511170	148511171	C, T	EZH2
chr7	148513755	148513756	C, G	EZH2
chr7	148514920	148514921	C, T	EZH2
chr7	148514933	148514934	A, G	EZH2
chr7	148524236	148524237	C, G	EZH2
chr7	148525903	148525904	C, G	EZH2
chr7	148543524	148543525	A, G	EZH2
chr7	151164347	151164348	A, G	RHEB
chr7	151167603	151167604	A, T	RHEB
chr7	151168533	151168534	A, G	RHEB
chr7	151174537	151174538	C, T	RHEB
chr7	151195312	151195313	A, G	RHEB
chr7	151195327	151195328	C, G	RHEB
chr7	152346006	152346007	C, T	XRCC2
chr7	152357876	152357877	A, G	XRCC2
chr7	152373232	152373233	A, C	XRCC2
chr7	152373251	152373252	C, G	XRCC2
chr7	155596352	155596353	A, G	SHH
chr7	155596412	155596413	C, T	SHH
chr7	155599381	155599382	A, G	SHH
chr7	155599413	155599414	G	SHH
chr8	6366573	6366574	A, G	ANGPT2
chr8	6371290	6371291	A, G	ANGPT2
chr8	6371302	6371303	A, G	ANGPT2
chr8	6377432	6377433	C, T	ANGPT2
chr8	6378690	6378691	A, G	ANGPT2
chr8	6378783	6378784	A, C	ANGPT2
chr8	6385066	6385067	G, T	ANGPT2
chr8	6385179	6385180	C, T	ANGPT2
chr8	6389888	6389889	A, C, G	ANGPT2
chr8	6420359	6420360	C, T	ANGPT2
chr8	9413874	9413875	C, T	TNKS
chr8	9413892	9413893	A, G	TNKS
chr8	9414048	9414049	A, G	TNKS
chr8	9414158	9414159	C, G	TNKS
chr8	9537426	9537427	A, G	TNKS
chr8	9538249	9538250	A, G	TNKS
chr8	9564309	9564310	C, T	TNKS
chr8	9564418	9564419	C, T	TNKS
chr8	9564436	9564437	A, G	TNKS
chr8	9564484	9564485	A, G	TNKS
chr8	9564510	9564511	C, T	TNKS
chr8	9567699	9567700	A, C	TNKS
chr8	9577939	9577940	C, T	TNKS
chr8	9627602	9627603	C, T	TNKS
chr8	9627790	9627791	A, G	TNKS
chr8	9629780	9629781	A, G	TNKS
chr8	9629809	9629810	A, G	TNKS
chr8	9629844	9629845	A, G	TNKS
chr8	9634151	9634152	C, T	TNKS
chr8	11612664	11612665	A, T	GATA4
chr8	11612697	11612698	A, C	GATA4
chr8	11614501	11614502	C, T	GATA4
chr8	11614558	11614559	A, G	GATA4
chr8	11615927	11615928	A, G	GATA4
chr8	18257703	18257704	A, G	NAT2
chr8	18257794	18257795	C, T	NAT2
chr8	18257853	18257854	C, T	NAT2
chr8	18257993	18257994	C, T	NAT2
chr8	18258102	18258103	A, G	NAT2
chr8	18258315	18258316	A, G	NAT2
chr8	18258350	18258351	A, G	NAT2
chr8	18258369	18258370	A, G	NAT2
chr8	22020258	22020259	A, G	SFTPC
chr8	22020974	22020975	G, T	SFTPC
chr8	22021036	22021037	A, C	SFTPC
chr8	22021795	22021796	A, G	SFTPC
chr8	22880161	22880162	C, G	TNFRSF10B
chr8	22880172	22880173	A, G	TNFRSF10B
chr8	22881851	22881852	C, T	TNFRSF10B
chr8	22886001	22886002	A, G	TNFRSF10B
chr8	22886019	22886020	A, G	TNFRSF10B
chr8	22900700	22900701	A, G	TNFRSF10B
chr8	22926312	22926313	A, G	TNFRSF10B
chr8	23049291	23049292	C, T	TNFRSF10A
chr8	23054634	23054635	A, C	TNFRSF10A
chr8	23054778	23054779	C, T	TNFRSF10A
chr8	23054791	23054792	C, T	TNFRSF10A
chr8	23056903	23056904	G, T	TNFRSF10A
chr8	23057466	23057467	A, G	TNFRSF10A
chr8	23058187	23058188	C, T	TNFRSF10A
chr8	23058219	23058220	G, T	TNFRSF10A
chr8	23059279	23059280	G, T	TNFRSF10A
chr8	23059323	23059324	C, G	TNFRSF10A
chr8	23069573	23069574	C, T	TNFRSF10A
chr8	23082476	23082477	A, G	TNFRSF10A
chr8	23155552	23155553	T	LOXL2
chr8	23167299	23167300	A, G	LOXL2
chr8	23167352	23167353	G, T	LOXL2
chr8	23167434	23167435	C, T	LOXL2
chr8	23167463	23167464	C, G	LOXL2
chr8	23174667	23174668	A, T	LOXL2
chr8	23177496	23177497	A, G	LOXL2
chr8	23186006	23186007	C, T	LOXL2
chr8	23190925	23190926	C, T	LOXL2
chr8	23190940	23190941	C, T	LOXL2
chr8	23190994	23190995	C, T	LOXL2
chr8	23225558	23225559	A, G	LOXL2
chr8	23225744	23225745	C, T	LOXL2
chr8	23282503	23282504	C	LOXL2
chr8	23282556	23282557	C, T	LOXL2
chr8	23282560	23282561	C, T	LOXL2
chr8	27255262	27255263	A, G	PTK2B
chr8	27277536	27277537	A, G	PTK2B
chr8	27277627	27277628	G	PTK2B
chr8	27279882	27279883	A, G	PTK2B
chr8	27287996	27287997	A, T	PTK2B
chr8	27291556	27291557	C, T	PTK2B
chr8	27293305	27293306	C, T	PTK2B
chr8	27293334	27293335	G, T	PTK2B
chr8	27293864	27293865	C, T	PTK2B
chr8	27294605	27294606	C, G	PTK2B
chr8	27297744	27297745	A, G	PTK2B
chr8	27301724	27301725	C, G	PTK2B
chr8	27308537	27308538	A, G	PTK2B
chr8	27308584	27308585	A, C	PTK2B
chr8	27311620	27311621	C, T	PTK2B
chr8	27311702	27311703	C, T	PTK2B
chr8	27312134	27312135	A, G	PTK2B
chr8	27315875	27315876	A, G	PTK2B
chr8	27315899	27315900	A, G	PTK2B
chr8	27455840	27455841	A, T	CLU
chr8	27456129	27456130	A, G	CLU
chr8	27457478	27457479	C, T	CLU
chr8	27457506	27457507	C, G	CLU
chr8	27457511	27457512	G, T	CLU
chr8	27462480	27462481	A, G	CLU
chr8	27464080	27464081	C, T	CLU
chr8	27466577	27466578	G	CLU
chr8	27467945	27467946	C, T	CLU
chr8	27467983	27467984	C, T	CLU
chr8	27468004	27468005	A, G	CLU
chr8	27469063	27469064	C	CLU
chr8	27469065	27469066	C, T	CLU
chr8	27469155	27469156	C, T	CLU
chr8	27472133	27472134	A, G	CLU
chr8	27472137	27472138	C, T	CLU
chr8	27472258	27472259	A, C	CLU
chr8	37553688	37553689	A, G	ZNF703
chr8	37654906	37654907	A, G	GPR124
chr8	37655043	37655044	C, G	GPR124
chr8	37690614	37690615	A, G	GPR124
chr8	37690783	37690784	A, G	GPR124
chr8	37692703	37692704	A, G	GPR124
chr8	37692730	37692731	C, T	GPR124
chr8	37696626	37696627	C, T	GPR124
chr8	37697588	37697589	C, G	GPR124
chr8	37698901	37698902	C, G	GPR124
chr8	37699105	37699106	A, T	GPR124
chr8	37699194	37699195	C, G	GPR124
chr8	37699393	37699394	C, G	GPR124
chr8	37699442	37699443	A, G	GPR124
chr8	37699515	37699516	C, T	GPR124
chr8	37888089	37888090	C, T	EIF4EBP1
chr8	38271300	38271301	A, G	FGFR1
chr8	38279247	38279248	A, G	FGFR1
chr8	38287237	38287238	A, G	FGFR1
chr8	38318714	38318715	A, G	FGFR1
chr8	48689365	48689366	C, T	PRKDC
chr8	48691636	48691637	A, G	PRKDC
chr8	48694955	48694956	A, G	PRKDC
chr8	48695174	48695175	C, T	PRKDC
chr8	48695180	48695181	A, C	PRKDC
chr8	48697704	48697705	C, T	PRKDC
chr8	48710879	48710880	C, T	PRKDC
chr8	48710954	48710955	A, G	PRKDC
chr8	48715853	48715854	A, G	PRKDC
chr8	48729958	48729959	C, T	PRKDC
chr8	48729959	48729960	C, T	PRKDC
chr8	48739304	48739305	A, G	PRKDC
chr8	48739338	48739339	A, G	PRKDC
chr8	48739439	48739440	A, C	PRKDC
chr8	48771242	48771243	C, T	PRKDC
chr8	48792041	48792042	A, T	PRKDC
chr8	48792198	48792199	A, C	PRKDC
chr8	48794625	48794626	A, C	PRKDC
chr8	48805787	48805788	C, T	PRKDC
chr8	48815185	48815186	C, T	PRKDC
chr8	48817589	48817590	A, G	PRKDC
chr8	48824964	48824965	C, G	PRKDC
chr8	48842424	48842425	C, T	PRKDC
chr8	48843309	48843310	C, G	PRKDC
chr8	48845530	48845531	C, T	PRKDC
chr8	48846518	48846519	C, T	PRKDC
chr8	48852224	48852225	C, T	PRKDC
chr8	48870029	48870030	A, T	PRKDC
chr8	56860112	56860113	C, T	LYN
chr8	56860128	56860129	A, G	LYN
chr8	56863150	56863151	A, G	LYN
chr8	56866451	56866452	A, G	LYN
chr8	56882381	56882382	G	LYN
chr8	56910927	56910928	C, T	LYN
chr8	63938763	63938764	A, G	GGH
chr8	63939838	63939839	C, T	GGH
chr8	63942716	63942717	C, T	GGH
chr8	63942732	63942733	C, T	GGH
chr8	63948197	63948198	A, C	GGH
chr8	108306154	108306155	C, G	ANGPT1
chr8	108315461	108315462	C, T	ANGPT1
chr8	108334923	108334924	A, G	ANGPT1
chr8	108335012	108335013	A, T	ANGPT1
chr8	108335036	108335037	A, T	ANGPT1
chr8	108335041	108335042	C, T	ANGPT1
chr8	128750539	128750540	A, G	MYC
chr8	128750606	128750607	A, G	MYC
chr8	128751200	128751201	A, G	MYC
chr8	143955915	143955916	C, G	CYP11B1
chr8	143956802	143956803	C, G	CYP11B1
chr8	143956807	143956808	A, C	CYP11B1
chr8	143956853	143956854	A, G	CYP11B1
chr8	143957332	143957333	C, G	CYP11B1
chr8	143957737	143957738	C, T	CYP11B1
chr8	143957824	143957825	A, G	CYP11B1
chr8	143958341	143958342	A, G	CYP11B1
chr8	143958426	143958427	C, T	CYP11B1
chr8	143959187	143959188	A, G, T	CYP11B1
chr8	143959218	143959219	A, G	CYP11B1
chr8	143959249	143959250	C, T	CYP11B1
chr8	143959271	143959272	C, T	CYP11B1
chr8	143959288	143959289	C, T	CYP11B1
chr8	143959310	143959311	A, G	CYP11B1
chr8	143960596	143960597	A, G	CYP11B1
chr8	143960625	143960626	A, G	CYP11B1
chr8	143961004	143961005	C, T	CYP11B1
chr8	143961101	143961102	C, T	CYP11B1
chr8	143994040	143994041	C, T	CYP11B2
chr8	143994265	143994266	A, G	CYP11B2
chr8	143994341	143994342	C, T	CYP11B2
chr8	143994805	143994806	A, G, T	CYP11B2
chr8	143995742	143995743	C, T	CYP11B2
chr8	143995760	143995761	C, T	CYP11B2
chr8	143995791	143995792	T	CYP11B2
chr8	143996362	143996363	A, G	CYP11B2
chr8	143996364	143996365	A, G	CYP11B2
chr8	143996538	143996539	C, T	CYP11B2
chr8	143996552	143996553	A, G	CYP11B2
chr8	143998661	143998662	A, G	CYP11B2
chr8	143999145	143999146	C, T	CYP11B2
chr8	143999171	143999172	C, T	CYP11B2
chr9	5050705	5050706	C, T	JAK2
chr9	5066746	5066747	C, T	JAK2
chr9	5066785	5066786	C, T	JAK2
chr9	5077516	5077517	C, T	JAK2
chr9	5081779	5081780	A, G	JAK2
chr9	5089687	5089688	C, T	JAK2
chr9	5126442	5126443	A, T	JAK2
chr9	5457295	5457296	C, T	CD274
chr9	5467800	5467801	C, T	CD274
chr9	5467924	5467925	A, G	CD274
chr9	5549539	5549540	C, T	PDCD1LG2
chr9	5557707	5557708	C, T	PDCD1LG2
chr9	5557792	5557793	A, T	PDCD1LG2
chr9	5563114	5563115	A, T	PDCD1LG2
chr9	8319805	8319806	C, T	PTPRD
chr9	8338877	8338878	A, C	PTPRD
chr9	8340300	8340301	C, G	PTPRD
chr9	8340315	8340316	G, T	PTPRD
chr9	8341184	8341185	A, G	PTPRD
chr9	8389342	8389343	A, G	PTPRD
chr9	8389363	8389364	C, G	PTPRD
chr9	8436702	8436703	C, G	PTPRD
chr9	8437140	8437141	C, G	PTPRD
chr9	8454494	8454495	A, G	PTPRD
chr9	8454565	8454566	C, T	PTPRD
chr9	8460590	8460591	A, G	PTPRD
chr9	8465579	8465580	G, T	PTPRD
chr9	8465597	8465598	A, G	PTPRD
chr9	8484189	8484190	A, G	PTPRD
chr9	8484239	8484240	G, T	PTPRD
chr9	8484297	8484298	A, C	PTPRD
chr9	8485786	8485787	C, G	PTPRD
chr9	8485833	8485834	A, G	PTPRD
chr9	8485927	8485928	A, G	PTPRD
chr9	8518051	8518052	C, G	PTPRD
chr9	8518142	8518143	C, T	PTPRD
chr9	8518394	8518395	A, G	PTPRD
chr9	8518437	8518438	C, G	PTPRD
chr9	8518469	8518470	C, G	PTPRD
chr9	8524853	8524854	C, T	PTPRD
chr9	21077370	21077371	C, T	IFNB1
chr9	21077640	21077641	A, G	IFNB1
chr9	21077688	21077689	G, T	IFNB1
chr9	21384791	21384792	A, G	IFNA2
chr9	21385311	21385312	G, T	IFNA2
chr9	21968158	21968159	A, G	CDKN2A
chr9	21968198	21968199	C, G	CDKN2A
chr9	21968711	21968712	A, C	CDKN2A
chr9	21970978	21970979	A, C	CDKN2A
chr9	21971183	21971184	T	CDKN2A
chr9	21974437	21974438	C	CDKN2A
chr9	22006272	22006273	G, T	CDKN2B
chr9	27157913	27157914	C, T	TEK
chr9	27158009	27158010	A, G	TEK
chr9	27168432	27168433	A, G	TEK
chr9	27168467	27168468	A, G	TEK
chr9	27168570	27168571	C, T	TEK
chr9	27173179	27173180	C, T	TEK
chr9	27183462	27183463	A, C	TEK
chr9	27183597	27183598	C, T	TEK
chr9	27190491	27190492	C, T	TEK
chr9	27190654	27190655	A, G	TEK
chr9	27197367	27197368	C, T	TEK
chr9	27203077	27203078	A, G	TEK
chr9	27203143	27203144	C, T	TEK
chr9	27205020	27205021	A, G	TEK
chr9	27213579	27213580	C, T	TEK
chr9	27213611	27213612	C, G	TEK
chr9	27218725	27218726	C, T	TEK
chr9	27220065	27220066	A, G	TEK
chr9	27220093	27220094	C, T	TEK
chr9	27220181	27220182	A, T	TEK
chr9	27228199	27228200	A, G	TEK
chr9	27229098	27229099	A, G	TEK
chr9	27229140	27229141	C, T	TEK
chr9	34655285	34655286	C, T	IL11RA
chr9	34656727	34656728	A, C	IL11RA
chr9	34657389	34657390	A, G	IL11RA
chr9	34657394	34657395	A, G	IL11RA
chr9	34658477	34658478	C, T	IL11RA
chr9	34658561	34658562	G	IL11RA
chr9	34658651	34658652	A, G	IL11RA
chr9	34661552	34661553	A, G	IL11RA
chr9	35074916	35074917	C, T	FANCG
chr9	35075968	35075969	A, G	FANCG
chr9	35076516	35076517	G	FANCG
chr9	35076623	35076624	C, T	FANCG
chr9	35076754	35076755	A, G	FANCG
chr9	35076905	35076906	C, G	FANCG
chr9	35076922	35076923	C, T	FANCG
chr9	35077440	35077441	C, T	FANCG
chr9	35079360	35079361	G, T	FANCG
chr9	35079444	35079445	C, T	FANCG
chr9	35674052	35674053	A, G	CA9
chr9	35674100	35674101	C, T	CA9
chr9	35674346	35674347	A, T	CA9
chr9	35675851	35675852	C, G	CA9
chr9	35675960	35675961	A, G	CA9
chr9	35676287	35676288	C, T	CA9
chr9	35679142	35679143	A, G	CA9
chr9	35679250	35679251	A, G	CA9
chr9	35680932	35680933	A, G	CA9
chr9	36840622	36840623	A, G	PAX5
chr9	36840684	36840685	C, T	PAX5
chr9	37002805	37002806	A, G	PAX5
chr9	37006493	37006494	C, T	PAX5
chr9	37015233	37015234	A, G	PAX5
chr9	37020621	37020622	A, C	PAX5
chr9	80412602	80412603	C, T	GNAQ
chr9	87338455	87338456	A, G	NTRK2
chr9	87339314	87339315	C, T	NTRK2
chr9	87342647	87342648	A, C	NTRK2
chr9	87356743	87356744	A, G	NTRK2
chr9	87356780	87356781	A, C	NTRK2
chr9	87366872	87366873	C, T	NTRK2
chr9	87563369	87563370	C, T	NTRK2
chr9	87636264	87636265	C, T	NTRK2
chr9	93606308	93606309	A, G	SYK
chr9	93626911	93626912	A, G	SYK
chr9	93626936	93626937	A, C	SYK
chr9	93629543	93629544	C, T	SYK
chr9	93636430	93636431	A, G	SYK
chr9	93637014	93637015	C, T	SYK
chr9	93639845	93639846	A, C, G	SYK
chr9	93639848	93639849	A, G	SYK
chr9	93639972	93639973	C, G	SYK
chr9	93640008	93640009	A, G	SYK
chr9	93641150	93641151	C, T	SYK
chr9	93641174	93641175	C, T	SYK
chr9	93641198	93641199	C, T	SYK
chr9	93650014	93650015	A, T	SYK
chr9	93657760	93657761	A, T	SYK
chr9	97869395	97869396	C	FANCC
chr9	97897654	97897655	A, G	FANCC
chr9	97934358	97934359	C, T	FANCC
chr9	97934366	97934367	C, T	FANCC
chr9	98011601	98011602	G, T	FANCC
chr9	98209593	98209594	A, G	PTCH1
chr9	98209692	98209693	A, G	PTCH1
chr9	98209741	98209742	A, G	PTCH1
chr9	98211548	98211549	A, G	PTCH1
chr9	98211571	98211572	A, T	PTCH1
chr9	98211587	98211588	G	PTCH1
chr9	98215821	98215822	A, G	PTCH1
chr9	98215967	98215968	C, G	PTCH1
chr9	98220321	98220322	A, C	PTCH1
chr9	98229388	98229389	C, G	PTCH1
chr9	98231099	98231100	A, G	PTCH1
chr9	98231345	98231346	C, G	PTCH1
chr9	98236303	98236304	C, T	PTCH1
chr9	98236308	98236309	C, T	PTCH1
chr9	98236396	98236397	A, G	PTCH1
chr9	98238357	98238358	A, G	PTCH1
chr9	98239146	98239147	A, G	PTCH1
chr9	98239189	98239190	C, G	PTCH1
chr9	98241377	98241378	A, G	PTCH1
chr9	98278939	98278940	C, G	PTCH1
chr9	101890979	101890980	A, G	TGFBR1
chr9	101908914	101908915	A, G	TGFBR1
chr9	110249504	110249505	C, T	KLF4
chr9	110250170	110250171	A, G	KLF4
chr9	117782890	117782891	C, T	TNC
chr9	117791616	117791617	C, T	TNC
chr9	117791663	117791664	C, T	TNC
chr9	117791708	117791709	A, G	TNC
chr9	117792598	117792599	C, T	TNC
chr9	117797524	117797525	G, T	TNC
chr9	117797596	117797597	C, T	TNC
chr9	117803270	117803271	C, T	TNC
chr9	117803379	117803380	C, G	TNC
chr9	117804543	117804544	C, T	TNC
chr9	117804552	117804553	C, T	TNC
chr9	117804666	117804667	C, T	TNC
chr9	117808784	117808785	A, T	TNC
chr9	117815010	117815011	C, T	TNC
chr9	117815035	117815036	A, G	TNC
chr9	117827037	117827038	G, T	TNC
chr9	117827059	117827060	C, T	TNC
chr9	117835930	117835931	A, G	TNC
chr9	117840275	117840276	C, T	TNC
chr9	117840333	117840334	A, G	TNC
chr9	117844019	117844020	C, T	TNC
chr9	117844065	117844066	G, T	TNC
chr9	117845010	117845011	C, T	TNC
chr9	117846569	117846570	C, T	TNC
chr9	117846579	117846580	C, T	TNC
chr9	117848196	117848197	C, T	TNC
chr9	117848393	117848394	C, T	TNC
chr9	117849228	117849229	C, T	TNC
chr9	117849313	117849314	C, T	TNC
chr9	117849372	117849373	C, T	TNC
chr9	117853021	117853022	C, T	TNC
chr9	117853222	117853223	C, G	TNC
chr9	120474720	120474721	C, T	TLR4
chr9	120475301	120475302	A, G	TLR4
chr9	120475601	120475602	C, T	TLR4
chr9	120475825	120475826	A, G	TLR4
chr9	120475935	120475936	G, T	TLR4
chr9	128000647	128000648	A, C	HSPA5
chr9	128001118	128001119	C, T	HSPA5
chr9	130549076	130549077	A, G	CDK9
chr9	130549789	130549790	C, T	CDK9
chr9	130550197	130550198	C, G	CDK9
chr9	130550486	130550487	C, T	CDK9
chr9	130551710	130551711	C, T	CDK9
chr9	130578005	130578006	A, G	ENG
chr9	130578279	130578280	A, G	ENG
chr9	130580938	130580939	C, T	ENG
chr9	130586620	130586621	C, G	ENG
chr9	130586656	130586657	A, G	ENG
chr9	130586687	130586688	A, G	ENG
chr9	130588153	130588154	A, G	ENG
chr9	130588168	130588169	C, T	ENG
chr9	130616620	130616621	A, G	ENG
chr9	132580900	132580901	C, G	TOR1A
chr9	132586415	132586416	A, C	TOR1A
chr9	133710245	133710246	A, T	ABL1
chr9	133730137	133730138	A, G	ABL1
chr9	133738319	133738320	A, G	ABL1
chr9	133747456	133747457	C, T	ABL1
chr9	133748201	133748202	C, T	ABL1
chr9	133755527	133755528	A, G	ABL1
chr9	133759545	133759546	A, G	ABL1
chr9	133760028	133760029	C, G	ABL1
chr9	133760591	133760592	C, T	ABL1
chr9	133760616	133760617	C, T	ABL1
chr9	133760676	133760677	C, T	ABL1
chr9	133761000	133761001	A, G	ABL1
chr9	135771729	135771730	A, G	TSC1
chr9	135771792	135771793	A, G	TSC1
chr9	135776924	135776925	C, T	TSC1
chr9	135781204	135781205	C, T	TSC1
chr9	135781238	135781239	A, G	TSC1
chr9	135782220	135782221	C, T	TSC1
chr9	135786903	135786904	A, G	TSC1
chr9	135804138	135804139	C, T	TSC1
chr9	139390675	139390676	A, C	NOTCH1
chr9	139390957	139390958	C, T	NOTCH1
chr9	139391199	139391200	C, T	NOTCH1
chr9	139391337	139391338	C, T	NOTCH1
chr9	139391413	139391414	A, G	NOTCH1
chr9	139391635	139391636	A, G	NOTCH1
chr9	139391736	139391737	C, G	NOTCH1
chr9	139393306	139393307	A, G	NOTCH1
chr9	139396407	139396408	A, G	NOTCH1
chr9	139397706	139397707	A, G	NOTCH1
chr9	139399131	139399132	C, T	NOTCH1
chr9	139399319	139399320	C, T	NOTCH1
chr9	139401288	139401289	C, G	NOTCH1
chr9	139401301	139401302	A, G	NOTCH1
chr9	139402379	139402380	A, C	NOTCH1
chr9	139402657	139402658	C, T	NOTCH1
chr9	139402662	139402663	C, T	NOTCH1
chr9	139402693	139402694	A, C	NOTCH1
chr9	139404171	139404172	A, G	NOTCH1
chr9	139405092	139405093	A, G	NOTCH1
chr9	139405741	139405742	C, T	NOTCH1
chr9	139407931	139407932	A, G	NOTCH1
chr9	139408963	139408964	A, G	NOTCH1
chr9	139410588	139410589	A, G	NOTCH1
chr9	139411872	139411873	A, G	NOTCH1
chr9	139411879	139411880	A, G	NOTCH1
chr9	139413268	139413269	A, G	NOTCH1
chr9	139413907	139413908	C, T	NOTCH1
chr9	139417332	139417333	A, G	NOTCH1
chr9	139417380	139417381	A, G	NOTCH1
chr9	139418259	139418260	A, G	NOTCH1
chr9	139438410	139438411	C, G	NOTCH1
chr9	139562992	139562993	C, T	EGFL7
chr9	139564105	139564106	C, G	EGFL7
chr9	139564473	139564474	C, G	EGFL7
chr9	139564667	139564668	A, G	EGFL7
chr9	139566777	139566778	C, T	EGFL7
chr10	6060056	6060057	A, G	IL2RA
chr10	6061406	6061407	C, T	IL2RA
chr10	6061478	6061479	A, C	IL2RA
chr10	6061498	6061499	C, T	IL2RA
chr10	6061780	6061781	C, T	IL2RA
chr10	6063507	6063508	A, G	IL2RA
chr10	6063566	6063567	C, T	IL2RA
chr10	6063673	6063674	C, T	IL2RA
chr10	8100631	8100632	C, T	GATA3
chr10	8100646	8100647	C, T	GATA3
chr10	8106134	8106135	A, G	GATA3
chr10	8111408	8111409	C, T	GATA3
chr10	8115907	8115908	A, G	GATA3
chr10	22615321	22615322	A, G	BMI1
chr10	22617644	22617645	C, T	BMI1
chr10	33190566	33190567	A, C	ITGB1
chr10	33200497	33200498	A, G	ITGB1
chr10	33200557	33200558	A, G	ITGB1
chr10	33200781	33200782	C, T	ITGB1
chr10	33208943	33208944	C, T	ITGB1
chr10	33209265	33209266	G, T	ITGB1
chr10	33211226	33211227	G, T	ITGB1
chr10	33214801	33214802	A, G	ITGB1
chr10	33215060	33215061	A, T	ITGB1
chr10	33217109	33217110	A, G	ITGB1
chr10	35929130	35929131	A, G	FZD8
chr10	35929139	35929140	A, G	FZD8
chr10	35929349	35929350	C, T	FZD8
chr10	43595967	43595968	A, G	RET
chr10	43596032	43596033	A, G	RET
chr10	43600606	43600607	A, C	RET
chr10	43600688	43600689	A, G	RET
chr10	43606649	43606650	C, T	RET
chr10	43606686	43606687	A, G	RET
chr10	43606855	43606856	A, G	RET
chr10	43608432	43608433	C	RET
chr10	43610118	43610119	A, G	RET
chr10	43613842	43613843	G, T	RET
chr10	43615093	43615094	C, T	RET
chr10	43615632	43615633	C, G	RET
chr10	43620366	43620367	A, G	RET
chr10	43622216	43622217	C, T	RET
chr10	44793298	44793299	C, T	CXCL12
chr10	44793354	44793355	A, G	CXCL12
chr10	44868855	44868856	A, C	CXCL12
chr10	44868863	44868864	C, T	CXCL12
chr10	44871547	44871548	A, G	CXCL12
chr10	44873212	44873213	G, T	CXCL12
chr10	48414515	48414516	A, T	GDF2
chr10	48416337	48416338	A, G	GDF2
chr10	54074756	54074757	A, G	DKK1
chr10	54076270	54076271	A, G	DKK1
chr10	54076310	54076311	C, T	DKK1
chr10	62551888	62551889	A, G	CDK1
chr10	70332579	70332580	A, G	TET1
chr10	70332671	70332672	A, T	TET1
chr10	70332861	70332862	C, T	TET1
chr10	70333397	70333398	A, G	TET1
chr10	70333554	70333555	C, T	TET1
chr10	70404980	70404981	A, G	TET1
chr10	70405236	70405237	A, G	TET1
chr10	70405438	70405439	G, T	TET1
chr10	70405538	70405539	A, G	TET1
chr10	70405854	70405855	A, G	TET1
chr10	70405900	70405901	C, T	TET1
chr10	70406746	70406747	A, G	TET1
chr10	70411535	70411536	A, G	TET1
chr10	70432643	70432644	C, T	TET1
chr10	70451546	70451547	A, G	TET1
chr10	74714293	74714294	A, G	PLA2G12B
chr10	75671397	75671398	A, C	PLAU
chr10	75671404	75671405	A, G	PLAU
chr10	75671570	75671571	C, T	PLAU
chr10	75671702	75671703	A, G	PLAU
chr10	75671874	75671875	A, G	PLAU
chr10	75673100	75673101	C, T	PLAU
chr10	75673730	75673731	C, T	PLAU
chr10	75673747	75673748	A, C	PLAU
chr10	89653685	89653686	A, G	PTEN
chr10	90749255	90749256	A, G	FAS
chr10	90750599	90750600	A, G	FAS
chr10	90762800	90762801	A, G	FAS
chr10	90762857	90762858	C, T	FAS
chr10	90762895	90762896	A, G	FAS
chr10	90767481	90767482	A, G	FAS
chr10	90771828	90771829	C, T	FAS
chr10	90773198	90773199	A, G	FAS
chr10	94353277	94353278	G, T	KIF11
chr10	94366834	94366835	G, T	KIF11
chr10	94366897	94366898	A, G	KIF11
chr10	94392325	94392326	A, C	KIF11
chr10	94393482	94393483	A, G	KIF11
chr10	94397294	94397295	A, T	KIF11
chr10	94409748	94409749	C, T	KIF11
chr10	94413507	94413508	C, G	KIF11
chr10	96534767	96534768	A, G	CYP2C19
chr10	96540409	96540410	A, G	CYP2C19
chr10	96541615	96541616	A, G	CYP2C19
chr10	96602621	96602622	C, T	CYP2C19
chr10	96602622	96602623	A, G	CYP2C19
chr10	96609774	96609775	A, C	CYP2C19
chr10	96701600	96701601	C, G	CYP2C9
chr10	96702046	96702047	C, T	CYP2C9
chr10	96702065	96702066	A, G	CYP2C9
chr10	96708973	96708974	A, G	CYP2C9
chr10	96740907	96740908	C, T	CYP2C9
chr10	96740980	96740981	C, T	CYP2C9
chr10	96741164	96741165	C, T	CYP2C9
chr10	96748736	96748737	A, T	CYP2C9
chr10	96798714	96798715	A, G	CYP2C8
chr10	96798748	96798749	C, T	CYP2C8
chr10	96802736	96802737	A, G	CYP2C8
chr10	96818118	96818119	C, G	CYP2C8
chr10	96827117	96827118	A, G	CYP2C8
chr10	96827149	96827150	C, T	CYP2C8
chr10	96827177	96827178	C, T	CYP2C8
chr10	96827484	96827485	A, G	CYP2C8
chr10	101542577	101542578	C, T	ABCC2
chr10	101544446	101544447	T	ABCC2
chr10	101560168	101560169	A, G	ABCC2
chr10	101563784	101563785	C, T	ABCC2
chr10	101563814	101563815	A, G	ABCC2
chr10	101567785	101567786	A, T	ABCC2
chr10	101569996	101569997	C, T	ABCC2
chr10	101571441	101571442	G, T	ABCC2
chr10	101577034	101577035	A, T	ABCC2
chr10	101590618	101590619	C, T	ABCC2
chr10	101591417	101591418	A, G	ABCC2
chr10	101595974	101595975	G, T	ABCC2
chr10	101595995	101595996	A, T	ABCC2
chr10	101603521	101603522	C, T	ABCC2
chr10	101603630	101603631	A	ABCC2
chr10	101604106	101604107	C, T	ABCC2
chr10	101605454	101605455	C, T	ABCC2
chr10	101605502	101605503	C, T	ABCC2
chr10	101606860	101606861	G, T	ABCC2
chr10	101610454	101610455	A, G	ABCC2
chr10	101610532	101610533	C, T	ABCC2
chr10	101611293	101611294	A, G	ABCC2
chr10	104264106	104264107	C, T	SUFU
chr10	104353324	104353325	C, G	SUFU
chr10	104386933	104386934	C, T	SUFU
chr10	104591392	104591393	G, T	CYP17A1
chr10	104596923	104596924	A, C	CYP17A1
chr10	104596980	104596981	A, G	CYP17A1
chr10	106014724	106014725	A, G	GSTO1
chr10	106019568	106019569	G, T	GSTO1
chr10	106022788	106022789	A, C	GSTO1
chr10	106025989	106025990	G, T	GSTO1
chr10	106027058	106027059	A, G	GSTO1
chr10	106034614	106034615	G, T	GSTO2
chr10	106035131	106035132	A, G	GSTO2
chr10	106035132	106035133	A, C	GSTO2
chr10	106039089	106039090	A, C	GSTO2
chr10	106039184	106039185	A, G	GSTO2
chr10	106045777	106045778	C, T	GSTO2
chr10	106058939	106058940	C, T	GSTO2
chr10	115451780	115451781	C, T	CASP7
chr10	115480756	115480757	C, T	CASP7
chr10	115480935	115480936	A, G	CASP7
chr10	115481470	115481471	C, T	CASP7
chr10	115489151	115489152	C, G	CASP7
chr10	115489166	115489167	A, G	CASP7
chr10	123239111	123239112	A, G	FGFR2
chr10	123243196	123243197	A, G	FGFR2
chr10	123247549	123247550	A, G	FGFR2
chr10	123277600	123277601	A, G	FGFR2
chr10	123298157	123298158	C, T	FGFR2
chr10	123310870	123310871	A, G	FGFR2
chr10	123324176	123324177	C, T	FGFR2
chr10	123325157	123325158	A, G	FGFR2
chr10	123353212	123353213	A, C	FGFR2
chr10	131265544	131265545	C, T	MGMT
chr10	131265641	131265642	C, T	MGMT
chr10	131265664	131265665	G, T	MGMT
chr10	131506310	131506311	A, G	MGMT
chr10	131565169	131565170	A, G	MGMT
chr11	534196	534197	C, T	HRAS
chr11	534241	534242	A, G	HRAS
chr11	838012	838013	C, T	CD151
chr11	838109	838110	C, T	CD151
chr11	2185555	2185556	A, G	TH
chr11	2186423	2186424	A, G	TH
chr11	2186517	2186518	C, T	TH
chr11	2187721	2187722	A, C	TH
chr11	2187854	2187855	C, G	TH
chr11	2188237	2188238	C, T	TH
chr11	2188788	2188789	A, T	TH
chr11	2189184	2189185	A, G	TH
chr11	2189903	2189904	A, G	TH
chr11	2190924	2190925	C, T	TH
chr11	2190950	2190951	C, T	TH
chr11	2190981	2190982	A, G	TH
chr11	2191005	2191006	C, T	TH
chr11	5247790	5247791	C, G	HBB
chr11	13514023	13514024	C, T	PTH
chr11	13514052	13514053	G, T	PTH
chr11	13514256	13514257	C, T	PTH
chr11	13514262	13514263	C, T	PTH
chr11	13514307	13514308	A, C	PTH
chr11	14991538	14991539	C, T	CALCA
chr11	22646570	22646571	C, T	FANCF
chr11	22646732	22646733	A, C	FANCF
chr11	22647260	22647261	A, G	FANCF
chr11	32410773	32410774	A, G	WT1
chr11	32421532	32421533	C, T	WT1
chr11	32421653	32421654	C, T	WT1
chr11	32449623	32449624	A, C	WT1
chr11	32449660	32449661	A, G	WT1
chr11	32452031	32452032	C, G	WT1
chr11	32456297	32456298	A, G	WT1
chr11	32456561	32456562	A, G	WT1
chr11	32456693	32456694	A, C	WT1
chr11	35160838	35160839	A, G	CD44
chr11	35198107	35198108	A, G	CD44
chr11	35201809	35201810	C, T	CD44
chr11	35201841	35201842	C, T	CD44
chr11	35201957	35201958	A, G	CD44
chr11	35201960	35201961	T	CD44
chr11	35222680	35222681	C, T	CD44
chr11	35222758	35222759	A, G	CD44
chr11	35223302	35223303	A, G	CD44
chr11	35226154	35226155	A, G	CD44
chr11	35229672	35229673	C, T	CD44
chr11	35231626	35231627	C, T	CD44
chr11	35236385	35236386	C, T	CD44
chr11	35250714	35250715	C, T	CD44
chr11	46740870	46740871	A, G	F2
chr11	46740906	46740907	C, G	F2
chr11	46742248	46742249	C, T	F2
chr11	46744924	46744925	C, G	F2
chr11	46744988	46744989	C, T	F2
chr11	46745002	46745003	C, T	F2
chr11	46749647	46749648	A, G	F2
chr11	46760755	46760756	A, G	F2
chr11	49168415	49168416	A, G	FOLH1
chr11	49176056	49176057	C, T	FOLH1
chr11	49176057	49176058	A, G	FOLH1
chr11	49194889	49194890	A, T	FOLH1
chr11	49194893	49194894	A, G	FOLH1
chr11	49196489	49196490	C, T	FOLH1
chr11	49197415	49197416	A, G	FOLH1
chr11	49207314	49207315	A, G	FOLH1
chr11	49208177	49208178	A, T	FOLH1
chr11	49214393	49214394	A, G	FOLH1
chr11	49221884	49221885	A, T	FOLH1
chr11	49227619	49227620	A, G	FOLH1
chr11	49228386	49228387	C, T	FOLH1
chr11	60229969	60229970	A, G	MS4A1
chr11	60230530	60230531	C, T	MS4A1
chr11	64003433	64003434	A, G	VEGFB
chr11	64003671	64003672	C, T	VEGFB
chr11	64004642	64004643	C, G	VEGFB
chr11	64004648	64004649	G, T	VEGFB
chr11	64004691	64004692	C, T	VEGFB
chr11	64004730	64004731	A, G	VEGFB
chr11	64004923	64004924	G	VEGFB
chr11	64004934	64004935	A, G	VEGFB
chr11	64037678	64037679	A, G	BAD
chr11	64039174	64039175	A, G	BAD
chr11	64051852	64051853	A, G	BAD
chr11	64572017	64572018	C, T	MEN1
chr11	64572556	64572557	A, G	MEN1
chr11	64572601	64572602	A, G	MEN1
chr11	64577146	64577147	A, G	MEN1
chr11	66082181	66082182	A, T	CD248
chr11	66082212	66082213	A, G	CD248
chr11	66082427	66082428	G, T	CD248
chr11	66083128	66083129	C, T	CD248
chr11	66083157	66083158	A, G	CD248
chr11	66083268	66083269	A, G	CD248
chr11	66083361	66083362	A, G	CD248
chr11	66083781	66083782	A, G	CD248
chr11	66084155	66084156	C, T	CD248
chr11	66084243	66084244	A, G	CD248
chr11	66084330	66084331	A, G	CD248
chr11	67351296	67351297	A, G	GSTP1
chr11	67351584	67351585	C, G	GSTP1
chr11	67351673	67351674	A, G	GSTP1
chr11	67352160	67352161	C, T	GSTP1
chr11	67352255	67352256	A, C	GSTP1
chr11	67352688	67352689	A, G	GSTP1
chr11	67353578	67353579	C, T	GSTP1
chr11	67353841	67353842	A, G	GSTP1
chr11	67353843	67353844	C, T	GSTP1
chr11	67353969	67353970	C, T	GSTP1
chr11	69458904	69458905	A, G	CCND1
chr11	69462855	69462856	C, T	CCND1
chr11	69462909	69462910	A, G	CCND1
chr11	69465859	69465860	A, G	CCND1
chr11	69588728	69588729	A, G	FGF4
chr11	69589555	69589556	A, G	FGF4
chr11	69625384	69625385	C, T	FGF3
chr11	69625472	69625473	A, G	FGF3
chr11	69633632	69633633	A, C	FGF3
chr11	88911234	88911235	A, G	TYR
chr11	88911298	88911299	C, T	TYR
chr11	88911695	88911696	A, C	TYR
chr11	89017960	89017961	A, G	TYR
chr11	94153325	94153326	C, T	MRE11A
chr11	94153399	94153400	A, C	MRE11A
chr11	94168987	94168988	C, T	MRE11A
chr11	94200961	94200962	A, G	MRE11A
chr11	94201044	94201045	A, C	MRE11A
chr11	94209424	94209425	C, G	MRE11A
chr11	94209612	94209613	A, G	MRE11A
chr11	94212047	94212048	C, T	MRE11A
chr11	94225919	94225920	C, T	MRE11A
chr11	100909990	100909991	C, T	PGR
chr11	100921664	100921665	A, C	PGR
chr11	100922201	100922202	A, G	PGR
chr11	100933411	100933412	A, C	PGR
chr11	100962527	100962528	G, T	PGR
chr11	100998471	100998472	A, C	PGR
chr11	100998622	100998623	A, G	PGR
chr11	100998761	100998762	C, G	PGR
chr11	100998770	100998771	C, G	PGR
chr11	100999012	100999013	C, T	PGR
chr11	100999189	100999190	A, G	PGR
chr11	100999240	100999241	C, T	PGR
chr11	100999653	100999654	C, T	PGR
chr11	100999654	100999655	C, T	PGR
chr11	102195500	102195501	A, G	BIRC3
chr11	102196018	102196019	A, G	BIRC3
chr11	102196176	102196177	C, T	BIRC3
chr11	102199612	102199613	A, T	BIRC3
chr11	102201847	102201848	A, G	BIRC3
chr11	102207592	102207593	C, T	BIRC3
chr11	102248376	102248377	C, T	BIRC2
chr11	106810557	106810558	A, G	GUCY1A2
chr11	106849396	106849397	C, T	GUCY1A2
chr11	106849399	106849400	A, G	GUCY1A2
chr11	108106442	108106443	A, T	ATM
chr11	108114726	108114727	C, G	ATM
chr11	108114748	108114749	A, G	ATM
chr11	108114751	108114752	A, T	ATM
chr11	108114839	108114840	C, T	ATM
chr11	108119769	108119770	C, G	ATM
chr11	108121732	108121733	A, G	ATM
chr11	108122591	108122592	C, G	ATM
chr11	108127009	108127010	C, T	ATM
chr11	108129656	108129657	A, G	ATM
chr11	108129777	108129778	A, C	ATM
chr11	108138044	108138045	C, T	ATM
chr11	108139182	108139183	A, G	ATM
chr11	108143298	108143299	A, G	ATM
chr11	108143455	108143456	C, G	ATM
chr11	108150315	108150316	A, G	ATM
chr11	108159731	108159732	C, T	ATM
chr11	108163486	108163487	C, T	ATM
chr11	108175461	108175462	A, G	ATM
chr11	108186652	108186653	C, T	ATM
chr11	108192158	108192159	G, T	ATM
chr11	108198390	108198391	C, T	ATM
chr11	108204517	108204518	A, C	ATM
chr11	108225660	108225661	A, G	ATM
chr11	118343847	118343848	C, T	MLL
chr11	118348962	118348963	G, T	MLL
chr11	118361853	118361854	C, T	MLL
chr11	118367006	118367007	G, T	MLL
chr11	118373570	118373571	A, T	MLL
chr11	118374295	118374296	A, G	MLL
chr11	118374646	118374647	C, T	MLL
chr11	118375567	118375568	A, T	MLL
chr11	118375997	118375998	A, G	MLL
chr11	118376815	118376816	A, G	MLL
chr11	118377296	118377297	C, T	MLL
chr11	119145666	119145667	A, G	CBL
chr11	119148572	119148573	G, T	CBL
chr11	119155885	119155886	C, T	CBL
chr11	119156192	119156193	C, T	CBL
chr11	119170361	119170362	C, T	CBL
chr11	125495718	125495719	A, G	CHEK1
chr11	125495739	125495740	A, G	CHEK1
chr11	125495745	125495746	C, G	CHEK1
chr11	125497465	125497466	G, T	CHEK1
chr11	125507276	125507277	C, T	CHEK1
chr11	125523666	125523667	A, G	CHEK1
chr12	401879	401880	A, T	KDM5A
chr12	404857	404858	C, G	KDM5A
chr12	406291	406292	A, G	KDM5A
chr12	416292	416293	C, T	KDM5A
chr12	420069	420070	A, G	KDM5A
chr12	427574	427575	A, G	KDM5A
chr12	432758	432759	C, T	KDM5A
chr12	438071	438072	C, T	KDM5A
chr12	461373	461374	C, G	KDM5A
chr12	463247	463248	C, G	KDM5A
chr12	465614	465615	C	KDM5A
chr12	498284	498285	C, T	KDM5A
chr12	4388083	4388084	C, G	CCND2
chr12	4479548	4479549	A, G	FGF23
chr12	4543360	4543361	A, G	FGF6
chr12	4543486	4543487	A, T	FGF6
chr12	4553331	4553332	A, G	FGF6
chr12	4553382	4553383	A, G	FGF6
chr12	4554547	4554548	C, G	FGF6
chr12	4554629	4554630	A, G	FGF6
chr12	6058402	6058403	A, G	VWF
chr12	6058912	6058913	A, G	VWF
chr12	6058919	6058920	A, G	VWF
chr12	6060959	6060960	A, G	VWF
chr12	6061068	6061069	G, T	VWF
chr12	6061558	6061559	C, T	VWF
chr12	6061674	6061675	A, G	VWF
chr12	6062776	6062777	A, G	VWF
chr12	6077215	6077216	A, G	VWF
chr12	6078407	6078408	C, T	VWF
chr12	6080931	6080932	A, C	VWF
chr12	6085444	6085445	A, G	VWF
chr12	6085446	6085447	A, G	VWF
chr12	6090999	6091000	A, G	VWF
chr12	6092441	6092442	A, G	VWF
chr12	6094289	6094290	A, T	VWF
chr12	6094783	6094784	C, T	VWF
chr12	6094844	6094845	A, G	VWF
chr12	6103071	6103072	C, T	VWF
chr12	6103280	6103281	A, T	VWF
chr12	6120957	6120958	A, G	VWF
chr12	6122751	6122752	A, G	VWF
chr12	6125819	6125820	A, G	VWF
chr12	6128169	6128170	C, G	VWF
chr12	6128279	6128280	C, T	VWF
chr12	6128442	6128443	C, T	VWF
chr12	6128445	6128446	C, T	VWF
chr12	6128788	6128789	C, T	VWF
chr12	6128891	6128892	C	VWF
chr12	6131160	6131161	A, G	VWF
chr12	6131957	6131958	C, T	VWF
chr12	6131958	6131959	A, G	VWF
chr12	6132017	6132018	A, G	VWF
chr12	6132029	6132030	A, G	VWF
chr12	6132783	6132784	C, T	VWF
chr12	6132789	6132790	G, T	VWF
chr12	6134714	6134715	A, G	VWF
chr12	6138574	6138575	C, T	VWF
chr12	6138594	6138595	C, T	VWF
chr12	6143983	6143984	C, T	VWF
chr12	6145589	6145590	G, T	VWF
chr12	6145648	6145649	A, T	VWF
chr12	6153513	6153514	A, G	VWF
chr12	6153533	6153534	C, T	VWF
chr12	6153658	6153659	G, T	VWF
chr12	6155949	6155950	C, T	VWF
chr12	6166173	6166174	A, G	VWF
chr12	6167117	6167118	C, T	VWF
chr12	6167195	6167196	A, G	VWF
chr12	6172201	6172202	C, T	VWF
chr12	6172229	6172230	A, G	VWF
chr12	6173432	6173433	C, T	VWF
chr12	6173514	6173515	A, G	VWF
chr12	6174413	6174414	G, T	VWF
chr12	6174422	6174423	A, T	VWF
chr12	6180581	6180582	A, T	VWF
chr12	6181634	6181635	A, G	VWF
chr12	6182752	6182753	C, T	VWF
chr12	6182827	6182828	A, T	VWF
chr12	6204614	6204615	G, T	VWF
chr12	6219681	6219682	A, G	VWF
chr12	6219986	6219987	A, C	VWF
chr12	6232425	6232426	A, G	VWF
chr12	6883721	6883722	C, T	LAG3
chr12	6887019	6887020	C, T	LAG3
chr12	6909387	6909388	A, G	CD4
chr12	6923461	6923462	C, T	CD4
chr12	6924121	6924122	A, G	CD4
chr12	6925148	6925149	C, T	CD4
chr12	6925293	6925294	C, T	CD4
chr12	6925312	6925313	G, T	CD4
chr12	6925406	6925407	C, T	CD4
chr12	6926362	6926363	C, T	CD4
chr12	6927664	6927665	C, T	CD4
chr12	6928074	6928075	C, T	CD4
chr12	6928485	6928486	C, T	CD4
chr12	11992167	11992168	A, G	ETV6
chr12	12043862	12043863	C, T	ETV6
chr12	12312795	12312796	A, G	LRP6
chr12	12317519	12317520	G, T	LRP6
chr12	12317520	12317521	C, T	LRP6
chr12	12332841	12332842	C, T	LRP6
chr12	12334005	12334006	C, G	LRP6
chr12	12336965	12336966	A, G	LRP6
chr12	12337060	12337061	C, T	LRP6
chr12	12397265	12397266	A, T	LRP6
chr12	12871098	12871099	G, T	CDKN1B
chr12	12874141	12874142	C, T	CDKN1B
chr12	21325759	21325760	C, G	SLCO1B1
chr12	21327666	21327667	A, C	SLCO1B1
chr12	21329737	21329738	A, G	SLCO1B1
chr12	21329760	21329761	A, G	SLCO1B1
chr12	21329812	21329813	A, C	SLCO1B1
chr12	21329831	21329832	G, T	SLCO1B1
chr12	21331548	21331549	C, T	SLCO1B1
chr12	21331598	21331599	C, T	SLCO1B1
chr12	21331624	21331625	C, T	SLCO1B1
chr12	21331859	21331860	A, G	SLCO1B1
chr12	21331986	21331987	C, T	SLCO1B1
chr12	21349884	21349885	A, G	SLCO1B1
chr12	21350033	21350034	A, G	SLCO1B1
chr12	21353556	21353557	C, T	SLCO1B1
chr12	21353628	21353629	A, G	SLCO1B1
chr12	21355488	21355489	C, G	SLCO1B1
chr12	21355536	21355537	A, G	SLCO1B1
chr12	21358921	21358922	C, T	SLCO1B1
chr12	21358932	21358933	C, G	SLCO1B1
chr12	21375158	21375159	A, G	SLCO1B1
chr12	21377701	21377702	A, G	SLCO1B1
chr12	25362853	25362854	C, T	KRAS
chr12	46125128	46125129	G, T	ARID2
chr12	46149586	46149587	A	ARID2
chr12	46215162	46215163	A, G	ARID2
chr12	46244416	46244417	A, T	ARID2
chr12	46244669	46244670	A, G	ARID2
chr12	46245076	46245077	A, G	ARID2
chr12	46246093	46246094	A, G	ARID2
chr12	46246205	46246206	G, T	ARID2
chr12	46246397	46246398	A, G	ARID2
chr12	46285748	46285749	A, G	ARID2
chr12	48238756	48238757	A, G	VDR
chr12	48249387	48249388	C	VDR
chr12	48251075	48251076	C, T	VDR
chr12	48251304	48251305	A, G	VDR
chr12	48272742	48272743	A, G	VDR
chr12	48272839	48272840	A, G	VDR
chr12	48272848	48272849	A, G	VDR
chr12	48298294	48298295	A, G	VDR
chr12	49418434	49418435	A, C	MLL2
chr12	49422794	49422795	A, G	MLL2
chr12	49422825	49422826	A, G	MLL2
chr12	49422856	49422857	C, T	MLL2
chr12	49424533	49424534	A, G	MLL2
chr12	49424615	49424616	A, G	MLL2
chr12	49424864	49424865	C, T	MLL2
chr12	49425442	49425443	C, G	MLL2
chr12	49425977	49425978	C, T	MLL2
chr12	49426459	49426460	A, G	MLL2
chr12	49426877	49426878	C, T	MLL2
chr12	49427918	49427919	C, T	MLL2
chr12	49428322	49428323	A, G	MLL2
chr12	49431093	49431094	C, T	MLL2
chr12	49433355	49433356	A, G	MLL2
chr12	49433414	49433415	A, G	MLL2
chr12	49434073	49434074	A, C	MLL2
chr12	49434364	49434365	A, G	MLL2
chr12	49434408	49434409	A, G	MLL2
chr12	49434745	49434746	A, G	MLL2
chr12	49435813	49435814	C, T	MLL2
chr12	49435823	49435824	A, C	MLL2
chr12	49436004	49436005	C, T	MLL2
chr12	49437398	49437399	G, T	MLL2
chr12	49438163	49438164	C, T	MLL2
chr12	49438252	49438253	A, G	MLL2
chr12	49438346	49438347	C, T	MLL2
chr12	49441904	49441905	C, G	MLL2
chr12	49444544	49444545	A, G	MLL2
chr12	49445027	49445028	A, G	MLL2
chr12	49445215	49445216	C, T	MLL2
chr12	49445527	49445528	C, G	MLL2
chr12	49446039	49446040	C, T	MLL2
chr12	49448462	49448463	C, T	MLL2
chr12	52306340	52306341	A, G	ACVRL1
chr12	52307027	52307028	C, T	ACVRL1
chr12	52307144	52307145	C, T	ACVRL1
chr12	52308343	52308344	A, G	ACVRL1
chr12	52308392	52308393	C	ACVRL1
chr12	52309901	52309902	A, G	ACVRL1
chr12	52310025	52310026	C, T	ACVRL1
chr12	52310035	52310036	C, T	ACVRL1
chr12	52312943	52312944	C, T	ACVRL1
chr12	52435631	52435632	A, C	NR4A1
chr12	52435690	52435691	A, G	NR4A1
chr12	52435743	52435744	C, T	NR4A1
chr12	52448156	52448157	A, G	NR4A1
chr12	52448187	52448188	C, G	NR4A1
chr12	52448730	52448731	C, T	NR4A1
chr12	52448858	52448859	C, T	NR4A1
chr12	52449026	52449027	A, G	NR4A1
chr12	52450383	52450384	A, G	NR4A1
chr12	52450479	52450480	C, T	NR4A1
chr12	52450830	52450831	A, G	NR4A1
chr12	52450934	52450935	A, G	NR4A1
chr12	52452605	52452606	C, T	NR4A1
chr12	52452756	52452757	C, T	NR4A1
chr12	54795409	54795410	A, G	ITGA5
chr12	54795844	54795845	A, G	ITGA5
chr12	54796756	54796757	C, T	ITGA5
chr12	54796997	54796998	A, G	ITGA5
chr12	54797041	54797042	G	ITGA5
chr12	54797570	54797571	C, G	ITGA5
chr12	54798008	54798009	A, G	ITGA5
chr12	54798010	54798011	C, T	ITGA5
chr12	54798011	54798012	A, G	ITGA5
chr12	54798047	54798048	A, G	ITGA5
chr12	54798692	54798693	A, G	ITGA5
chr12	54799681	54799682	C, T	ITGA5
chr12	54801524	54801525	A, G	ITGA5
chr12	54802029	54802030	G, T	ITGA5
chr12	54802579	54802580	A, G	ITGA5
chr12	54802637	54802638	A, G	ITGA5
chr12	54802669	54802670	C, G	ITGA5
chr12	54805752	54805753	G, T	ITGA5
chr12	54805764	54805765	C, T	ITGA5
chr12	56360875	56360876	A, G	CDK2
chr12	56363356	56363357	A, G	CDK2
chr12	56364792	56364793	A, G	CDK2
chr12	56481333	56481334	C, G	ERBB3
chr12	56481734	56481735	C, G	ERBB3
chr12	56482858	56482859	A, G	ERBB3
chr12	56487200	56487201	C, T	ERBB3
chr12	56493821	56493822	A, C	ERBB3
chr12	56494990	56494991	A, G	ERBB3
chr12	56494997	56494998	A, T	ERBB3
chr12	56495305	56495306	C, T	ERBB3
chr12	58143087	58143088	C, T	CDK4
chr12	58144780	58144781	C, T	CDK4
chr12	58144920	58144921	C, G	CDK4
chr12	68551930	68551931	A, G	IFNG
chr12	69202325	69202326	C, T	MDM2
chr12	69207323	69207324	A, C	MDM2
chr12	69209571	69209572	A, G	MDM2
chr12	69233214	69233215	A, G	MDM2
chr12	104324265	104324266	A, G	HSP90B1
chr12	104325458	104325459	C, G	HSP90B1
chr12	104332256	104332257	C, T	HSP90B1
chr12	104335379	104335380	A, C	HSP90B1
chr12	104337666	104337667	A, G	HSP90B1
chr12	104340740	104340741	A, G	HSP90B1
chr12	104341102	104341103	C, T	HSP90B1
chr12	112856953	112856954	C, G	PTPN11
chr12	112856982	112856983	A, C	PTPN11
chr12	120762764	120762765	C, T	PLA2G1B
chr12	120762836	120762837	A, G	PLA2G1B
chr12	121592688	121592689	C, T	P2RX7
chr12	121598651	121598652	A, G	P2RX7
chr12	121598790	121598791	A, C	P2RX7
chr12	121600179	121600180	C, T	P2RX7
chr12	121600251	121600252	A, G	P2RX7
chr12	121600252	121600253	C, T	P2RX7
chr12	121603293	121603294	C, T	P2RX7
chr12	121603807	121603808	A, T	P2RX7
chr12	121603839	121603840	C, T	P2RX7
chr12	121603855	121603856	C, G	P2RX7
chr12	121605353	121605354	C, T	P2RX7
chr12	121605354	121605355	A, G	P2RX7
chr12	121613143	121613144	C, G	P2RX7
chr12	121614933	121614934	C, T	P2RX7
chr12	121615102	121615103	A, G	P2RX7
chr12	121615130	121615131	C, G	P2RX7
chr12	121618140	121618141	A, C	P2RX7
chr12	121618234	121618235	A, G	P2RX7
chr12	121618256	121618257	C, G	P2RX7
chr12	121622114	121622115	C, T	P2RX7
chr12	121622195	121622196	A, G	P2RX7
chr12	121622238	121622239	C, T	P2RX7
chr12	121622303	121622304	A, C	P2RX7
chr12	121622379	121622380	C, G	P2RX7
chr12	121622380	121622381	A, G	P2RX7
chr12	121622418	121622419	G, T	P2RX7
chr12	121622562	121622563	A, G	P2RX7
chr12	122694296	122694297	C, T	DIABLO
chr12	122701000	122701001	A, T	DIABLO
chr12	125397552	125397553	C, T	UBC
chr12	125398038	125398039	C, G	UBC
chr12	125398318	125398319	A, G	UBC
chr12	130647708	130647709	C, G	FZD10
chr12	130649133	130649134	C, T	FZD10
chr12	133201326	133201327	A, T	POLE
chr12	133201946	133201947	C, T	POLE
chr12	133202003	133202004	C, T	POLE
chr12	133202214	133202215	A, G	POLE
chr12	133208978	133208979	C, T	POLE
chr12	133212484	133212485	C, T	POLE
chr12	133214694	133214695	G, T	POLE
chr12	133215910	133215911	C, T	POLE
chr12	133218209	133218210	C, G	POLE
chr12	133218276	133218277	A, G	POLE
chr12	133219830	133219831	C, T	POLE
chr12	133219948	133219949	A, G	POLE
chr12	133219988	133219989	A, T	POLE
chr12	133220525	133220526	C, T	POLE
chr12	133235999	133236000	C, T	POLE
chr12	133236029	133236030	C, T	POLE
chr12	133237686	133237687	A, G	POLE
chr12	133238075	133238076	C, T	POLE
chr12	133240966	133240967	A, G	POLE
chr12	133241062	133241063	C, T	POLE
chr12	133242048	133242049	C, T	POLE
chr12	133245148	133245149	A, G	POLE
chr12	133245546	133245547	A, G	POLE
chr12	133250117	133250118	C, T	POLE
chr12	133250196	133250197	C, T	POLE
chr12	133251938	133251939	A, G	POLE
chr12	133252692	133252693	C, T	POLE
chr12	133252795	133252796	C, G	POLE
chr12	133253194	133253195	G	POLE
chr12	133253994	133253995	A, G	POLE
chr12	133254082	133254083	C, T	POLE
chr12	133256697	133256698	C, T	POLE
chr12	133263824	133263825	A, G	POLE
chr13	26828915	26828916	C, T	CDK8
chr13	26928054	26928055	C, T	CDK8
chr13	26971194	26971195	A, G	CDK8
chr13	26974561	26974562	A, G	CDK8
chr13	26974573	26974574	C, T	CDK8
chr13	28578208	28578209	C, G	FLT3
chr13	28578212	28578213	C, T	FLT3
chr13	28601172	28601173	C, T	FLT3
chr13	28602255	28602256	C, T	FLT3
chr13	28602291	28602292	C, T	FLT3
chr13	28608282	28608283	A, G	FLT3
chr13	28608458	28608459	C, T	FLT3
chr13	28608472	28608473	C, T	FLT3
chr13	28609650	28609651	C, G	FLT3
chr13	28610044	28610045	C, T	FLT3
chr13	28610182	28610183	A, G	FLT3
chr13	28611381	28611382	G, T	FLT3
chr13	28622355	28622356	A, G	FLT3
chr13	28623698	28623699	G, T	FLT3
chr13	28623758	28623759	C, T	FLT3
chr13	28624293	28624294	A, G	FLT3
chr13	28636083	28636084	A, G	FLT3
chr13	28644585	28644586	C, T	FLT3
chr13	28674557	28674558	A, G	FLT3
chr13	28674627	28674628	C, T	FLT3
chr13	28882947	28882948	A, G	FLT1
chr13	28883060	28883061	A, G	FLT1
chr13	28893641	28893642	A, G	FLT1
chr13	28893687	28893688	A, G	FLT1
chr13	28896978	28896979	C, T	FLT1
chr13	28959076	28959077	A, G	FLT1
chr13	28964197	28964198	C, T	FLT1
chr13	28971023	28971024	C, T	FLT1
chr13	28973172	28973173	A, G	FLT1
chr13	28973312	28973313	A, G	FLT1
chr13	28979993	28979994	A, G	FLT1
chr13	29001429	29001430	A, G	FLT1
chr13	29004324	29004325	A, C	FLT1
chr13	29041006	29041007	A, T	FLT1
chr13	29041580	29041581	A, C	FLT1
chr13	29041592	29041593	G, T	FLT1
chr13	32890571	32890572	A, G	BRCA2
chr13	32900439	32900440	A, T	BRCA2
chr13	32903684	32903685	C, T	BRCA2
chr13	32906479	32906480	A, C	BRCA2
chr13	32906728	32906729	A, C	BRCA2
chr13	32906979	32906980	A, G	BRCA2
chr13	32907402	32907403	C, T	BRCA2
chr13	32910720	32910721	C, T	BRCA2
chr13	32910841	32910842	A, G	BRCA2
chr13	32911462	32911463	A, G	BRCA2
chr13	32911755	32911756	C, T	BRCA2
chr13	32912360	32912361	G	BRCA2
chr13	32913054	32913055	A, G	BRCA2
chr13	32913909	32913910	A, G	BRCA2
chr13	32914195	32914196	A, G	BRCA2
chr13	32914838	32914839	A, G	BRCA2
chr13	32915004	32915005	C, G	BRCA2
chr13	32929006	32929007	C, G	BRCA2
chr13	32929231	32929232	A, G	BRCA2
chr13	32929308	32929309	A, G	BRCA2
chr13	32929386	32929387	C, T	BRCA2
chr13	32930597	32930598	C, T	BRCA2
chr13	32944666	32944667	A, C	BRCA2
chr13	32953528	32953529	A, T	BRCA2
chr13	32953549	32953550	A, G	BRCA2
chr13	32972379	32972380	A, G	BRCA2
chr13	48916861	48916862	C, T	RB1
chr13	48916894	48916895	C, T	RB1
chr13	48919357	48919358	G, T	RB1
chr13	48919380	48919381	A, G	RB1
chr13	48921922	48921923	A, G	RB1
chr13	48934297	48934298	A, T	RB1
chr13	48947468	48947469	G, T	RB1
chr13	48955457	48955458	C, G	RB1
chr13	49047416	49047417	A, G	RB1
chr13	49051011	49051012	C, T	RB1
chr13	49051480	49051481	A, T	RB1
chr13	78473967	78473968	C, T	EDNRB
chr13	78475312	78475313	C, T	EDNRB
chr13	78477664	78477665	A, G	EDNRB
chr13	78477673	78477674	A, G	EDNRB
chr13	95097955	95097956	C, T	DCT
chr13	95114397	95114398	A, G	DCT
chr13	95117925	95117926	C, T	DCT
chr13	95121252	95121253	A, G	DCT
chr13	95121342	95121343	C	DCT
chr13	102375149	102375150	C, T	FGF14
chr13	102379087	102379088	A, G	FGF14
chr13	103460018	103460019	A, G	ERCC5
chr13	103474030	103474031	C, T	ERCC5
chr13	103483990	103483991	C, T	ERCC5
chr13	103498542	103498543	A, G	ERCC5
chr13	103498544	103498545	C, T	ERCC5
chr13	103504516	103504517	C, T	ERCC5
chr13	103506685	103506686	C, G	ERCC5
chr13	103511300	103511301	C, T	ERCC5
chr13	103513950	103513951	A, G	ERCC5
chr13	103514938	103514939	C, T	ERCC5
chr13	103515378	103515379	A, C	ERCC5
chr13	103518161	103518162	A, C	ERCC5
chr13	103524761	103524762	C, T	ERCC5
chr13	103528001	103528002	C, G	ERCC5
chr13	108922642	108922643	C, G	TNFSF13B
chr13	108955574	108955575	C, T	TNFSF13B
chr13	108955932	108955933	C, T	TNFSF13B
chr13	110408582	110408583	C, T	IRS2
chr13	110435230	110435231	C, T	IRS2
chr13	110435405	110435406	C, T	IRS2
chr13	110435769	110435770	C, T	IRS2
chr13	110435952	110435953	A, G	IRS2
chr13	110436057	110436058	A, G	IRS2
chr13	110436231	110436232	A, G	IRS2
chr13	110436486	110436487	A, G	IRS2
chr13	110436666	110436667	C, T	IRS2
chr13	110436866	110436867	C, T	IRS2
chr14	20811771	20811772	A, C	PARP2
chr14	20811910	20811911	C, G	PARP2
chr14	20813641	20813642	A, G	PARP2
chr14	20813671	20813672	A, G	PARP2
chr14	20814939	20814940	C, G	PARP2
chr14	20815012	20815013	C, T	PARP2
chr14	20819226	20819227	A, G	PARP2
chr14	20822255	20822256	A, G	PARP2
chr14	20822307	20822308	A, G	PARP2
chr14	20823051	20823052	A, G	PARP2
chr14	20823094	20823095	A, G	PARP2
chr14	20824180	20824181	C, T	PARP2
chr14	20824620	20824621	A, G	PARP2
chr14	20824624	20824625	C, T	PARP2
chr14	20824858	20824859	C, T	PARP2
chr14	20824901	20824902	C, T	PARP2
chr14	20825322	20825323	G, T	PARP2
chr14	20942743	20942744	A, G	PNP
chr14	20942752	20942753	C, T	PNP
chr14	20942755	20942756	A, G	PNP
chr14	20943141	20943142	A, G	PNP
chr14	23504020	23504021	A, G	PSMB5
chr14	23777080	23777081	A, G	BCL2L2
chr14	23777098	23777099	A, G	BCL2L2
chr14	23844978	23844979	A, C	IL25
chr14	25042908	25042909	A, G	CTSG
chr14	25043670	25043671	C, T	CTSG
chr14	25043835	25043836	C, G	CTSG
chr14	25043950	25043951	A, G	CTSG
chr14	25045385	25045386	C, G	CTSG
chr14	35871216	35871217	A, G	NFKBIA
chr14	35871959	35871960	A, G	NFKBIA
chr14	35872093	35872094	C, T	NFKBIA
chr14	35872925	35872926	A, G	NFKBIA
chr14	35872988	35872989	A, G	NFKBIA
chr14	35873769	35873770	A, G	NFKBIA
chr14	36988828	36988829	A, G	NKX2-1
chr14	38679001	38679002	A, G	SSTR1
chr14	38679472	38679473	C, T	SSTR1
chr14	62188396	62188397	C, T	HIF1A
chr14	62207556	62207557	C, T	HIF1A
chr14	62207574	62207575	A, G	HIF1A
chr14	62213847	62213848	C, T	HIF1A
chr14	64694194	64694195	C, T	ESR2
chr14	64694234	64694235	C, T	ESR2
chr14	64700044	64700045	C, T	ESR2
chr14	64716312	64716313	C, G	ESR2
chr14	64724050	64724051	C, T	ESR2
chr14	64726853	64726854	A, T	ESR2
chr14	64735495	64735496	A, G	ESR2
chr14	64735534	64735535	A, G	ESR2
chr14	64746765	64746766	A, T	ESR2
chr14	64749322	64749323	G, T	ESR2
chr14	64749696	64749697	C, T	ESR2
chr14	75409340	75409341	C, T	PGF
chr14	75413010	75413011	C, T	PGF
chr14	75415338	75415339	G, T	PGF
chr14	75415999	75416000	C, T	PGF
chr14	81422177	81422178	A, C	TSHR
chr14	81534708	81534709	A, T	TSHR
chr14	81554262	81554263	C, T	TSHR
chr14	81554393	81554394	A, T	TSHR
chr14	81558964	81558965	A, G	TSHR
chr14	81562997	81562998	C, T	TSHR
chr14	81574815	81574816	C, G	TSHR
chr14	81574958	81574959	A, G	TSHR
chr14	81609722	81609723	A, C	TSHR
chr14	81609778	81609779	A, G	TSHR
chr14	81610633	81610634	C, G	TSHR
chr14	90865461	90865462	C, G	CALM1
chr14	90866467	90866468	A, G	CALM1
chr14	94844842	94844843	G, T	SERPINA1
chr14	94847261	94847262	A, T	SERPINA1
chr14	94847284	94847285	A, G	SERPINA1
chr14	94847350	94847351	C, T	SERPINA1
chr14	94847414	94847415	A, G	SERPINA1
chr14	94849150	94849151	A, G	SERPINA1
chr14	94849200	94849201	C, T	SERPINA1
chr14	102548150	102548151	A, G	HSP90AA1
chr14	102548440	102548441	G, T	HSP90AA1
chr14	102549982	102549983	C, T	HSP90AA1
chr14	102550085	102550086	A, C	HSP90AA1
chr14	102551787	102551788	A, G	HSP90AA1
chr14	102552489	102552490	C, T	HSP90AA1
chr14	102552772	102552773	A, G	HSP90AA1
chr14	102552774	102552775	G, T	HSP90AA1
chr14	102568366	102568367	A, T	HSP90AA1
chr14	105238669	105238670	C, T	AKT1
chr14	105238782	105238783	A, G	AKT1
chr14	105239435	105239436	A, G	AKT1
chr14	105240226	105240227	C, G	AKT1
chr14	105241303	105241304	A, G	AKT1
chr14	105241377	105241378	C, T	AKT1
chr14	105241398	105241399	C, T	AKT1
chr14	105241421	105241422	A, G	AKT1
chr14	105242965	105242966	C, T	AKT1
chr14	105258891	105258892	C, T	AKT1
chr14	105258892	105258893	A, G	AKT1
chr15	41020860	41020861	G, T	RAD51
chr15	41021050	41021051	A, T	RAD51
chr15	41221986	41221987	C, T	DLL4
chr15	41222024	41222025	C, T	DLL4
chr15	41227148	41227149	C, T	DLL4
chr15	41795739	41795740	A, G	LTK
chr15	41796497	41796498	A, T	LTK
chr15	41796598	41796599	C, T	LTK
chr15	41797295	41797296	C, T	LTK
chr15	41798216	41798217	C, T	LTK
chr15	41799710	41799711	C, T	LTK
chr15	41799847	41799848	A, G	LTK
chr15	41803795	41803796	G, T	LTK
chr15	41803806	41803807	A, G	LTK
chr15	41803826	41803827	C, T	LTK
chr15	41805114	41805115	A, G	LTK
chr15	41805236	41805237	C, T	LTK
chr15	51502843	51502844	A, C	CYP19A1
chr15	51503880	51503881	A, T	CYP19A1
chr15	51503896	51503897	A, G	CYP19A1
chr15	51507873	51507874	A, G	CYP19A1
chr15	51507967	51507968	A, G	CYP19A1
chr15	51510867	51510868	A, C	CYP19A1
chr15	51514571	51514572	A, G	CYP19A1
chr15	51529111	51529112	C, T	CYP19A1
chr15	51529165	51529166	A, G	CYP19A1
chr15	51529232	51529233	A, G	CYP19A1
chr15	51529264	51529265	C, T	CYP19A1
chr15	51534994	51534995	A, G	CYP19A1
chr15	66679797	66679798	C, G	MAP2K1
chr15	66679818	66679819	C, G	MAP2K1
chr15	66727596	66727597	C, G	MAP2K1
chr15	66729249	66729250	C, T	MAP2K1
chr15	66735550	66735551	C, T	MAP2K1
chr15	66779596	66779597	A, T	MAP2K1
chr15	67430336	67430337	A, G	SMAD3
chr15	67457334	67457335	A, G	SMAD3
chr15	67457697	67457698	A, G	SMAD3
chr15	67482695	67482696	A, G	SMAD3
chr15	67482696	67482697	C, T	SMAD3
chr15	80259963	80259964	C, T	BCL2A1
chr15	80260013	80260014	C, T	BCL2A1
chr15	80263110	80263111	A, C	BCL2A1
chr15	80263216	80263217	C, T	BCL2A1
chr15	80263344	80263345	A, C	BCL2A1
chr15	80263405	80263406	C, T	BCL2A1
chr15	88476364	88476365	A, G	NTRK3
chr15	88522551	88522552	A, C	NTRK3
chr15	88576184	88576185	C, G	NTRK3
chr15	88576214	88576215	A, G	NTRK3
chr15	88669444	88669445	C, T	NTRK3
chr15	88670347	88670348	C, G	NTRK3
chr15	88726764	88726765	A, G	NTRK3
chr15	90627615	90627616	C, T	IDH2
chr15	90628536	90628537	A, G	IDH2
chr15	90628590	90628591	A, G	IDH2
chr15	90628593	90628594	C, T	IDH2
chr15	90630629	90630630	A, G	IDH2
chr15	90645664	90645665	C, T	IDH2
chr15	91292916	91292917	A, G	BLM
chr15	91295109	91295110	C, T	BLM
chr15	91308511	91308512	T	BLM
chr15	91308513	91308514	G, T	BLM
chr15	91312312	91312313	A, G	BLM
chr15	91326098	91326099	C, T	BLM
chr15	91337478	91337479	A, G	BLM
chr15	91341598	91341599	G, T	BLM
chr15	91346922	91346923	A, C	BLM
chr15	91354504	91354505	C, T	BLM
chr15	91354519	91354520	C, T	BLM
chr15	91354520	91354521	A, G	BLM
chr15	99251097	99251098	A, G	IGF1R
chr15	99434776	99434777	C, T	IGF1R
chr15	99434797	99434798	A, G	IGF1R
chr15	99434815	99434816	A, C	IGF1R
chr15	99454538	99454539	A, C	IGF1R
chr15	99456248	99456249	C, T	IGF1R
chr15	99456252	99456253	C, T	IGF1R
chr15	99465472	99465473	C, T	IGF1R
chr15	99467933	99467934	A, C	IGF1R
chr15	99473407	99473408	A, T	IGF1R
chr15	99500604	99500605	C, T	IGF1R
chr16	1128894	1128895	A, G	SSTR5
chr16	1129009	1129010	A, C	SSTR5
chr16	1129022	1129023	C, T	SSTR5
chr16	1129192	1129193	C, T	SSTR5
chr16	1129224	1129225	C, T	SSTR5
chr16	1129269	1129270	C, T	SSTR5
chr16	1129350	1129351	C, T	SSTR5
chr16	1129383	1129384	A, G	SSTR5
chr16	1129524	1129525	A, G	SSTR5
chr16	1129619	1129620	C, T	SSTR5
chr16	1129865	1129866	C, T	SSTR5
chr16	1129871	1129872	C, T	SSTR5
chr16	1129911	1129912	A, G	SSTR5
chr16	1131062	1131063	C, T	SSTR5
chr16	1131174	1131175	A, C	SSTR5
chr16	1131180	1131181	C, T	SSTR5
chr16	2103485	2103486	G, T	TSC2
chr16	2105562	2105563	C, T	TSC2
chr16	2107185	2107186	A, G	TSC2
chr16	2108846	2108847	G	TSC2
chr16	2113071	2113072	C	TSC2
chr16	2114371	2114372	C, T	TSC2
chr16	2115463	2115464	C, G	TSC2
chr16	2115480	2115481	C, T	TSC2
chr16	2115505	2115506	C, T	TSC2
chr16	2125787	2125788	C, T	TSC2
chr16	2125833	2125834	C, T	TSC2
chr16	2129191	2129192	C, G	TSC2
chr16	2130189	2130190	C	TSC2
chr16	2132378	2132379	C, T	TSC2
chr16	2132512	2132513	C, G	TSC2
chr16	2133639	2133640	C, G	TSC2
chr16	2133725	2133726	C, T	TSC2
chr16	2133726	2133727	A, G	TSC2
chr16	2133797	2133798	A, G	TSC2
chr16	2134437	2134438	C, T	TSC2
chr16	2135070	2135071	C, T	TSC2
chr16	2136865	2136866	C, T	TSC2
chr16	2137856	2137857	C, T	TSC2
chr16	2138217	2138218	A, C	TSC2
chr16	2138218	2138219	C, T	TSC2
chr16	2138268	2138269	C, T	TSC2
chr16	2138397	2138398	C, T	TSC2
chr16	2138421	2138422	C, G	TSC2
chr16	2138507	2138508	C, G	TSC2
chr16	2138583	2138584	C, G	TSC2
chr16	2138636	2138637	A, G	TSC2
chr16	2692463	2692464	A, G	PDPK1
chr16	3293887	3293888	C, T	MEFV
chr16	3293895	3293896	C, T	MEFV
chr16	3293921	3293922	A, T	MEFV
chr16	3294245	3294246	A, G	MEFV
chr16	3296615	3296616	C, T	MEFV
chr16	3297072	3297073	A, G	MEFV
chr16	3297099	3297100	A, G	MEFV
chr16	3297174	3297175	C, T	MEFV
chr16	3297180	3297181	C, T	MEFV
chr16	3298946	3298947	C, G	MEFV
chr16	3299031	3299032	C, T	MEFV
chr16	3299467	3299468	C, T	MEFV
chr16	3299585	3299586	A, G	MEFV
chr16	3299748	3299749	A, G	MEFV
chr16	3301896	3301897	A, G	MEFV
chr16	3304128	3304129	C, G	MEFV
chr16	3304157	3304158	C, T	MEFV
chr16	3304462	3304463	C, T	MEFV
chr16	3304572	3304573	G, T	MEFV
chr16	3304625	3304626	C, G	MEFV
chr16	3304653	3304654	C, T	MEFV
chr16	3304734	3304735	C, T	MEFV
chr16	3304738	3304739	A, G	MEFV
chr16	3304761	3304762	A, G	MEFV
chr16	3778336	3778337	A, G	CREBBP
chr16	3779059	3779060	A, G	CREBBP
chr16	3779377	3779378	A, G	CREBBP
chr16	3781249	3781250	A, G	CREBBP
chr16	3781312	3781313	A, G	CREBBP
chr16	3794790	3794791	A, G	CREBBP
chr16	3795291	3795292	G, T	CREBBP
chr16	3795362	3795363	A, G	CREBBP
chr16	3817842	3817843	A, G	CREBBP
chr16	3819260	3819261	C, T	CREBBP
chr16	3820666	3820667	C, T	CREBBP
chr16	3824731	3824732	C, T	CREBBP
chr16	3827552	3827553	A, G	CREBBP
chr16	3831186	3831187	A, T	CREBBP
chr16	3832958	3832959	A, C	CREBBP
chr16	3860639	3860640	A, G	CREBBP
chr16	3929940	3929941	C, T	CREBBP
chr16	9916203	9916204	C, G	GRIN2A
chr16	9943665	9943666	C, T	GRIN2A
chr16	9984972	9984973	C, G	GRIN2A
chr16	15797842	15797843	C, G	MYH11
chr16	15809116	15809117	C, T	MYH11
chr16	15811022	15811023	C, T	MYH11
chr16	15811061	15811062	C, T	MYH11
chr16	15811130	15811131	A, G	MYH11
chr16	15812095	15812096	A, G	MYH11
chr16	15812308	15812309	A, G	MYH11
chr16	15812990	15812991	A, C	MYH11
chr16	15814920	15814921	C, T	MYH11
chr16	15814936	15814937	A, G	MYH11
chr16	15815350	15815351	A, G	MYH11
chr16	15818140	15818141	A, C	MYH11
chr16	15818652	15818653	A, G	MYH11
chr16	15818841	15818842	A, G	MYH11
chr16	15820862	15820863	C, T	MYH11
chr16	15826383	15826384	C, T	MYH11
chr16	15829418	15829419	C, T	MYH11
chr16	15838939	15838940	C, G	MYH11
chr16	15838970	15838971	C, G	MYH11
chr16	15839033	15839034	A, G	MYH11
chr16	15839102	15839103	G, T	MYH11
chr16	15841772	15841773	A, G	MYH11
chr16	15841829	15841830	A, G	MYH11
chr16	15841838	15841839	A, G	MYH11
chr16	15841861	15841862	C, T	MYH11
chr16	15842004	15842005	A, G	MYH11
chr16	15843957	15843958	C, T	MYH11
chr16	15843964	15843965	A, G	MYH11
chr16	15851654	15851655	A, G	MYH11
chr16	15865471	15865472	A, G	MYH11
chr16	15872747	15872748	G, T	MYH11
chr16	15917226	15917227	C, T	MYH11
chr16	15917320	15917321	C, T	MYH11
chr16	15931974	15931975	A, G	MYH11
chr16	16130356	16130357	C, T	ABCC1
chr16	16130513	16130514	A, C	ABCC1
chr16	16139713	16139714	C, T	ABCC1
chr16	16139719	16139720	A, G	ABCC1
chr16	16139877	16139878	A, G	ABCC1
chr16	16146575	16146576	C, G	ABCC1
chr16	16161975	16161976	A, G	ABCC1
chr16	16162018	16162019	C, T	ABCC1
chr16	16162038	16162039	C, T	ABCC1
chr16	16173226	16173227	C, T	ABCC1
chr16	16177201	16177202	A, C	ABCC1
chr16	16177274	16177275	A, G	ABCC1
chr16	16196493	16196494	C, T	ABCC1
chr16	16200755	16200756	C, T	ABCC1
chr16	16208682	16208683	C, G	ABCC1
chr16	16208947	16208948	C, G	ABCC1
chr16	16219728	16219729	C, T	ABCC1
chr16	16225804	16225805	C	ABCC1
chr16	16228241	16228242	A, G	ABCC1
chr16	16232379	16232380	C, T	ABCC1
chr16	16244128	16244129	C, T	ABCC6
chr16	16244662	16244663	C, T	ABCC6
chr16	16248679	16248680	C, T	ABCC6
chr16	16248680	16248681	A, G	ABCC6
chr16	16251530	16251531	C, T	ABCC6
chr16	16251598	16251599	C, T	ABCC6
chr16	16253291	16253292	C, G	ABCC6
chr16	16255436	16255437	A, G	ABCC6
chr16	16259595	16259596	A, G	ABCC6
chr16	16263662	16263663	A, G	ABCC6
chr16	16267220	16267221	C, G	ABCC6
chr16	16271356	16271357	C, T	ABCC6
chr16	16271408	16271409	A, G	ABCC6
chr16	16272669	16272670	C, T	ABCC6
chr16	16276291	16276292	C, T	ABCC6
chr16	16276340	16276341	A, T	ABCC6
chr16	16278862	16278863	G, T	ABCC6
chr16	16278868	16278869	C, G	ABCC6
chr16	16281006	16281007	A, G	ABCC6
chr16	16281153	16281154	A, C	ABCC6
chr16	16284264	16284265	C, T	ABCC6
chr16	16284271	16284272	C, T	ABCC6
chr16	16291857	16291858	C, G	ABCC6
chr16	16291870	16291871	C, G	ABCC6
chr16	16291970	16291971	C, T	ABCC6
chr16	16295956	16295957	C, T	ABCC6
chr16	16306058	16306059	C, T	ABCC6
chr16	23646941	23646942	C, T	PALB2
chr16	23647237	23647238	A, G	PALB2
chr16	23690252	23690253	C, T	PLK1
chr16	23691415	23691416	A, G	PLK1
chr16	23691589	23691590	A, G	PLK1
chr16	23692203	23692204	T	PLK1
chr16	23699916	23699917	C, G	PLK1
chr16	23700058	23700059	C, T	PLK1
chr16	23701254	23701255	A, G	PLK1
chr16	23701457	23701458	A, G	PLK1
chr16	23701537	23701538	A, G	PLK1
chr16	23847574	23847575	A, C	PRKCB
chr16	23848761	23848762	A, G	PRKCB
chr16	23999927	23999928	G, T	PRKCB
chr16	24104187	24104188	C, T	PRKCB
chr16	24105668	24105669	A, G	PRKCB
chr16	24166129	24166130	C, T	PRKCB
chr16	24192106	24192107	A, G	PRKCB
chr16	24202457	24202458	C, T	PRKCB
chr16	27352591	27352592	A, G	IL4R
chr16	27353588	27353589	C, G	IL4R
chr16	27356223	27356224	A, G	IL4R
chr16	27356270	27356271	C, T	IL4R
chr16	27357926	27357927	C, T	IL4R
chr16	27363900	27363901	A, G	IL4R
chr16	27367225	27367226	C, G	IL4R
chr16	27367259	27367260	C, T	IL4R
chr16	27367278	27367279	A, G	IL4R
chr16	27370164	27370165	A, G	IL4R
chr16	27373557	27373558	A, C	IL4R
chr16	27373611	27373612	C, T	IL4R
chr16	27373871	27373872	A, C	IL4R
chr16	27373914	27373915	G, T	IL4R
chr16	27373965	27373966	C, T	IL4R
chr16	27373971	27373972	C, T	IL4R
chr16	27374146	27374147	A, G	IL4R
chr16	27374179	27374180	C, T	IL4R
chr16	27374399	27374400	A, G	IL4R
chr16	27374407	27374408	A, G	IL4R
chr16	27374926	27374927	G, T	IL4R
chr16	27375024	27375025	C, T	IL4R
chr16	27375069	27375070	C, T	IL4R
chr16	27414440	27414441	C, T	IL21R
chr16	27414523	27414524	C, T	IL21R
chr16	27414535	27414536	C, T	IL21R
chr16	27441282	27441283	A, G	IL21R
chr16	27455885	27455886	A, G	IL21R
chr16	27457264	27457265	C, T	IL21R
chr16	27460436	27460437	A, G	IL21R
chr16	28944281	28944282	C, T	CD19
chr16	28944395	28944396	C, G	CD19
chr16	28944699	28944700	G, T	CD19
chr16	28950050	28950051	A, G	CD19
chr16	30128433	30128434	A, G	MAPK3
chr16	31102588	31102589	A, G	VKORC1
chr16	31105553	31105554	A, C	VKORC1
chr16	31106014	31106015	C, T	VKORC1
chr16	31273128	31273129	C, T	ITGAM
chr16	31283163	31283164	A, G	ITGAM
chr16	31289395	31289396	C, T	ITGAM
chr16	31308990	31308991	A, C	ITGAM
chr16	31332654	31332655	C, T	ITGAM
chr16	31332889	31332890	C, T	ITGAM
chr16	31335905	31335906	C, T	ITGAM
chr16	31336718	31336719	A, G	ITGAM
chr16	31336887	31336888	C, T	ITGAM
chr16	31340509	31340510	C, T	ITGAM
chr16	31340519	31340520	C, T	ITGAM
chr16	31343004	31343005	C, T	ITGAM
chr16	50733742	50733743	A, G	NOD2
chr16	50733858	50733859	C, G	NOD2
chr16	50741762	50741763	C, T	NOD2
chr16	50744623	50744624	C, T	NOD2
chr16	50745198	50745199	C, T	NOD2
chr16	50745274	50745275	C, T	NOD2
chr16	50745582	50745583	G, T	NOD2
chr16	50745925	50745926	C, T	NOD2
chr16	50745944	50745945	A, G	NOD2
chr16	50745995	50745996	C, G	NOD2
chr16	50746190	50746191	A, G	NOD2
chr16	50750759	50750760	C, T	NOD2
chr16	50750790	50750791	G	NOD2
chr16	50757275	50757276	A, G	NOD2
chr16	55515759	55515760	A, G	MMP2
chr16	55515825	55515826	A, C	MMP2
chr16	55517898	55517899	A, G	MMP2
chr16	55519534	55519535	C, G	MMP2
chr16	55519606	55519607	C, T	MMP2
chr16	55522415	55522416	C, T	MMP2
chr16	55523621	55523622	C, T	MMP2
chr16	55523653	55523654	C, T	MMP2
chr16	55523704	55523705	C, T	MMP2
chr16	55525758	55525759	A, G	MMP2
chr16	55527112	55527113	A, G	MMP2
chr16	55530999	55531000	C, T	MMP2
chr16	55536686	55536687	A, G	MMP2
chr16	55536726	55536727	C, T	MMP2
chr16	55536762	55536763	C, G	MMP2
chr16	55536781	55536782	C, G	MMP2
chr16	55539190	55539191	C, G	MMP2
chr16	55725893	55725894	C, G	SLC6A2
chr16	55725974	55725975	A, G	SLC6A2
chr16	55728080	55728081	G, T	SLC6A2
chr16	55729189	55729190	A, G	SLC6A2
chr16	55730095	55730096	A, G	SLC6A2
chr16	55730123	55730124	A, C	SLC6A2
chr16	55731834	55731835	A, G	SLC6A2
chr16	55731945	55731946	A, G	SLC6A2
chr16	55733588	55733589	C, T	SLC6A2
chr16	55734105	55734106	C, T	SLC6A2
chr16	55735911	55735912	C, T	SLC6A2
chr16	55739091	55739092	A, T	SLC6A2
chr16	55739233	55739234	C, T	SLC6A2
chr16	56792438	56792439	A, T	NUP93
chr16	56852643	56852644	A, G	NUP93
chr16	56863026	56863027	A, G	NUP93
chr16	56864397	56864398	C, T	NUP93
chr16	56864398	56864399	C, T	NUP93
chr16	56865704	56865705	G, T	NUP93
chr16	56868308	56868309	C, T	NUP93
chr16	56868699	56868700	A, G	NUP93
chr16	56868732	56868733	G	NUP93
chr16	56873494	56873495	C, T	NUP93
chr16	56878548	56878549	A, G	NUP93
chr16	57467935	57467936	A, T	CIAPIN1
chr16	57467980	57467981	A, G	CIAPIN1
chr16	57468109	57468110	A, G	CIAPIN1
chr16	57470563	57470564	C, G	CIAPIN1
chr16	57474667	57474668	A, G	CIAPIN1
chr16	57474686	57474687	C, G	CIAPIN1
chr16	66420884	66420885	C, T	CDH5
chr16	66422317	66422318	A, G	CDH5
chr16	66430136	66430137	G, T	CDH5
chr16	66432380	66432381	C, T	CDH5
chr16	66432422	66432423	C, T	CDH5
chr16	66432423	66432424	C, T	CDH5
chr16	66847574	66847575	C, T	NAE1
chr16	66847657	66847658	A, T	NAE1
chr16	66850763	66850764	C, G	NAE1
chr16	66851223	66851224	C, T	NAE1
chr16	66857572	66857573	C, G	NAE1
chr16	66861965	66861966	A, G	NAE1
chr16	66864713	66864714	G, T	NAE1
chr16	67063611	67063612	G, T	CBFB
chr16	67116168	67116169	C, T	CBFB
chr16	67663290	67663291	C, T	CTCF
chr16	68771370	68771371	C, G	CDH1
chr16	68771371	68771372	C, T	CDH1
chr16	68842479	68842480	C, G	CDH1
chr16	68847442	68847443	C, G	CDH1
chr16	68856040	68856041	A, G	CDH1
chr16	68856087	68856088	C, T	CDH1
chr16	68857440	68857441	C, T	CDH1
chr16	69745144	69745145	A, G	NQO1
chr16	69748927	69748928	C, G	NQO1
chr16	69752372	69752373	C, T	NQO1
chr16	69760260	69760261	G, T	NQO1
chr16	69760285	69760286	C, G	NQO1
chr16	69760340	69760341	A, G	NQO1
chr16	71674881	71674882	C, G	PHLPP2
chr16	71674954	71674955	C, T	PHLPP2
chr16	71678662	71678663	C, T	PHLPP2
chr16	71678761	71678762	C, G	PHLPP2
chr16	71682920	71682921	C, T	PHLPP2
chr16	71683717	71683718	A, G	PHLPP2
chr16	71692546	71692547	A, C	PHLPP2
chr16	71703251	71703252	A, G	PHLPP2
chr16	71710427	71710428	A, G	PHLPP2
chr16	71712785	71712786	A, G	PHLPP2
chr16	71718365	71718366	C, T	PHLPP2
chr16	71718423	71718424	A, G	PHLPP2
chr16	88709711	88709712	A, G	CYBA
chr16	88709827	88709828	A, G	CYBA
chr16	88713212	88713213	C, G	CYBA
chr16	88713235	88713236	A, G	CYBA
chr16	88713500	88713501	A, G	CYBA
chr16	89574833	89574834	G, T	SPG7
chr16	89577045	89577046	C, T	SPG7
chr16	89590242	89590243	A, G	SPG7
chr16	89597056	89597057	G, T	SPG7
chr16	89597109	89597110	A, G	SPG7
chr16	89603355	89603356	G, T	SPG7
chr16	89613122	89613123	A, G	SPG7
chr16	89615465	89615466	C, T	SPG7
chr16	89615541	89615542	G	SPG7
chr16	89615764	89615765	G, T	SPG7
chr16	89616886	89616887	A, C	SPG7
chr16	89619554	89619555	C, T	SPG7
chr16	89620147	89620148	A, G	SPG7
chr16	89620157	89620158	A, G	SPG7
chr16	89620185	89620186	C, G	SPG7
chr16	89620301	89620302	A, G	SPG7
chr16	89623300	89623301	A, G	SPG7
chr16	89623407	89623408	C, T	SPG7
chr16	89805260	89805261	A, G	FANCA
chr16	89805671	89805672	C, T	FANCA
chr16	89805913	89805914	C, T	FANCA
chr16	89805969	89805970	C, T	FANCA
chr16	89805976	89805977	A, G	FANCA
chr16	89806062	89806063	C, G	FANCA
chr16	89806342	89806343	A, C	FANCA
chr16	89806346	89806347	A, T	FANCA
chr16	89806476	89806477	C, T	FANCA
chr16	89807232	89807233	C, G	FANCA
chr16	89809170	89809171	C, T	FANCA
chr16	89809318	89809319	C, T	FANCA
chr16	89813193	89813194	C, T	FANCA
chr16	89813205	89813206	A, G	FANCA
chr16	89815048	89815049	C, T	FANCA
chr16	89815151	89815152	A, G	FANCA
chr16	89816313	89816314	A, G	FANCA
chr16	89816332	89816333	C, T	FANCA
chr16	89825064	89825065	A, G	FANCA
chr16	89828436	89828437	A, G	FANCA
chr16	89831492	89831493	C, G	FANCA
chr16	89831509	89831510	A, C	FANCA
chr16	89831519	89831520	A, T	FANCA
chr16	89836322	89836323	C, T	FANCA
chr16	89836508	89836509	C, G	FANCA
chr16	89836550	89836551	A, G	FANCA
chr16	89837137	89837138	G, T	FANCA
chr16	89838077	89838078	A, G	FANCA
chr16	89838085	89838086	A, C	FANCA
chr16	89839751	89839752	C, T	FANCA
chr16	89839765	89839766	C, G	FANCA
chr16	89839853	89839854	C, T	FANCA
chr16	89845193	89845194	A, G	FANCA
chr16	89845286	89845287	A, G	FANCA
chr16	89846396	89846397	A, G	FANCA
chr16	89849479	89849480	C, T	FANCA
chr16	89857879	89857880	C, T	FANCA
chr16	89858416	89858417	A, C	FANCA
chr16	89858504	89858505	C, T	FANCA
chr16	89858524	89858525	C, G	FANCA
chr16	89862416	89862417	C	FANCA
chr16	89862433	89862434	C, T	FANCA
chr16	89866042	89866043	C, T	FANCA
chr16	89869703	89869704	C, T	FANCA
chr16	89869760	89869761	C, T	FANCA
chr16	89874755	89874756	A, G	FANCA
chr16	89877234	89877235	A, T	FANCA
chr16	89877268	89877269	C, T	FANCA
chr16	89882358	89882359	G, T	FANCA
chr16	89882999	89883000	C, G	FANCA
chr16	89883006	89883007	A, T	FANCA
chr17	6902178	6902179	A, G	ALOX12
chr17	6902294	6902295	A, G	ALOX12
chr17	6902742	6902743	A, G	ALOX12
chr17	6902759	6902760	A, G	ALOX12
chr17	6909837	6909838	A, G	ALOX12
chr17	6913651	6913652	A, G	ALOX12
chr17	7462554	7462555	A, G	TNFSF13
chr17	7462580	7462581	C, G	TNFSF13
chr17	7462968	7462969	A, G	TNFSF13
chr17	7464218	7464219	C, T	TNFSF13
chr17	7579471	7579472	C, G	TP53
chr17	7579547	7579548	A, G	TP53
chr17	7579595	7579596	A, G	TP53
chr17	7579800	7579801	C, G	TP53
chr17	7976916	7976917	A, T	ALOX12B
chr17	7979451	7979452	G, T	ALOX12B
chr17	7979462	7979463	A, G	ALOX12B
chr17	7983680	7983681	A, G	ALOX12B
chr17	7984156	7984157	A, C	ALOX12B
chr17	7989405	7989406	C, T	ALOX12B
chr17	7990718	7990719	A, G	ALOX12B
chr17	8108330	8108331	A, G	AURKB
chr17	8108338	8108339	A, G	AURKB
chr17	8109964	8109965	A, G	AURKB
chr17	8109992	8109993	A, G	AURKB
chr17	8110939	8110940	A, G	AURKB
chr17	9729444	9729445	A, T	GLP2R
chr17	9739700	9739701	C, T	GLP2R
chr17	9745902	9745903	A, G	GLP2R
chr17	9760715	9760716	G, T	GLP2R
chr17	9763474	9763475	C, T	GLP2R
chr17	9764530	9764531	A, G	GLP2R
chr17	9764546	9764547	C, G, T	GLP2R
chr17	9769059	9769060	A, T	GLP2R
chr17	9769061	9769062	A, T	GLP2R
chr17	9769198	9769199	C, T	GLP2R
chr17	9773983	9773984	C, G	GLP2R
chr17	9774056	9774057	G, T	GLP2R
chr17	9791158	9791159	A, G	GLP2R
chr17	9792767	9792768	A, G	GLP2R
chr17	9792773	9792774	C, T	GLP2R
chr17	9792871	9792872	C, T	GLP2R
chr17	9792927	9792928	A, G	GLP2R
chr17	9793416	9793417	A, T	GLP2R
chr17	12043293	12043294	C, T	MAP2K4
chr17	15134320	15134321	A, G	PMP22
chr17	15142754	15142755	A, G	PMP22
chr17	16285929	16285930	C, T	UBB
chr17	29486151	29486152	A, G	NF1
chr17	29508774	29508775	A, G	NF1
chr17	29508882	29508883	A	NF1
chr17	29528561	29528562	A, G	NF1
chr17	29546174	29546175	C, T	NF1
chr17	29550597	29550598	A, T	NF1
chr17	29552199	29552200	A, G	NF1
chr17	29553472	29553473	C, T	NF1
chr17	29553484	29553485	A, G	NF1
chr17	29554201	29554202	C, T	NF1
chr17	29559917	29559918	T	NF1
chr17	29559931	29559932	A, C	NF1
chr17	29559941	29559942	A, C	NF1
chr17	29562904	29562905	A, G	NF1
chr17	29592392	29592393	C, T	NF1
chr17	29652883	29652884	C, T	NF1
chr17	29652930	29652931	A, G	NF1
chr17	29653036	29653037	A, G	NF1
chr17	29653292	29653293	C, T	NF1
chr17	29677183	29677184	C, T	NF1
chr17	29679245	29679246	A, G	NF1
chr17	29683993	29683994	C, T	NF1
chr17	29685688	29685689	C, T	NF1
chr17	29694380	29694381	C, T	NF1
chr17	29705946	29705947	C, T	NF1
chr17	33433202	33433203	C, T	RAD51L3
chr17	33445548	33445549	A, G	RAD51L3
chr17	33446669	33446670	A, C	RAD51L3
chr17	34416150	34416151	A, C	CCL3
chr17	34416664	34416665	A, G	CCL3
chr17	34417291	34417292	A, G	CCL3
chr17	34417308	34417309	C, G	CCL3
chr17	37561612	37561613	A, G	MED1
chr17	37580083	37580084	A, G	MED1
chr17	37581029	37581030	C, T	MED1
chr17	37603994	37603995	G, T	MED1
chr17	37618594	37618595	C, T	CDK12
chr17	37619037	37619038	A, G	CDK12
chr17	37682090	37682091	A, G	CDK12
chr17	37682199	37682200	A, G	CDK12
chr17	37682291	37682292	A, G	CDK12
chr17	37682374	37682375	A, T	CDK12
chr17	37855833	37855834	A, C	ERBB2
chr17	37856588	37856589	A, G	ERBB2
chr17	37863267	37863268	A, G	ERBB2
chr17	37864728	37864729	C, G	ERBB2
chr17	37866004	37866005	C, T	ERBB2
chr17	37866740	37866741	G, T	ERBB2
chr17	37868347	37868348	C, T	ERBB2
chr17	37872004	37872005	G, T	ERBB2
chr17	37872034	37872035	G, T	ERBB2
chr17	37872049	37872050	A, G	ERBB2
chr17	37879587	37879588	A, G	ERBB2
chr17	37884036	37884037	C, G	ERBB2
chr17	38512822	38512823	G	RARA
chr17	38545823	38545824	A, C	TOP2A
chr17	38547867	38547868	C, T	TOP2A
chr17	38547908	38547909	A, G	TOP2A
chr17	38555205	38555206	A, G	TOP2A
chr17	38556532	38556533	C, T	TOP2A
chr17	38556769	38556770	C, T	TOP2A
chr17	38560394	38560395	C, T	TOP2A
chr17	40469125	40469126	A, G	STAT3
chr17	40469179	40469180	A, G	STAT3
chr17	40475055	40475056	A, G	STAT3
chr17	40475382	40475383	C, G	STAT3
chr17	40476945	40476946	A, T	STAT3
chr17	40477063	40477064	C, G	STAT3
chr17	40481528	40481529	C, G	STAT3
chr17	40483465	40483466	A, C	STAT3
chr17	41197828	41197829	G, T	BRCA1
chr17	41222974	41222975	C, T	BRCA1
chr17	41223093	41223094	C, T	BRCA1
chr17	41234469	41234470	A, G	BRCA1
chr17	41243999	41244000	C, T	BRCA1
chr17	41244129	41244130	C, T	BRCA1
chr17	41244428	41244429	C, T	BRCA1
chr17	41244434	41244435	C, T	BRCA1
chr17	41244935	41244936	A, G	BRCA1
chr17	41244981	41244982	A, G	BRCA1
chr17	41245089	41245090	C, T	BRCA1
chr17	41245236	41245237	A, G	BRCA1
chr17	41245465	41245466	A, G	BRCA1
chr17	41245470	41245471	C, T	BRCA1
chr17	41245576	41245577	C, T	BRCA1
chr17	41246480	41246481	C, T	BRCA1
chr17	41251930	41251931	A, G	BRCA1
chr17	41258449	41258450	A, T	BRCA1
chr17	41267762	41267763	C, T	BRCA1
chr17	41607596	41607597	C, T	ETV4
chr17	41611331	41611332	C, G	ETV4
chr17	41622397	41622398	A, G	ETV4
chr17	42635964	42635965	C, T	FZD2
chr17	42636441	42636442	A, C	FZD2
chr17	45331266	45331267	A, G	ITGB3
chr17	45331283	45331284	G, T	ITGB3
chr17	45331284	45331285	C, T	ITGB3
chr17	45331357	45331358	C, G	ITGB3
chr17	45331396	45331397	A, G	ITGB3
chr17	45360679	45360680	C, T	ITGB3
chr17	45360729	45360730	C, T	ITGB3
chr17	45361778	45361779	A, G	ITGB3
chr17	45364539	45364540	C, T	ITGB3
chr17	45366990	45366991	A, G	ITGB3
chr17	45367510	45367511	C, T	ITGB3
chr17	45368336	45368337	A, C	ITGB3
chr17	45384909	45384910	C, T	ITGB3
chr17	45385011	45385012	C, T	ITGB3
chr17	47685199	47685200	C, G	SPOP
chr17	47698019	47698020	G, T	SPOP
chr17	56432375	56432376	A, G	RNF43
chr17	56434875	56434876	C	RNF43
chr17	56435079	56435080	C, G	RNF43
chr17	56435166	56435167	C, G	RNF43
chr17	56435551	56435552	A, G	RNF43
chr17	56436108	56436109	C, T	RNF43
chr17	56439929	56439930	C, T	RNF43
chr17	56440605	56440606	A, G	RNF43
chr17	56448296	56448297	C, T	RNF43
chr17	56492799	56492800	C, T	RNF43
chr17	61557199	61557200	C, T	ACE
chr17	61557772	61557773	A, G	ACE
chr17	61557821	61557822	C, T	ACE
chr17	61557822	61557823	G, T	ACE
chr17	61557938	61557939	C, T	ACE
chr17	61558397	61558398	A, G	ACE
chr17	61558950	61558951	C, T	ACE
chr17	61559818	61559819	C, T	ACE
chr17	61559922	61559923	C, T	ACE
chr17	61560048	61560049	C, G	ACE
chr17	61560762	61560763	C, T	ACE
chr17	61561755	61561756	A, G	ACE
chr17	61562308	61562309	C, T	ACE
chr17	61562321	61562322	C, T	ACE
chr17	61562372	61562373	A, G	ACE
chr17	61562773	61562774	C, T	ACE
chr17	61564051	61564052	A, G	ACE
chr17	61564280	61564281	C, T	ACE
chr17	61565989	61565990	C, G	ACE
chr17	61565997	61565998	A, C	ACE
chr17	61566030	61566031	A, G	ACE
chr17	61566084	61566085	A, G	ACE
chr17	61568616	61568617	C, T	ACE
chr17	61568620	61568621	C, T	ACE
chr17	61571835	61571836	C, T	ACE
chr17	61573760	61573761	C, T	ACE
chr17	61574661	61574662	A, C	ACE
chr17	61574674	61574675	A, G	ACE
chr17	62007497	62007498	A, G	CD79B
chr17	62007776	62007777	A, G	CD79B
chr17	62496669	62496670	A, C	DDX5
chr17	62499700	62499701	C, G	DDX5
chr17	62500752	62500753	C, T	DDX5
chr17	63049708	63049709	C, T	GNA13
chr17	63049823	63049824	A, C	GNA13
chr17	64685077	64685078	A, G	PRKCA
chr17	64737716	64737717	A, T	PRKCA
chr17	64737762	64737763	A, G	PRKCA
chr17	64784938	64784939	C, T	PRKCA
chr17	64785021	64785022	A, G	PRKCA
chr17	66511626	66511627	A, G	PRKAR1A
chr17	66519971	66519972	C, T	PRKAR1A
chr17	66520243	66520244	C, T	PRKAR1A
chr17	66521876	66521877	A, G	PRKAR1A
chr17	66524986	66524987	A, G	PRKAR1A
chr17	66526026	66526027	G, T	PRKAR1A
chr17	71166700	71166701	A, G	SSTR2
chr17	76210366	76210367	C, G	BIRC5
chr17	76218868	76218869	A, G	BIRC5
chr17	76219522	76219523	A, G	BIRC5
chr17	76219590	76219591	A, G	BIRC5
chr17	76219610	76219611	C, T	BIRC5
chr17	78519518	78519519	C, T	RPTOR
chr17	78599468	78599469	G, T	RPTOR
chr17	78599561	78599562	C, G	RPTOR
chr17	78617438	78617439	C, T	RPTOR
chr17	78681589	78681590	A, G	RPTOR
chr17	78727791	78727792	A, G	RPTOR
chr17	78811769	78811770	A, G	RPTOR
chr17	78820328	78820329	C, T	RPTOR
chr17	78820373	78820374	A, G	RPTOR
chr17	78829174	78829175	A, G	RPTOR
chr17	78854222	78854223	A, G	RPTOR
chr17	78858815	78858816	C, T	RPTOR
chr17	78865545	78865546	C, T	RPTOR
chr17	78865629	78865630	A, G	RPTOR
chr17	78896528	78896529	C, T	RPTOR
chr17	78921107	78921108	A, G	RPTOR
chr17	78921116	78921117	C, T	RPTOR
chr17	78923177	78923178	C, T	RPTOR
chr17	78931413	78931414	A, G	RPTOR
chr17	78934033	78934034	C, G	RPTOR
chr17	78935196	78935197	C, T	RPTOR
chr17	78936702	78936703	C, G	RPTOR
chr17	78936704	78936705	C, T	RPTOR
chr18	658000	658001	A, G	TYMS
chr18	662134	662135	A, G	TYMS
chr18	662246	662247	A, G	TYMS
chr18	662369	662370	C, T	TYMS
chr18	669186	669187	C, T	TYMS
chr18	671519	671520	C, T	TYMS
chr18	673015	673016	C, T	TYMS
chr18	724611	724612	A, G	YES1
chr18	732811	732812	C, G	YES1
chr18	742890	742891	A, T	YES1
chr18	743435	743436	C, T	YES1
chr18	745883	745884	A, C	YES1
chr18	745932	745933	C, T	YES1
chr18	25532303	25532304	C, T	CDH2
chr18	25543386	25543387	A, G	CDH2
chr18	25565081	25565082	A, G	CDH2
chr18	25572836	25572837	A, G	CDH2
chr18	25572848	25572849	C, T	CDH2
chr18	25583095	25583096	A, G	CDH2
chr18	25589674	25589675	A, T	CDH2
chr18	25589686	25589687	C	CDH2
chr18	25616450	25616451	A, T	CDH2
chr18	25727747	25727748	C, T	CDH2
chr18	45371685	45371686	C, T	SMAD2
chr18	45371694	45371695	A, G	SMAD2
chr18	45375014	45375015	C, T	SMAD2
chr18	48577781	48577782	C, G	SMAD4
chr18	48586183	48586184	A, G	SMAD4
chr18	48586343	48586344	C, T	SMAD4
chr18	59157763	59157764	C, T	CDH20
chr18	59157902	59157903	A, G	CDH20
chr18	59166387	59166388	A, G	CDH20
chr18	59166522	59166523	C, T	CDH20
chr18	59166540	59166541	C, T	CDH20
chr18	59167580	59167581	G, T	CDH20
chr18	59174601	59174602	A, G	CDH20
chr18	59174758	59174759	A, C	CDH20
chr18	59195352	59195353	C	CDH20
chr18	59195353	59195354	C, T	CDH20
chr18	59203706	59203707	A, G	CDH20
chr18	59212413	59212414	A, T	CDH20
chr18	59217171	59217172	C, T	CDH20
chr18	59221549	59221550	A, G	CDH20
chr18	60985603	60985604	C, T	BCL2
chr18	60985609	60985610	A, G	BCL2
chr18	60985618	60985619	G, T	BCL2
chr18	60985621	60985622	A, G	BCL2
chr18	60985772	60985773	C, T	BCL2
chr18	60985878	60985879	C, T	BCL2
chr18	61066462	61066463	A, G	VPS4B
chr18	61067817	61067818	A, G	VPS4B
chr18	61067958	61067959	C, T	VPS4B
chr18	61077632	61077633	A, G	VPS4B
chr19	1000419	1000420	A, G	GRIN3B
chr19	1000716	1000717	A, C	GRIN3B
chr19	1000784	1000785	C, T	GRIN3B
chr19	1000798	1000799	C, G	GRIN3B
chr19	1003136	1003137	C, T	GRIN3B
chr19	1003157	1003158	C, T	GRIN3B
chr19	1003161	1003162	C, T	GRIN3B
chr19	1003171	1003172	C, T	GRIN3B
chr19	1003220	1003221	A, C	GRIN3B
chr19	1003373	1003374	A, G	GRIN3B
chr19	1003438	1003439	A, G	GRIN3B
chr19	1003656	1003657	A, G	GRIN3B
chr19	1004686	1004687	C, T	GRIN3B
chr19	1004708	1004709	A, G	GRIN3B
chr19	1004709	1004710	C, T	GRIN3B
chr19	1004723	1004724	A, G	GRIN3B
chr19	1004739	1004740	C, T	GRIN3B
chr19	1004807	1004808	C, T	GRIN3B
chr19	1004822	1004823	A, G	GRIN3B
chr19	1004843	1004844	C, T	GRIN3B
chr19	1004871	1004872	A, G	GRIN3B
chr19	1004882	1004883	C, T	GRIN3B
chr19	1005065	1005066	C	GRIN3B
chr19	1005185	1005186	A, G	GRIN3B
chr19	1005223	1005224	A, G	GRIN3B
chr19	1005229	1005230	C, T	GRIN3B
chr19	1005333	1005334	A, G	GRIN3B
chr19	1005426	1005427	C, T	GRIN3B
chr19	1005530	1005531	C, G	GRIN3B
chr19	1008215	1008216	A, G	GRIN3B
chr19	1008703	1008704	A, G	GRIN3B
chr19	1008744	1008745	A, G	GRIN3B
chr19	1008878	1008879	C, G	GRIN3B
chr19	1009188	1009189	A, G	GRIN3B
chr19	1009364	1009365	A, T	GRIN3B
chr19	1009484	1009485	C, G	GRIN3B
chr19	1009526	1009527	C, T	GRIN3B
chr19	1207175	1207176	A, C	STK11
chr19	1218383	1218384	C, T	STK11
chr19	1219273	1219274	A, G	STK11
chr19	1221160	1221161	C, T	STK11
chr19	1221292	1221293	C, T	STK11
chr19	1222011	1222012	C, G	STK11
chr19	1223124	1223125	C, G	STK11
chr19	2164350	2164351	A, T	DOT1L
chr19	2199813	2199814	C, T	DOT1L
chr19	2202789	2202790	A, T	DOT1L
chr19	2208858	2208859	C, T	DOT1L
chr19	2211220	2211221	C, T	DOT1L
chr19	2213523	2213524	C, T	DOT1L
chr19	2213894	2213895	A, G	DOT1L
chr19	2216918	2216919	C, T	DOT1L
chr19	2222470	2222471	A, T	DOT1L
chr19	2223274	2223275	C, T	DOT1L
chr19	2223326	2223327	A, G	DOT1L
chr19	2226675	2226676	A, G	DOT1L
chr19	2226771	2226772	C, G	DOT1L
chr19	2226854	2226855	C, T	DOT1L
chr19	2226876	2226877	A, G	DOT1L
chr19	2227129	2227130	C, G	DOT1L
chr19	2227140	2227141	C, T	DOT1L
chr19	2229692	2229693	A, G	DOT1L
chr19	3110348	3110349	G, T	GNA11
chr19	3110360	3110361	C, T	GNA11
chr19	3119238	3119239	C, T	GNA11
chr19	3119364	3119365	C, G	GNA11
chr19	3119404	3119405	G, T	GNA11
chr19	3119405	3119406	G, T	GNA11
chr19	3976704	3976705	C, T	EEF2
chr19	3976759	3976760	A, G	EEF2
chr19	3977470	3977471	A, G	EEF2
chr19	3977485	3977486	A, G	EEF2
chr19	3977500	3977501	C, T	EEF2
chr19	3978193	3978194	C, T	EEF2
chr19	3979407	3979408	A, G	EEF2
chr19	3979469	3979470	C, T	EEF2
chr19	3979841	3979842	C, T	EEF2
chr19	3980823	3980824	A, G	EEF2
chr19	3981441	3981442	A, G	EEF2
chr19	3982080	3982081	T	EEF2
chr19	3982323	3982324	A, G	EEF2
chr19	3982784	3982785	C, T	EEF2
chr19	3982791	3982792	C, G	EEF2
chr19	3982849	3982850	A, G	EEF2
chr19	3982930	3982931	A, G	EEF2
chr19	3982966	3982967	A, G	EEF2
chr19	3983081	3983082	A, G	EEF2
chr19	3983183	3983184	A, G	EEF2
chr19	3983301	3983302	A, G	EEF2
chr19	4101195	4101196	A, G	MAP2K2
chr19	4102353	4102354	C, T	MAP2K2
chr19	4102448	4102449	A, G	MAP2K2
chr19	4110551	4110552	C, G	MAP2K2
chr19	4117527	4117528	A, G	MAP2K2
chr19	6586267	6586268	A, G	CD70
chr19	7125518	7125519	A, G	INSR
chr19	7128822	7128823	C, T	INSR
chr19	7132135	7132136	C, T	INSR
chr19	7141726	7141727	A, G	INSR
chr19	7141774	7141775	A, G	INSR
chr19	7141870	7141871	C, G	INSR
chr19	7142920	7142921	C, T	INSR
chr19	7142998	7142999	C, T	INSR
chr19	7150490	7150491	A, G	INSR
chr19	7163082	7163083	C, T	INSR
chr19	7163139	7163140	G, T	INSR
chr19	7163153	7163154	A, G	INSR
chr19	7163213	7163214	C, T	INSR
chr19	7163229	7163230	C, T	INSR
chr19	7166137	7166138	A, G	INSR
chr19	7166387	7166388	A, G	INSR
chr19	7184391	7184392	C, T	INSR
chr19	7184430	7184431	G	INSR
chr19	7184517	7184518	A, G	INSR
chr19	7267745	7267746	A, G	INSR
chr19	10599964	10599965	A, G	KEAP1
chr19	10600441	10600442	C, G	KEAP1
chr19	10600538	10600539	C, T	KEAP1
chr19	10610235	10610236	A, G	KEAP1
chr19	10679239	10679240	C, G	CDKN2D
chr19	11097708	11097709	C, T	SMARCA4
chr19	11098396	11098397	A, G	SMARCA4
chr19	11098411	11098412	A, C	SMARCA4
chr19	11105607	11105608	C, T	SMARCA4
chr19	11105864	11105865	C, G	SMARCA4
chr19	11106599	11106600	C, T	SMARCA4
chr19	11107084	11107085	A, G	SMARCA4
chr19	11107132	11107133	C, T	SMARCA4
chr19	11107133	11107134	A, G	SMARCA4
chr19	11118558	11118559	T	SMARCA4
chr19	11123737	11123738	C, T	SMARCA4
chr19	11129599	11129600	C, T	SMARCA4
chr19	11136214	11136215	C, G	SMARCA4
chr19	11145690	11145691	C, T	SMARCA4
chr19	11152083	11152084	G	SMARCA4
chr19	11169068	11169069	A, G	SMARCA4
chr19	11169513	11169514	C, T	SMARCA4
chr19	11169576	11169577	A, G	SMARCA4
chr19	11170695	11170696	A, G	SMARCA4
chr19	11170838	11170839	C, T	SMARCA4
chr19	15271449	15271450	A, T	NOTCH3
chr19	15271468	15271469	C	NOTCH3
chr19	15271625	15271626	A, G	NOTCH3
chr19	15271685	15271686	A, G	NOTCH3
chr19	15271770	15271771	A, G	NOTCH3
chr19	15272000	15272001	C, T	NOTCH3
chr19	15272336	15272337	A, G	NOTCH3
chr19	15273380	15273381	A, G	NOTCH3
chr19	15273423	15273424	C, T	NOTCH3
chr19	15276142	15276143	C, T	NOTCH3
chr19	15276738	15276739	A, G	NOTCH3
chr19	15276918	15276919	A, G	NOTCH3
chr19	15278056	15278057	A, G	NOTCH3
chr19	15281385	15281386	A, C	NOTCH3
chr19	15281458	15281459	C, G	NOTCH3
chr19	15285051	15285052	C, T	NOTCH3
chr19	15288694	15288695	A, G	NOTCH3
chr19	15289822	15289823	A, C	NOTCH3
chr19	15290006	15290007	C, T	NOTCH3
chr19	15290124	15290125	A, G	NOTCH3
chr19	15291095	15291096	A, G	NOTCH3
chr19	15291575	15291576	C, G	NOTCH3
chr19	15291698	15291699	C, T	NOTCH3
chr19	15291714	15291715	C, T	NOTCH3
chr19	15292436	15292437	C, T	NOTCH3
chr19	15295133	15295134	A, G	NOTCH3
chr19	15296402	15296403	C, T	NOTCH3
chr19	15297973	15297974	A, G	NOTCH3
chr19	15298135	15298136	A, C	NOTCH3
chr19	15300068	15300069	C, T	NOTCH3
chr19	15302843	15302844	C, T	NOTCH3
chr19	15303224	15303225	A, G	NOTCH3
chr19	15311544	15311545	C, G	NOTCH3
chr19	17937515	17937516	C, T	JAK3
chr19	17940815	17940816	C, G	JAK3
chr19	17940841	17940842	A, G	JAK3
chr19	17946803	17946804	A, G	JAK3
chr19	17948731	17948732	C, T	JAK3
chr19	17951018	17951019	C, T	JAK3
chr19	17952184	17952185	G, T	JAK3
chr19	17952404	17952405	C, T	JAK3
chr19	17954214	17954215	G, T	JAK3
chr19	17954596	17954597	C, G	JAK3
chr19	17983502	17983503	G, T	SLC5A5
chr19	17985290	17985291	A, C	SLC5A5
chr19	17988793	17988794	C, T	SLC5A5
chr19	17994572	17994573	A, C	SLC5A5
chr19	17994593	17994594	A, G	SLC5A5
chr19	17994604	17994605	A, C	SLC5A5
chr19	17994634	17994635	C, T	SLC5A5
chr19	17994643	17994644	C, T	SLC5A5
chr19	17994835	17994836	A, G	SLC5A5
chr19	18001838	18001839	A, G	SLC5A5
chr19	18266698	18266699	C, T	PIK3R2
chr19	18271763	18271764	C, T	PIK3R2
chr19	18272189	18272190	A, C	PIK3R2
chr19	18278127	18278128	C, T	PIK3R2
chr19	18279637	18279638	C, T	PIK3R2
chr19	18279996	18279997	C, T	PIK3R2
chr19	18684562	18684563	C, T	UBA52
chr19	18685822	18685823	A, G	UBA52
chr19	18685963	18685964	G, T	UBA52
chr19	30312873	30312874	C, T	CCNE1
chr19	30313343	30313344	C, T	CCNE1
chr19	30314537	30314538	G, T	CCNE1
chr19	35823434	35823435	G, T	CD22
chr19	35823603	35823604	A, G	CD22
chr19	35828772	35828773	C, T	CD22
chr19	35828902	35828903	A, G	CD22
chr19	35829255	35829256	A, G	CD22
chr19	35829380	35829381	A, G	CD22
chr19	35831985	35831986	C, T	CD22
chr19	35832388	35832389	A, G	CD22
chr19	35832822	35832823	A, G	CD22
chr19	35835939	35835940	C, T	CD22
chr19	35836529	35836530	A, G	CD22
chr19	35836599	35836600	A, C	CD22
chr19	35837095	35837096	C, T	CD22
chr19	35837149	35837150	C, T	CD22
chr19	39787142	39787143	A, G	IL29
chr19	39789114	39789115	A, G	IL29
chr19	40739512	40739513	A, G	AKT2
chr19	40739720	40739721	G, T	AKT2
chr19	40747819	40747820	C, G	AKT2
chr19	40748638	40748639	C, T	AKT2
chr19	41725270	41725271	A, G	AXL
chr19	41725409	41725410	A, G	AXL
chr19	41737016	41737017	A, G	AXL
chr19	41745008	41745009	A, G	AXL
chr19	41748752	41748753	C, T	AXL
chr19	41758879	41758880	C, G	AXL
chr19	41759473	41759474	C, T	AXL
chr19	41765574	41765575	C, T	AXL
chr19	41765616	41765617	C, T	AXL
chr19	41854384	41854385	A, C	TGFB1
chr19	41858589	41858590	C, T	TGFB1
chr19	42212796	42212797	A, G	CEACAM5
chr19	42213669	42213670	A, G	CEACAM5
chr19	42213743	42213744	C, T	CEACAM5
chr19	42213771	42213772	A, G	CEACAM5
chr19	42213781	42213782	C, T	CEACAM5
chr19	42213832	42213833	C, T	CEACAM5
chr19	42213840	42213841	C, T	CEACAM5
chr19	42213867	42213868	A, G	CEACAM5
chr19	42213871	42213872	C, T	CEACAM5
chr19	42213943	42213944	A, C	CEACAM5
chr19	42221354	42221355	C, T	CEACAM5
chr19	42221417	42221418	A, G	CEACAM5
chr19	42221433	42221434	A, C	CEACAM5
chr19	42221606	42221607	A, G	CEACAM5
chr19	42222258	42222259	A, G	CEACAM5
chr19	42222340	42222341	C, T	CEACAM5
chr19	42224907	42224908	C, T	CEACAM5
chr19	42224909	42224910	C, T	CEACAM5
chr19	42224938	42224939	A, G	CEACAM5
chr19	42225059	42225060	A, C	CEACAM5
chr19	42470841	42470842	A, G	ATP1A3
chr19	42470982	42470983	A, G	ATP1A3
chr19	42471049	42471050	C, G	ATP1A3
chr19	42474638	42474639	A, G	ATP1A3
chr19	42489434	42489435	A, T	ATP1A3
chr19	42489515	42489516	A, C	ATP1A3
chr19	42492237	42492238	A, T	ATP1A3
chr19	42492549	42492550	A, G	ATP1A3
chr19	42791461	42791462	C, T	CIC
chr19	42793944	42793945	C, T	CIC
chr19	42795553	42795554	C, T	CIC
chr19	42796697	42796698	G, T	CIC
chr19	42798899	42798900	C, T	CIC
chr19	42798917	42798918	C, T	CIC
chr19	42798959	42798960	A, G	CIC
chr19	42799048	42799049	C, T	CIC
chr19	44047696	44047697	A, G	XRCC1
chr19	44050194	44050195	C, T	XRCC1
chr19	44050965	44050966	C, T	XRCC1
chr19	44050980	44050981	A, G	XRCC1
chr19	44055725	44055726	C, T	XRCC1
chr19	44056340	44056341	C, T	XRCC1
chr19	44056411	44056412	C, T	XRCC1
chr19	44057718	44057719	G	XRCC1
chr19	44065101	44065102	A, G	XRCC1
chr19	45854918	45854919	G, T	ERCC2
chr19	45855454	45855455	C, T	ERCC2
chr19	45855523	45855524	A, G	ERCC2
chr19	45856467	45856468	C, G	ERCC2
chr19	45862193	45862194	A, G	ERCC2
chr19	45867258	45867259	C, T	ERCC2
chr19	45867675	45867676	A, C	ERCC2
chr19	45868290	45868291	G, T	ERCC2
chr19	45868308	45868309	G, T	ERCC2
chr19	45871963	45871964	C, T	ERCC2
chr19	47104778	47104779	A, C	CALM3
chr19	47109150	47109151	C, G	CALM3
chr19	47111644	47111645	A, G	CALM3
chr19	47111662	47111663	C, T	CALM3
chr19	47112206	47112207	C, T	CALM3
chr19	47735874	47735875	C, T	BBC3
chr19	49838890	49838891	A, C	CD37
chr19	49838953	49838954	A, G	CD37
chr19	49839014	49839015	C, T	CD37
chr19	49839032	49839033	C, G	CD37
chr19	49841202	49841203	A, G	CD37
chr19	49842609	49842610	A, G	CD37
chr19	49977928	49977929	A, G	FLT3LG
chr19	49978014	49978015	A, G	FLT3LG
chr19	49979397	49979398	A, G	FLT3LG
chr19	49983672	49983673	C, T	FLT3LG
chr19	50902163	50902164	A, G	POLD1
chr19	50902330	50902331	C, T	POLD1
chr19	50902658	50902659	C, G	POLD1
chr19	50905073	50905074	A, G	POLD1
chr19	50905188	50905189	G, T	POLD1
chr19	50905189	50905190	C, T	POLD1
chr19	50905309	50905310	A, G	POLD1
chr19	50905411	50905412	A, G	POLD1
chr19	50905654	50905655	A, G	POLD1
chr19	50905761	50905762	C, T	POLD1
chr19	50905876	50905877	G, T	POLD1
chr19	50906274	50906275	C, T	POLD1
chr19	50906297	50906298	C, T	POLD1
chr19	50906784	50906785	C, T	POLD1
chr19	50909628	50909629	A, G	POLD1
chr19	50909764	50909765	C, T	POLD1
chr19	50910283	50910284	A, G	POLD1
chr19	50910292	50910293	C, T	POLD1
chr19	50910533	50910534	C, T	POLD1
chr19	50910537	50910538	C, T	POLD1
chr19	50910609	50910610	C, T	POLD1
chr19	50912125	50912126	A, G	POLD1
chr19	50912417	50912418	C, G	POLD1
chr19	50916771	50916772	C, T	POLD1
chr19	50916810	50916811	A, G	POLD1
chr19	50916975	50916976	A, G	POLD1
chr19	50918757	50918758	C, T	POLD1
chr19	50918968	50918969	A, G	POLD1
chr19	50919796	50919797	C, T	POLD1
chr19	50919827	50919828	A, G	POLD1
chr19	50919837	50919838	C, T	POLD1
chr19	50920409	50920410	C, T	POLD1
chr19	50920534	50920535	C, T	POLD1
chr19	50920535	50920536	A, G	POLD1
chr19	51359542	51359543	A, G	KLK3
chr19	51359565	51359566	A, G	KLK3
chr19	51359715	51359716	A, G	KLK3
chr19	51361381	51361382	A, G	KLK3
chr19	51361471	51361472	A, C	KLK3
chr19	51361756	51361757	C, T	KLK3
chr19	51362803	51362804	A, G	KLK3
chr19	51363397	51363398	C, T	KLK3
chr19	51376836	51376837	C, G	KLK2
chr19	51379892	51379893	C, T	KLK2
chr19	51380109	51380110	A, T	KLK2
chr19	51381776	51381777	C, T	KLK2
chr19	51381792	51381793	A, C	KLK2
chr19	52693456	52693457	A, C	PPP2R1A
chr19	52693508	52693509	G, T	PPP2R1A
chr19	52705298	52705299	A, G	PPP2R1A
chr19	52714578	52714579	A, C	PPP2R1A
chr19	52714718	52714719	C, T	PPP2R1A
chr19	52716142	52716143	A, G	PPP2R1A
chr19	52716411	52716412	C, T	PPP2R1A
chr19	52719189	52719190	A, G	PPP2R1A
chr19	52719961	52719962	C, T	PPP2R1A
chr19	52723366	52723367	A, G	PPP2R1A
chr19	52723435	52723436	C, T	PPP2R1A
chr19	52724215	52724216	C, G	PPP2R1A
chr19	52729029	52729030	C, T	PPP2R1A
chr19	52729081	52729082	A, C	PPP2R1A
chr19	55281314	55281315	G, T	KIR2DL1
chr19	55286843	55286844	A, G	KIR2DL1
chr19	55286863	55286864	A, C	KIR2DL1
chr19	55294361	55294362	A, C	KIR2DL1
chr19	55294926	55294927	A, G	KIR2DL1
chr19	55295021	55295022	C, G	KIR2DL1
chr19	55295035	55295036	C, G	KIR2DL1
chr19	57742488	57742489	C, T	AURKC
chr19	57744008	57744009	A, G	AURKC
chr19	57744818	57744819	C, T	AURKC
chr19	57746287	57746288	A, G	AURKC
chr19	57746602	57746603	C, T	AURKC
chr20	3193841	3193842	A, C	ITPA
chr20	3193892	3193893	A, C	ITPA
chr20	3193977	3193978	A, G	ITPA
chr20	3195914	3195915	G, T	ITPA
chr20	3195940	3195941	A, G	ITPA
chr20	3203949	3203950	A, T	ITPA
chr20	3204083	3204084	A, G	ITPA
chr20	23016083	23016084	A, C	SSTR4
chr20	23016147	23016148	G, T	SSTR4
chr20	23016170	23016171	C, G	SSTR4
chr20	23016969	23016970	G, T	SSTR4
chr20	23017016	23017017	C, T	SSTR4
chr20	23017043	23017044	C, T	SSTR4
chr20	23017081	23017082	C, T	SSTR4
chr20	30954294	30954295	A, G	ASXL1
chr20	31017118	31017119	C, T	ASXL1
chr20	31022468	31022469	A, G	ASXL1
chr20	31022479	31022480	C, T	ASXL1
chr20	31022764	31022765	C, T	ASXL1
chr20	31022765	31022766	A, G	ASXL1
chr20	31022909	31022910	G, T	ASXL1
chr20	31023027	31023028	A, G	ASXL1
chr20	31023499	31023500	C, T	ASXL1
chr20	31024012	31024013	C, G	ASXL1
chr20	31024033	31024034	A, G	ASXL1
chr20	31024206	31024207	C, T	ASXL1
chr20	31024273	31024274	C, T	ASXL1
chr20	31024487	31024488	C, T	ASXL1
chr20	31025162	31025163	A, G	ASXL1
chr20	32264847	32264848	C	E2F1
chr20	32264959	32264960	A, G	E2F1
chr20	32273959	32273960	A, G	E2F1
chr20	36022404	36022405	C, T	SRC
chr20	36024559	36024560	C, T	SRC
chr20	36030944	36030945	C, T	SRC
chr20	36760710	36760711	A, G	TGM2
chr20	36767849	36767850	A, G	TGM2
chr20	36769791	36769792	A, G	TGM2
chr20	36770482	36770483	A, G	TGM2
chr20	36770518	36770519	C, T	TGM2
chr20	36770587	36770588	C, T	TGM2
chr20	36775131	36775132	A, G	TGM2
chr20	36775134	36775135	A, G	TGM2
chr20	36775242	36775243	A, G	TGM2
chr20	36776392	36776393	C, G	TGM2
chr20	36793500	36793501	A, G	TGM2
chr20	36793528	36793529	A, G	TGM2
chr20	36793550	36793551	C, G	TGM2
chr20	39657624	39657625	A, C	TOP1
chr20	39728766	39728767	A, G	TOP1
chr20	39743904	39743905	A, G	TOP1
chr20	39743920	39743921	G, T	TOP1
chr20	39788685	39788686	C, T	PLCG1
chr20	39788815	39788816	A, G	PLCG1
chr20	39791993	39791994	C, T	PLCG1
chr20	39792001	39792002	C, T	PLCG1
chr20	39792062	39792063	A, G	PLCG1
chr20	39792537	39792538	C, T	PLCG1
chr20	39793746	39793747	C, G	PLCG1
chr20	39793846	39793847	A, C	PLCG1
chr20	39794488	39794489	A, G	PLCG1
chr20	39795462	39795463	C, T	PLCG1
chr20	39797464	39797465	C, T	PLCG1
chr20	39801011	39801012	C, T	PLCG1
chr20	39802501	39802502	G, T	PLCG1
chr20	39803077	39803078	C, T	PLCG1
chr20	43252914	43252915	C, T	ADA
chr20	43254297	43254298	C, T	ADA
chr20	43254375	43254376	A, C	ADA
chr20	43255219	43255220	C, T	ADA
chr20	43264926	43264927	C, T	ADA
chr20	43264993	43264994	A, G	ADA
chr20	43280226	43280227	C, T	ADA
chr20	44746981	44746982	C, T	CD40
chr20	44747085	44747086	A, G	CD40
chr20	44747103	44747104	C, T	CD40
chr20	44750423	44750424	C, T	CD40
chr20	44751362	44751363	C, T	CD40
chr20	44756822	44756823	C, T	CD40
chr20	44756889	44756890	G, T	CD40
chr20	44756890	44756891	A, G	CD40
chr20	44756907	44756908	A, C	CD40
chr20	44757017	44757018	C, T	CD40
chr20	44757212	44757213	A, G	CD40
chr20	44757288	44757289	G, T	CD40
chr20	44757406	44757407	A, G	CD40
chr20	44757523	44757524	C, G	CD40
chr20	52188375	52188376	A, T	ZNF217
chr20	52192307	52192308	A, C	ZNF217
chr20	52192407	52192408	C, T	ZNF217
chr20	52192452	52192453	A, G	ZNF217
chr20	52192594	52192595	C, T	ZNF217
chr20	52192636	52192637	C, T	ZNF217
chr20	52192647	52192648	C, G	ZNF217
chr20	52192689	52192690	G, T	ZNF217
chr20	52192697	52192698	A, G	ZNF217
chr20	52192788	52192789	C, T	ZNF217
chr20	52193087	52193088	C, T	ZNF217
chr20	52193213	52193214	A, G	ZNF217
chr20	52193367	52193368	C, T	ZNF217
chr20	52193659	52193660	A, G	ZNF217
chr20	52193697	52193698	A, G	ZNF217
chr20	52193721	52193722	A, G	ZNF217
chr20	52198137	52198138	C, T	ZNF217
chr20	52198339	52198340	A, T	ZNF217
chr20	52198618	52198619	A, C	ZNF217
chr20	52198966	52198967	A, G	ZNF217
chr20	54959295	54959296	C, G	AURKA
chr20	54961540	54961541	A, T	AURKA
chr20	54963302	54963303	C, T	AURKA
chr20	54963319	54963320	C, T	AURKA
chr20	57415454	57415455	C, T	GNAS
chr20	57415875	57415876	A, C	GNAS
chr20	57428299	57428300	C, T	GNAS
chr20	57428819	57428820	A, G	GNAS
chr20	57428844	57428845	C, T	GNAS
chr20	57428946	57428947	A, G	GNAS
chr20	57429446	57429447	C, T	GNAS
chr20	57430556	57430557	A, T	GNAS
chr20	57430567	57430568	A, T	GNAS
chr20	57478680	57478681	C, T	GNAS
chr20	57478779	57478780	C, T	GNAS
chr20	57478797	57478798	A, G	GNAS
chr20	57478806	57478807	C, T	GNAS
chr20	57480366	57480367	G, T	GNAS
chr20	57480419	57480420	C, T	GNAS
chr20	57484240	57484241	C, T	GNAS
chr20	57484325	57484326	C, G	GNAS
chr20	57485116	57485117	C, T	GNAS
chr20	57485811	57485812	C, T	GNAS
chr20	62331932	62331933	A, G	ARFRP1
chr20	62331988	62331989	G, T	ARFRP1
chr20	62332024	62332025	C, T	ARFRP1
chr20	62332536	62332537	C, T	ARFRP1
chr20	62332640	62332641	C, T	ARFRP1
chr20	62338144	62338145	A, G	ARFRP1
chr21	36164343	36164344	A, C	RUNX1
chr21	36164361	36164362	A, G	RUNX1
chr21	36164485	36164486	C, G	RUNX1
chr21	36171637	36171638	A, G	RUNX1
chr21	36259307	36259308	C, T	RUNX1
chr21	36262008	36262009	A, G	RUNX1
chr21	37507500	37507501	A, G	CBR3
chr21	37507739	37507740	C, G	CBR3
chr21	37507768	37507769	C, T	CBR3
chr21	37510223	37510224	C, T	CBR3
chr21	37518581	37518582	A, G	CBR3
chr21	37518678	37518679	A, T	CBR3
chr21	37518705	37518706	A, G	CBR3
chr21	37518797	37518798	A, G	CBR3
chr21	37518812	37518813	A, G	CBR3
chr21	37518849	37518850	A, G	CBR3
chr21	39755606	39755607	A, G	ERG
chr21	39762882	39762883	C, T	ERG
chr21	39763535	39763536	C, G	ERG
chr21	39764210	39764211	A, T	ERG
chr21	39764260	39764261	C, G	ERG
chr21	39870309	39870310	A, G	ERG
chr21	39947521	39947522	C, T	ERG
chr21	39947696	39947697	A, G	ERG
chr21	42838103	42838104	C, G	TMPRSS2
chr21	42842542	42842543	C, T	TMPRSS2
chr21	42845382	42845383	A, G	TMPRSS2
chr21	42852496	42852497	C, T	TMPRSS2
chr21	42860306	42860307	C, T	TMPRSS2
chr21	42860484	42860485	C, G	TMPRSS2
chr21	42860493	42860494	C, G	TMPRSS2
chr21	42861544	42861545	A, G	TMPRSS2
chr21	42866295	42866296	C, T	TMPRSS2
chr21	42879908	42879909	A, C	TMPRSS2
chr21	46308794	46308795	A, G	ITGB2
chr21	46311812	46311813	A, G	ITGB2
chr21	46313441	46313442	G, T	ITGB2
chr21	46318939	46318940	A, G	ITGB2
chr21	46319068	46319069	C, T	ITGB2
chr21	46326814	46326815	C, T	ITGB2
chr21	46330182	46330183	C, T	ITGB2
chr21	46330301	46330302	C, T	ITGB2
chr21	46330486	46330487	A, G	ITGB2
chr21	46330608	46330609	T	ITGB2
chr21	46330627	46330628	C, T	ITGB2
chr21	46918385	46918386	C, T	SLC19A1
chr21	46918573	46918574	C, T	SLC19A1
chr21	46935941	46935942	A, G	SLC19A1
chr21	46951555	46951556	A, G	SLC19A1
chr21	46952093	46952094	C, T	SLC19A1
chr21	46954446	46954447	C, T	SLC19A1
chr21	46957793	46957794	C, T	SLC19A1
chr22	21288415	21288416	A, G	CRKL
chr22	22127316	22127317	A, G	MAPK1
chr22	22221679	22221680	C, T	MAPK1
chr22	22890491	22890492	A, G	PRAME
chr22	22890751	22890752	A, G	PRAME
chr22	22890755	22890756	A, G	PRAME
chr22	22890791	22890792	C, T	PRAME
chr22	22890868	22890869	C, T	PRAME
chr22	22890932	22890933	G	PRAME
chr22	22892334	22892335	A, G	PRAME
chr22	22892489	22892490	C, T	PRAME
chr22	22893391	22893392	C, G	PRAME
chr22	22895351	22895352	A, G	PRAME
chr22	22895391	22895392	A, G	PRAME
chr22	22895402	22895403	C, T	PRAME
chr22	22899233	22899234	A, G	PRAME
chr22	22899323	22899324	G, T	PRAME
chr22	23523308	23523309	C, T	BCR
chr22	23523629	23523630	A, C	BCR
chr22	23523752	23523753	C	BCR
chr22	23523968	23523969	A, G	BCR
chr22	23524465	23524466	G, T	BCR
chr22	23540509	23540510	A, G	BCR
chr22	23540608	23540609	A, G	BCR
chr22	23541424	23541425	A	BCR
chr22	23541487	23541488	C, T	BCR
chr22	23595923	23595924	T	BCR
chr22	23595995	23595996	C	BCR
chr22	23627237	23627238	A, C	BCR
chr22	23627368	23627369	A, G	BCR
chr22	23631800	23631801	C, T	BCR
chr22	23631822	23631823	C, T	BCR
chr22	23632512	23632513	A, G	BCR
chr22	23632546	23632547	A, G	BCR
chr22	23632620	23632621	A, C, G	BCR
chr22	23632635	23632636	A, C	BCR
chr22	23632664	23632665	A, C	BCR
chr22	23657612	23657613	C, T	BCR
chr22	24129325	24129326	C, T	SMARCB1
chr22	24135881	24135882	C, T	SMARCB1
chr22	24143205	24143206	A, G	SMARCB1
chr22	24143383	24143384	C, T	SMARCB1
chr22	24167512	24167513	A, G	SMARCB1
chr22	29130457	29130458	C, T	CHEK2
chr22	29664407	29664408	A, G	EWSR1
chr22	29664422	29664423	A, G	EWSR1
chr22	29668198	29668199	C, T	EWSR1
chr22	29678560	29678561	C, T	EWSR1
chr22	29688218	29688219	A, C	EWSR1
chr22	29688631	29688632	G, T	EWSR1
chr22	29693989	29693990	A, G	EWSR1
chr22	29694916	29694917	A, G	EWSR1
chr22	29695870	29695871	C, T	EWSR1
chr22	29695998	29695999	C, T	EWSR1
chr22	29696017	29696018	C, T	EWSR1
chr22	29696068	29696069	C, T	EWSR1
chr22	30038151	30038152	A, C	NF2
chr22	30054301	30054302	C, T	NF2
chr22	31532959	31532960	C, T	PLA2G3
chr22	31533795	31533796	C, G	PLA2G3
chr22	31533842	31533843	A, G	PLA2G3
chr22	31533951	31533952	A, G	PLA2G3
chr22	31533966	31533967	A, G	PLA2G3
chr22	31535871	31535872	C, G	PLA2G3
chr22	31535994	31535995	C, G	PLA2G3
chr22	31536132	31536133	A, C	PLA2G3
chr22	37602601	37602602	C, T	SSTR3
chr22	37602610	37602611	C, G	SSTR3
chr22	37603020	37603021	A, G	SSTR3
chr22	37603050	37603051	C, T	SSTR3
chr22	37603389	37603390	C, T	SSTR3
chr22	37603743	37603744	C, T	SSTR3
chr22	37603744	37603745	A, G	SSTR3
chr22	38071706	38071707	A, G	LGALS1
chr22	38074433	38074434	A, G	LGALS1
chr22	38369975	38369976	A, G	SOX10
chr22	38379542	38379543	A, G	SOX10
chr22	38508467	38508468	C, T	PLA2G6
chr22	38512243	38512244	A, G	PLA2G6
chr22	38512401	38512402	A, G	PLA2G6
chr22	38522548	38522549	A, G	PLA2G6
chr22	38525560	38525561	A, G	PLA2G6
chr22	38528957	38528958	C, T	PLA2G6
chr22	38539083	38539084	A, C	PLA2G6
chr22	38543409	38543410	A, G	PLA2G6
chr22	38543452	38543453	C, T	PLA2G6
chr22	38544456	38544457	C, T	PLA2G6
chr22	38544571	38544572	C, T	PLA2G6
chr22	38564040	38564041	C, G	PLA2G6
chr22	38565208	38565209	A, G	PLA2G6
chr22	38565261	38565262	C, T	PLA2G6
chr22	38565346	38565347	C, T	PLA2G6
chr22	39621796	39621797	G, T	PDGFB
chr22	39621892	39621893	C, T	PDGFB
chr22	39629417	39629418	C, T	PDGFB
chr22	39631712	39631713	C, T	PDGFB
chr22	39631746	39631747	C, G	PDGFB
chr22	39631767	39631768	G, T	PDGFB
chr22	39636828	39636829	A, T	PDGFB
chr22	39639852	39639853	G, T	PDGFB
chr22	41513174	41513175	C, T	EP300
chr22	41523525	41523526	C, T	EP300
chr22	41537191	41537192	C, T	EP300
chr22	41537233	41537234	G, T	EP300
chr22	41543982	41543983	C, G	EP300
chr22	41545883	41545884	A, G	EP300
chr22	41548007	41548008	A, G	EP300
chr22	41551038	41551039	A, T	EP300
chr22	41553258	41553259	A, G	EP300
chr22	41553336	41553337	C, T	EP300
chr22	41558837	41558838	C, G	EP300
chr22	41559962	41559963	C, T	EP300
chr22	41564707	41564708	A, C	EP300
chr22	41568552	41568553	A, G	EP300
chr22	41572540	41572541	C, T	EP300
chr22	41574086	41574087	C, T	EP300
chr22	42522612	42522613	C, G	CYP2D6
chr22	42523942	42523943	A, G	CYP2D6
chr22	42524946	42524947	C, T	CYP2D6
chr22	42525131	42525132	C, G	CYP2D6
chr22	42525133	42525134	C, T	CYP2D6
chr22	42525727	42525728	A, C	CYP2D6
chr22	42525755	42525756	A, G	CYP2D6
chr22	42525771	42525772	A, G	CYP2D6
chr22	42525797	42525798	C, G	CYP2D6
chr22	42525810	42525811	C, T	CYP2D6
chr22	42525951	42525952	A, C	CYP2D6
chr22	42526570	42526571	C, G	CYP2D6
chr22	42526572	42526573	G, T	CYP2D6
chr22	42526579	42526580	C, G	CYP2D6
chr22	42526693	42526694	A, G	CYP2D6
chr22	42526762	42526763	C, T	CYP2D6
chr22	42540356	42540357	C, G	CYP2D6
chr22	46611262	46611263	A, G	PPARA
chr22	46614273	46614274	C, G	PPARA
chr22	46615879	46615880	C, T	PPARA
chr22	46615904	46615905	C, T	PPARA
chr22	46628118	46628119	C, G	PPARA

	APPENDIX 2
	chr1	36768200	rs1573020
	chr1	159174683	rs2814778
	chr1	204790977	rs2065160
	chr2	7149155	rs896788
	chr2	109513601	rs3827760
	chr2	136616754	rs182549
	chr3	168645035	rs1498444
	chr4	38803255	rs4540055
	chr4	159181963	rs2026721
	chr5	33951693	rs16891982
	chr7	4457003	rs917118
	chr10	17064992	rs7897550
	chr10	34755348	rs1978806
	chr11	32424389	rs5030240
	chr12	29369871	rs10843344
	chr12	56603834	rs773658
	chr13	20901724	rs1335873
	chr13	22374700	rs1886510
	chr13	34864240	rs2065982
	chr14	36170607	rs10141763
	chr14	101142890	rs730570
	chr15	28365618	rs12913832
	chr15	48426484	rs1426654
	chr16	31079371	rs881929
	chr16	90105333	rs3785181
	chr17	75551667	rs2304925
	chr18	75432386	rs1024116
	chr19	42410331	rs2303798
	chr20	38849642	rs1321333
	chr21	16685598	rs722098
	chr21	17710424	rs239031
	chr21	25672460	rs2572307
	chr22	26350103	rs5997008
	chr22	47836412	rs2040411

Claims

1. A method for genomic and/or genetic analysis of a human nucleic acid sample comprising the following steps: a) providing a group of human reference genomes;b) testing of the human nucleic acid sample for sex and/or ancestry;c) selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis on the results of the sex and/or ancestry test in step b); andd) aligning the human nucleic acid sample to the selected PHREGs.

2. The method of claim 1, wherein the alignment is performed on a majority allele level, or on a non-rare alleles level.

3. The method of claim 1, comprising the additional step: e) performing variant calling of the aligned human nucleic acid sample with respect to the selected PHREGs.

4. The method of claim 3, wherein the variant calling is performed on a majority allele level, or on a non-rare alleles level.

5. The method of claim 1, wherein the human reference genomes provided in step a) are published human reference genomes or are derived from published human reference genomes.

6. The method of claim 1, wherein step a) comprises adjusting the human reference genomes to an encoding level, the encoding level comprising either unique nucleotide codes or ambiguous nucleotide codes.

7. The method of claim 1, wherein the human reference genomes provided in step a) are PHREGs.

8. The method of claim 1, wherein the sex test comprises one or more of the following: testing at least one position in a sex-specific gene on chromosome X and/or on chromosome Y;leveraging alignment differences of human genome samples on chromosome X and/or chromosome Y; cytogenetic tests; FISH analysis; CGH analysis.

9. The method of claim 1, wherein the ancestry test is based on a machine learning algorithm used on a human nucleic acid sample, or on another classification scheme that leverages ancestry-specific variants.

10. The method of claim 1, wherein the ancestry test comprises using the genotype of at least one genomic position and/or testing of SNP arrays or SNP chips and/or testing of markers from Sanger sequencing or mass spectroscopy.

11. The method of claim 1, wherein the ancestry test comprises testing at least one gene selected from the group of genes consisting of ABL2, ATP1A3, CIC, CYP2C8, CYP2C9, EPHA3, EPHA7, ERBB3, ERG, ETV1, F2, FAS, HFE, IL11RA, IL2RA, ITGB6, KIF11, KIT, KLK3, LRP6, MDM4, NAT2, NTRK2, PDGFB, PIK3R1, PLA2G3, PLAU, PRKCB, RICTOR, SLC7A11, STAT3, T, TSC1, VCAM1, VDR, VEGFB, ACVRL1, AXL, CA9, CALCR, CASP9, ENG, EPHB1, ERBB4, ESR1, FGFR2, HPSE, HSP90AA1, ITK, MRE11A, PLK1, PTPRC, SERPINE1, SMC4, TERT, TLR3, WISP3, WT1, XRCC1, ANGPT2, ARID2, BARD1, CBR3, CDH2, CYP1B1, DDR2, DNMT3A, EPCAM, ERCC2, FANCG, FANCL, GSTP1, IRS2, ITGB1, JAK3, LHCGR, MSH6, NCF2, RNF43, SLC5A5, TMPRSS2, TNFRSF8, AKT1, CD248, CD4, ESR2, EZH2, IGF1R, ITGAV, ITGB2, KLHL6, MAP3K1, MET, MLL, MTHFR, NFKB1, NUP93, PARP8, RB1, RPE65, TSHR, ABL1, BLM, CYP19A1, DPP4, EPHA6, ERBB2, EWSR1, FOXP4, ITGAM, KDM5A, LPA, LTK, MLH1, PBRM1, PHLPP2, SF3B1, TNFRSF10A, ABCG2, ACPP, ADAM15, DPYD, EPHA5, EPHB6, FOLH1, KDR, MSH3, MST1R, NTRK1, ROCK2, SLC6A2, TET2, TGM2, TH, ABCB1, CD22, CD40, CD44, CDH20, CYP11B2, ERCC5, GPR124, IL7R, ITGB3, ITGB5, NCL, NOD2, NR4A1, PGR, PLCG1, PPP2R1A, PRAME, PTCH2, RET, SETD2, XPC, ASXL1, EPHB4, PLA2G6, SYK, TET1, EP300, FLT1, ITGA1, LOXL2, PDGFRB, PIK3CD, SSTR5, TEC, APC, ATR, CLU, CREBBP, CYP2D6, EML4, MMP2, PARP2, PDGFRA, TRPM8, CSF1R, DOT1L, FGFR3, FGFR4, GLP2R, IKBKE, JAK1, NOTCH2, SPEN, SPG7, BRCA1, CYP11B1, GNAS, ITGA5, LTF, NRP2, PTK2B, TNKS, ABCC1, CEACAM5, CYP4B1, EGFR, FLT3, INSR, PTCH1, SMARCA4, ZNF217, BCR, EEF2, SELP, SLCO1B1, ABCC2, FLT4, MTR, IL4R, MTOR, RPTOR, TEK, ATM, CARD11, FANCD2, MEFV, NF1, TP73, BRCA2, CD109, PTPRD, ABCC6, IGF2R, P2RX7, ROS1, ACE, PARP1, PRKDC, CENPE, TSC2, ALK, NOTCH1, TNC, NOTCH3, POLE, MLL2, MYH11, POLD1, GRIN3B, F5, FANCA, LRP1B, LRP2, VWF.

12. The method of claim 1, wherein the human nucleic acid sample comprises a set of reads issued from a next-generation sequencing procedure, NGS, and wherein the alignment comprises a step of mapping the reads to the selected PHREGs.

13. A computer system for genomic and/or genetic analysis of a human nucleic acid sample, the computer system comprising: a) a first module comprising computer instructions for providing a group of human reference genomes;b) a second module for testing of a human nucleic acid sample for sex and/or ancestry;c) a third module comprising computer instructions for selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis of the results of the sex and/or ancestry test; andd) a fourth module comprising computer instructions for aligning the human nucleic acid sample to the determined PHREGs.

14. Computer program comprising instructions which, when the program is executed by a computer, cause the computer to carry out the steps a), b), c) and d) of the method of claim 1.

15. Computer-readable storage medium comprising instructions which, when executed by a computer, cause the computer to carry out the steps a), b), c) and d) of the method of claim 1.

16. A method of treating a patient comprising Retrieving an identification of a disease indication of the patient, Obtaining a nucleic acid sample from the patientPerforming genomic and/or genetic analysis of the nucleic acid sample according to the method of claim 1,Retrieving possible treatments for the disease indication of the patientPerforming variant calling and interpretationClassification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patientSelecting one of the indicated treatmentsTreating of the patient according to the selected treatment.