Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
EPHA10	284656	broad.mit.edu	37	1	38186483	38186483	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38186483C>T	uc009vvi.2	-	12	2266	c.2180G>A	c.(2179-2181)AGC>AAC	p.S727N	EPHA10_uc001cbt.2_5'Flank|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	727	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGCCCCATGGCTCATGTACTC	0.562													7	68	---	---	---	---	PASS
CTSS	1520	broad.mit.edu	37	1	150724283	150724283	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150724283C>G	uc001evn.2	-	5	734	c.601G>C	c.(601-603)GAC>CAC	p.D201H	CTSS_uc010pcj.1_Missense_Mutation_p.D151H|CTSS_uc001evo.1_Missense_Mutation_p.D201H	NM_004079	NP_004070	P25774	CATS_HUMAN	cathepsin S preproprotein	201					immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			TAGGAAGCGTCTGAGTCGATG	0.473													128	245	---	---	---	---	PASS
IFI16	3428	broad.mit.edu	37	1	158988366	158988366	+	Silent	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158988366G>A	uc001ftf.1	+	6	1504	c.897G>A	c.(895-897)AAG>AAA	p.K299K	IFI16_uc001ftg.2_Silent_p.K299K|IFI16_uc010pis.1_Silent_p.K243K	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	299	HIN-200 1.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					ACAGAGCAAAGGAAACTCTGA	0.348													102	198	---	---	---	---	PASS
PTGS2	5743	broad.mit.edu	37	1	186643675	186643675	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186643675A>C	uc001gsb.2	-	10	1762	c.1625T>G	c.(1624-1626)TTT>TGT	p.F542C	PTGS2_uc009wyo.2_Missense_Mutation_p.F389C	NM_000963	NP_000954	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 precursor	542					cellular component movement|cyclooxygenase pathway|hormone biosynthetic process|positive regulation of brown fat cell differentiation|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of fever generation|positive regulation of fibroblast growth factor production|positive regulation of nitric oxide biosynthetic process|positive regulation of platelet-derived growth factor production|positive regulation of prostaglandin biosynthetic process|positive regulation of transforming growth factor-beta production|positive regulation vascular endothelial growth factor production|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome|neuron projection|nucleus	enzyme binding|heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|central_nervous_system(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Carprofen(DB00821)|Celecoxib(DB00482)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Epoprostenol(DB01240)|Etodolac(DB00749)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Valdecoxib(DB00580)	GATGATTTGAAAACCCACTTC	0.433													100	214	---	---	---	---	PASS
SUSD4	55061	broad.mit.edu	37	1	223395438	223395438	+	3'UTR	SNP	A	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223395438A>C	uc001hnx.2	-	8					SUSD4_uc001hny.3_3'UTR|SUSD4_uc010puw.1_3'UTR	NM_017982	NP_060452	Q5VX71	SUSD4_HUMAN	sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)		CAAGTTAGACATTTTGCCCCC	0.478													32	87	---	---	---	---	PASS
TP53BP2	7159	broad.mit.edu	37	1	223983853	223983853	+	Silent	SNP	T	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223983853T>A	uc010pvb.1	-	13	2680	c.2388A>T	c.(2386-2388)CCA>CCT	p.P796P	TP53BP2_uc001hod.2_Silent_p.P667P|TP53BP2_uc010puz.1_Silent_p.P29P|TP53BP2_uc010pva.1_Silent_p.P435P	NM_001031685	NP_001026855	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein, 2 isoform 1	790					apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)		CATGTAAATATGGATTCTGGA	0.512													119	217	---	---	---	---	PASS
TEKT4	150483	broad.mit.edu	37	2	95542556	95542556	+	3'UTR	SNP	C	T	T	rs62147444	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95542556C>T	uc002stw.1	+	6					uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4						cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3						AAATAAACAGCGCGTTAGCTT	0.607													4	27	---	---	---	---	PASS
BMPR2	659	broad.mit.edu	37	2	203420922	203420922	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203420922A>T	uc002uzf.3	+	12	3682	c.2534A>T	c.(2533-2535)GAA>GTA	p.E845V	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	845	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						AGGGCCCAAGAAATGTTGCAG	0.468													71	135	---	---	---	---	PASS
BMPR2	659	broad.mit.edu	37	2	203420924	203420924	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203420924A>T	uc002uzf.3	+	12	3684	c.2536A>T	c.(2536-2538)ATG>TTG	p.M846L	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	846	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						GGCCCAAGAAATGTTGCAGAA	0.468													70	135	---	---	---	---	PASS
PTPRN	5798	broad.mit.edu	37	2	220159737	220159737	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220159737C>T	uc002vkz.2	-	19	2724	c.2635G>A	c.(2635-2637)GGC>AGC	p.G879S	PTPRN_uc010zlc.1_Missense_Mutation_p.G789S|PTPRN_uc002vla.2_Missense_Mutation_p.G850S|uc010zld.1_5'Flank|MIR153-1_hsa-mir-153-1|MI0000463_5'Flank	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	879	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCCGGTGTGCCCTCTGCCGGC	0.716													6	7	---	---	---	---	PASS
SDHAP1	255812	broad.mit.edu	37	3	195711423	195711423	+	Intron	SNP	A	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195711423A>G	uc011btq.1	-						SDHAP1_uc003fvx.3_RNA|SDHAP1_uc011btp.1_Intron					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						CTCTTGTACTAGAAACAGACC	0.552													3	17	---	---	---	---	PASS
ISL1	3670	broad.mit.edu	37	5	50685635	50685635	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50685635G>C	uc003jor.2	+	4	1182	c.634G>C	c.(634-636)GAG>CAG	p.E212Q		NM_002202	NP_002193	P61371	ISL1_HUMAN	islet-1	212	Homeobox.				generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)				GCTCATGAAGGAGCAACTGGT	0.587													11	56	---	---	---	---	PASS
RGMB	285704	broad.mit.edu	37	5	98115300	98115300	+	Silent	SNP	A	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98115300A>T	uc003knc.2	+	4	678	c.276A>T	c.(274-276)CCA>CCT	p.P92P	RGMB_uc003knb.2_Silent_p.P92P	NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B	51					axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		GCCAACAGCCAGCCCAATGTC	0.463													31	62	---	---	---	---	PASS
C5orf25	375484	broad.mit.edu	37	5	175716597	175716597	+	Intron	SNP	A	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175716597A>G	uc003mdt.3	+						C5orf25_uc003mds.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc011dfk.1_Intron|uc003mdu.1_5'UTR	NM_198567	NP_940969	Q8NDZ2	CE025_HUMAN	hypothetical protein LOC375484												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)		GACTTAAGTCATCTCAGATAA	0.368													10	203	---	---	---	---	PASS
EGFL8	80864	broad.mit.edu	37	6	32134517	32134517	+	Silent	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32134517G>A	uc003oab.1	+	4	322	c.264G>A	c.(262-264)GAG>GAA	p.E88E	PPT2_uc003nzy.1_RNA|EGFL8_uc003oac.1_Silent_p.E88E	NM_030652	NP_085155	Q99944	EGFL8_HUMAN	NG3 protein precursor	88	EMI.					extracellular region|integral to membrane	calcium ion binding				0						TGAGGCGGGAGGTTCAGCAGA	0.657													17	31	---	---	---	---	PASS
MRPL14	64928	broad.mit.edu	37	6	44084332	44084332	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44084332C>T	uc003owp.2	-	2	146	c.17G>A	c.(16-18)GGG>GAG	p.G6E		NM_032111	NP_115487	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14 precursor	6					translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)			GCCCCAGAGCCCAGTAAAGAA	0.448													66	146	---	---	---	---	PASS
LRP11	84918	broad.mit.edu	37	6	150174142	150174142	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150174142C>A	uc003qng.2	-	2	1092	c.768G>T	c.(766-768)ATG>ATT	p.M256I	LRP11_uc003qnh.1_Missense_Mutation_p.M256I	NM_032832	NP_116221	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein	256	PKD.|Extracellular (Potential).					integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		GCGTTACCTTCATGTCCACTG	0.527													25	61	---	---	---	---	PASS
PON3	5446	broad.mit.edu	37	7	94993300	94993300	+	Silent	SNP	C	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94993300C>A	uc003unt.2	-	6	595	c.570G>T	c.(568-570)CTG>CTT	p.L190L	PON1_uc011kih.1_Intron|PON3_uc011kii.1_Silent_p.L238L	NM_000940	NP_000931	Q15166	PON3_HUMAN	paraoxonase 3	190					aromatic compound catabolic process|carboxylic acid catabolic process|response to external stimulus	extracellular space	aryldialkylphosphatase activity|arylesterase activity|metal ion binding|protein homodimerization activity			ovary(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)			CAAAAAATGACAGGAGGGAGT	0.433													31	304	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	156974262	156974262	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156974262A>G	uc010lqs.2	+	7	979	c.667A>G	c.(667-669)ATT>GTT	p.I223V	UBE3C_uc003wnf.2_Missense_Mutation_p.I180V|UBE3C_uc003wng.2_Missense_Mutation_p.I223V	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	223					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TCCATCAAGTATTGAATATTC	0.328													137	299	---	---	---	---	PASS
REXO1L1	254958	broad.mit.edu	37	8	86786310	86786310	+	RNA	SNP	G	T	T	rs150998281		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86786310G>T	uc011lfx.1	-	1		c.2539C>A			REXO1L1_uc010mah.2_RNA	NM_172239	NP_758439	Q8IX06	GOR_HUMAN	exonuclease GOR							cytoplasm|nucleus	exonuclease activity|nucleic acid binding				0						ccttcatttcgttatgtaccc	0.000													3	15	---	---	---	---	PASS
LAMC3	10319	broad.mit.edu	37	9	133914603	133914603	+	Silent	SNP	C	A	A	rs148513856		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133914603C>A	uc004caa.1	+	6	1349	c.1251C>A	c.(1249-1251)CCC>CCA	p.P417P		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	417	Laminin EGF-like 3.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GCTGTCTGCCCGGGTTCCACT	0.632													3	37	---	---	---	---	PASS
KIAA1598	57698	broad.mit.edu	37	10	118719667	118719667	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118719667C>T	uc009xyw.2	-	4	745	c.247G>A	c.(247-249)GCT>ACT	p.A83T	KIAA1598_uc001lcz.3_Missense_Mutation_p.A83T|KIAA1598_uc010qso.1_Missense_Mutation_p.A23T|KIAA1598_uc010qsp.1_Missense_Mutation_p.A83T|KIAA1598_uc010qsq.1_Missense_Mutation_p.A23T|KIAA1598_uc001lcy.3_Missense_Mutation_p.A53T	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a	83	Potential.				axon guidance	axon					0				all cancers(201;0.00494)		AAAGCTTCAGCACTTTCTCGA	0.373													90	242	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62790158	62790158	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62790158G>C	uc001src.1	+	20	2663	c.2654G>C	c.(2653-2655)GGA>GCA	p.G885A	USP15_uc001srb.1_Missense_Mutation_p.G856A	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	885					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AACCACTATGGAGGGATGGGA	0.373													56	500	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88496844	88496844	+	Intron	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88496844C>T	uc001tar.2	-						CEP290_uc001taq.2_Translation_Start_Site|CEP290_uc001tat.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TGGTCAAGCACTAGCCACTTT	0.299													8	35	---	---	---	---	PASS
DGKH	160851	broad.mit.edu	37	13	42729884	42729884	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42729884G>A	uc001uyl.1	+	5	592	c.571G>A	c.(571-573)GTG>ATG	p.V191M	DGKH_uc010tfh.1_Missense_Mutation_p.V191M|DGKH_uc001uym.1_Missense_Mutation_p.V191M|DGKH_uc010tfi.1_Silent_p.T23T|DGKH_uc010tfj.1_Missense_Mutation_p.V46M|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.V46M|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	191	Phorbol-ester/DAG-type 1.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CTTCTGTAACGTGTGCAGAGA	0.517													6	174	---	---	---	---	PASS
C14orf4	64207	broad.mit.edu	37	14	77491664	77491664	+	3'UTR	SNP	A	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77491664A>G	uc001xsy.2	-	1						NM_024496	NP_078772	Q9H1B7	I2BPL_HUMAN	chromosome 14 open reading frame 4							nucleus					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)		GAGGGGAGGGAGGGTCGAGTT	0.483													4	45	---	---	---	---	PASS
SLC24A5	283652	broad.mit.edu	37	15	48428782	48428782	+	Intron	SNP	C	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48428782C>A	uc001zwe.2	+						SLC24A5_uc010bel.2_Intron|uc001zwf.1_RNA	NM_205850	NP_995322	Q71RS6	NCKX5_HUMAN	solute carrier family 24, member 5 precursor						response to stimulus	integral to membrane|melanosome|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity				0		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TCTATGGCTACTTTTGTTAGA	0.279													20	126	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101606305	101606305	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101606305C>T	uc002bwr.2	+	32	5982	c.5663C>T	c.(5662-5664)TCC>TTC	p.S1888F	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1888					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGTGCTGCCTCCGACAGGTCT	0.617													7	69	---	---	---	---	PASS
TRAP1	10131	broad.mit.edu	37	16	3726076	3726076	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3726076A>G	uc002cvt.3	-	7	864	c.775T>C	c.(775-777)TCC>CCC	p.S259P	TRAP1_uc002cvs.2_Missense_Mutation_p.S50P|TRAP1_uc010uxf.1_Missense_Mutation_p.S206P	NM_016292	NP_057376	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1 precursor	259					cellular response to oxidative stress|protein folding	mitochondrion	ATP binding|tumor necrosis factor receptor binding|unfolded protein binding			central_nervous_system(1)	1		Ovarian(90;0.0261)				TTGCAGTCGGATTTCAGGTGG	0.577													82	155	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15225426	15225426	+	Intron	SNP	C	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15225426C>G	uc002ddc.2	+						uc010uzs.1_RNA|uc002ddh.2_5'UTR|uc002ddi.2_5'Flank|uc010uzt.1_5'UTR	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	GTTGAGCACGCGGGAGCGCGT	0.697													3	9	---	---	---	---	PASS
TMCO7	79613	broad.mit.edu	37	16	68953056	68953056	+	Silent	SNP	C	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68953056C>A	uc002ewi.3	+	12	2073	c.2061C>A	c.(2059-2061)ACC>ACA	p.T687T		NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	687						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		CAGAGAGCACCGTGGAATCAC	0.527													106	256	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													8	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													6	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268158A>C	uc010cfp.1	-	3		c.257T>G								Homo sapiens cDNA, FLJ98908.																		TTCTTCATTAAAACAGCTACT	0.333													4	86	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	74425826	74425826	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74425826G>A	uc010vmt.1	+	6	998	c.997G>A	c.(997-999)GCA>ACA	p.A333T						RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		ggaggccgaggcacaacaatt	0.229													7	68	---	---	---	---	PASS
TBC1D26	353149	broad.mit.edu	37	17	15643627	15643627	+	Intron	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15643627C>T	uc010cov.2	+						TBC1D26_uc010cou.1_3'UTR|TBC1D26_uc002gpb.3_Intron	NM_178571	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26							intracellular	Rab GTPase activator activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		GAAGCCCAGACTCCTGGTGTC	0.547													24	48	---	---	---	---	PASS
LOXHD1	125336	broad.mit.edu	37	18	44114298	44114298	+	Silent	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44114298G>A	uc010xcw.1	-	27	4212	c.4212C>T	c.(4210-4212)GAC>GAT	p.D1404D	LOXHD1_uc002lcg.1_Silent_p.D1126D|LOXHD1_uc002lce.3_Silent_p.D197D|LOXHD1_uc002lcf.3_Silent_p.D293D|LOXHD1_uc010xcv.1_Silent_p.D337D|LOXHD1_uc010xcx.1_RNA	NM_144612	NP_653213	Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1 isoform 1	1126	PLAT 8.				sensory perception of sound	stereocilium	protein binding				0						AACAACTCACGTCTTTATCCG	0.493													8	239	---	---	---	---	PASS
ZNF653	115950	broad.mit.edu	37	19	11598181	11598181	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11598181G>A	uc002mrz.1	-	4	1150	c.1097C>T	c.(1096-1098)ACC>ATC	p.T366I		NM_138783	NP_620138	Q96CK0	ZN653_HUMAN	zinc finger protein 653	366					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTCTGTCTGGGTGTAGGCTGC	0.647													13	35	---	---	---	---	PASS
NOTCH3	4854	broad.mit.edu	37	19	15290202	15290202	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15290202G>C	uc002nan.2	-	21	3509	c.3433C>G	c.(3433-3435)CTC>GTC	p.L1145V	NOTCH3_uc002nao.1_Missense_Mutation_p.L1093V	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	1145	Extracellular (Potential).|EGF-like 29; calcium-binding (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CAGGAGCAGAGATAGCGGGCC	0.607													9	44	---	---	---	---	PASS
GIPR	2696	broad.mit.edu	37	19	46185190	46185190	+	Silent	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46185190C>T	uc002pcu.1	+	14	1497	c.1398C>T	c.(1396-1398)TGC>TGT	p.C466C	GIPR_uc002pct.1_3'UTR|GIPR_uc010xxp.1_Silent_p.C430C|GIPR_uc010xxq.1_RNA	NM_000164	NP_000155	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	466	Cytoplasmic (Potential).				generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane				skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		AAAGTTACTGCTAGGGGGCGG	0.448													3	31	---	---	---	---	PASS
MORC2	22880	broad.mit.edu	37	22	31328363	31328363	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31328363G>C	uc003aje.1	-	25	4002	c.2638C>G	c.(2638-2640)CTA>GTA	p.L880V		NM_014941	NP_055756	Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	942							ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2						AAAGATATTAGCTCATCTGAA	0.463													82	162	---	---	---	---	PASS
TFDP3	51270	broad.mit.edu	37	X	132351243	132351243	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132351243T>G	uc004exb.1	-	1	1134	c.1045A>C	c.(1045-1047)AAT>CAT	p.N349H		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	349						transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					CACGTGCCATTAGACCTGGAA	0.552													34	120	---	---	---	---	PASS
OPN1MW	2652	broad.mit.edu	37	X	153461744	153461744	+	3'UTR	SNP	C	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153461744C>T	uc004fkb.2	+	6						NM_000513	NP_000504	P04001	OPSG_HUMAN	opsin 1 (cone pigments), medium-wave-sensitive						phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GAGAGCGCTTCATAGACTTTA	0.542													6	26	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9932	9932	+	RNA	SNP	G	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9932G>A	uc011mfi.1	+	1		c.1270G>A			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		GCCTGATACTGGCATTTTGTA	0.383													42	21	---	---	---	---	PASS
CALML6	163688	broad.mit.edu	37	1	1844944	1844944	+	5'Flank	DEL	T	-	-	rs71578352		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1844944delT	uc001aih.1	+							NM_138705	NP_619650	Q8TD86	CALL6_HUMAN	calmodulin-like 6							cytoplasm|nucleus	calcium ion binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		ttttcttttcttttttttttt	0.020													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2515193	2515193	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2515193delC								TNFRSF14 (19928 upstream) : C1orf93 (3056 downstream)																							ctgtgcagtgcccacccaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5775592	5775592	+	IGR	DEL	A	-	-	rs149917812	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5775592delA								AJAP1 (931742 upstream) : NPHP4 (147278 downstream)																							tacagatgggaaaaccaaggc	0.035													4	2	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8677842	8677842	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8677842delG	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCAGTCATATGGAAAACTCAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	12840038	12840038	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12840038delC								PRAMEF12 (1992 upstream) : PRAMEF1 (11508 downstream)																							GAAAACTTTTCCATTCTCTAG	0.398													4	2	---	---	---	---	
ARHGEF19	128272	broad.mit.edu	37	1	16528470	16528471	+	Intron	DEL	CC	-	-	rs58225172		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16528470_16528471delCC	uc001ayc.1	-						ARHGEF19_uc009voo.1_Intron|ARHGEF19_uc001ayb.1_Intron	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		AGGACCCAGGCCTACCCTAGGG	0.619													10	5	---	---	---	---	
ARHGEF19	128272	broad.mit.edu	37	1	16528473	16528484	+	Intron	DEL	ACCCTAGGGACC	-	-	rs57272462		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16528473_16528484delACCCTAGGGACC	uc001ayc.1	-						ARHGEF19_uc009voo.1_Intron|ARHGEF19_uc001ayb.1_Intron	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		ACCCAGGCCTACCCTAGGGACCCATGTCTGCC	0.623													9	6	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18631220	18631221	+	Intron	INS	-	AT	AT	rs5009445		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18631220_18631221insAT	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		cacacacacacacatacacaca	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	21754481	21754482	+	5'Flank	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21754481_21754482insG	uc001bep.1	-											Homo sapiens cDNA FLJ25572 fis, clone JTH05111.																		AGAATAAGCCAGGGGGGGCGTT	0.272													8	8	---	---	---	---	
NBPF3	84224	broad.mit.edu	37	1	21791623	21791624	+	Intron	INS	-	C	C	rs144217242	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21791623_21791624insC	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ATTTCCTTTTTTCAGAaatgag	0.183													4	2	---	---	---	---	
EPHB2	2048	broad.mit.edu	37	1	23064383	23064383	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23064383delG	uc009vqj.1	+						EPHB2_uc001bge.2_Intron|EPHB2_uc001bgf.2_Intron|EPHB2_uc010odu.1_Intron	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor						axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		CTTGGAAGTAGGAGGAAATTA	0.453									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
FUCA1	2517	broad.mit.edu	37	1	24191197	24191197	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24191197delT	uc001bie.2	-						FUCA1_uc009vqt.1_Intron|FUCA1_uc010oed.1_Intron	NM_000147	NP_000138	P04066	FUCO_HUMAN	fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		gtcttttttcttttttttttt	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	26281135	26281135	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26281135delA								STMN1 (47767 upstream) : PAFAH2 (5125 downstream)																							CGCCGGGGGGAAAGAGAGATT	0.428													4	2	---	---	---	---	
SESN2	83667	broad.mit.edu	37	1	28595994	28595994	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28595994delT	uc001bps.2	+							NM_031459	NP_113647	P58004	SESN2_HUMAN	sestrin 2						cell cycle arrest	cytoplasm|nucleus				skin(3)|ovary(2)|pancreas(1)|lung(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		GTGGCCAAACTTTTTTTTTTT	0.219													4	2	---	---	---	---	
EPB41	2035	broad.mit.edu	37	1	29439863	29439863	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29439863delA	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron|EPB41_uc009vtn.1_Intron	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		GAGTGCCTTTAAAAAAAGAAA	0.473													4	2	---	---	---	---	
HCRTR1	3061	broad.mit.edu	37	1	32081717	32081720	+	5'Flank	DEL	CACG	-	-	rs148334907		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32081717_32081720delCACG	uc009vtx.2	+						HCRTR1_uc001btb.2_5'Flank|HCRTR1_uc001btc.3_5'Flank|HCRTR1_uc001btd.2_5'Flank|HCRTR1_uc010ogl.1_5'Flank	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1						feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		cacatgcacacacgcacacacaca	0.284													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	32373167	32373167	+	RNA	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32373167delT	uc001btx.1	-	1		c.546delA								Homo sapiens BM-008 mRNA, complete cds.																		AAACCAGGGATTTTTTTTTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35147058	35147059	+	IGR	DEL	TT	-	-	rs67758544		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35147058_35147059delTT								MIR552 (11763 upstream) : GJB5 (73662 downstream)																							AAAACTATTCTTTTTTTTTTTT	0.252													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35897322	35897322	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35897322delC								ZMYM4 (9778 upstream) : KIAA0319L (1770 downstream)																							AGGGGCATTACCTGGGGAAAA	0.428													4	2	---	---	---	---	
KIAA0319L	79932	broad.mit.edu	37	1	35914599	35914599	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35914599delG	uc001byx.2	-						KIAA0319L_uc001byw.2_Intron|KIAA0319L_uc010ohv.1_Intron	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTGATTGTTTGGAATGCCTTA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37509146	37509147	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37509146_37509147insT								GRIK3 (9302 upstream) : ZC3H12A (430972 downstream)																							TGTCTTTATGATTTTTTTTCAA	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38122494	38122495	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38122494_38122495delGT								RSPO1 (22003 upstream) : C1orf109 (24755 downstream)																							gtgtgtttgagtgtgtgtgtgt	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39073631	39073631	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39073631delT								POU3F1 (561181 upstream) : RRAGC (231384 downstream)																							CCCCCAGTACTTTTTTTTTTT	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39247016	39247016	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39247016delA								POU3F1 (734566 upstream) : RRAGC (57999 downstream)																							ggcccctgataaaaaaaaatg	0.025													3	3	---	---	---	---	
FOXJ3	22887	broad.mit.edu	37	1	42733197	42733197	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42733197delA	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron|FOXJ3_uc001chh.1_Intron	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				tatttaactcaacgtctacca	0.000													4	2	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	45046745	45046746	+	Intron	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45046745_45046746delGA	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						AGCCTTGGCTGAGAGAGAGAGT	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	45285227	45285227	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45285227delT								BTBD19 (5426 upstream) : PTCH2 (2861 downstream)																							AAACTTCTGAtttttttttgt	0.204													4	2	---	---	---	---	
MAST2	23139	broad.mit.edu	37	1	46402440	46402442	+	Intron	DEL	CAT	-	-	rs150419924	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46402440_46402442delCAT	uc001cov.2	+						MAST2_uc001cow.2_Intron|MAST2_uc001cox.1_Intron|MAST2_uc001coy.1_Intron|MAST2_uc001coz.1_Intron|MAST2_uc009vya.2_Intron	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					ACATGGCCACCATCATCATCATC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	46915291	46915291	+	IGR	DEL	G	-	-	rs5773910		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46915291delG								FAAH (35771 upstream) : DMBX1 (57377 downstream)																							GAATGAAGGAGTAAGCTGAGC	0.498													2	7	---	---	---	---	
MKNK1	8569	broad.mit.edu	37	1	47072012	47072013	+	5'Flank	INS	-	TGGG	TGGG	rs142319347	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47072012_47072013insTGGG	uc001cqb.2	-						MKNK1_uc010omd.1_5'Flank|MKNK1_uc001cqc.2_5'Flank|MKNK1_uc009vyi.2_5'Flank|MKNK1_uc010ome.1_5'Flank|MKNK1_uc009vyj.2_5'Flank|MKNK1_uc001cqd.2_5'Flank|MKNK1_uc010omf.1_Intron	NM_003684	NP_003675	Q9BUB5	MKNK1_HUMAN	MAP kinase-interacting serine/threonine kinase 1						intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)					TTTTAGAATGCTGGGATTGGGC	0.366													4	3	---	---	---	---	
CYP4X1	260293	broad.mit.edu	37	1	47471371	47471371	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47471371delA	uc001cqr.2	+						CYP4X1_uc001cqs.2_Intron	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2						taactttactaaaaaagctgg	0.000													4	2	---	---	---	---	
SLC5A9	200010	broad.mit.edu	37	1	48693242	48693243	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48693242_48693243delGT	uc001cro.2	+						SLC5A9_uc010oms.1_Intron|SLC5A9_uc001crn.2_Intron|SLC5A9_uc010omt.1_Intron|SLC5A9_uc001crp.2_Intron|SLC5A9_uc010omu.1_Intron	NM_001011547	NP_001011547	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/glucose							integral to membrane|plasma membrane	low-affinity glucose:sodium symporter activity			ovary(3)	3						gtgtgtcagagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49002721	49002721	+	Intron	DEL	G	-	-	rs2798109	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49002721delG	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		GATTAGTTTTGAGTCAAAACA	0.378													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49238922	49238922	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49238922delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron|BEND5_uc001crx.3_Intron|BEND5_uc001crw.3_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		TGAGCCTCCTAAAAAAAAAAT	0.413													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49331227	49331227	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49331227delT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		GCAGTGCTGATTTTTTTTTCA	0.403													4	2	---	---	---	---	
LRP8	7804	broad.mit.edu	37	1	53731854	53731854	+	Intron	DEL	C	-	-	rs34790867		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53731854delC	uc001cvi.1	-						LRP8_uc001cvh.1_Intron|LRP8_uc001cvk.1_Intron|LRP8_uc001cvj.1_Intron|LRP8_uc001cvl.1_Intron|LRP8_uc001cvm.1_Intron	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein						cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0						TTCTTCCTTTCTGCCCTGGCC	0.542											OREG0013489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
TACSTD2	4070	broad.mit.edu	37	1	59045499	59045499	+	5'Flank	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59045499delA	uc001cyz.3	-							NM_002353	NP_002344	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2						cell proliferation|cell surface receptor linked signaling pathway|visual perception	cytosol|integral to plasma membrane	receptor activity				0	all_cancers(7;6.54e-05)					ACTCAGGGATATGCCTCTCTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59408404	59408405	+	IGR	DEL	CC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59408404_59408405delCC								JUN (158619 upstream) : LOC729467 (189205 downstream)																							attcccacagccactctgagag	0.114													2	4	---	---	---	---	
CYP2J2	1573	broad.mit.edu	37	1	60375861	60375861	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60375861delA	uc001czq.2	-							NM_000775	NP_000766	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J,						epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)					gcttgccaccaAAAAAAAATA	0.035													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61429487	61429487	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61429487delA	uc001czu.2	-											Homo sapiens cDNA clone IMAGE:4796864.																		CTGTCAGGAGAAAAAAAAATT	0.473													4	2	---	---	---	---	
EFCAB7	84455	broad.mit.edu	37	1	64034374	64034374	+	Intron	DEL	T	-	-	rs67539131		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64034374delT	uc001dbf.2	+							NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7								calcium ion binding				0						TTTTATATGATTTTTAAAGGT	0.254													10	5	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64263947	64263947	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64263947delG	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						acgctctgcagggaaattgga	0.065													4	2	---	---	---	---	
CACHD1	57685	broad.mit.edu	37	1	64963248	64963248	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64963248delA	uc001dbo.1	+							NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1						calcium ion transport	integral to membrane				ovary(2)	2						ATAGTTCAGGAAAAAAAATAC	0.413													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67206038	67206041	+	Intron	DEL	ATTG	-	-	rs146106863		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67206038_67206041delATTG	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Intron|SGIP1_uc001dcu.2_Intron	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						ACCTTAATTAATTGATTAACACTC	0.309													4	3	---	---	---	---	
RPE65	6121	broad.mit.edu	37	1	68897751	68897751	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68897751delA	uc001dei.1	-							NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						TGACAAAAAGAAAAAAAAAAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	71831133	71831134	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71831133_71831134delAC								ZRANB2 (284388 upstream) : NEGR1 (37492 downstream)																							ATTGCTATGTACACACACCAAA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74122999	74122999	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74122999delA								None (None upstream) : LRRIQ3 (368705 downstream)																							TATGTCATAGAAAAAAAAATA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74416944	74416944	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74416944delA								None (None upstream) : LRRIQ3 (74760 downstream)																							taaataaatGAAAAAAAAATG	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80294852	80294852	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80294852delT								ELTD1 (822357 upstream) : None (None downstream)																							atattgtcactttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84088880	84088881	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84088880_84088881delAC	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																		GTATACACATACACACACACAC	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88702905	88702908	+	IGR	DEL	CTCC	-	-	rs142556581		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88702905_88702908delCTCC								LMO4 (888302 upstream) : PKN2 (447014 downstream)																							TCGCCCACAGCTCCCTTCTCAAAG	0.495													4	3	---	---	---	---	
PKN2	5586	broad.mit.edu	37	1	89150151	89150151	+	5'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89150151delT	uc001dmn.2	+	1					PKN2_uc001dmm.1_5'UTR|PKN2_uc010osp.1_5'UTR|PKN2_uc010osq.1_5'UTR|PKN2_uc009wcv.2_5'UTR	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TCCCTAGTTGTTTTTTTTTTT	0.637													5	3	---	---	---	---	
C1orf146	388649	broad.mit.edu	37	1	92709514	92709514	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92709514delA	uc001doq.2	+						C1orf146_uc010ote.1_Intron	NM_001012425	NP_001012425	Q5VVC0	CA146_HUMAN	hypothetical protein LOC388649											ovary(1)	1		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		TTCATCTAGGAAAAAAAAAAA	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96724249	96724250	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96724249_96724250delAC								None (None upstream) : PTBP2 (462925 downstream)																							CTATGCACAAACACACACACAT	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	97029104	97029104	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97029104delT								None (None upstream) : PTBP2 (158071 downstream)																							TGGATTCACATTTTTTTTTTC	0.244													4	2	---	---	---	---	
DPYD	1806	broad.mit.edu	37	1	98280000	98280001	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98280000_98280001insA	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	tgtaaaaagggaaattagtagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	105786189	105786189	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105786189delA								None (None upstream) : None (None downstream)																							CTCCTCTTTGAACAACATCTT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	109189187	109189187	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109189187delG								FAM102B (7239 upstream) : C1orf59 (1725 downstream)																							gatacggtttggatctgtgtc	0.000													4	2	---	---	---	---	
ATP5F1	515	broad.mit.edu	37	1	112002965	112002965	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112002965delT	uc001ebc.2	+						ATP5F1_uc001ebd.3_Intron	NM_001688	NP_001679	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial F0						ATP catabolic process|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transporting ATP synthase activity, rotational mechanism|protein binding				0		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		TATGACTTGATTTTTTTTTTC	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115379467	115379470	+	IGR	DEL	CAGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115379467_115379470delCAGA								SIKE1 (56159 upstream) : SYCP1 (17985 downstream)																							ATGAAGAGTTCAGACAAAATTTTT	0.255													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116496258	116496259	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116496258_116496259insA								NHLH2 (112511 upstream) : SLC22A15 (22860 downstream)																							AGCTCTGAAGGAAAAAAAAATA	0.351													4	2	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119451543	119451544	+	Intron	INS	-	CA	CA	rs146145670	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119451543_119451544insCA	uc001ehl.1	-							NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		cactcaacattcacacacacac	0.168													2	4	---	---	---	---	
HSD3B1	3283	broad.mit.edu	37	1	120055205	120055205	+	Intron	DEL	A	-	-	rs151061429		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120055205delA	uc001ehv.1	+						HSD3B1_uc001ehw.2_Intron	NM_000862	NP_000853	P14060	3BHS1_HUMAN	3 beta-hydroxysteroid dehydrogenase 1						androgen biosynthetic process|estrogen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	NADH(DB00157)|Trilostane(DB01108)	ACCATAAAAGAAAAAAAAAAA	0.433													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120819495	120819495	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120819495delA								NOTCH2 (207219 upstream) : FAM72B (19510 downstream)																							gtgctgagtgaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143191464	143191464	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143191464delT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		TAAACTTttctttttttttct	0.104													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144855491	144855491	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144855491delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTCACACCCCTTCATCTTCTT	0.453			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145060586	145060586	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145060586delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CCAAGCACACTTTTTTTTCTT	0.353													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145275507	145275508	+	Intron	INS	-	T	T	rs143422176	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145275507_145275508insT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gagagccagtctgagttccaaa	0.005													2	4	---	---	---	---	
IQGAP3	128239	broad.mit.edu	37	1	156532119	156532120	+	Intron	INS	-	C	C	rs138515696	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156532119_156532120insC	uc001fpf.2	-						IQGAP3_uc009wsb.1_Intron	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGTCCAACTGCCCCCCCGGCA	0.569													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157451336	157451336	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157451336delA								ETV3 (342953 upstream) : FCRL5 (31832 downstream)																							GTCCAGCTGCAACTAAACTCC	0.438													4	2	---	---	---	---	
IGSF9	57549	broad.mit.edu	37	1	159896888	159896889	+	3'UTR	DEL	AG	-	-	rs35733433		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159896888_159896889delAG	uc001fur.2	-	21					IGSF9_uc001fuq.2_3'UTR|CCDC19_uc001ful.2_5'Flank|TAGLN2_uc001fun.1_5'Flank|TAGLN2_uc001fuo.1_5'Flank|TAGLN2_uc010piy.1_5'Flank|IGSF9_uc001fup.2_3'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a							cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			acacacacacagagagagagag	0.302													4	2	---	---	---	---	
UCK2	7371	broad.mit.edu	37	1	165877195	165877195	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165877195delT	uc001gdp.2	+	7					UCK2_uc010plb.1_3'UTR	NM_012474	NP_036606	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					ATGCCTTTGATTTTTTTTTTC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172486324	172486324	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172486324delT								C1orf105 (48359 upstream) : C1orf9 (15936 downstream)																							CATTTGGTGATTTTTTTTTTC	0.373													4	2	---	---	---	---	
FASLG	356	broad.mit.edu	37	1	172632163	172632163	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172632163delG	uc001gis.2	+						FASLG_uc001git.2_Intron	NM_000639	NP_000630	P48023	TNFL6_HUMAN	fas ligand						activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of necroptosis by extracellular signals|induction of necroptosis of activated-T cells|necrotic cell death|negative regulation of angiogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction	extracellular space|integral to plasma membrane	cytokine activity			lung(2)|breast(1)	3						TCTGTGGATTGGGCCATTCTC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172739159	172739159	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172739159delA								FASLG (103149 upstream) : TNFSF18 (271201 downstream)																							cagaaaacataagtccaatat	0.000													4	2	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176456836	176456837	+	Intron	DEL	TG	-	-	rs150463929		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176456836_176456837delTG	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						tctaggaccttgtaggggtaga	0.134													2	4	---	---	---	---	
FAM5B	57795	broad.mit.edu	37	1	177147982	177147982	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177147982delT	uc001glf.2	+							NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						ctcaagttgcttccattctag	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177767874	177767875	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177767874_177767875insG								FAM5B (516317 upstream) : SEC16B (129614 downstream)																							GTGAAAAAAAAAAACTTTCAGG	0.515													4	2	---	---	---	---	
SEC16B	89866	broad.mit.edu	37	1	177919084	177919084	+	Intron	DEL	A	-	-	rs71963792		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177919084delA	uc001gli.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwy.1_5'Flank|SEC16B_uc001glh.1_Intron|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron|SEC16B_uc001gll.3_Intron	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						CTACTATTACAAAAAAAAAAA	0.373													4	2	---	---	---	---	
SEC16B	89866	broad.mit.edu	37	1	177919086	177919087	+	Intron	INS	-	AAG	AAG	rs71799486		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177919086_177919087insAAG	uc001gli.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwy.1_5'Flank|SEC16B_uc001glh.1_Intron|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron|SEC16B_uc001gll.3_Intron	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						ACTATTACAAAAAAAAAAAATG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	179234418	179234419	+	IGR	INS	-	A	A	rs150508845	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179234418_179234419insA								ABL2 (35599 upstream) : SOAT1 (28598 downstream)																							CAGGTAAATTTAAAAAAAAATG	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182257423	182257423	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182257423delT								ZNF648 (226576 upstream) : GLUL (94246 downstream)																							GAGCTGCCCATTTTTTGGGGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	189689151	189689152	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189689151_189689152insA								None (None upstream) : FAM5C (377645 downstream)																							GATTCACAACtaaaaaaaaaat	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191228744	191228745	+	IGR	INS	-	T	T	rs147870995	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191228744_191228745insT								FAM5C (781985 upstream) : RGS18 (898847 downstream)																							CCAAATGATTACACAAACTTAT	0.327													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191660711	191660711	+	IGR	DEL	A	-	-	rs68115728		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191660711delA								None (None upstream) : RGS18 (466881 downstream)																							ACCATGGCTTAAAAAAAAAAC	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192770565	192770565	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192770565delA								RGS13 (141178 upstream) : RGS2 (7604 downstream)																							AATAAAGTTTAAAAAAAGTAG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195816191	195816191	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195816191delA								None (None upstream) : KCNT2 (378722 downstream)																							catgtaagggaggcagcatag	0.154													4	2	---	---	---	---	
CACNA1S	779	broad.mit.edu	37	1	201019881	201019881	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201019881delA	uc001gvv.2	-							NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TAACCAAAACAAAAAAAAAAA	0.289													8	4	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206624920	206624920	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206624920delA	uc001hdy.2	+						SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TTCAAAGGAGAAAAAAAAAAA	0.413													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	207124385	207124385	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207124385delT								PIGR (4574 upstream) : FCAMR (7019 downstream)																							TGGAGACTACTAGGAGCATGT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208875905	208875905	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208875905delT								PLXNA2 (458240 upstream) : LOC642587 (726263 downstream)																							agcagttgactcccacagccc	0.030													4	2	---	---	---	---	
SYT14	255928	broad.mit.edu	37	1	210281631	210281631	+	Intron	DEL	G	-	-	rs11353212		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210281631delG	uc009xcv.2	+						SYT14_uc001hhs.3_Intron|SYT14_uc001hht.3_Intron|SYT14_uc001hhu.3_Intron|SYT14_uc010psn.1_Intron|SYT14_uc010pso.1_Intron	NM_153262	NP_694994	Q8NB59	SYT14_HUMAN	synaptotagmin XIV isoform 4							integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)		ggaagaaagaggcaataagag	0.050													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213644432	213644433	+	IGR	DEL	TG	-	-	rs141376692		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213644432_213644433delTG								RPS6KC1 (197625 upstream) : PROX1 (516853 downstream)																							tggtgatttttgtgtgtgtgta	0.000													1	5	---	---	---	---	
RAB3GAP2	25782	broad.mit.edu	37	1	220394441	220394442	+	Intron	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220394441_220394442delGA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron|RAB3GAP2_uc010pum.1_Intron	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		TAGTGCATCTGAGACTGGGTTT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	220498852	220498853	+	IGR	DEL	CT	-	-	rs72069202		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220498852_220498853delCT								RAB3GAP2 (53009 upstream) : MARK1 (202715 downstream)																							GCAGGGGTTACTCTCTCAGCAC	0.510													3	3	---	---	---	---	
CNIH3	149111	broad.mit.edu	37	1	224838767	224838770	+	Intron	DEL	ACAC	-	-	rs76720153		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224838767_224838770delACAC	uc001hos.1	+							NM_152495	NP_689708	Q8TBE1	CNIH3_HUMAN	cornichon homolog 3						intracellular signal transduction|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic shaft|postsynaptic membrane					0	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		AGGGACATGGacacacacacacac	0.412													4	3	---	---	---	---	
PARP1	142	broad.mit.edu	37	1	226569949	226569949	+	Intron	DEL	A	-	-	rs75468693		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226569949delA	uc001hqd.3	-							NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1						cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		TTCTCCTGCCAAAAAAATACG	0.478								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					4	2	---	---	---	---	
NUP133	55746	broad.mit.edu	37	1	229593374	229593374	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229593374delT	uc001htn.2	-						uc001hto.1_5'Flank	NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GTTGTTTTAATTTTTTTGTTA	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230157956	230157956	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230157956delA								URB2 (362010 upstream) : GALNT2 (35580 downstream)																							AATAGTAAGCAAAAAAAAAGA	0.294													3	4	---	---	---	---	
GNPAT	8443	broad.mit.edu	37	1	231404693	231404694	+	Intron	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231404693_231404694delTT	uc001hup.3	+						GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TGGAAATGCGTTTTTTTTTAAA	0.149													4	2	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236694189	236694189	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236694189delT	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACCCTGGTACTTAGTTTTACT	0.289													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237679291	237679291	+	Intron	DEL	C	-	-	rs77066700	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237679291delC	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			cctccctcttcttttttctct	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	886809	886810	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:886809_886810insT								TMEM18 (209370 upstream) : SNTG2 (59745 downstream)																							ccaagctttgatttttttaatt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2668292	2668293	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2668292_2668293delCA								MYT1L (333247 upstream) : TSSC1 (524448 downstream)																							CTCATATGCTCACACACACAGG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16384913	16384914	+	IGR	DEL	TC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16384913_16384914delTC								MYCN (297785 upstream) : FAM49A (348987 downstream)																							tttctctctgtctctctctctc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17460257	17460258	+	IGR	INS	-	C	C	rs144320909	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17460257_17460258insC								FAM49A (613161 upstream) : RAD51AP2 (231728 downstream)																							TTACTCATCAACTGAGCACTCA	0.401													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17568514	17568514	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17568514delA								FAM49A (721418 upstream) : RAD51AP2 (123472 downstream)																							GGTCTGAGCCACCAAAGCCCA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18832852	18832853	+	IGR	INS	-	C	C	rs150630393	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18832852_18832853insC								NT5C1B (62014 upstream) : OSR1 (718394 downstream)																							TTGCCTTTAATATGGGCTTTAG	0.455													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19078608	19078609	+	IGR	INS	-	AAAG	AAAG	rs10641825		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19078608_19078609insAAAG								NT5C1B (307770 upstream) : OSR1 (472638 downstream)																							CTTACAGTCTCAAATTATTTTT	0.317													12	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19731307	19731308	+	IGR	DEL	GT	-	-	rs74816574		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19731307_19731308delGT								OSR1 (172935 upstream) : TTC32 (365210 downstream)																							GAGTAATCACGTGTGTGTGTGT	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22170217	22170219	+	IGR	DEL	GAC	-	-	rs149780899		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22170217_22170219delGAC								APOB (903272 upstream) : None (None downstream)																							gcaaccgactgacgacagggttg	0.177													4	5	---	---	---	---	
KLHL29	114818	broad.mit.edu	37	2	23850601	23850607	+	Intron	DEL	GTGTGGC	-	-	rs67522253		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23850601_23850607delGTGTGGC	uc002reg.2	+						KLHL29_uc002ref.2_Intron			Q96CT2	KLH29_HUMAN	RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2						CAGGATTGTTGTGTGGCGTCAAGAGTC	0.527													6	3	---	---	---	---	
DNAJC27	51277	broad.mit.edu	37	2	25170158	25170159	+	3'UTR	INS	-	C	C	rs139553812	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25170158_25170159insC	uc002rft.1	-	7					DNAJC27_uc010ykn.1_3'UTR|DNAJC27_uc002rfu.1_RNA|DNAJC27_uc010eyg.1_3'UTR	NM_016544	NP_057628	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27						protein folding|small GTPase mediated signal transduction		GTP binding|heat shock protein binding|unfolded protein binding			skin(1)	1						CTCTCTTCCCTCCTCCAGGAAC	0.361													3	5	---	---	---	---	
OTOF	9381	broad.mit.edu	37	2	26757552	26757552	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26757552delG	uc002rhk.2	-							NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					acagtcccgtggggcagatag	0.269													4	2	---	---	---	---	
PPP1CB	5500	broad.mit.edu	37	2	29011026	29011026	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29011026delA	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron|SPDYA_uc002rmi.2_Intron	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)					gacaatcctgaaaaaaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34852574	34852575	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34852574_34852575insT								MYADML (899290 upstream) : None (None downstream)																							AAAATAATTCAttttttttttg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36452351	36452352	+	IGR	DEL	GA	-	-	rs113865516	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36452351_36452352delGA								None (None upstream) : CRIM1 (131045 downstream)																							gtgtgtgtgtgagagagagaga	0.257													4	2	---	---	---	---	
STRN	6801	broad.mit.edu	37	2	37119572	37119572	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37119572delA	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153	O43815	STRN_HUMAN	striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)				gttgaaaaagaaaaaaacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38519217	38519218	+	IGR	INS	-	AA	AA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38519217_38519218insAA								C2orf58 (110226 upstream) : ATL2 (2813 downstream)																							CTAATTACCATAAAAATTTGTC	0.446													4	2	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39085574	39085575	+	Intron	DEL	TG	-	-	rs144247886		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39085574_39085575delTG	uc002rrf.2	-						DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				CACATGACTCTGAGACTATTTG	0.327													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41456156	41456156	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41456156delT								SLC8A1 (716581 upstream) : PKDCC (819005 downstream)																							agacacaaactttttttttta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41722884	41722885	+	IGR	INS	-	G	G	rs72530123		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41722884_41722885insG								SLC8A1 (983309 upstream) : PKDCC (552276 downstream)																							ccgctccccaacatcactctta	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42040099	42040100	+	IGR	DEL	TA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42040099_42040100delTA								None (None upstream) : PKDCC (235061 downstream)																							tctttgcatttatgtggaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42133228	42133228	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42133228delT								None (None upstream) : PKDCC (141933 downstream)																							AAACTGTCCATTTTTTTTCTA	0.378													4	2	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44133595	44133595	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44133595delA	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TACAGGATTTAAAAAAAGCAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	44327414	44327414	+	IGR	DEL	T	-	-	rs71880837		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44327414delT								LRPPRC (104270 upstream) : PPM1B (68586 downstream)																							accgggtttgttttttttttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46431791	46431792	+	IGR	DEL	TT	-	-	rs72531853		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46431791_46431792delTT								PRKCE (16663 upstream) : EPAS1 (92771 downstream)																							ttcagtctcatttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48329706	48329707	+	IGR	INS	-	A	A	rs141552997	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48329706_48329707insA								FBXO11 (196892 upstream) : FOXN2 (212088 downstream)																							ggaatttatttaaaagggagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49490064	49490065	+	IGR	INS	-	TCTT	TCTT	rs147929971	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49490064_49490065insTCTT								FSHR (108434 upstream) : NRXN1 (655579 downstream)																							CATTCTCTCTCGTTTTGAAGTG	0.366													2	4	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50167895	50167895	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50167895delA	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc010yon.1_Intron|NRXN1_uc002rxa.3_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AGGTGGACAGAAAAAGCTAAT	0.363													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	51132128	51132128	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51132128delT	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CATTCATTCATTTTTTTTATT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54291601	54291602	+	IGR	INS	-	C	C	rs143914425	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54291601_54291602insC								PSME4 (93624 upstream) : ACYP2 (50808 downstream)																							GGGGGCCATATCTTTTATAAAT	0.153													3	6	---	---	---	---	
CCDC85A	114800	broad.mit.edu	37	2	56603301	56603302	+	Intron	INS	-	T	T	rs144830752	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56603301_56603302insT	uc002rzn.2	+							NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTTGTTTTGAGAATGTGATTCA	0.287													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57297343	57297343	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57297343delT								CCDC85A (684035 upstream) : VRK2 (837443 downstream)																							TGTGAATCACTTTTTTTTTTA	0.274													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60590205	60590206	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60590205_60590206delAC								None (None upstream) : BCL11A (88097 downstream)																							ACACACACGGACACACACACAC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60966341	60966341	+	IGR	DEL	T	-	-	rs36139227		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60966341delT								BCL11A (185708 upstream) : PAPOLG (17042 downstream)																							TTGTGTTAGGTCACACATGTC	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62858713	62858715	+	Intron	DEL	AAA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62858713_62858715delAAA	uc002sbw.1	-											Homo sapiens cDNA clone IMAGE:5271366.																		gtaaatgaataAAAAAAAAaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64969607	64969607	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64969607delT								SERTAD2 (88561 upstream) : SLC1A4 (245972 downstream)																							TTAAGCTAAATTACATATTGC	0.274													4	2	---	---	---	---	
APLF	200558	broad.mit.edu	37	2	68730375	68730376	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68730375_68730376insT	uc002sep.2	+						APLF_uc010fdf.2_Intron	NM_173545	NP_775816	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor						double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2						CCTTTTCCTCATTTTTTTAGCT	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71496099	71496099	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71496099delA								PAIP2B (41866 upstream) : ZNF638 (7624 downstream)																							TCTTCTGTACAAAAAAAAAAG	0.259													2	4	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80201221	80201221	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80201221delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						tctttttgtcattttttttaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81243685	81243686	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81243685_81243686insA								CTNNA2 (367781 upstream) : None (None downstream)																							cagaatggattaaaaaaaaaag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83840189	83840190	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83840189_83840190insT								None (None upstream) : FUNDC2P2 (677616 downstream)																							TGACCACCAAATTTTTTTTCGC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90233322	90233324	+	Intron	DEL	GAT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90233322_90233324delGAT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		CTTGAAGACAGATGATGATGCGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91737719	91737720	+	IGR	DEL	AT	-	-	rs4005136		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91737719_91737720delAT								None (None upstream) : LOC654342 (67472 downstream)																							atctcatctcatatttttgata	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91799030	91799031	+	IGR	INS	-	T	T	rs149067363		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91799030_91799031insT								None (None upstream) : LOC654342 (6161 downstream)																							TTTTACCTGACtttttttaaat	0.025													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91895810	91895810	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91895810delT								LOC654342 (47835 upstream) : GGT8P (67558 downstream)																							TTAAAAGCAGTTTTTTTTGgt	0.139													4	2	---	---	---	---	
RNF149	284996	broad.mit.edu	37	2	101904184	101904184	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101904184delA	uc002taz.1	-						RNF149_uc002tax.1_Intron	NM_173647	NP_775918	Q8NC42	RN149_HUMAN	ring finger protein 149 precursor							integral to membrane	ligase activity|zinc ion binding			ovary(1)|breast(1)	2						TTGTAGGTTTAAACCAGCTAC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104316074	104316074	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104316074delA								TMEM182 (881938 upstream) : LOC150568 (734731 downstream)																							aaaactaatcaaaaaaattaa	0.000													4	2	---	---	---	---	
NCK2	8440	broad.mit.edu	37	2	106366494	106366495	+	Intron	INS	-	ACAC	ACAC	rs72315025		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106366494_106366495insACAC	uc002tdg.2	+						NCK2_uc002tdh.2_Intron	NM_003581	NP_003572	O43639	NCK2_HUMAN	NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2						aaaGCAAacaaacacacacaca	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106878640	106878640	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106878640delG								UXS1 (67845 upstream) : PLGLA (124129 downstream)																							gctgggtcccgaaggatggaa	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114912431	114912432	+	IGR	INS	-	AT	AT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114912431_114912432insAT								ACTR3 (196264 upstream) : DPP10 (287467 downstream)																							ctatctccaccatatatataca	0.084													4	2	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116461817	116461818	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116461817_116461818insA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						CCTAGCCATTTAAAAAAAAAAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118662381	118662382	+	IGR	DEL	TT	-	-	rs34594326		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118662381_118662382delTT								DDX18 (72428 upstream) : CCDC93 (10767 downstream)																							ttctcaactctttgtattttcg	0.168													3	4	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121560945	121560946	+	Intron	INS	-	GT	GT	rs10660529		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121560945_121560946insGT	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				tgggcacagagGGCCTTGTGTG	0.203													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124405673	124405674	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124405673_124405674insA								None (None upstream) : CNTNAP5 (377190 downstream)																							AAGTCACTATGAAAAAAAATAA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127066557	127066558	+	IGR	INS	-	AA	AA	rs144425461	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127066557_127066558insAA								None (None upstream) : GYPC (347126 downstream)																							GTTGCTATGCTAGTTattgccc	0.198													2	4	---	---	---	---	
SAP130	79595	broad.mit.edu	37	2	128772210	128772211	+	Intron	INS	-	A	A	rs141768063	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128772210_128772211insA	uc002tpp.2	-						SAP130_uc002tpn.2_5'Flank|SAP130_uc002tpo.2_Intron|SAP130_uc010fmd.2_Intron|SAP130_uc002tpq.1_Intron	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		agcacctggccTTTTTTTCttt	0.089													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129572352	129572352	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129572352delA								HS6ST1 (496181 upstream) : None (None downstream)																							tggctaagataaaaatggtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131622767	131622767	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131622767delG	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																		AAATTGCCCTGGGCCTTCTAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133034857	133034858	+	IGR	INS	-	AAGA	AAGA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133034857_133034858insAAGA								NCRNA00164 (19315 upstream) : GPR39 (139289 downstream)																							AGCAAGCAAGCAAGCAAATGAT	0.233													2	5	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137523845	137523845	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137523845delG	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATTTATCGGTGGAGTGTCAGG	0.542													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137630505	137630505	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137630505delA	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		cataactgctaaattgcttca	0.000													4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	144870983	144870983	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144870983delA	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		acaacagtggaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146662669	146662670	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146662669_146662670insT								None (None upstream) : PABPC1P2 (681955 downstream)																							tccaacttttctttttttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	149616742	149616742	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149616742delA								EPC2 (71607 upstream) : KIF5C (16077 downstream)																							CCTTTGCCCTAAAActttgtg	0.035													4	2	---	---	---	---	
PKP4	8502	broad.mit.edu	37	2	159326991	159326991	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159326991delT	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						AGTATCTAACTTTTTTGTGGT	0.279										HNSCC(62;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162453128	162453129	+	IGR	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162453128_162453129delTT								TBR1 (171555 upstream) : SLC4A10 (27716 downstream)																							TATGACTGAGTTTTTTTTTTTT	0.267													4	4	---	---	---	---	
FAP	2191	broad.mit.edu	37	2	163050783	163050784	+	Intron	DEL	CA	-	-	rs67094128		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163050783_163050784delCA	uc002ucd.2	-						FAP_uc010fpc.2_Intron|FAP_uc010zct.1_Intron|FAP_uc010fpd.2_Intron	NM_004460	NP_004451	Q12884	SEPR_HUMAN	fibroblast activation protein, alpha subunit						endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3						GGGATGTTACcacacacacaca	0.282													4	2	---	---	---	---	
COBLL1	22837	broad.mit.edu	37	2	165668575	165668575	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165668575delA	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucs.1_Intron|COBLL1_uc002uct.2_Intron	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1											ovary(2)|pancreas(1)	3						TAAGGCTCTGAAAAAAAAAAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	167371435	167371435	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167371435delT								SCN7A (20718 upstream) : XIRP2 (373562 downstream)																							AGTTTTCACCTTTTTTTCTTT	0.368													4	2	---	---	---	---	
XIRP2	129446	broad.mit.edu	37	2	167809234	167809234	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167809234delT	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CTTTACTCTGTTTTTTTTTCA	0.279													2	4	---	---	---	---	
XIRP2	129446	broad.mit.edu	37	2	168066493	168066493	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168066493delT	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Intron|XIRP2_uc010fpq.2_Intron|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TTAACACTACTTCCAGATATG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168429390	168429390	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168429390delA								XIRP2 (313131 upstream) : B3GALT1 (245792 downstream)																							GGTTAGCGGGAAAAAAATATT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168594611	168594612	+	IGR	INS	-	A	A	rs142192960	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168594611_168594612insA								XIRP2 (478352 upstream) : B3GALT1 (80570 downstream)																							GAAAAGAACTTACAATGACAGT	0.391													3	3	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171259144	171259144	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171259144delA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ctactgcttgaaaaaaaaaag	0.239													9	4	---	---	---	---	
TLK1	9874	broad.mit.edu	37	2	171998235	171998235	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171998235delC	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_Intron	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						ccagctccctccccccaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	175126277	175126278	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175126277_175126278insT								OLA1 (12912 upstream) : SP9 (73543 downstream)																							agtacggaggatttttacggca	0.000													4	2	---	---	---	---	
CHN1	1123	broad.mit.edu	37	2	175680318	175680318	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175680318delT	uc002uji.2	-						CHN1_uc010zeq.1_Intron|CHN1_uc002ujj.2_Intron|CHN1_uc002ujg.2_Intron	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)			ggatatttccttttttttttt	0.000			T	TAF15	extraskeletal myxoid chondrosarcoma								3	5	---	---	---	---	
TTC30A	92104	broad.mit.edu	37	2	178484441	178484441	+	5'Flank	DEL	A	-	-	rs116183267	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178484441delA	uc002ulo.2	-							NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			TACTGCCCATAAATCTTTTCT	0.323													4	2	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179534646	179534646	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179534646delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAGAGCACACTTTTTTTTTTC	0.308													8	5	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179557609	179557609	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179557609delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGAAGTTAGTTTTTTTTTTT	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186017003	186017003	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186017003delT								ZNF804A (212791 upstream) : None (None downstream)																							TTTACTTTACTTTTTTTTTTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190132797	190132797	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190132797delT								COL5A2 (88192 upstream) : WDR75 (173362 downstream)																							ATCCACTGTCTTTTTACATTC	0.299													4	2	---	---	---	---	
WDR75	84128	broad.mit.edu	37	2	190315377	190315382	+	Intron	DEL	CCTCTT	-	-	rs72128461		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190315377_190315382delCCTCTT	uc002uql.1	+						WDR75_uc002uqm.1_Intron|WDR75_uc002uqn.1_5'UTR	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75							nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			TTACCATCTCCCTCTTCAAGACAGAA	0.257													10	8	---	---	---	---	
STAT4	6775	broad.mit.edu	37	2	191974034	191974035	+	Intron	INS	-	T	T	rs138988001	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191974034_191974035insT	uc002usm.1	-						STAT4_uc002usn.1_Intron|STAT4_uc002uso.2_Intron|STAT4_uc002usp.3_Intron	NM_003151	NP_003142	Q14765	STAT4_HUMAN	signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			tttgttttttgttttttttttA	0.248													4	2	---	---	---	---	
MYO1B	4430	broad.mit.edu	37	2	192229249	192229250	+	Intron	DEL	GT	-	-	rs66471334		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192229249_192229250delGT	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			ctagcccgtggtgtatgatcag	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200461127	200461127	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200461127delC								FLJ32063 (119469 upstream) : C2orf69 (314852 downstream)																							ttttaagccaccagtgtgtgg	0.100													4	2	---	---	---	---	
C2orf60	129450	broad.mit.edu	37	2	200795492	200795493	+	3'UTR	INS	-	AGAA	AGAA	rs149629914	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200795492_200795493insAGAA	uc002uvi.3	-	8					C2orf60_uc002uvj.3_3'UTR|C2orf60_uc002uvk.3_RNA|C2orf60_uc010fss.2_3'UTR	NM_001039693	NP_001034782	A2RUC4	TYW5_HUMAN	hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0						GCACATTAGGGAGAATGGAGAA	0.381													3	3	---	---	---	---	
ALS2CR12	130540	broad.mit.edu	37	2	202153880	202153881	+	Intron	INS	-	C	C	rs142645837	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202153880_202153881insC	uc010ftg.2	-						ALS2CR12_uc002uya.3_Intron|ALS2CR12_uc010fth.2_Intron	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)						regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						GGATTTAAAAACCACCCTCAGT	0.436													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203635685	203635688	+	IGR	DEL	CTTT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203635685_203635688delCTTT								FAM117B (1206 upstream) : ICA1L (2185 downstream)																							AGTTTTCTCCCTTTCTTTCTTAGT	0.373													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206259934	206259939	+	Intron	DEL	ACTTAT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206259934_206259939delACTTAT	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ttgtacagacacttatacttacccac	0.000													5	6	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206421089	206421089	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206421089delA	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ACACAGAGAGAAAATGCTCCA	0.458													4	2	---	---	---	---	
MDH1B	130752	broad.mit.edu	37	2	207617274	207617274	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207617274delG	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		GTAGGAGGGTGGGGAGGGTGG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210121930	210121931	+	IGR	INS	-	A	A	rs143600015	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210121930_210121931insA								PTH2R (417112 upstream) : MAP2 (166840 downstream)																							TAAATAGACTCAGAGAATATTT	0.297													4	2	---	---	---	---	
MARCH4	57574	broad.mit.edu	37	2	217147011	217147012	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217147011_217147012delAC	uc002vgb.2	-							NM_020814	NP_065865	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TGTGTGTGCAacacacacacac	0.446													4	2	---	---	---	---	
DIRC3	729582	broad.mit.edu	37	2	218225253	218225254	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218225253_218225254insA	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0						CTTCGTTGACTAAAACCTTTCT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221135810	221135811	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221135810_221135811insT								SLC4A3 (629109 upstream) : None (None downstream)																							tttcttttttcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221626326	221626326	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221626326delT								None (None upstream) : EPHA4 (656423 downstream)																							ccgatttcacttttttttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222795773	222795773	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222795773delG								EPHA4 (356851 upstream) : PAX3 (268834 downstream)																							TGGAGAGTCTGAACAAAGCAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	223871545	223871545	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223871545delA								ACSL3 (62191 upstream) : KCNE4 (45317 downstream)																							tcatgggatcaaagactgacg	0.109													4	2	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225783167	225783168	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225783167_225783168delTG	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002vod.1_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		ggtgtgtgtatgtgttatgtga	0.045													2	4	---	---	---	---	
RHBDD1	84236	broad.mit.edu	37	2	227715898	227715898	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227715898delT	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GACGCTAAACTTTTTTCCATC	0.423													4	2	---	---	---	---	
RHBDD1	84236	broad.mit.edu	37	2	227773299	227773300	+	Intron	DEL	AC	-	-	rs10559846		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227773299_227773300delAC	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		ATTTTCCACTacacacacacac	0.371													10	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228641521	228641521	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228641521delG								SLC19A3 (58776 upstream) : CCL20 (37037 downstream)																							cctccactgtgggcaacttac	0.000													4	2	---	---	---	---	
SP140	11262	broad.mit.edu	37	2	231089249	231089250	+	5'Flank	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231089249_231089250delGA	uc002vql.2	+						SP140_uc010zma.1_5'Flank|SP140_uc002vqj.2_5'Flank|SP140_uc002vqk.2_5'Flank|SP140_uc002vqn.2_5'Flank|SP140_uc002vqm.2_5'Flank|SP140_uc010fxl.2_5'Flank	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1						defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		agagagagaggagagagagaga	0.178													3	3	---	---	---	---	
EFHD1	80303	broad.mit.edu	37	2	233505168	233505170	+	Intron	DEL	ATG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233505168_233505170delATG	uc002vtc.2	+						EFHD1_uc010fyf.2_Intron	NM_025202	NP_079478	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1								calcium ion binding|protein binding				0		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		GTACCATATCATGATGATGATGA	0.438													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238581823	238581823	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238581823delA	uc002vxc.2	+							NM_001137550	NP_001131022	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TGTTTCAGTGAAAAAAAAATA	0.443											OREG0015331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240146192	240146192	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240146192delG	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc002vyl.1_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ctcctgaccaggtcttcggcc	0.080													4	2	---	---	---	---	
ANKMY1	51281	broad.mit.edu	37	2	241437495	241437495	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241437495delC	uc002vyz.1	-						ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Intron|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		cttgcaggaaccctggccagg	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5344590	5344590	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5344590delT								EDEM1 (82941 upstream) : None (None downstream)																							TGTCTATGACTAAGATTAGGA	0.318													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191569	10191569	+	Frame_Shift_Del	DEL	C	-	-	rs5030824		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191569delC	uc003bvc.2	+	3	775	c.562delC	c.(562-564)CTGfs	p.L188fs	VHL_uc003bvd.2_Frame_Shift_Del_p.L147fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	188			L -> Q (in VHLD; type I).|L -> P (in VHLD; type I-II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L188fs*14(2)|p.L188P(2)|p.D187_L188del(2)|p.L188Q(2)|p.L188V(1)|p.D187_N193del(1)|p.E186fs*14(1)|p.Y185fs*11(1)|p.L188R(1)|p.D187fs*14(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CTACGAAGATCTGGAAGACCA	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				69	55	---	---	---	---	
SLC6A11	6538	broad.mit.edu	37	3	10885049	10885049	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10885049delT	uc003bvz.2	+							NM_014229	NP_055044	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)		cctttcctgctttttccttct	0.224													4	2	---	---	---	---	
LOC152024	152024	broad.mit.edu	37	3	24138195	24138196	+	RNA	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24138195_24138196insT	uc003ccu.3	-	4		c.2552_2553insA								Homo sapiens hypothetical protein LOC152024, mRNA (cDNA clone IMAGE:4829078).												0						GTTTTTTCCTGTTTTTTTTGAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35347191	35347191	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35347191delC								None (None upstream) : ARPP21 (333890 downstream)																							TCATTTTTTTCCCTATAATAT	0.378													4	2	---	---	---	---	
TRANK1	9881	broad.mit.edu	37	3	36879646	36879647	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36879646_36879647delAC	uc003cgj.2	-							NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1						DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2						TAacacacaaacacacacacac	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	37016013	37016013	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37016013delT								TRANK1 (113602 upstream) : EPM2AIP1 (11345 downstream)																							CCTTCAACAAttttttttttt	0.159													5	3	---	---	---	---	
MLH1	4292	broad.mit.edu	37	3	37082032	37082033	+	Intron	INS	-	TTTG	TTTG	rs147362928	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37082032_37082033insTTTG	uc003cgl.2	+						MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Intron|MLH1_uc010hge.2_Intron|MLH1_uc003cgn.3_Intron|MLH1_uc011ayc.1_Intron|MLH1_uc011ayd.1_Intron|MLH1_uc003cgo.2_Intron|MLH1_uc010hgk.2_Intron|MLH1_uc010hgn.2_Intron|MLH1_uc010hgm.2_Intron|MLH1_uc010hgo.2_Intron|MLH1_uc010hgp.2_5'Flank|MLH1_uc010hgq.2_5'Flank	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1						mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						catgcagggGTtttgtttgttt	0.168		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				2	5	---	---	---	---	
ITGA9	3680	broad.mit.edu	37	3	37789675	37789675	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37789675delT	uc003chd.2	+							NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CATGGAGTTGTTTTTTTGGCC	0.403													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41654564	41654564	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41654564delC	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GCATGCAGGGCCCCACACAAT	0.443													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41763727	41763727	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41763727delA	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AGAGAAGGCTAACACTCTGTT	0.423													4	2	---	---	---	---	
CYP8B1	1582	broad.mit.edu	37	3	42909495	42909495	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42909495delA	uc010hif.2	-						CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,						bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		aagtatctgtaaaatgcatgG	0.249													6	3	---	---	---	---	
ZDHHC3	51304	broad.mit.edu	37	3	44968020	44968020	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44968020delT	uc003cod.2	-	8					ZDHHC3_uc003cog.2_3'UTR|ZDHHC3_uc011bad.1_Intron	NM_016598	NP_057682	Q9NYG2	ZDHC3_HUMAN	zinc finger, DHHC-type containing 3 isoform 2							Golgi membrane|integral to membrane	zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)		ATGTGGGGACTTTTTTTTTTC	0.338													4	4	---	---	---	---	
LARS2	23395	broad.mit.edu	37	3	45489880	45489880	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45489880delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	TTAGTCTTGGTTTTTTTCCAG	0.323													4	2	---	---	---	---	
MAP4	4134	broad.mit.edu	37	3	47920988	47920988	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47920988delT	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc011bbe.1_Intron|MAP4_uc003cry.2_Intron|MAP4_uc003csa.3_Intron|MAP4_uc003crz.3_Intron|MAP4_uc003csd.2_Intron|MAP4_uc003cse.1_Intron	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		ctgtgtacccttttacccagt	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	51967046	51967047	+	IGR	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51967046_51967047insC								IQCF1 (29660 upstream) : RRP9 (399 downstream)																							CCTGACCCCCACACCTCACGGC	0.579													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	61319671	61319671	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61319671delT								FHIT (82538 upstream) : PTPRG (227572 downstream)																							TTTTCATATCTTACCATCTTT	0.259													4	2	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71021129	71021129	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71021129delA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron|FOXP1_uc003dor.1_3'UTR	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCAACAGCAGAAAAAAAAAAC	0.443			T	PAX5	ALL								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	82751289	82751289	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82751289delG								GBE1 (940339 upstream) : None (None downstream)																							ggtgtgagatggtatctcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	84462325	84462325	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84462325delA								None (None upstream) : CADM2 (545808 downstream)																							ccaactaaggaagtctctcca	0.000													4	2	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85127838	85127838	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85127838delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		tctttctttcttttttttttC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	89052736	89052740	+	IGR	DEL	AAACT	-	-	rs79992092		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89052736_89052740delAAACT								C3orf38 (845623 upstream) : EPHA3 (103934 downstream)																							ttaaaaagaaaaactaaacaacaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	95122928	95122929	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95122928_95122929delAC								LOC255025 (227849 upstream) : None (None downstream)																							acacacacaaacacacacacac	0.312													4	2	---	---	---	---	
TMEM45A	55076	broad.mit.edu	37	3	100245542	100245543	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100245542_100245543insA	uc003dtz.1	+						TMEM45A_uc003dua.1_Intron	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A							integral to membrane				skin(2)|ovary(1)	3						AATTATCTGCCAAAAAAATTCT	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105049380	105049381	+	IGR	DEL	TC	-	-	rs79826398	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105049380_105049381delTC								None (None upstream) : ALCAM (36332 downstream)																							ccagttttgttctttttgctca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110722656	110722656	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110722656delT								None (None upstream) : PVRL3 (68209 downstream)																							accagcaacctacagaatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110766890	110766890	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110766890delT								None (None upstream) : PVRL3 (23975 downstream)																							CAAATGGTACTTTTCCCTACC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112816344	112816345	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112816344_112816345insT								C3orf17 (77789 upstream) : BOC (114067 downstream)																							CTTTTCCTTACTTTTTTTTTTC	0.327													4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115366220	115366220	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115366220delG	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		taatagcagtgggaactaaaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116625053	116625053	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116625053delT								LOC285194 (189168 upstream) : None (None downstream)																							AAATGCCTACTTTTAGAAGGA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117969038	117969038	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117969038delT								None (None upstream) : IGSF11 (650443 downstream)																							AAAGCCAAGGTTTTTTTTTCC	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120255028	120255029	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120255028_120255029insA								FSTL1 (85110 upstream) : NDUFB4 (60099 downstream)																							agactccatttaaaaaaaaaga	0.000													4	2	---	---	---	---	
DTX3L	151636	broad.mit.edu	37	3	122290765	122290765	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122290765delT	uc003efk.2	+	5					DTX3L_uc010hrj.2_3'UTR	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like						histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)	4				GBM - Glioblastoma multiforme(114;0.0459)		GGAGTGATACttttttttttg	0.159													6	3	---	---	---	---	
LOC100129550	100129550	broad.mit.edu	37	3	122608187	122608187	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122608187delT	uc010hrn.2	+	1						NR_024618				Homo sapiens cDNA FLJ45384 fis, clone BRHIP3021987.												0						TTCATTCATGTTTTTTTTAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125451532	125451537	+	IGR	DEL	AACAAA	-	-	rs112932427		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125451532_125451537delAACAAA								OSBPL11 (137151 upstream) : MIR548I1 (57710 downstream)																							atctcaaaacaacaaaaacaaaaaca	0.039													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126385091	126385091	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126385091delC	uc003eje.1	+	3	347	c.103delC	c.(103-105)CTTfs	p.L35fs						RecName: Full=Putative uncharacterized protein C3orf46;																		GGTGCTGCTGCTTGGAGCCGT	0.607													10	7	---	---	---	---	
COL29A1	256076	broad.mit.edu	37	3	130132669	130132669	+	Intron	DEL	C	-	-	rs71639083		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130132669delC	uc010htj.1	+						COL29A1_uc010hti.1_Intron	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0						AAATATTGTGCATTTGACTGC	0.423													10	6	---	---	---	---	
CEP63	80254	broad.mit.edu	37	3	134229815	134229816	+	Intron	INS	-	T	T	rs113047401		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134229815_134229816insT	uc003eqo.1	+						CEP63_uc003eql.1_Intron|CEP63_uc003eqm.2_Intron|CEP63_uc003eqn.1_Intron	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a						cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1						TCCACCTTTGATTTTTTTTTTT	0.470													9	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134404429	134404429	+	IGR	DEL	A	-	-	rs35224201		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134404429delA								KY (33951 upstream) : EPHB1 (109831 downstream)																							TGGTTTGGGGACAGAAGAGCT	0.453													1	5	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140243340	140243340	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140243340delA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						attgtgagggacttcaacagc	0.139										HNSCC(16;0.037)			4	2	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141138830	141138830	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141138830delA	uc003etw.2	+						ZBTB38_uc010hun.2_Intron|ZBTB38_uc010huo.2_Intron|ZBTB38_uc003ety.2_Intron	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						actccgtctcaaaaaaaaGTG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144565387	144565387	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144565387delA								C3orf58 (854178 upstream) : None (None downstream)																							AGAGAAGCATAAAAGGAAGCA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147462720	147462721	+	IGR	INS	-	A	A	rs141049785	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147462720_147462721insA								ZIC1 (328216 upstream) : AGTR1 (952937 downstream)																							acttacaagagaaaaaaaaaat	0.000													2	4	---	---	---	---	
HLTF	6596	broad.mit.edu	37	3	148767867	148767867	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148767867delA	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			GCAAAAAGTCAAAAAAAAAAA	0.318													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157709974	157709975	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157709974_157709975insT								C3orf55 (390955 upstream) : SHOX2 (103826 downstream)																							tcagagccttcttttttttttt	0.000													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	159361060	159361060	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159361060delG	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			ttctcaatgaggtagaatttg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162215663	162215663	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162215663delA								OTOL1 (993935 upstream) : None (None downstream)																							AGGACCACCTAAAAAATCAGA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162953646	162953646	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162953646delC	uc003feh.2	-											Homo sapiens hypothetical protein LOC647107, mRNA (cDNA clone IMAGE:5103171), partial cds.																		gaggcatttgccttaatgggc	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163998327	163998328	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163998327_163998328insA								MIR1263 (108983 upstream) : MIR720 (60801 downstream)																							tcaatctgaagaaaaaaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165342049	165342050	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165342049_165342050insA								SLITRK3 (427580 upstream) : BCHE (148644 downstream)																							tgcagggctgtatcaaaatgaa	0.000													4	2	---	---	---	---	
WDR49	151790	broad.mit.edu	37	3	167369027	167369028	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167369027_167369028insA	uc003fev.1	-						WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49											large_intestine(1)|ovary(1)|skin(1)	3						ATCTGTGTAAGAAAAAAAAAAT	0.376													4	3	---	---	---	---	
LRRC34	151827	broad.mit.edu	37	3	169515506	169515506	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169515506delA	uc003ffx.2	-						LRRC34_uc003ffy.2_Intron|LRRC34_uc011bpn.1_Intron|LRRC34_uc003ffz.2_Intron|LRRC34_uc003fga.3_Intron	NM_153353	NP_699184	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34												0	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			AGGTACTTTGAAAAAAACTTT	0.179													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170543760	170543760	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170543760delC	uc011bpt.1	+							NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ACTACACATTCCCCCGCCTCC	0.403													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175185159	175185166	+	Intron	DEL	ACCTTCAA	-	-	rs76733066		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175185159_175185166delACCTTCAA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		ACTACGTATGACCTTCAAATATCTTACC	0.351													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176511584	176511587	+	IGR	DEL	GAGA	-	-	rs72312837		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176511584_176511587delGAGA								NAALADL2 (988158 upstream) : TBL1XR1 (226956 downstream)																							CAAGACCCTGGAGAGAGAAACCAG	0.451													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177410096	177410096	+	IGR	DEL	G	-	-	rs76713587		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177410096delG								TBL1XR1 (495048 upstream) : KCNMB2 (844128 downstream)																							TGGGCAGCTAGGTGAGGTGTT	0.109													4	3	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178320362	178320362	+	Intron	DEL	G	-	-	rs68166687		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178320362delG	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			gttcgggggtgggggggagga	0.000													3	5	---	---	---	---	
GNB4	59345	broad.mit.edu	37	3	179119234	179119236	+	Intron	DEL	AAT	-	-	rs74384746		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179119234_179119236delAAT	uc003fjv.3	-						GNB4_uc003fju.3_Intron	NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			TCAGttaaaaaataataataatt	0.271													17	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182729727	182729727	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182729727delA								DCUN1D1 (31401 upstream) : MCCC1 (3281 downstream)																							AATGGGTCTTATCCAACAGAG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184351413	184351414	+	IGR	INS	-	TG	TG	rs145001857	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184351413_184351414insTG								EPHB3 (51218 upstream) : MAGEF1 (76742 downstream)																							gtgtgtgcatatgtgtgtgtgt	0.450													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187674433	187674434	+	IGR	INS	-	AC	AC	rs140849237	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187674433_187674434insAC								BCL6 (210958 upstream) : LPP (197285 downstream)																							catgagccactacacttggccT	0.208													3	4	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192034062	192034062	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192034062delA	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ctacctacacaaaaaaaaatc	0.010													4	3	---	---	---	---	
ATP13A5	344905	broad.mit.edu	37	3	192993372	192993373	+	Intron	INS	-	C	C	rs141138095		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192993372_192993373insC	uc011bsq.1	-							NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTCCCCTCAGACTGAAATGGTA	0.416													4	2	---	---	---	---	
MUC20	200958	broad.mit.edu	37	3	195445330	195445331	+	5'Flank	INS	-	AAAC	AAAC	rs139697185	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195445330_195445331insAAAC	uc010hzo.2	+							NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ctaaacgaaaacaaCAAATCAC	0.099													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197194709	197194709	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197194709delT								DLG1 (168566 upstream) : BDH1 (41946 downstream)																							TATGAACTGAtttttttttgt	0.159													4	2	---	---	---	---	
IQCG	84223	broad.mit.edu	37	3	197681208	197681208	+	Intron	DEL	T	-	-	rs112330576		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197681208delT	uc003fyp.2	-						RPL35A_uc003fyr.2_Intron|RPL35A_uc003fys.2_Intron	NM_032263	NP_115639	Q9H095	IQCG_HUMAN	IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		ttgttttttgttttttttttg	0.149													4	2	---	---	---	---	
LMLN	89782	broad.mit.edu	37	3	197730355	197730355	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197730355delA	uc011buo.1	+						LMLN_uc003fyt.2_Intron|LMLN_uc010iar.2_Intron|LMLN_uc010ias.2_Intron|LMLN_uc003fyu.2_Intron	NM_033029	NP_149018	Q96KR4	LMLN_HUMAN	leishmanolysin-like isoform 2						cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		ATTCAGTATCAAAAAAAAGGC	0.199													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	16484	16485	+	IGR	INS	-	GC	GC			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16484_16485insGC								None (None upstream) : ZNF595 (36742 downstream)																							tgtgtgtgtgtgtgtgtCTTCC	0.144													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	67784	67785	+	Intron	DEL	TT	-	-	rs146895580		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67784_67785delTT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ggattgCttctttttttttttt	0.005													6	3	---	---	---	---	
ZNF721	170960	broad.mit.edu	37	4	459571	459572	+	Intron	INS	-	AA	AA	rs150785605	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:459571_459572insAA	uc003gag.2	-						ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc003gae.2_Intron|ABCA11P_uc010ibd.1_Intron|ZNF721_uc003gaf.3_Intron|ZNF721_uc010ibe.2_Intron	NM_133474	NP_597731	D9N162	D9N162_HUMAN	zinc finger protein 721							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						ttggaaattacaaaaaaaaaac	0.025													4	2	---	---	---	---	
FAM53A	152877	broad.mit.edu	37	4	1653956	1653957	+	Intron	INS	-	AC	AC	rs142090008		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1653956_1653957insAC	uc011bve.1	-						FAM53A_uc010ibw.2_Intron	NM_001013622	NP_001013644	Q6NSI3	FA53A_HUMAN	dorsal neural-tube nuclear protein							nucleus					0		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			ccacacacactagtcgcacaca	0.000													5	4	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2271922	2271923	+	3'UTR	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2271922_2271923delGA	uc003gex.1	-	13					ZFYVE28_uc011bvk.1_3'UTR|ZFYVE28_uc011bvl.1_3'UTR|ZFYVE28_uc003gew.1_3'UTR	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						GAAGGATGGTGAGGGGTGAGGG	0.584													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2311479	2311480	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2311479_2311480delAC	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gew.1_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						acaacagacaacacacacacag	0.000													4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3231147	3231148	+	Intron	DEL	AG	-	-	rs116275868	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3231147_3231148delAG	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGCcacacacagcacacaacca	0.163													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3604323	3604325	+	IGR	DEL	CTG	-	-	rs10571400		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3604323_3604325delCTG								LRPAP1 (70099 upstream) : ADRA2C (163750 downstream)																							GGTAGTGAGACTGCTGCTGGGTC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	5504993	5504993	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5504993delC								STK32B (2268 upstream) : C4orf6 (21890 downstream)																							CTTCTTGTGACCCTCCTCCCA	0.313													4	2	---	---	---	---	
CRMP1	1400	broad.mit.edu	37	4	5868824	5868824	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5868824delT	uc003gip.2	-						CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Intron|CRMP1_uc003gir.2_Intron|CRMP1_uc003gis.2_Intron	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)		caagctgcacttttttttcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9117904	9117904	+	IGR	DEL	C	-	-	rs1811572	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9117904delC								LOC650293 (165778 upstream) : USP17 (242205 downstream)																							ttttgagacacggcctcgctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10235309	10235310	+	IGR	INS	-	T	T	rs149862997	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10235309_10235310insT								WDR1 (116736 upstream) : ZNF518B (206195 downstream)																							tttcccttagcctttttctgtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12871269	12871271	+	IGR	DEL	AAC	-	-	rs79250820		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12871269_12871271delAAC								None (None upstream) : HSP90AB2P (463766 downstream)																							GTCTCAAAATAACAACACCATAT	0.241													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14277270	14277270	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14277270delC								BOD1L (647942 upstream) : CPEB2 (728252 downstream)																							aatggattttcccaggaaata	0.060													4	2	---	---	---	---	
TAPT1	202018	broad.mit.edu	37	4	16227341	16227341	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16227341delT	uc010ied.1	-						FLJ39653_uc011bxf.1_5'Flank|FLJ39653_uc011bxg.1_5'Flank|TAPT1_uc011bxe.1_Intron|TAPT1_uc003gow.3_Intron|FLJ39653_uc003gox.1_5'Flank	NM_153365	NP_699196	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0						AGATGCAACATTTTATGGAGT	0.358													4	2	---	---	---	---	
MED28	80306	broad.mit.edu	37	4	17622991	17622991	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17622991delT	uc003gpi.1	+						MED28_uc003gpj.2_Intron	NM_025205	NP_079481	Q9H204	MED28_HUMAN	mediator complex subunit 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0						TATCTCTCTCTTTTTTTTTTT	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18243830	18243830	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18243830delT								LCORL (220445 upstream) : None (None downstream)																							tgtatatatatttttttgttt	0.000													6	3	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21229107	21229107	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21229107delT	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				CCTCCAAGAGTTTTTTTGAAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24802556	24802556	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24802556delT								SOD3 (90 upstream) : CCDC149 (5184 downstream)																							ttcgttttccttttttttctt	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25960139	25960141	+	IGR	DEL	GGC	-	-	rs138493868		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25960139_25960141delGGC								C4orf52 (28639 upstream) : RBPJ (361191 downstream)																							tgaggagaatggcagacaactgc	0.089													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	30566125	30566125	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30566125delT								None (None upstream) : PCDH7 (155912 downstream)																							tgagcaaggatttttttttaa	0.000													4	2	---	---	---	---	
PCDH7	5099	broad.mit.edu	37	4	30975868	30975869	+	Intron	INS	-	TTCCT	TTCCT	rs148370231	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30975868_30975869insTTCCT	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						ttctttctttcttcctttcctt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34179155	34179155	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34179155delT								None (None upstream) : None (None downstream)																							TGCAATTATCTTTTTTTTTTG	0.358													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38392430	38392431	+	IGR	DEL	CT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38392430_38392431delCT								TBC1D1 (251637 upstream) : FLJ13197 (221891 downstream)																							ccccttggcactctctctctcc	0.000													4	2	---	---	---	---	
KLHL5	51088	broad.mit.edu	37	4	39120478	39120478	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39120478delT	uc003gts.2	+						KLHL5_uc003gtp.2_Intron|KLHL5_uc003gtq.2_Intron|KLHL5_uc003gtt.2_Intron	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1							cytoplasm|cytoskeleton	actin binding			ovary(1)	1						GTACAGGGAGTTTTTAAGTGA	0.398													4	2	---	---	---	---	
N4BP2	55728	broad.mit.edu	37	4	40115854	40115855	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40115854_40115855insT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron|N4BP2_uc010ifr.2_Intron	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						TGGTTAGGCTATTTTTTTTTTC	0.243													4	2	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40454187	40454187	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40454187delA	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron|RBM47_uc003gvg.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						actccatctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	41229908	41229908	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41229908delT								APBB2 (13273 upstream) : UCHL1 (28990 downstream)																							AAGGGGTAGGTTAGAGGGAAA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	41837815	41837815	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41837815delC								PHOX2B (86828 upstream) : TMEM33 (99322 downstream)																							CCCTCACCATCCCACTGTGCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43854865	43854865	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43854865delT								GRXCR1 (822192 upstream) : KCTD8 (321057 downstream)																							TCATGACCTATTTTTTCCCAC	0.229													4	2	---	---	---	---	
COX7B2	170712	broad.mit.edu	37	4	46778411	46778412	+	Intron	DEL	GT	-	-	rs34113475		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46778411_46778412delGT	uc003gxf.2	-						COX7B2_uc010ige.2_Intron	NM_130902	NP_570972	Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2 precursor							integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TAGTTTCAGAgtgtgtgtgtgt	0.267													5	3	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47280632	47280633	+	Intron	INS	-	T	T	rs142132373	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47280632_47280633insT	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	CAAGCCCTAGGTTTTTGCCTTT	0.421													3	3	---	---	---	---	
TEC	7006	broad.mit.edu	37	4	48178432	48178432	+	Intron	DEL	C	-	-	rs35859358		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48178432delC	uc003gxz.2	-							NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						TTCTGTCCTGCCCCCCCAAAA	0.194													6	3	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48596196	48596201	+	Intron	DEL	TATAAG	-	-	rs78630567		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48596196_48596201delTATAAG	uc003gyh.1	-						FRYL_uc003gyk.2_Intron	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						aatacatgattataagtATATTATTT	0.087													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49247788	49247788	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49247788delA								CWH43 (183695 upstream) : None (None downstream)																							CACAATATGTAAAAAAAAGTT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49266139	49266140	+	IGR	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49266139_49266140delAG								CWH43 (202046 upstream) : None (None downstream)																							tgggtgaaacagagactctgtg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49274524	49274525	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49274524_49274525insA								CWH43 (210431 upstream) : None (None downstream)																							cagcaagattgaaatggtaatt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53109634	53109634	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53109634delG								SPATA18 (146177 upstream) : USP46 (347495 downstream)																							CTCCATGTGAGGGACATAAGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59577033	59577033	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59577033delT								None (None upstream) : None (None downstream)																							CCCATCGTCATTCTACTGTGG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60265277	60265278	+	IGR	INS	-	C	C	rs141972176		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60265277_60265278insC								None (None upstream) : None (None downstream)																							TGTGCTGTGCAAAGGTAAGCAG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60265279	60265280	+	IGR	INS	-	ACACT	ACACT	rs140129401	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60265279_60265280insACACT								None (None upstream) : None (None downstream)																							TGCTGTGCAAAGGTAAGCAGTG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70056779	70056779	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70056779delA								UGT2B7 (78075 upstream) : UGT2B11 (9274 downstream)																							taggttaggtaaaaacctcat	0.000													4	2	---	---	---	---	
RUFY3	22902	broad.mit.edu	37	4	71634619	71634620	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71634619_71634620delAC	uc003hfq.2	+						RUFY3_uc003hfp.3_Intron|RUFY3_uc011cax.1_Intron|RUFY3_uc003hfr.2_Intron|RUFY3_uc011cay.1_Intron	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			acatacatatacacacacacac	0.139													4	3	---	---	---	---	
AFM	173	broad.mit.edu	37	4	74361402	74361402	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74361402delT	uc003hhb.2	+							NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor						vitamin transport		vitamin E binding			ovary(2)|central_nervous_system(1)	3	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TAAATTTACATTTTTCTTTAT	0.284													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79089663	79089664	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79089663_79089664insT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						AAAACTTCAAATTTTTTTTTTC	0.386													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79440334	79440337	+	Intron	DEL	TAAG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79440334_79440337delTAAG	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						tttttttAAATAAGTAAGTGCAAT	0.176													7	12	---	---	---	---	
BMP2K	55589	broad.mit.edu	37	4	79704620	79704620	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79704620delA	uc003hlk.2	+						BMP2K_uc010ijl.1_Intron|BMP2K_uc003hlj.2_Intron	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						TCAGTATTCCAAAAAAACAGT	0.239													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81377787	81377787	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81377787delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						ggatacatggaggattggaat	0.000													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81472079	81472079	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81472079delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						TCCTGAAAGTAATGGGTTTTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	86362524	86362524	+	IGR	DEL	T	-	-	rs111926140	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86362524delT								C4orf12 (434356 upstream) : ARHGAP24 (33760 downstream)																							TGAGTTGCAGTTTTTTTTTAC	0.284													4	2	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87628406	87628406	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87628406delA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GAACAGATACAACTAATTTCT	0.358													4	2	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87673077	87673078	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87673077_87673078delTG	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATtgtatgtatgtgtgtgtgtg	0.257													4	2	---	---	---	---	
IBSP	3381	broad.mit.edu	37	4	88733232	88733233	+	3'UTR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88733232_88733233insT	uc003hqx.3	+	7						NM_004967	NP_004958	P21815	SIAL_HUMAN	integrin-binding sialoprotein precursor						biomineral tissue development|cell adhesion|ossification						0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		CTTCTTGTCCCTTTTTTTTCTG	0.351													4	2	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	93481781	93481781	+	Intron	DEL	C	-	-	rs111708737		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93481781delC	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	CCTGGAACATCCTCTCATTTC	0.338													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97940768	97940768	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97940768delG								None (None upstream) : C4orf37 (539266 downstream)																							AAAGAAATATGGGCCTCAGGT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	101720779	101720779	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101720779delT								EMCN (281529 upstream) : PPP3CA (223808 downstream)																							TTCAATGTTGTTTTTTTTTTT	0.323													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104453499	104453499	+	IGR	DEL	C	-	-	rs34788610		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104453499delC								CENPE (333933 upstream) : TACR3 (57126 downstream)																							CCTTACATGGCCCTAAAGCAT	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	116169504	116169504	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116169504delT								NDST4 (134472 upstream) : None (None downstream)																							AAAAAATACATTTTTTTTACC	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117258278	117258278	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117258278delT								MIR1973 (37354 upstream) : TRAM1L1 (746438 downstream)																							tttatatttgtttttttttct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117997165	117997167	+	IGR	DEL	CTT	-	-	rs71593943		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117997165_117997167delCTT								MIR1973 (776241 upstream) : TRAM1L1 (7549 downstream)																							CCCCTTTCTCCTTCTCTCCACCA	0.394													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118162731	118162732	+	IGR	INS	-	ACA	ACA	rs141611156	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118162731_118162732insACA								TRAM1L1 (155995 upstream) : NDST3 (792041 downstream)																							GAGCAGGTGGTACAAGTATACA	0.287													1	5	---	---	---	---	
SYNPO2	171024	broad.mit.edu	37	4	119913845	119913846	+	Intron	INS	-	ACCT	ACCT	rs144881851	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119913845_119913846insACCT	uc003icm.3	+						SYNPO2_uc010ina.2_Intron|SYNPO2_uc010inb.2_Intron|SYNPO2_uc011cgh.1_Intron	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b							nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2						CCCTCTCCATGACCTACTCACC	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122444025	122444025	+	IGR	DEL	T	-	-	rs35375893		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122444025delT								QRFPR (141844 upstream) : ANXA5 (145128 downstream)																							aactatttcattttttttttt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128404746	128404746	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128404746delA								None (None upstream) : INTU (149374 downstream)																							GAAAAATATGAAAAAAAAAAA	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132771993	132771993	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132771993delA								None (None upstream) : None (None downstream)																							atttttgcataaatgctatct	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	133639617	133639617	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133639617delT								None (None upstream) : PCDH10 (430853 downstream)																							TCCTTTTTAATTTTTTTCTAT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	133798328	133798337	+	IGR	DEL	AGAGAGAGAG	-	-	rs13122045		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133798328_133798337delAGAGAGAGAG								None (None upstream) : PCDH10 (272133 downstream)																							actaacaaaaagagagagagagagagagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134893264	134893264	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134893264delT								PCDH10 (780533 upstream) : PABPC4L (224227 downstream)																							cctaattgaatgctaagatct	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142708325	142708325	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142708325delA								IL15 (53714 upstream) : INPP4B (240859 downstream)																							ccactctgggattcctgacac	0.085													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148820460	148820461	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148820460_148820461delGT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		agcagctggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	149811002	149811002	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149811002delG								NR3C2 (447359 upstream) : None (None downstream)																							ACAAAAAGCtggggggttaaa	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158301574	158301574	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158301574delG								GRIA2 (14350 upstream) : LOC340017 (192068 downstream)																							TATTTTAATTGGGCTTTAATA	0.294													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164869716	164869716	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164869716delA	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GATCGAGGATAGGTTGTTTTT	0.358													4	2	---	---	---	---	
CPE	1363	broad.mit.edu	37	4	166414988	166414988	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166414988delT	uc003irg.3	+							NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCCATTTCCATTTCCCCAGTT	0.378											OREG0016391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166794335	166794335	+	5'Flank	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166794335delT	uc003irh.1	+						TLL1_uc011cjn.1_5'Flank|TLL1_uc011cjo.1_5'Flank	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GGTGCGAATATTTTTTTTTTT	0.453													3	3	---	---	---	---	
GALNTL6	442117	broad.mit.edu	37	4	173915569	173915569	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173915569delT	uc003isv.2	+						uc003isx.1_Intron	NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						TGAAGATGTATTTTTACCACA	0.368													4	2	---	---	---	---	
HPGD	3248	broad.mit.edu	37	4	175419472	175419473	+	Intron	INS	-	T	T	rs139375173	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175419472_175419473insT	uc003itu.2	-						HPGD_uc003itt.2_5'Flank|HPGD_uc003itv.2_Intron|HPGD_uc011ckf.1_Intron|HPGD_uc010irp.2_Intron|HPGD_uc010irq.2_Intron|HPGD_uc011ckg.1_Intron|HPGD_uc011ckh.1_Intron|HPGD_uc003itw.2_Intron	NM_000860	NP_000851	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)						female pregnancy|lipoxygenase pathway|negative regulation of cell cycle|parturition|prostaglandin metabolic process|transforming growth factor beta receptor signaling pathway	cytosol|nucleus	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|NAD+ binding|prostaglandin E receptor activity|protein homodimerization activity				0		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)	NADH(DB00157)	TCCTTTTTTCATttttttttta	0.114													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	178157399	178157399	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178157399delT								VEGFC (443504 upstream) : NEIL3 (73592 downstream)																							aaagtattgatttttttttca	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179007440	179007441	+	IGR	INS	-	T	T	rs143612718	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179007440_179007441insT								LOC285501 (95537 upstream) : None (None downstream)																							GGATTTTCCGATTTTTTTCTGT	0.332													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185302790	185302790	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185302790delC								ENPP6 (163676 upstream) : IRF2 (6088 downstream)																							ATTCTCAGCTCCTTTTATGCC	0.328													4	2	---	---	---	---	
CYP4V2	285440	broad.mit.edu	37	4	187131994	187131994	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187131994delT	uc003iyw.3	+	11					CYP4V2_uc010ism.2_RNA	NM_207352	NP_997235	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily v,						response to stimulus|visual perception	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		tttttctttattttttttttt	0.139													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188203875	188203875	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188203875delT								FAT1 (556025 upstream) : ZFP42 (713050 downstream)																							AAACTTCTTATTTTTGGAACA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188250312	188250312	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188250312delC								FAT1 (602462 upstream) : ZFP42 (666613 downstream)																							TTCACATTTTCCCCAGTCAGA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189554940	189554940	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189554940delA								TRIML1 (486291 upstream) : None (None downstream)																							attctgtttcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190635800	190635801	+	IGR	INS	-	AA	AA	rs62333661		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190635800_190635801insAA								None (None upstream) : FRG1 (226173 downstream)																							tacacacacacatacatacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190704722	190704723	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190704722_190704723insA								None (None upstream) : FRG1 (157251 downstream)																							aggcaaacaccaaaaaaaagaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190825290	190825290	+	Intron	DEL	C	-	-	rs78560680	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190825290delC	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		CATAAAAAAACCATTACTTTT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	191029820	191029822	+	IGR	DEL	CTT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191029820_191029822delCTT								LOC653545 (19644 upstream) : None (None downstream)																							atcatcattccttcttcttcagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	744986	744986	+	IGR	DEL	A	-	-	rs79366496		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:744986delA								TPPP (51476 upstream) : ZDHHC11 (50734 downstream)																							actctgtctcaaaaaaaaaaa	0.154													3	3	---	---	---	---	
SLC6A3	6531	broad.mit.edu	37	5	1424643	1424644	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1424643_1424644delCA	uc003jck.2	-							NM_001044	NP_001035	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter						cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)	CTCAGTGCCTCACACACACACG	0.594													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1562597	1562598	+	IGR	DEL	CA	-	-	rs114997852	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1562597_1562598delCA								LPCAT1 (38521 upstream) : SDHAP3 (6039 downstream)																							TATAAATGCGcacacacacaca	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1936653	1936654	+	IGR	INS	-	C	C	rs145634078	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1936653_1936654insC								IRX4 (53773 upstream) : IRX2 (809627 downstream)																							GGTGTCTCCTTGCTATGACGCC	0.505													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3682106	3682107	+	IGR	INS	-	AG	AG	rs144453254	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3682106_3682107insAG								IRX1 (80590 upstream) : None (None downstream)																							TGTGGACATAAAGAGTCCAAAG	0.475													4	3	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7790325	7790326	+	Intron	INS	-	T	T	rs144023753	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7790325_7790326insT	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						TAAACCATGCCTCCCACACGCC	0.530													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9299851	9299851	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9299851delC	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						TCTCTGCTCTCCCAACTGAAA	0.398													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9450869	9450869	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9450869delA	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						CTACCACATCAAAAAAAAAAA	0.318													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10405429	10405429	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10405429delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CCAATGAATGTTTTTTTTTTC	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13234984	13234987	+	IGR	DEL	CTGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13234984_13234987delCTGA								None (None upstream) : DNAH5 (455450 downstream)																							tcctgggaagctgactaaggtacc	0.000													2	4	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16776514	16776514	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16776514delT	uc003jft.3	-							NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						GTTTGTGATATTAATAAACAT	0.184													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21548269	21548275	+	Intron	DEL	AAGAAGA	-	-	rs67715168		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21548269_21548275delAAGAAGA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ATATTTCTTGAAGAAGAAAGAAAGAAG	0.396													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23022923	23022923	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23022923delT								CDH12 (169192 upstream) : PRDM9 (484801 downstream)																							GTCATTTTAATTTTTTTTTTC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25900094	25900095	+	IGR	INS	-	T	T	rs138407898	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25900094_25900095insT								None (None upstream) : CDH9 (980614 downstream)																							ACAGTGTTGGAttttttgtttg	0.307													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27415555	27415555	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27415555delA								CDH9 (376866 upstream) : None (None downstream)																							tgtgaccttcaacctccctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28143999	28143999	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28143999delC								None (None upstream) : None (None downstream)																							TTTACTCCTTCCATTGTCTTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33188707	33188707	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33188707delT								C5orf23 (396888 upstream) : TARS (252095 downstream)																							ccttcaataattttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34540294	34540294	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34540294delT								C1QTNF3 (496977 upstream) : RAI14 (116139 downstream)																							ACTCCTCATATTTTTAGACCA	0.289													6	4	---	---	---	---	
TTC23L	153657	broad.mit.edu	37	5	34856482	34856483	+	Intron	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34856482_34856483insC	uc003jiu.2	+							NM_144725	NP_653326	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1						tccaaaaacctccccccatcca	0.040													4	2	---	---	---	---	
C5orf42	65250	broad.mit.edu	37	5	37168327	37168327	+	Intron	DEL	T	-	-	rs72062104		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37168327delT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TAATCACAGATTCTGGGTCTA	0.308													3	3	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38261272	38261272	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38261272delA	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					CTCTGGTGAGAAAAAACTGAG	0.403													4	2	---	---	---	---	
HEATR7B2	133558	broad.mit.edu	37	5	41052312	41052313	+	Intron	DEL	AA	-	-	rs33979852		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41052312_41052313delAA	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8						GTGATTTTAGAAAAAAAAAAAA	0.287													2	4	---	---	---	---	
C5orf28	64417	broad.mit.edu	37	5	43484959	43484960	+	5'Flank	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43484959_43484960insC	uc003jny.2	-						C5orf28_uc003jnv.3_5'Flank|C5orf28_uc003jnx.2_5'Flank	NM_022483	NP_071928	Q0VDI3	CE028_HUMAN	hypothetical protein LOC64417							integral to membrane					0	Lung NSC(6;2.07e-05)					CTCCTAGGCCACCCCCAGAATC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	44837728	44837728	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44837728delT								MRPS30 (22114 upstream) : HCN1 (421625 downstream)																							TTTTTCTTCCTTTTTTTTTTC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50151859	50151859	+	IGR	DEL	G	-	-	rs76271841		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50151859delG								PARP8 (13690 upstream) : ISL1 (527099 downstream)																							gctaggcactggggggatgca	0.209													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50728058	50728061	+	IGR	DEL	GAGA	-	-	rs67129718	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50728058_50728061delGAGA								ISL1 (37501 upstream) : None (None downstream)																							gtgtgtgtgtgagagagagagaga	0.230													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50932064	50932064	+	IGR	DEL	T	-	-	rs113073536		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50932064delT								ISL1 (241507 upstream) : None (None downstream)																							tcttaggatattttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53966019	53966019	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53966019delA								SNX18 (123604 upstream) : ESM1 (307677 downstream)																							tatccctggcaaaaggcaaag	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	54873776	54873776	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54873776delG								PPAP2A (42903 upstream) : SLC38A9 (47900 downstream)																							AGAAATCTGTGTATACCCATC	0.423													1	5	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	57987331	57987332	+	Intron	INS	-	A	A	rs149180823	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57987331_57987332insA	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		AACACTTTTACATCTTTAAATC	0.396													4	2	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	58062844	58062845	+	Intron	INS	-	G	G	rs149854082	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58062844_58062845insG	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		ATATAGCCAGCGGGGGGGACTC	0.490													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62379047	62379047	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62379047delT								ISCA1P1 (305877 upstream) : HTR1A (877232 downstream)																							TACTCATAAAttttttttttt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	64333241	64333241	+	IGR	DEL	A	-	-	rs113464229		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64333241delA								CWC27 (18651 upstream) : ADAMTS6 (111323 downstream)																							AGGTTACAGGAAAAAAAAAGT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66711288	66711288	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66711288delT								CD180 (218671 upstream) : PIK3R1 (800316 downstream)																							tggtgccttctttttttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66767767	66767767	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66767767delA								CD180 (275150 upstream) : PIK3R1 (743837 downstream)																							CTTTATACACAAAAAATTGGA	0.383													4	2	---	---	---	---	
EDIL3	10085	broad.mit.edu	37	5	83304551	83304551	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83304551delA	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		GAGGAAGGTTAAAAATAAGTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85179425	85179426	+	IGR	DEL	AA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85179425_85179426delAA								None (None upstream) : NBPF22P (398836 downstream)																							cttctcaaccaaaaaaaaaaag	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	86371537	86371537	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86371537delA								COX7C (454956 upstream) : RASA1 (192614 downstream)																							AACTGAAAAGAAAAAAAAAAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	86822098	86822098	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86822098delT								CCNH (113262 upstream) : TMEM161B (668926 downstream)																							ctgcgattgattagagcagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87323857	87323857	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87323857delG								CCNH (615021 upstream) : TMEM161B (167167 downstream)																							CTGCAGGTCCGGGTCATCATA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	89501458	89501458	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89501458delA								None (None upstream) : CETN3 (188073 downstream)																							taaataacctaaaaaaaaaac	0.000													4	2	---	---	---	---	
LYSMD3	116068	broad.mit.edu	37	5	89815390	89815390	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89815390delA	uc003kjr.2	-						LYSMD3_uc010jaz.1_Intron|LYSMD3_uc003kjs.1_Intron	NM_198273	NP_938014	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain						cell wall macromolecule catabolic process	integral to membrane					0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		CTTTTGGAGGAAAAAAAAAGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92193783	92193783	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92193783delG								None (None upstream) : FLJ42709 (551282 downstream)																							TCCTAGGCATGGATCTTATGA	0.378													4	2	---	---	---	---	
ANKRD32	84250	broad.mit.edu	37	5	93972286	93972288	+	Intron	DEL	TTC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93972286_93972288delTTC	uc003kkr.3	+						ANKRD32_uc011cul.1_Intron	NM_032290	NP_115666	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32											ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		agcaattatattcttcatctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95595104	95595105	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95595104_95595105delTG								MIR583 (180188 upstream) : PCSK1 (131014 downstream)																							TAGATCTGAATGTGAATTTAGT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95600196	95600196	+	IGR	DEL	G	-	-	rs10709093		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95600196delG								MIR583 (185280 upstream) : PCSK1 (125923 downstream)																							GTCAGGGTCTGAGTTTGTGGG	0.388													6	5	---	---	---	---	
LNPEP	4012	broad.mit.edu	37	5	96341750	96341751	+	Intron	INS	-	TA	TA	rs139363188	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96341750_96341751insTA	uc003kmv.1	+						LNPEP_uc003kmw.1_Intron	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1						cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		ggaaaaagttttatatatatat	0.243													15	7	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108192465	108192465	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108192465delT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		GAGTTAAATCTTTTTTTTTTC	0.244													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111668161	111668161	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111668161delT	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TGCGTATTGATTTTTATTTTT	0.433													4	2	---	---	---	---	
TMED7-TICAM2	100302736	broad.mit.edu	37	5	114915343	114915344	+	3'UTR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114915343_114915344delCA	uc003krd.2	-	4					TMED7-TICAM2_uc003kre.2_3'UTR|TICAM2_uc003krc.2_3'UTR	NM_021649	NP_067681	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2						I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	Golgi apparatus|intrinsic to membrane|plasma membrane	protein binding|transmembrane receptor activity				0						AATAACCTATCACACACACACA	0.406													4	2	---	---	---	---	
CDO1	1036	broad.mit.edu	37	5	115153910	115153911	+	5'Flank	INS	-	A	A	rs140264734	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115153910_115153911insA	uc003krg.2	-							NM_001801	NP_001792	Q16878	CDO1_HUMAN	cysteine dioxygenase						inflammatory response|sulfur amino acid biosynthetic process|taurine biosynthetic process	cytosol	cysteine dioxygenase activity			large_intestine(1)|skin(1)	2		all_cancers(142;0.0046)|all_epithelial(76;0.000161)|Prostate(80;0.0132)|Ovarian(225;0.0776)		OV - Ovarian serous cystadenocarcinoma(64;7.8e-08)|Epithelial(69;7.32e-07)|all cancers(49;3.24e-05)	L-Cysteine(DB00151)|NADH(DB00157)	ttcacgtagttaaaaaaaatca	0.094													4	2	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115432603	115432604	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115432603_115432604insA	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		TTTTCATTTTTAAAAAAAATTC	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116439313	116439316	+	IGR	DEL	TCTG	-	-	rs72382486		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116439313_116439316delTCTG								SEMA6A (528762 upstream) : None (None downstream)																							CTTTAAActatctgtctgtctgtc	0.245													1	5	---	---	---	---	
HSD17B4	3295	broad.mit.edu	37	5	118825369	118825369	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118825369delT	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	tggggctTTCTTGTGACAACT	0.169													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122275692	122275692	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122275692delT	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		tttcattttcttttttttttt	0.124													4	2	---	---	---	---	
CSNK1G3	1456	broad.mit.edu	37	5	122902538	122902538	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122902538delA	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375	Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		ggaaaagtttaaaaaaaaaag	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123171637	123171637	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123171637delA								CSNK1G3 (219175 upstream) : ZNF608 (800973 downstream)																							CATGGACAATAAAAAAAAAAC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123323008	123323008	+	IGR	DEL	T	-	-	rs35045413		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123323008delT								CSNK1G3 (370546 upstream) : ZNF608 (649602 downstream)																							cttttcattcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123556069	123556069	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123556069delC								CSNK1G3 (603607 upstream) : ZNF608 (416541 downstream)																							GTTAACTATACAAAAAAAAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124628316	124628316	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124628316delC								ZNF608 (543816 upstream) : None (None downstream)																							GAGACCCTGTCCAGCTCTTGA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124757823	124757823	+	IGR	DEL	T	-	-	rs72086716		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124757823delT								ZNF608 (673323 upstream) : GRAMD3 (937965 downstream)																							TTCTGCATGATTTTTTTTTTT	0.373													4	2	---	---	---	---	
SLC12A2	6558	broad.mit.edu	37	5	127496536	127496537	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127496536_127496537delTG	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron|SLC12A2_uc003kut.1_Intron	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	Ggtgtgtgtttgtgtgtgtgtg	0.327													3	5	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127596182	127596182	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127596182delA	uc003kuu.2	-							NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		AAGATAGGATAAAAACCACAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128706211	128706211	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128706211delA								ISOC1 (256494 upstream) : ADAMTS19 (89892 downstream)																							atgaaacaggaaatactttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129721212	129721212	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129721212delT								CHSY3 (198886 upstream) : HINT1 (773663 downstream)																							TTCCTTACAATTTTTCTTCAG	0.294													4	2	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132859151	132859157	+	Intron	DEL	GATAGTG	-	-	rs113214823		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132859151_132859157delGATAGTG	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAAACCACCAGATAGTGGATGACATAG	0.333													4	3	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132891362	132891363	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132891362_132891363delAC	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAAAAAATAAACACACACACAC	0.356													4	2	---	---	---	---	
C5orf24	134553	broad.mit.edu	37	5	134188172	134188172	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134188172delT	uc003kzx.2	+						C5orf24_uc003kzy.3_Intron|C5orf24_uc003kzz.2_Intron	NM_152409	NP_689622	Q7Z6I8	CE024_HUMAN	hypothetical protein LOC134553												0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCATGCTCATTTCCTTTTGC	0.363													4	2	---	---	---	---	
SMAD5	4090	broad.mit.edu	37	5	135498017	135498017	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135498017delT	uc003lbj.1	+						SMAD5_uc003lbk.1_Intron|SMAD5_uc003lbl.1_Intron	NM_001001419	NP_001001419	Q99717	SMAD5_HUMAN	SMAD family member 5						BMP signaling pathway|embryonic pattern specification|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			tgggaatggattttttttctc	0.030													4	2	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138227086	138227086	+	Intron	DEL	T	-	-	rs72359808		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138227086delT	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|CTNNA1_uc003ldl.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TACAACCTCCTTTTTTTTTTG	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	138581767	138581767	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138581767delA								SIL1 (47702 upstream) : SNHG4 (28011 downstream)																							AAAGGCTTTGAAAGGGGAGGA	0.468													4	2	---	---	---	---	
CXXC5	51523	broad.mit.edu	37	5	139042024	139042024	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139042024delA	uc010jfg.1	+						CXXC5_uc003let.2_Intron	NM_016463	NP_057547	Q7LFL8	CXXC5_HUMAN	CXXC finger 5						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|nucleus	DNA binding|signal transducer activity|zinc ion binding			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATATGCTGCCAAAAAAAAAGC	0.498													6	3	---	---	---	---	
PCDHA1	56147	broad.mit.edu	37	5	140171169	140171170	+	Intron	INS	-	T	T	rs148113956	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140171169_140171170insT	uc003lhb.2	+						PCDHA1_uc003lha.2_Intron	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor						homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGGGGGGCATTTTTTTTACA	0.337													3	4	---	---	---	---	
FGF1	2246	broad.mit.edu	37	5	142005459	142005459	+	Intron	DEL	T	-	-	rs77096526		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142005459delT	uc003lmn.3	-						FGF1_uc003lmp.3_Intron|FGF1_uc003lmq.2_Intron|FGF1_uc010jgj.2_Intron|FGF1_uc003lmr.2_Intron|FGF1_uc003lms.3_Intron	NM_000800	NP_000791	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic) isoform 1						angiogenesis|cellular response to heat|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cell migration|positive regulation of cholesterol biosynthetic process|positive regulation of intracellular protein kinase cascade|positive regulation of transcription from RNA polymerase II promoter	cell cortex|cytosol|extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|S100 alpha binding				0		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Pentosan Polysulfate(DB00686)	TGGCTGCATCTTTTTTTTCTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	142939415	142939415	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142939415delT								NR3C1 (124338 upstream) : HMHB1 (252311 downstream)																							AGGAAAAGGCTTTTTTTTTTT	0.438													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144829806	144829806	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144829806delA								KCTD16 (972862 upstream) : PRELID2 (308776 downstream)																							AGTCCGTTGTAAAGAATTTCC	0.383													4	2	---	---	---	---	
LOC728264	728264	broad.mit.edu	37	5	148799500	148799501	+	Intron	INS	-	C	C	rs34670039	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148799500_148799501insC	uc003lqq.2	+						LOC728264_uc003lqs.2_Intron|LOC728264_uc003lqp.2_Intron					Homo sapiens cDNA FLJ44517 fis, clone UTERU3002667.												0						CTTTTTTTTTTCCTCTCTTCCC	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	148861328	148861328	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148861328delG								LOC728264 (48929 upstream) : CSNK1A1 (11621 downstream)																							ATGTCCCCCTGGAGAGAAATG	0.438													4	2	---	---	---	---	
IRGM	345611	broad.mit.edu	37	5	150240449	150240449	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150240449delT	uc011dcl.1	+									A1A4Y4	IRGM_HUMAN	Homo sapiens immunity-related GTPase family, M, mRNA (cDNA clone IMAGE:5183529).						autophagy|inflammatory response|innate immune response	autophagic vacuole membrane|cell projection|Golgi membrane|phagocytic cup|phagocytic vesicle membrane	GTP binding|hydrolase activity, acting on acid anhydrides				0						AGGAAACTGATTTTTTTTTCA	0.363													4	2	---	---	---	---	
GM2A	2760	broad.mit.edu	37	5	150950485	150950485	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150950485delC	uc011dcs.1	+						FAT2_uc003lue.3_5'Flank|FAT2_uc010jhx.1_5'Flank	NM_000405		P17900	SAP3_HUMAN	GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAAAGTCTGCCTAAATCGGG	0.522													4	2	---	---	---	---	
GLRA1	2741	broad.mit.edu	37	5	151228693	151228694	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151228693_151228694insT	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	ttctttctttctttctttcttt	0.099													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151712338	151712338	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151712338delA								GLRA1 (407941 upstream) : NMUR2 (58764 downstream)																							AAAAAATAAGAAAAAAAAAAT	0.249													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154283046	154283046	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154283046delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCTTTGCTTCAAAAAAAAAGT	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154523370	154523370	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154523370delG								KIF4B (125685 upstream) : SGCD (611693 downstream)																							CTGACTCAGTGGGTTTTTTGC	0.393													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155795107	155795108	+	Intron	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155795107_155795108insC	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCtttttttttttctttttttc	0.178													4	2	---	---	---	---	
TIMD4	91937	broad.mit.edu	37	5	156380012	156380012	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156380012delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGAGCTTCATTAGCTACCGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157327752	157327752	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157327752delC								CLINT1 (41584 upstream) : EBF1 (795172 downstream)																							tctgtggtctccaggcctctc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157514475	157514476	+	IGR	INS	-	T	T	rs143832112	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157514475_157514476insT								CLINT1 (228307 upstream) : EBF1 (608448 downstream)																							ATAAATACAAGTTTTTTTTTAC	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157828284	157828284	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157828284delA								CLINT1 (542116 upstream) : EBF1 (294640 downstream)																							gtctcaaaacaaaaaaacaaa	0.209													4	2	---	---	---	---	
UBLCP1	134510	broad.mit.edu	37	5	158697815	158697815	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158697815delA	uc003lxq.2	+							NM_145049	NP_659486	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase							nucleus	phosphoprotein phosphatase activity			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			acagataagcaaaaaaaaaag	0.119													4	2	---	---	---	---	
ATP10B	23120	broad.mit.edu	37	5	160152424	160152424	+	Intron	DEL	T	-	-	rs7724022	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160152424delT	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCGTCTTACCTAGATCTAATT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162281914	162281914	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162281914delG								GABRG2 (699370 upstream) : CCNG1 (582663 downstream)																							ttaaatttcagggagtgcagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163475205	163475205	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163475205delT								MAT2B (528872 upstream) : None (None downstream)																							CTTCAATACCTTTGTGCTCCT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163763697	163763697	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163763697delT								MAT2B (817364 upstream) : None (None downstream)																							GATGGGCCTATTTTTTTTTTC	0.343													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164375039	164375039	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164375039delA								None (None upstream) : None (None downstream)																							TGCAGTAGTTAAAAAAAAAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164642971	164642972	+	IGR	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164642971_164642972delGA								None (None upstream) : None (None downstream)																							AGGATTGGGGGAGGATATGTCA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166604129	166604130	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166604129_166604130insG								None (None upstream) : ODZ2 (107713 downstream)																							GTTGAGACAAAGGGGAAATGAA	0.361													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167275930	167275931	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167275930_167275931insT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TGTTTTTTGGGTTTTTTTGGCC	0.252													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167484316	167484317	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167484316_167484317delAC	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GCCTCGCCCAacacacacacac	0.396													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167595272	167595272	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167595272delG	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron|uc003lzs.1_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TTCCCTGGGTGGGCTCACCCA	0.294													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169398193	169398193	+	Intron	DEL	A	-	-	rs148665749		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169398193delA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AAAGAAAGGCAAAAAAAAAAA	0.438													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171025392	171025392	+	IGR	DEL	T	-	-	rs67437957		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171025392delT								FGF18 (141230 upstream) : FBXW11 (263164 downstream)																							aagctagttGTTTTTTTTTTG	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172051151	172051152	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172051151_172051152insT								SH3PXD2B (169624 upstream) : NEURL1B (17124 downstream)																							TCCTCAGTCTGTTTTCATGTAA	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172248417	172248418	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172248417_172248418delCA								DUSP1 (50214 upstream) : ERGIC1 (12805 downstream)																							GGTGTGCACTCACACACACACA	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173901450	173901450	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173901450delA								HMP19 (365269 upstream) : MSX2 (250125 downstream)																							aaaaaaaaagaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174577609	174577609	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174577609delT								MSX2 (419708 upstream) : DRD1 (290067 downstream)																							tgctaagagcttttttttttt	0.139													4	4	---	---	---	---	
C5orf25	375484	broad.mit.edu	37	5	175738556	175738556	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175738556delA	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc003mdv.2_5'Flank			Q8NDZ2	CE025_HUMAN	RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)		CACATTATTTAAAAAAAAAAA	0.154													4	2	---	---	---	---	
CDHR2	54825	broad.mit.edu	37	5	176015725	176015726	+	Intron	INS	-	GA	GA	rs149030593	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176015725_176015726insGA	uc003mem.1	+						CDHR2_uc003men.1_Intron	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor						homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2						tgtgtgtgtgtgAGAGAGAGAG	0.139													5	5	---	---	---	---	
UNC5A	90249	broad.mit.edu	37	5	176284523	176284524	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176284523_176284524delCA	uc003mey.2	+						UNC5A_uc003mex.1_Intron	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			acatgcatgccacacacacatg	0.455													4	2	---	---	---	---	
UNC5A	90249	broad.mit.edu	37	5	176284537	176284538	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176284537_176284538delCA	uc003mey.2	+						UNC5A_uc003mex.1_Intron	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cacacatgcgcacacacacaca	0.446													4	2	---	---	---	---	
RMND5B	64777	broad.mit.edu	37	5	177570300	177570300	+	Intron	DEL	A	-	-	rs11329795		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177570300delA	uc003mim.2	+						RMND5B_uc003min.2_Intron|RMND5B_uc003mio.2_Intron|RMND5B_uc003mip.2_Intron|RMND5B_uc011dgf.1_Intron|RMND5B_uc003miq.2_Intron	NM_022762	NP_073599	Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog											ovary(1)|skin(1)	2	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			tggtaaaagtaaaagattttc	0.104													2	5	---	---	---	---	
CANX	821	broad.mit.edu	37	5	179154863	179154863	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179154863delA	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	agagaaagggaacagtcaCTG	0.214													4	2	---	---	---	---	
MAPK9	5601	broad.mit.edu	37	5	179707178	179707178	+	Intron	DEL	A	-	-	rs67561166		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179707178delA	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743	P45984	MK09_HUMAN	mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGagaaatgaaaaaaaaaat	0.289													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180514068	180514070	+	IGR	DEL	GGA	-	-	rs150538329		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180514068_180514070delGGA								BTNL9 (25546 upstream) : OR2V2 (67873 downstream)																							CGGTCCTGGGGGATCAGTGCTAA	0.512													4	2	---	---	---	---	
C6orf195	154386	broad.mit.edu	37	6	2635010	2635010	+	5'UTR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2635010delA	uc003mtw.2	-	1						NM_152554	NP_689767	Q96MT4	CF195_HUMAN	hypothetical protein LOC154386												0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGGAAGCGTTAAGGCCAGGAA	0.507											OREG0017140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3406247	3406248	+	Intron	INS	-	A	A	rs151324129	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3406247_3406248insA	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc010jno.2_Intron	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				ATCTTTGAGAGACTTTTTCAAG	0.371													4	2	---	---	---	---	
C6orf145	221749	broad.mit.edu	37	6	3748796	3748797	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3748796_3748797delGT	uc003mvt.2	-							NM_183373	NP_899229	Q5TGL8	CF145_HUMAN	hypothetical protein LOC221749						cell communication		phosphatidylinositol binding			breast(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)				CCACTCCACAGTGTGTGTGTGC	0.530											OREG0017153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
LYRM4	57128	broad.mit.edu	37	6	5157486	5157486	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5157486delA	uc003mwp.2	-						LYRM4_uc010jnu.2_Intron|LYRM4_uc003mwq.2_Intron|uc003mwn.1_Intron	NM_020408	NP_065141	Q9HD34	LYRM4_HUMAN	LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)				GTTACCATTTAATGCCTACAT	0.338													4	2	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5501166	5501167	+	Intron	INS	-	GA	GA	rs138118700	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5501166_5501167insGA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	TTCAAATCCCCgagagagagag	0.371													3	3	---	---	---	---	
BMP6	654	broad.mit.edu	37	6	7746209	7746210	+	Intron	DEL	AG	-	-	rs35704083		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7746209_7746210delAG	uc003mxu.3	+							NM_001718	NP_001709	P22004	BMP6_HUMAN	bone morphogenetic protein 6 preproprotein						BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)					caagaaaaaaaGAGAGAGAGAG	0.228													2	4	---	---	---	---	
EEF1E1	9521	broad.mit.edu	37	6	8098302	8098303	+	Intron	INS	-	T	T	rs145208758	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8098302_8098303insT	uc003mxz.2	-						EEF1E1_uc011dic.1_Intron	NM_004280	NP_004271	O43324	MCA3_HUMAN	eukaryotic translation elongation factor 1						negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of DNA damage response, signal transduction by p53 class mediator|tRNA aminoacylation for protein translation	cytosol|nucleus					0	Ovarian(93;0.0398)					AAAAAGAATTGTTTTTTTGGGA	0.223													4	3	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10907587	10907587	+	Intron	DEL	A	-	-	rs71550743		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10907587delA	uc003mzo.2	+						SYCP2L_uc011din.1_Intron|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			agacaatctcaaaaaaaaaaa	0.149													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11150180	11150183	+	IGR	DEL	TTCT	-	-	rs144178688		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11150180_11150183delTTCT								LOC221710 (11216 upstream) : NEDD9 (33348 downstream)																							ttacctcccattctttctttgttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14393895	14393895	+	IGR	DEL	A	-	-	rs79208548		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14393895delA								CD83 (256749 upstream) : JARID2 (851839 downstream)																							TGTGTGACAGAAAAAAAAAAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16947968	16947968	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16947968delT								ATXN1 (186247 upstream) : RBM24 (333841 downstream)																							CTCTATTTCCTGAAATCTGAC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21318269	21318269	+	IGR	DEL	A	-	-	rs35864637		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21318269delA								CDKAL1 (85637 upstream) : SOX4 (275703 downstream)																							CACCGTGGTGAAAAAAAAAGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23254664	23254664	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23254664delC								HDGFL1 (683915 upstream) : NRSN1 (871750 downstream)																							cctccccactccccccacccc	0.000													4	2	---	---	---	---	
HLA-F	3134	broad.mit.edu	37	6	29701137	29701138	+	Intron	INS	-	TT	TT	rs143436896	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29701137_29701138insTT	uc011dly.1	+						LOC285830_uc003nnp.2_Intron|LOC285830_uc011dlz.1_Intron			P30511	HLAF_HUMAN	Homo sapiens cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F precursor.						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						TGTGTATTTTATTTTTTTTAAT	0.332													1	5	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29875463	29875463	+	Intron	DEL	G	-	-	rs35863317		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29875463delG	uc011dmb.1	+						HCG4P6_uc003nog.1_Intron	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						TGGGGTTCCTGGGGGGTGGTG	0.617													3	3	---	---	---	---	
TNXB	7148	broad.mit.edu	37	6	32049694	32049694	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32049694delG	uc003nzl.2	-							NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor						actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						GCCCTGGAGTGGGGCCGGGAA	0.662													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33895978	33895983	+	IGR	DEL	TAGAGA	-	-	rs67295791		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33895978_33895983delTAGAGA								MLN (124185 upstream) : MIR1275 (71766 downstream)																							GACAGCACATTAGAgaagactgctcc	0.233													4	2	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34040282	34040283	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34040282_34040283delCA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	agatacaaaccacacacacaca	0.000													4	2	---	---	---	---	
STK38	11329	broad.mit.edu	37	6	36499237	36499238	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36499237_36499238insT	uc003omg.2	-						STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202	Q15208	STK38_HUMAN	serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6						CTAAAACATTGTTTTTTAATGA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41591484	41591484	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41591484delT								FOXP4 (21363 upstream) : MDFI (13446 downstream)																							ttcttctttcttttttttttg	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44745415	44745416	+	IGR	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44745415_44745416insC								CDC5L (330636 upstream) : SUPT3H (31638 downstream)																							aattccctcctccccccatcta	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	45654892	45654892	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45654892delT								RUNX2 (136074 upstream) : CLIC5 (211298 downstream)																							ctttttgttctttagggtttg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47435040	47435041	+	IGR	DEL	AA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47435040_47435041delAA								TNFRSF21 (157360 upstream) : CD2AP (10484 downstream)																							ATTGAGGGGCAAAAAGAGGGCA	0.416													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	55964485	55964486	+	Intron	INS	-	AT	AT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55964485_55964486insAT	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			cacccacatacacacacacacC	0.277													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56486770	56486770	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56486770delA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GGTTTCTAATAATAATTCATA	0.294													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57345003	57345004	+	Intron	INS	-	ATTTA	ATTTA	rs140856200	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57345003_57345004insATTTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGTACATTTGTATTTAGTAAGC	0.292													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57366676	57366676	+	Intron	DEL	A	-	-	rs11337169		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57366676delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTTAAATAACAAAGGCTATTT	0.279													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57398707	57398707	+	Intron	DEL	G	-	-	rs67468005		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57398707delG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGAAACTTTTGGttttttttt	0.134													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404193	57404193	+	Intron	DEL	T	-	-	rs11331163		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404193delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATTGTGTCTCTAGATACCTTT	0.299													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57439748	57439750	+	Intron	DEL	TTC	-	-	rs78957849		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57439748_57439750delTTC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATCCTCAGCTTTCTTTTTTTATT	0.281													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57511529	57511533	+	Intron	DEL	ATAAC	-	-	rs148539245		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511529_57511533delATAAC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTGAGAAAAAATAACATAAGTTATG	0.317													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72327844	72327844	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72327844delC								C6orf155 (197396 upstream) : RIMS1 (268806 downstream)																							GTTGGGTGTGCCCCAGGCCTA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72400974	72400974	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72400974delT								C6orf155 (270526 upstream) : RIMS1 (195676 downstream)																							aaattcaatgtttagacaggt	0.030													4	2	---	---	---	---	
TMEM30A	55754	broad.mit.edu	37	6	75995155	75995156	+	5'Flank	INS	-	CTT	CTT	rs146206354	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75995155_75995156insCTT	uc003phw.2	-						TMEM30A_uc003phx.2_5'Flank|uc010kbd.1_Intron	NM_018247	NP_060717	Q9NV96	CC50A_HUMAN	transmembrane protein 30A isoform 1							integral to membrane					0						TTACATTTCCCCTTTTCTGTGT	0.351													2	5	---	---	---	---	
KIAA1009	22832	broad.mit.edu	37	6	84881834	84881834	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84881834delA	uc010kbp.2	-						KIAA1009_uc003pkj.3_Intron|KIAA1009_uc003pki.3_Intron	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein						cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		AAGAGAGGGGAAAAAAAAAAT	0.483													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85635378	85635379	+	IGR	INS	-	GT	GT	rs143552477	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85635378_85635379insGT								TBX18 (161479 upstream) : NT5E (523923 downstream)																							ATCAATGAAGGgtgtgtgtgtg	0.307													4	4	---	---	---	---	
HTR1E	3354	broad.mit.edu	37	6	87699620	87699621	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87699620_87699621insA	uc003pli.2	+							NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E						G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)	TAAGTTGAGCCAAAAAAAAAAG	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91905851	91905851	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91905851delT								MAP3K7 (608944 upstream) : None (None downstream)																							TCCCTTTCTATTTTTTTTTTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92365550	92365550	+	Intron	DEL	A	-	-	rs111536030		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92365550delA	uc003pod.2	-											Homo sapiens cDNA clone IMAGE:5284581.																		AGTCTGGCTTAAAAAAATTAT	0.219													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	93414076	93414077	+	IGR	INS	-	TGA	TGA	rs57132958	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93414076_93414077insTGA								None (None upstream) : EPHA7 (535665 downstream)																							GGCAGCgatgctgatgatgatg	0.347													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96677904	96677904	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96677904delA								FUT9 (14417 upstream) : KIAA0776 (291798 downstream)																							taacaataccaaaaaaagatt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	97099083	97099083	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97099083delT								FHL5 (34571 upstream) : GPR63 (146806 downstream)																							gatttatgcatttttttgctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99039079	99039079	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99039079delC								MIR2113 (566582 upstream) : POU3F2 (243501 downstream)																							gccctagattcccacagtaaa	0.090													4	2	---	---	---	---	
C6orf168	84553	broad.mit.edu	37	6	99781673	99781673	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99781673delG	uc003ppj.3	-						C6orf168_uc003ppi.3_Intron	NM_032511	NP_115900	Q5TGI0	CF168_HUMAN	hypothetical protein LOC84553											ovary(2)|central_nervous_system(1)	3		all_cancers(76;1.63e-06)|Acute lymphoblastic leukemia(125;5.12e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00898)|Colorectal(196;0.0699)|Lung NSC(302;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.073)		TGATGGAAAAGGAAAAAAAAG	0.398													5	3	---	---	---	---	
ASCC3	10973	broad.mit.edu	37	6	101294781	101294784	+	Intron	DEL	AATT	-	-	rs72212752		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101294781_101294784delAATT	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		cctgctagacaattaattctgaga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	101402024	101402024	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101402024delA								ASCC3 (72800 upstream) : GRIK2 (444881 downstream)																							ATGCTGTTTTAAAAATCCTTT	0.303													4	2	---	---	---	---	
SESN1	27244	broad.mit.edu	37	6	109381427	109381427	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109381427delT	uc003psu.2	-							NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		ATTTGTTGAGTTTTTTTTCTA	0.209													4	2	---	---	---	---	
HS3ST5	222537	broad.mit.edu	37	6	114378234	114378234	+	3'UTR	DEL	T	-	-	rs80329057		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114378234delT	uc003pwg.3	-	2					uc003pwf.2_Intron|HS3ST5_uc003pwh.3_3'UTR	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CAGACAGCAATTTTTTTTTTT	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	117557826	117557826	+	IGR	DEL	G	-	-	rs145152978	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117557826delG								RFX6 (304518 upstream) : VGLL2 (28895 downstream)																							ttctggcactgaaaaaaaaat	0.000													4	2	---	---	---	---	
ROS1	6098	broad.mit.edu	37	6	117726831	117726831	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117726831delA	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GATACATATGAAAAAAAAAAG	0.318			T	GOPC|ROS1	glioblastoma|NSCLC								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119909112	119909112	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119909112delT								MAN1A1 (238186 upstream) : None (None downstream)																							AATGTCAGACTTTTTTTTTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	121245699	121245699	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121245699delA								None (None upstream) : C6orf170 (154928 downstream)																							AGTATGGGTGAAAAAAAATCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	122212712	122212712	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122212712delC								GJA1 (441840 upstream) : HSF2 (507984 downstream)																							GGTGATTTTACCTGACACatt	0.154													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123873170	123873170	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123873170delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|TRDN_uc010keo.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		ttaaaactggaaaaaaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	125463109	125463109	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125463109delA								RNF217 (58452 upstream) : TPD52L1 (11770 downstream)																							AGCTATAAAGAAAAAAAAAGG	0.224													4	2	---	---	---	---	
THEMIS	387357	broad.mit.edu	37	6	128038347	128038347	+	Intron	DEL	A	-	-	rs68131056		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128038347delA	uc003qbi.2	-						THEMIS_uc010kfa.2_Intron|THEMIS_uc011ebt.1_Intron|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform						negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						tataatcttcaaaaaaaaaaa	0.065													1	5	---	---	---	---	
THEMIS	387357	broad.mit.edu	37	6	128166198	128166199	+	Intron	INS	-	A	A	rs71834993		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128166198_128166199insA	uc003qbi.2	-						THEMIS_uc010kfa.2_Intron|THEMIS_uc011ebt.1_Intron|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform						negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						CAAATTTTAGTAAAAAAAAAAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	128901157	128901158	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128901157_128901158insT								PTPRK (59287 upstream) : LAMA2 (303128 downstream)																							tcttttctttcttttttttttt	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130056628	130056628	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130056628delT								ARHGAP18 (25258 upstream) : C6orf191 (95763 downstream)																							attctttgccttttttttttg	0.000													5	4	---	---	---	---	
EYA4	2070	broad.mit.edu	37	6	133850247	133850247	+	3'UTR	DEL	C	-	-	rs5880184		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133850247delC	uc003qec.3	+	20					EYA4_uc011ecq.1_3'UTR|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_3'UTR|EYA4_uc003qee.3_3'UTR|EYA4_uc011ecs.1_3'UTR|uc003qeg.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		AGAACTCTTACCCTGGCAAAG	0.428													5	3	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136931832	136931832	+	Intron	DEL	A	-	-	rs112503301		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136931832delA	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTTGAGAATTAAAAAAAAAAA	0.279													4	2	---	---	---	---	
KIAA1244	57221	broad.mit.edu	37	6	138542323	138542324	+	Intron	INS	-	G	G	rs139145804	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138542323_138542324insG	uc003qhu.2	+						PBOV1_uc003qhv.2_5'Flank	NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		tggcagtggcagggaaaattga	0.000													4	2	---	---	---	---	
HIVEP2	3097	broad.mit.edu	37	6	143187661	143187662	+	Intron	INS	-	A	A	rs140429520	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143187661_143187662insA	uc003qjd.2	-							NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ACTCCTTTATTACCTCTTTCTC	0.376													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145488208	145488208	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145488208delT								UTRN (314040 upstream) : EPM2A (458238 downstream)																							GAAGTGTGAATTTTTTTTTTC	0.328													4	2	---	---	---	---	
C6orf103	79747	broad.mit.edu	37	6	147119813	147119813	+	Intron	DEL	A	-	-	rs72393169		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147119813delA	uc010khx.2	+						C6orf103_uc003qlp.2_Intron|C6orf103_uc003qlq.2_Intron|C6orf103_uc003qlr.2_Intron	NM_024694	NP_078970	Q8N7X0	CAN7L_HUMAN	hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)		taaaaaacagaaaaaaaaaaa	0.000													4	4	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152949719	152949720	+	Intron	INS	-	A	A	rs74643030		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152949719_152949720insA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_5'Flank	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGGTACAACATAAAAAAAAAAT	0.297										HNSCC(10;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156717158	156717158	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156717158delG								MIR1202 (449145 upstream) : ARID1B (381928 downstream)																							AGTTATCTCAGGTAACCAGTT	0.408													4	2	---	---	---	---	
TULP4	56995	broad.mit.edu	37	6	158807979	158807979	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158807979delT	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TTTCTGTTTATTTCTGTCAAA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159256561	159256561	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159256561delA								EZR (16105 upstream) : OSTCL (5599 downstream)																							CACAAACTGTAAAAATCGCCT	0.303													4	2	---	---	---	---	
OSTCL	202459	broad.mit.edu	37	6	159262512	159262512	+	3'UTR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159262512delA	uc003qrw.2	-	3						NM_145303	NP_660346			oligosaccharyltransferase complex subunit-like												0						TCAGCAGGGGAAAAAAAAATA	0.328													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160120593	160120593	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160120593delA								SOD2 (6240 upstream) : WTAP (27536 downstream)																							ACTCCACGAGAAAAAAAAAAA	0.438													4	3	---	---	---	---	
AGPAT4	56895	broad.mit.edu	37	6	161558679	161558679	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161558679delA	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		AGGAGTAAAGAACACAAACAC	0.517													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	161708387	161708387	+	IGR	DEL	G	-	-	rs112272508		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161708387delG								AGPAT4 (13280 upstream) : PARK2 (60204 downstream)																							gcaaggaattggggggaaaaa	0.000													3	6	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162926825	162926826	+	Intron	INS	-	T	T	rs149598338	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162926825_162926826insT	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CTGGAAAACTGTGAGTATTTGT	0.356													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164182884	164182885	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164182884_164182885insT	uc003quk.1	+											Homo sapiens cDNA FLJ35795 fis, clone TESTI2005827.																		tctcctaggTCTTTTTTTTTTT	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164460282	164460282	+	IGR	DEL	A	-	-	rs74313040		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164460282delA								QKI (465390 upstream) : None (None downstream)																							atctgaatttaagtgtaaatt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169234894	169234894	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169234894delG								SMOC2 (166223 upstream) : THBS2 (380982 downstream)																							ATAGTTGTGTGGGGTTTTTTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169666957	169666957	+	IGR	DEL	T	-	-	rs142701386		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169666957delT								THBS2 (12820 upstream) : WDR27 (190350 downstream)																							GTGTGGGAGCTTGTGTGTCCC	0.577													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169770551	169770551	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169770551delT								THBS2 (116414 upstream) : WDR27 (86756 downstream)																							ATACTGTGTATTTTTTTCAGT	0.542													4	2	---	---	---	---	
WDR27	253769	broad.mit.edu	37	6	169857351	169857352	+	3'UTR	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169857351_169857352insC	uc003qwx.2	-	26					WDR27_uc003qwv.1_RNA|WDR27_uc010kkw.1_3'UTR|WDR27_uc003qwy.2_3'UTR			A2RRH5	WDR27_HUMAN	RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		AAATTCTCTCTTTTTTCTTCCA	0.371													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945073	945073	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945073delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						gagaaaggagaaagggagaaa	0.060													4	3	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	1887069	1887069	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1887069delG	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc003sld.1_Intron|uc003slj.1_RNA	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		AGGAGACAGTGGAGACCTCTA	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20800046	20800046	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20800046delA								ABCB5 (3410 upstream) : SP8 (21849 downstream)																							aaAGGAAAGGAAAAAAAAGAA	0.204													4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30891616	30891616	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30891616delT	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_5'Flank	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						TTTCCATTTCTTTTTTTTTTC	0.438													3	5	---	---	---	---	
CCDC129	223075	broad.mit.edu	37	7	31691382	31691382	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31691382delT	uc003tcj.1	+						CCDC129_uc011kad.1_Intron|CCDC129_uc003tci.1_Intron|CCDC129_uc011kae.1_Intron|CCDC129_uc003tck.1_Intron	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129												0						aataaagttgtttttttTTTT	0.139													23	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	32394595	32394595	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32394595delC								PDE1C (55654 upstream) : LSM5 (130350 downstream)																							TGGAGGACTTCGTCTTGTTTC	0.478													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32866776	32866776	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32866776delT	uc011kai.1	+						uc003tda.1_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						AGAGACCAAGTTTGGGAATGT	0.428													4	2	---	---	---	---	
DPY19L1	23333	broad.mit.edu	37	7	35076026	35076026	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35076026delT	uc003tem.3	-							NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1							integral to membrane					0						GTCAACTTTGTTTTTTTTTTT	0.458													5	3	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38433274	38433275	+	Intron	INS	-	C	C	rs140891605		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38433274_38433275insC	uc003tgu.2	-						AMPH_uc003tgv.2_Intron|AMPH_uc003tgt.2_Intron|AMPH_uc003tgw.1_Intron|AMPH_uc010kxl.1_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						GCTCACTTCATCACATTCTCTT	0.421													4	3	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39459731	39459731	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39459731delG	uc003thb.1	+							NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						CAAATAACATGGACAAAACCA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41413699	41413699	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41413699delT								C7orf10 (513342 upstream) : INHBA (314904 downstream)																							TGTACGTGTGTTTTTTTTTTA	0.343													3	4	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42180245	42180245	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42180245delA	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						cggttactctaaattaaccca	0.000									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				4	2	---	---	---	---	
GCK	2645	broad.mit.edu	37	7	44224671	44224672	+	Intron	DEL	AG	-	-	rs144685104	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44224671_44224672delAG	uc003tkl.2	-							NM_000162	NP_000153	P35557	HXK4_HUMAN	glucokinase isoform 1						cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4						aggtagacacagagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48955398	48955399	+	IGR	DEL	TG	-	-	rs138420464	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48955398_48955399delTG								ABCA13 (268307 upstream) : CDC14C (8758 downstream)																							ATTTTTTTTTTGATGAATGGCA	0.337													4	3	---	---	---	---	
GRB10	2887	broad.mit.edu	37	7	50687623	50687624	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50687623_50687624delAC	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)					GTGGacacgtacacacacacac	0.431									Russell-Silver_syndrome				4	2	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55623049	55623049	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55623049delT	uc003tqs.2	-						VOPP1_uc010kzi.2_5'Flank|VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						AGCACTACCATTTCCGCACAT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57648800	57648800	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57648800delT								ZNF716 (115535 upstream) : None (None downstream)																							ggattacaggtgtgcgtcact	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57696378	57696380	+	5'Flank	DEL	TGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57696378_57696380delTGA	uc003tso.1	+											Homo sapiens macronuclear mRNA.																		aggataatggtgatgatgatgag	0.069													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57932687	57932688	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57932687_57932688delCA								ZNF716 (399422 upstream) : None (None downstream)																							agaaacagagcaaaagggataa	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67186181	67186181	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67186181delG								STAG3L4 (399669 upstream) : None (None downstream)																							ataatttggtgggcggggctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67920626	67920626	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67920626delC								None (None upstream) : None (None downstream)																							GCTGTCACAGCCACCACCACA	0.353													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70123316	70123316	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70123316delC	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		AAAGACCACTCCCCCCCAACA	0.557													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	71119493	71119493	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71119493delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				gtgtacctacttcccctgtaa	0.000													4	2	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73187518	73187518	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73187518delA	uc011kfa.1	-						CLDN3_uc003tzg.3_5'Flank	NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						GTCATCTTGTAGGAGTCAAGG	0.507													4	2	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73334727	73334727	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73334727delT	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						ttgtcacctataaaaagctCT	0.244													4	2	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75266670	75266670	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75266670delG	uc003uds.1	-							NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						GTGCAGGGCTGGGAGGATGCT	0.502			T	PDGFRB	CMML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76328963	76328963	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76328963delG								POMZP3 (72343 upstream) : PMS2L11 (281176 downstream)																							TGTaaaaaaagaaagaaagaa	0.299													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76429624	76429625	+	IGR	INS	-	C	C	rs146622719	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76429624_76429625insC								POMZP3 (173004 upstream) : PMS2L11 (180514 downstream)																							AAAAAAGAAAACACACATGTAA	0.282													4	2	---	---	---	---	
RSBN1L	222194	broad.mit.edu	37	7	77372376	77372377	+	Intron	INS	-	T	T	rs140081040		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77372376_77372377insT	uc010ldt.1	+						RSBN1L_uc003ugm.2_Intron	NM_198467	NP_940869	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like							nucleus				ovary(1)	1						TTCCATGGGAAttttttttttt	0.074													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82291196	82291196	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82291196delA								CACNA2D1 (218165 upstream) : PCLO (92125 downstream)																							GTCTGGCACCAAAAAAAAAAA	0.358													4	2	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82777886	82777886	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82777886delT	uc003uhx.2	-						PCLO_uc003uhv.2_Intron	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TAGGTCCTTATTTTTTAGACC	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84922689	84922689	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84922689delT								SEMA3D (106518 upstream) : None (None downstream)																							CATAACTTACTTTTTTTTTTT	0.328													4	3	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92020810	92020810	+	Intron	DEL	T	-	-	rs11311575		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92020810delT	uc003ulw.2	+						ANKIB1_uc010lew.1_Intron	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTTTGGTGATTTTTTTTTTC	0.279													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95233571	95233571	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95233571delC								PDK4 (7646 upstream) : DYNC1I1 (168247 downstream)																							GAGTCATGGTCCAGTTGCCCA	0.343													4	2	---	---	---	---	
PTCD1	26024	broad.mit.edu	37	7	99062883	99062883	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99062883delA	uc011kiw.1	-						ATP5J2_uc003uql.2_Intron|ATP5J2_uc003uqm.2_Intron|ATP5J2_uc003uqn.2_Intron|ATP5J2_uc003uqo.2_Intron	NM_015545	NP_056360	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			acgccatctcaaaaaaaaaat	0.020													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103207862	103207862	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103207862delG	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACATGATCCAGGGGACTGCAC	0.453													4	2	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105123625	105123625	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105123625delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						ctttctttccttttttttttt	0.070													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109968970	109968970	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109968970delT								EIF3IP1 (368700 upstream) : IMMP2L (334140 downstream)																							aaaaaggggattttttttttt	0.000													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	111115466	111115466	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111115466delT	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		AAACAGTGCCTTTTTTTTTTC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115312680	115312681	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115312680_115312681insA								MDFIC (653417 upstream) : TFEC (262521 downstream)																							GCTCATTGATGAAAGAAAAAGC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	119578340	119578340	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119578340delA								None (None upstream) : KCND2 (335382 downstream)																							gtggtaagggaaaggcaaagt	0.000													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	120313044	120313045	+	Intron	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120313044_120313045delAG	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					agagaaagaaagagagagagag	0.000													5	3	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	120381960	120381960	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120381960delA	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					TGGTAAAGGTAAAAAAAAATG	0.343													5	3	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122186603	122186604	+	Intron	INS	-	TCTT	TCTT	rs140799880	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122186603_122186604insTCTT	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						ACCTCTGCTGATCTTAAGCTTT	0.406													3	4	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122214070	122214071	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122214070_122214071insA	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AATCAAATGGCAAAAAAAATGT	0.297													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126387853	126387853	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126387853delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	aactgaagaattataaatttt	0.085										HNSCC(24;0.065)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131617300	131617300	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131617300delG								PODXL (375924 upstream) : PLXNA4 (190792 downstream)																							ccttacttctggcacaacgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	134372191	134372192	+	IGR	INS	-	T	T	rs146983175	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134372191_134372192insT								BPGM (7626 upstream) : CALD1 (91979 downstream)																							actgttctgccttgagttaagc	0.000													5	8	---	---	---	---	
WDR91	29062	broad.mit.edu	37	7	134893948	134893948	+	Intron	DEL	C	-	-	rs112551663		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134893948delC	uc003vsp.2	-						WDR91_uc010lmq.2_5'Flank|WDR91_uc010lmr.2_5'Flank	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4						AGCTGAAGTTCTAATGATAAA	0.343													5	7	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135282462	135282463	+	Intron	INS	-	TTTTC	TTTTC	rs146889702	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135282462_135282463insTTTTC	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						AGAGTTAATTATTTTCTTTTCT	0.297													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	137559456	137559456	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137559456delA								DGKI (27847 upstream) : CREB3L2 (271 downstream)																							AGGAGACAATAAAAATAACAG	0.388													4	2	---	---	---	---	
AKR1D1	6718	broad.mit.edu	37	7	137692151	137692152	+	Intron	INS	-	AGC	AGC	rs148090100	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137692151_137692152insAGC	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1						CTACAGGTACGAGCAGCCAGAG	0.540													2	4	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138475050	138475050	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138475050delT	uc003vug.2	-						ATP6V0A4_uc003vuh.2_Intron	NM_020632	NP_065683	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						GTTGCTGttgtttttttgaga	0.080													4	2	---	---	---	---	
TTC26	79989	broad.mit.edu	37	7	138867302	138867302	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138867302delT	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1						TGCTTGGAGCTTTGGTATTCA	0.383													4	2	---	---	---	---	
ATG9B	285973	broad.mit.edu	37	7	150709313	150709314	+	3'UTR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150709313_150709314insT	uc011kvc.1	-	19					NOS3_uc003wif.2_Intron|NOS3_uc011kuy.1_Intron|ATG9B_uc003wig.3_RNA	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B						autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		tttgttttttgtttttttttta	0.391													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153582201	153582202	+	5'Flank	INS	-	T	T	rs10693546		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153582201_153582202insT	uc003wli.2	+							NM_001039350	NP_001034439	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 3						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ATGCTTGGTGGGAAAGAGAGGG	0.441													3	4	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153582202	153582203	+	5'Flank	INS	-	GT	GT	rs80143673		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153582202_153582203insGT	uc003wli.2	+							NM_001039350	NP_001034439	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 3						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGCTTGGTGGGAAAGAGAGGGA	0.441													2	5	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153868994	153868994	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153868994delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			AATTTCTGTCTTAGTGTATTT	0.348													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154388884	154388885	+	Intron	INS	-	AG	AG	rs140516065	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154388884_154388885insAG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ggagagaagacagagagagaga	0.272													3	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157921639	157921640	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157921639_157921640delAC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		AGGCAACCAAacacacacacac	0.381													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157940449	157940450	+	Intron	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157940449_157940450insC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCTCAATGACACCCCACCTCAC	0.584													5	4	---	---	---	---	
ERICH1	157697	broad.mit.edu	37	8	591808	591808	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:591808delC	uc011kwh.1	-						ERICH1_uc003wpe.1_Intron|uc003wpf.1_RNA	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1											large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		TTGGTTCCTGCCCAGACCTCA	0.602													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1784458	1784458	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1784458delG	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CTGCAGCCCAGGCAGGTATGA	0.453													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1813891	1813892	+	Intron	INS	-	CT	CT	rs138928609	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1813891_1813892insCT	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_Intron|ARHGEF10_uc010lrd.1_Intron|ARHGEF10_uc003wpu.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CACGTGATTCCGTTAGTGACCC	0.550													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4967634	4967635	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4967634_4967635insT								CSMD1 (115306 upstream) : None (None downstream)																							TTTTGGTGGCATTTAATACAAG	0.416													4	2	---	---	---	---	
DEFB1	1672	broad.mit.edu	37	8	6731266	6731266	+	Intron	DEL	A	-	-	rs5743470		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6731266delA	uc003wqs.2	-							NM_005218	NP_005209	P60022	DEFB1_HUMAN	defensin, beta 1 preproprotein						chemotaxis|defense response to bacterium|G-protein coupled receptor protein signaling pathway|innate immune response	extracellular region					0			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)		gggtgacaagatcacattcca	0.005													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10578653	10578653	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10578653delC								C8orf74 (20550 upstream) : SOX7 (2626 downstream)																							CCACATCAGACCCAGCCTCAG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	11810817	11810817	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11810817delA								CTSB (85171 upstream) : DEFB136 (20631 downstream)																							TCTCACCATTAAAAAATGGCA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13390088	13390091	+	IGR	DEL	TCTC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13390088_13390091delTCTC								DLC1 (17659 upstream) : C8orf48 (34261 downstream)																							tctctctctttctctctctctctc	0.029													32	16	---	---	---	---	
MTMR7	9108	broad.mit.edu	37	8	17177535	17177535	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17177535delA	uc003wxm.2	-						MTMR7_uc003wxn.2_Intron	NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)		tgctacacacaaaaaatgcaa	0.000													4	2	---	---	---	---	
SLC7A2	6542	broad.mit.edu	37	8	17377692	17377692	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17377692delT	uc011kyc.1	+							NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2						cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TGCAAACATGTTTTAGGAAAG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18335871	18335871	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18335871delA								NAT2 (77148 upstream) : PSD3 (48943 downstream)																							TGCAAACTTTAAAACTTAAGA	0.338													4	2	---	---	---	---	
XPO7	23039	broad.mit.edu	37	8	21807226	21807229	+	Intron	DEL	TGTT	-	-	rs67297450		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21807226_21807229delTGTT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltj.1_Intron	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		ATGGCCAGGCTGTttgttgttgtt	0.284													5	4	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25665406	25665406	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25665406delC	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GTCCCTGGGACCCCGGCCTGG	0.607													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	26045755	26045761	+	Intron	DEL	TATTCAC	-	-	rs142066164		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26045755_26045761delTATTCAC	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GAAGGAAAATTATTCACTATTCTGTGT	0.377													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32240321	32240321	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32240321delC	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		atctatctgtcccatacactg	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	32855487	32855487	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32855487delA	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																		caaacaaaccaaaaaaaaaac	0.000													4	4	---	---	---	---	
UNC5D	137970	broad.mit.edu	37	8	35573312	35573313	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35573312_35573313insA	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron|UNC5D_uc003xjt.1_Intron	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TCAGGGAACAGAAAAAAAAAAG	0.233													4	2	---	---	---	---	
ADAM32	203102	broad.mit.edu	37	8	39044800	39044801	+	Intron	INS	-	T	T	rs138677663	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39044800_39044801insT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CTTAGTATGGAttttttttgag	0.119													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47076876	47076877	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47076876_47076877insA								None (None upstream) : BEYLA (675631 downstream)																							ttgcagattctaaaaaaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49550000	49550000	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49550000delG								UBE2V2 (575548 upstream) : EFCAB1 (73351 downstream)																							acctggctgtggtagtgctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49864710	49864711	+	IGR	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49864710_49864711insC								SNAI2 (30722 upstream) : C8orf22 (120192 downstream)																							agccactacttccccatggaat	0.000													3	3	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	50824135	50824136	+	Intron	INS	-	A	A	rs150815249	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50824135_50824136insA	uc010lxy.1	+						SNTG1_uc003xqs.1_5'Flank|SNTG1_uc010lxz.1_5'Flank	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				aaagaaaaaagaaaaaaaaaag	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	51985575	51985576	+	IGR	INS	-	T	T	rs76982274		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51985575_51985576insT								SNTG1 (280148 upstream) : PXDNL (246568 downstream)																							ttgttttgttATTTttttttta	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53878598	53878599	+	IGR	INS	-	A	A	rs143208859	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53878598_53878599insA								NPBWR1 (25145 upstream) : OPRK1 (259677 downstream)																							TTTTTGTAAGGAAAAAATACCC	0.376													3	3	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56135396	56135396	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56135396delT	uc003xsf.2	+							NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			AAGGAGGGGATTTTTTTTTTA	0.363													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58651158	58651159	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58651158_58651159delTG								C8orf71 (453870 upstream) : FAM110B (255954 downstream)																							agaaggaggctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	59698681	59698681	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59698681delT								NSMAF (126277 upstream) : TOX (19296 downstream)																							TGGCAGCAAATTTTTTTTTTA	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62140422	62140423	+	IGR	INS	-	A	A	rs138200551	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62140422_62140423insA								CHD7 (360959 upstream) : CLVS1 (60102 downstream)																							aaggcccagacaaaAAAATACT	0.292													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66080558	66080558	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66080558delC								CYP7B1 (369210 upstream) : ARMC1 (434514 downstream)																							actttgagaaccacAGCCCTG	0.124													4	2	---	---	---	---	
RDH10	157506	broad.mit.edu	37	8	74225701	74225701	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74225701delT	uc003xzi.2	+						RDH10_uc003xzj.2_Intron|uc003xzk.1_Intron	NM_172037	NP_742034	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10						retinal metabolic process|retinol metabolic process|visual perception	endoplasmic reticulum membrane|integral to membrane|microsome	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity				0	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			TGTCCTTCCCTTTTTTTTTTT	0.393													4	2	---	---	---	---	
PI15	51050	broad.mit.edu	37	8	75747096	75747113	+	Intron	DEL	CACATTCTCCTGATGATT	-	-	rs67423924		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75747096_75747113delCACATTCTCCTGATGATT	uc003yal.2	+						uc003yak.1_Intron|PI15_uc003yam.2_Intron	NM_015886	NP_056970	O43692	PI15_HUMAN	protease inhibitor 15 preproprotein							extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			AGTCAGTGGGCACATTCTCCTGATGATTCACATTCTCC	0.390													3	4	---	---	---	---	
ZFHX4	79776	broad.mit.edu	37	8	77733029	77733029	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77733029delA	uc003yav.2	+						ZFHX4_uc003yau.1_Intron|ZFHX4_uc003yaw.1_Intron	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACCTACAATGAAAAAGTAATG	0.343										HNSCC(33;0.089)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77827367	77827369	+	IGR	DEL	TTA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77827367_77827369delTTA								ZFHX4 (47847 upstream) : PEX2 (65127 downstream)																							TAGAAAAACGTTATTATTATTAG	0.399													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79291528	79291528	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79291528delA								None (None upstream) : PKIA (136808 downstream)																							Ctttttttttaaaaaaaaaaa	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79761998	79761998	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79761998delT								IL7 (44240 upstream) : STMN2 (761382 downstream)																							cctccagaactttaagaaaat	0.050													4	2	---	---	---	---	
WWP1	11059	broad.mit.edu	37	8	87356036	87356037	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87356036_87356037delTG	uc003ydt.2	+						uc003yds.2_5'Flank	NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2						AATTTTTTTCTGTGTGTGTGTA	0.277													4	2	---	---	---	---	
CNBD1	168975	broad.mit.edu	37	8	88094882	88094883	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88094882_88094883delTG	uc003ydy.2	+							NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1											ovary(3)	3						aactgaaccctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92746852	92746853	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92746852_92746853insT								SLC26A7 (336472 upstream) : RUNX1T1 (224299 downstream)																							ATTAGAGCCACtttttttttga	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93131171	93131171	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93131171delC								RUNX1T1 (23465 upstream) : C8orf83 (764694 downstream)																							accttggaggccacaagttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94242674	94242674	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94242674delC								C8orf83 (212773 upstream) : FAM92A1 (470099 downstream)																							AGAAAGTTTACCATTTCTCAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94904719	94904719	+	IGR	DEL	G	-	-	rs35911249		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94904719delG								TMEM67 (74373 upstream) : PDP1 (24364 downstream)																							CCCCACTGCAGGACTGTAGCA	0.537													0	8	---	---	---	---	
PDP1	54704	broad.mit.edu	37	8	94929882	94929883	+	Intron	INS	-	TG	TG			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94929882_94929883insTG	uc003yge.2	+						PDP1_uc003ygf.2_Intron|PDP1_uc010max.2_Intron|PDP1_uc011lgm.1_Intron|PDP1_uc011lgn.1_5'Flank	NM_018444	NP_060914	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						TGTGGCTTTGCCTCCCCGGCGG	0.693													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96469655	96469655	+	IGR	DEL	A	-	-	rs1466875	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96469655delA								C8orf37 (188218 upstream) : GDF6 (684905 downstream)																							GAACAAAAATACCTTTCACAG	0.423													4	2	---	---	---	---	
MTDH	92140	broad.mit.edu	37	8	98680789	98680789	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98680789delT	uc003yhz.2	+							NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			ctgtaacaacttttttttttt	0.000													3	3	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99688905	99688905	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99688905delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		ataaaaaaGTAAAAAAAAATa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101407400	101407400	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101407400delT								RNF19A (85073 upstream) : ANKRD46 (114587 downstream)																							CAAGAGAAACTTTTTTTTCCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101461708	101461710	+	IGR	DEL	GCT	-	-	rs34823749		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101461708_101461710delGCT								RNF19A (139381 upstream) : ANKRD46 (60277 downstream)																							gatggtggtggctgcctaatgca	0.158													3	8	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103322566	103322566	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103322566delT	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			ttttaaaatgttttttgtttg	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109444119	109444119	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109444119delA								EIF3E (183160 upstream) : TTC35 (11734 downstream)																							taggaaagAGAAAAAAAATGT	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111086509	111086509	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111086509delT								KCNV1 (98433 upstream) : None (None downstream)																							TTTATATGTGTTTATGTTAGA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	115415171	115415172	+	IGR	DEL	CT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115415171_115415172delCT								CSMD3 (965929 upstream) : None (None downstream)																							cctcctcttcctctctctctct	0.000													6	4	---	---	---	---	
SLC30A8	169026	broad.mit.edu	37	8	118127826	118127826	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118127826delT	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			caaacacatgttttttcctca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118510660	118510661	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118510660_118510661insT								SLC30A8 (321708 upstream) : MED30 (22304 downstream)																							attttccagggtttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120666083	120666083	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120666083delG								ENPP2 (14977 upstream) : TAF2 (76932 downstream)																							GCGTAGATGAGGGGAGAAGGT	0.284													4	2	---	---	---	---	
COL14A1	7373	broad.mit.edu	37	8	121373302	121373302	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121373302delT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			tccagtcacattttttttttc	0.000													4	2	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121817956	121817956	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121817956delA	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			ttatagcagcaatagaaaact	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	121864185	121864185	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121864185delT								SNTB1 (39876 upstream) : HAS2 (761086 downstream)																							ACTCAAACTCTTGACTCTTTA	0.428													4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123839860	123839860	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123839860delA	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TCTTTAGGGGAAAAAAAGAGA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124010634	124010634	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124010634delT								ZHX2 (23879 upstream) : DERL1 (14934 downstream)																							CTAATTCAGAttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127703088	127703088	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127703088delG								FAM84B (132622 upstream) : LOC727677 (598974 downstream)																							TAGGAAAAATGGGACACAGAG	0.383													4	2	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	128858940	128858940	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128858940delT	uc003ysj.2	+						PVT1_uc010mdq.2_Intron|PVT1_uc010mdp.1_Intron					Human proto-oncogene myc mRNA, 5' end, clone DMmyc.												0						TGGTACTCTCtttttttttga	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132571299	132571299	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132571299delA								ADCY8 (518464 upstream) : EFR3A (345060 downstream)																							taattaatacaaaaagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139102814	139102815	+	IGR	INS	-	AT	AT	rs72541573		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139102814_139102815insAT								None (None upstream) : FAM135B (39453 downstream)																							cagcttaactcgggtcaaacaa	0.000													3	4	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143312398	143312401	+	Intron	DEL	ATCC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143312398_143312401delATCC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					ctacccacctatccatccatccat	0.074													4	2	---	---	---	---	
TOP1MT	116447	broad.mit.edu	37	8	144403652	144403653	+	Intron	DEL	CG	-	-	rs67407424		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144403652_144403653delCG	uc003yxz.2	-						TOP1MT_uc011lkd.1_Intron|TOP1MT_uc011lke.1_Intron|TOP1MT_uc010mfb.2_Intron|TOP1MT_uc011lkf.1_Intron|TOP1MT_uc010mfd.1_Intron	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	gcacgccacacgcacgccacac	0.168													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1530509	1530509	+	IGR	DEL	A	-	-	rs111795010		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1530509delA								DMRT2 (472956 upstream) : SMARCA2 (484833 downstream)																							atctgtcaggaacttgtggaa	0.139													2	4	---	---	---	---	
RFX3	5991	broad.mit.edu	37	9	3332912	3332912	+	Intron	DEL	T	-	-	rs147142725		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3332912delT	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc003zht.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		cGGAAGCACCTTATCTCAAAA	0.224													3	3	---	---	---	---	
SLC1A1	6505	broad.mit.edu	37	9	4560434	4560434	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4560434delT	uc003zij.1	+						C9orf68_uc003zik.2_Intron	NM_004170	NP_004161	P43005	EAA3_HUMAN	solute carrier family 1, member 1						D-aspartate import|L-glutamate import|synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)	agagagagggttagaaactat	0.124													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9775647	9775647	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9775647delA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GGAGATTACTAAAAAGCGAAT	0.204										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	12118205	12118205	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12118205delA								None (None upstream) : TYRP1 (575181 downstream)																							gtcctttttcaacatatttat	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	12437054	12437054	+	IGR	DEL	T	-	-	rs112139127		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12437054delT								None (None upstream) : TYRP1 (256332 downstream)																							gtccataccattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16078226	16078226	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16078226delA								C9orf93 (106331 upstream) : BNC2 (331276 downstream)																							aaagctggggaaaAAAATGAC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	21638094	21638094	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21638094delA								LOC554202 (78262 upstream) : MTAP (164541 downstream)																							aaatgagtttaaaaaattagt	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22501796	22501796	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22501796delC								DMRTA1 (49324 upstream) : None (None downstream)																							gagccagtaaccatgtcctta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	23590894	23590894	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23590894delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																		CTTATTTGCCTTTTACATTGT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	24303309	24303309	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24303309delG								ELAVL2 (477246 upstream) : None (None downstream)																							atatgttggtgggcttgatcg	0.000													4	2	---	---	---	---	
IFT74	80173	broad.mit.edu	37	9	26955649	26955649	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26955649delT	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_5'Flank|IFT74_uc003zqg.3_5'Flank	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a							cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		CATTATCTCATTTTGTGTTGT	0.214													4	2	---	---	---	---	
LINGO2	158038	broad.mit.edu	37	9	28136558	28136559	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28136558_28136559insT	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CACTTTTTCTCTTTTTTTGTGG	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31677080	31677081	+	IGR	INS	-	T	T	rs143146343		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31677080_31677081insT								None (None upstream) : ACO1 (707520 downstream)																							gagttggtgccttttttttttt	0.000													4	2	---	---	---	---	
DDX58	23586	broad.mit.edu	37	9	32525794	32525795	+	Intron	INS	-	AG	AG	rs141984562		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32525794_32525795insAG	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mjk.1_Intron|DDX58_uc011lnr.1_Intron	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		ataaatgaaACAAAATTTCTTC	0.069													3	3	---	---	---	---	
NDUFB6	4712	broad.mit.edu	37	9	32553603	32553606	+	3'UTR	DEL	AAAC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32553603_32553606delAAAC	uc003zre.1	-	4					TOPORS_uc003zrb.2_5'Flank|TOPORS_uc003zrc.2_5'Flank|NDUFB6_uc003zrf.1_3'UTR	NM_002493	NP_002484	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)	NADH(DB00157)	TGTAAGAAAAAAACAAACAAACAT	0.324													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35010935	35010935	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35010935delA								DNAJB5 (12507 upstream) : C9orf131 (30167 downstream)																							GAAGAAGGAGAAAAAAAAAAG	0.363													8	6	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37701172	37701172	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37701172delA	uc004aag.1	+						FRMPD1_uc004aah.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		TGCCAAGTGGAAGATAACGGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38405939	38405939	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38405939delT								ALDH1B1 (7284 upstream) : IGFBPL1 (3053 downstream)																							ccccgactcctttttgcatgc	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44890105	44890105	+	IGR	DEL	T	-	-	rs78386507		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44890105delT								None (None upstream) : FAM27C (100131 downstream)																							CAAACCAAAATCGAGGTAAAT	0.507													3	4	---	---	---	---	
LOC442421	442421	broad.mit.edu	37	9	66495777	66495777	+	5'Flank	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66495777delG	uc004aed.1	+											Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						ttttagaattgtttttgtaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67067623	67067623	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67067623delA								LOC442421 (564596 upstream) : AQP7P1 (186644 downstream)																							agagtgatatagatcagaaac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68410436	68410437	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68410436_68410437insT	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																		tcatttctgccttttagatttt	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68450734	68450735	+	IGR	INS	-	AAA	AAA	rs111991274		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68450734_68450735insAAA								FAM27B (656545 upstream) : MIR1299 (551504 downstream)																							atcgttatgataaaaactgcca	0.000													6	3	---	---	---	---	
APBA1	320	broad.mit.edu	37	9	72225876	72225877	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72225876_72225877insT	uc004ahh.2	-							NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						cttctaagttcttttttttttt	0.000													4	2	---	---	---	---	
GDA	9615	broad.mit.edu	37	9	74788736	74788737	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74788736_74788737delGT	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron	NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		CATTCTGTGAGTGTGTGTGTGT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	79018251	79018251	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79018251delT								RPSAP9 (3297 upstream) : GCNT1 (16501 downstream)																							CCTGTATGGCTTTTTGATTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81521394	81521394	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81521394delA								PSAT1 (576387 upstream) : TLE4 (665484 downstream)																							GCCTACGGCCAAACCATGTTT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84419445	84419445	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84419445delT								TLE1 (115849 upstream) : FLJ43950 (108907 downstream)																							GTGCGTTCTATTTTGGATGCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95882745	95882746	+	IGR	INS	-	C	C	rs149212027	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95882745_95882746insC								C9orf89 (7181 upstream) : NINJ1 (1026 downstream)																							GCCCAGTTAGACCCCCTCACTC	0.579													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95936350	95936351	+	IGR	INS	-	T	T	rs78570296		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95936350_95936351insT								NINJ1 (39780 upstream) : WNK2 (10861 downstream)																							ATGGCTCAGCCttttttttaga	0.213													4	2	---	---	---	---	
PTPDC1	138639	broad.mit.edu	37	9	96793739	96793739	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96793739delA	uc004auf.1	+						PTPDC1_uc004aug.1_Intron	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1								protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1						gcaatcaattaaaaaaaaaag	0.060													4	3	---	---	---	---	
FANCC	2176	broad.mit.edu	37	9	97911011	97911011	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97911011delA	uc004avh.2	-						FANCC_uc004avi.3_Intron	NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				gtgtgttggcaaaaaagatcc	0.000			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98360568	98360569	+	IGR	INS	-	C	C			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98360568_98360569insC								PTCH1 (81321 upstream) : C9orf130 (207803 downstream)																							CCAAATAATTTCCCTGCATAGC	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98965073	98965073	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98965073delT								NCRNA00092 (181036 upstream) : HSD17B3 (32516 downstream)																							caagactccatttcaaaaaaa	0.000													4	2	---	---	---	---	
CDC14B	8555	broad.mit.edu	37	9	99280925	99280925	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99280925delA	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron|CDC14B_uc004awi.2_Intron	NM_033331	NP_201588	O60729	CC14B_HUMAN	CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				ATCTTCCCACAAAAAAAACAA	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102392733	102392734	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102392733_102392734delCA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																		TATACACATGCACACACACAca	0.178													5	3	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107672870	107672871	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107672870_107672871delTG	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	CAAGAGAGTATGTGTGTGTGTG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110458410	110458410	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110458410delG								KLF4 (206363 upstream) : None (None downstream)																							ggagaggaaaggggggctgaa	0.000													4	2	---	---	---	---	
FKBP15	23307	broad.mit.edu	37	9	115974032	115974033	+	Intron	INS	-	AA	AA	rs111510294		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115974032_115974033insAA	uc004bgs.2	-						FKBP15_uc010muu.1_Intron|FKBP15_uc011lxd.1_Intron|FKBP15_uc010mut.1_Intron|FKBP15_uc004bgt.2_Intron	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						atttaaaaattaaaaaaaaaaa	0.332													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116564747	116564748	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116564747_116564748delAC								RGS3 (204730 upstream) : ZNF618 (73814 downstream)																							tctcaaaactacagtgatcaag	0.000													4	2	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116661418	116661418	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116661418delT	uc004bid.2	+						ZNF618_uc004bib.1_Intron|ZNF618_uc004bic.2_Intron|ZNF618_uc011lxi.1_Intron|ZNF618_uc011lxj.1_Intron	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTTTCCCTAGttttttttttt	0.219													3	3	---	---	---	---	
C9orf91	203197	broad.mit.edu	37	9	117386314	117386314	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117386314delG	uc004bjd.3	+						C9orf91_uc004bje.3_Intron|C9orf91_uc004bjf.3_5'Flank	NM_153045	NP_694590	Q5VZI3	CI091_HUMAN	hypothetical protein LOC203197							integral to membrane				pancreas(1)	1						tccttgtgttggggaacattt	0.080													4	2	---	---	---	---	
DEC1	50514	broad.mit.edu	37	9	117997944	117997945	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117997944_117997945insA	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1						GATGTTTTGCTAAAAAAAACCA	0.233													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126365560	126365560	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126365560delA	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						AATGCAAAGGAAAAAAAATCC	0.318													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126569040	126569040	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126569040delC	uc004bnz.1	-						DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						actactgtatccccagcgcct	0.100													4	2	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127288844	127288844	+	Intron	DEL	A	-	-	rs111378093		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127288844delA	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						CAGTTTGAAGAAAAAAAAAAA	0.418													5	4	---	---	---	---	
RABEPK	10244	broad.mit.edu	37	9	127968225	127968226	+	Intron	INS	-	TC	TC	rs35136218		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127968225_127968226insTC	uc004bpi.2	+						RABEPK_uc004bph.1_Intron|RABEPK_uc004bpj.2_Intron|RABEPK_uc004bpk.2_Intron|RABEPK_uc004bpl.1_Intron|RABEPK_uc004bpm.2_Intron	NM_005833	NP_005824	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs						receptor-mediated endocytosis|vesicle docking involved in exocytosis	endosome membrane|plasma membrane				ovary(1)	1						ggaaaagagaattgagaatgac	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	129307930	129307930	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129307930delC								FAM125B (34231 upstream) : LMX1B (68818 downstream)																							gttcctgatgcccagggaggC	0.408													4	2	---	---	---	---	
CAMSAP1	157922	broad.mit.edu	37	9	138741702	138741703	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138741702_138741703insT	uc004cgr.3	-						CAMSAP1_uc004cgq.3_Intron|CAMSAP1_uc010nbg.2_Intron	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein							cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		TGTAGTAAACATTTTTTTTTTT	0.238													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	532092	532093	+	Intron	INS	-	AAT	AAT	rs139890243	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:532092_532093insAAT	uc001ifp.2	-						DIP2C_uc009xhk.1_5'Flank	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TCTCTAAACCAAATATGTTGAA	0.376													3	5	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1780486	1780486	+	5'Flank	DEL	T	-	-	rs148088220		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1780486delT	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		TTTTAAGCAATTTTTTTTTCC	0.328													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	1863560	1863561	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1863560_1863561insA								ADARB2 (83842 upstream) : None (None downstream)																							TATAATCGAGGAAAAAAAGGAG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2035671	2035672	+	IGR	INS	-	CAAAA	CAAAA	rs150756406	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2035671_2035672insCAAAA								ADARB2 (255953 upstream) : None (None downstream)																							CTCAGTAATATcaaaacaaaac	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2079408	2079409	+	IGR	INS	-	ATG	ATG	rs139862634	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2079408_2079409insATG								ADARB2 (299690 upstream) : None (None downstream)																							TACGAGCAATAATgatgatgat	0.198													4	2	---	---	---	---	
FBXO18	84893	broad.mit.edu	37	10	5955326	5955326	+	Intron	DEL	C	-	-	rs3841704		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5955326delC	uc001iis.2	+						FBXO18_uc001iir.2_Intron|FBXO18_uc009xig.2_Intron|FBXO18_uc001iit.2_Intron	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2						DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3						GTTTTATCCACAGGTGTAGTA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6758480	6758481	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6758480_6758481delTG								PRKCQ (136242 upstream) : SFMBT2 (445768 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8685557	8685557	+	IGR	DEL	T	-	-	rs66744803		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8685557delT								GATA3 (568395 upstream) : None (None downstream)																							AATGACTCTCTTTTTTTTTGG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	12385690	12385690	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12385690delT								CDC123 (93103 upstream) : CAMK1D (5893 downstream)																							ttcttgcctcttttttttttt	0.000													3	3	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12812434	12812435	+	Intron	INS	-	T	T	rs140339479	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12812434_12812435insT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		CATTAGAATACTTGTGATTGTT	0.312													4	2	---	---	---	---	
FAM171A1	221061	broad.mit.edu	37	10	15318181	15318181	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15318181delT	uc001iob.2	-							NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4						AGAAGttttcttttttttttc	0.149													9	4	---	---	---	---	
FAM171A1	221061	broad.mit.edu	37	10	15354307	15354312	+	Intron	DEL	TCTAAG	-	-	rs72403746		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15354307_15354312delTCTAAG	uc001iob.2	-							NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4						CAACTGTCACTCTAAGTCTAAAGCCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	17258281	17258282	+	Intron	INS	-	A	A	rs139642521	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17258281_17258282insA	uc001iot.1	-											Homo sapiens cDNA clone IMAGE:5760022, partial cds.																		TGTCTGAGTCCAAAAAAAAAGA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	17362669	17362670	+	IGR	INS	-	ATC	ATC	rs150271971		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17362669_17362670insATC								VIM (83077 upstream) : ST8SIA6 (7 downstream)																							ATGAGTCAGATATGGTGTCCAT	0.332													10	7	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17419839	17419839	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17419839delT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						ACGAAATTACTTTTTTATCGC	0.378													4	2	---	---	---	---	
PIP4K2A	5305	broad.mit.edu	37	10	22882276	22882277	+	Intron	INS	-	A	A	rs76422289		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22882276_22882277insA	uc001irl.3	-						PIP4K2A_uc010qcu.1_5'Flank	NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						TTGAGAGAAGGAAAAAAAAAAA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	23602952	23602953	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23602952_23602953insA								PTF1A (119773 upstream) : C10orf67 (2568 downstream)																							ATTTAGGAGGTAAAAAAACTGG	0.213													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27378822	27378826	+	Intron	DEL	ATTCT	-	-	rs112167562		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27378822_27378826delATTCT	uc001ith.2	-						ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						ATTCACTGCCATTCTAAAATTACCT	0.307													16	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	28051174	28051175	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28051174_28051175delCA								MKX (16396 upstream) : ARMC4 (49924 downstream)																							catgcatctccacacacacaca	0.074													4	2	---	---	---	---	
ARMC4	55130	broad.mit.edu	37	10	28101114	28101115	+	3'UTR	DEL	TT	-	-	rs67356646		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28101114_28101115delTT	uc009xky.2	-	20					ARMC4_uc010qds.1_3'UTR|ARMC4_uc010qdt.1_3'UTR|ARMC4_uc001itz.2_3'UTR	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4								binding			ovary(4)|skin(2)	6						GGCCATATCCTTTTTATTAAAA	0.347													2	8	---	---	---	---	
ARHGAP12	94134	broad.mit.edu	37	10	32202705	32202705	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32202705delT	uc001ivz.1	-						ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				TCTAGCAGGGTTTTTTTTTTT	0.184													6	3	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34954834	34954835	+	Intron	INS	-	G	G	rs60764123		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34954834_34954835insG	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				agaacagaacaaaaagaaaaga	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35242060	35242060	+	IGR	DEL	T	-	-	rs144676017	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35242060delT								PARD3 (138137 upstream) : CUL2 (56748 downstream)																							tttatctatcttttttttgag	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35973473	35973473	+	IGR	DEL	A	-	-	rs112104980		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35973473delA								FZD8 (43111 upstream) : None (None downstream)																							atttttaaacaaaaaaaaatt	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42626811	42626811	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42626811delC								None (None upstream) : LOC441666 (200504 downstream)																							gcctgggcagctttttgacat	0.000													4	2	---	---	---	---	
FAM21C	253725	broad.mit.edu	37	10	46259161	46259161	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46259161delT	uc001jcu.2	+						FAM21C_uc001jcs.1_Intron|FAM21C_uc001jct.2_Intron|FAM21C_uc010qfi.1_Intron|FAM21C_uc010qfj.1_Intron|FAM21C_uc010qfk.1_Intron	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725											ovary(1)	1						GACGCAGttcttttttttttt	0.149													7	7	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47138198	47138199	+	Intron	INS	-	CA	CA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47138198_47138199insCA	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aaacacaaatgcacacacacac	0.366													8	5	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49467679	49467680	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49467679_49467680delGT	uc001jgi.2	-						FRMPD2_uc001jgj.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		gtgtgtgtaagtgtgtgtgtgt	0.203													4	2	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50185470	50185471	+	Intron	INS	-	CATC	CATC			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50185470_50185471insCATC	uc001jha.3	+						WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						acccatccactcatccatccat	0.069													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51124338	51124339	+	Intron	INS	-	A	A	rs150322660	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51124338_51124339insA	uc001jif.2	-						PARG_uc001jih.2_Intron|PARG_uc001jig.2_Intron|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Intron|PARG_uc009xoj.2_Intron|PARG_uc010qgx.1_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		aaactggatcttgaggggtaaa	0.084													1	5	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56046388	56046389	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56046388_56046389insT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ACTCTTCCTGAtttttttttct	0.144										HNSCC(58;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57551603	57551604	+	IGR	INS	-	T	T	rs141864864	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57551603_57551604insT								PCDH15 (163901 upstream) : ZWINT (565595 downstream)																							CTGACCTAGAGATTTTATTCTC	0.351													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57694877	57694877	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57694877delT								PCDH15 (307175 upstream) : ZWINT (422322 downstream)																							gtctataaaattttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58392589	58392589	+	IGR	DEL	T	-	-	rs112808363		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58392589delT								ZWINT (271555 upstream) : None (None downstream)																							atccccttccttttttgtgtg	0.000													5	6	---	---	---	---	
BICC1	80114	broad.mit.edu	37	10	60335073	60335074	+	Intron	INS	-	A	A	rs138650617	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60335073_60335074insA	uc001jki.1	+							NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						caaagatccccgggtccctgga	0.030													0	6	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65224472	65224472	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65224472delG	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron|LOC84989_uc010qir.1_5'Flank	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					AAAAAAAAAAGATAATCAATT	0.333													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68767839	68767839	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68767839delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmz.1_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						ttTTTTCTTGTTTTTTTTTAA	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71376950	71376950	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71376950delT								NEUROG3 (43828 upstream) : C10orf35 (13053 downstream)																							TCTTCAAACATTTTTTTTTGT	0.378													5	4	---	---	---	---	
PCBD1	5092	broad.mit.edu	37	10	72646976	72646976	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72646976delA	uc001jrn.1	-							NM_000281	NP_000272	P61457	PHS_HUMAN	pterin-4 alpha-carbinolamine						L-phenylalanine catabolic process|regulation of transcription, DNA-dependent|tetrahydrobiopterin biosynthetic process|transcription, DNA-dependent	cytosol|nucleus	4-alpha-hydroxytetrahydrobiopterin dehydratase activity|identical protein binding|transcription coactivator activity				0						TCTGCATTACAAAAAAAAAAC	0.468													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	74123589	74123590	+	IGR	INS	-	C	C	rs140826772	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74123589_74123590insC								DNAJB12 (8682 upstream) : CBARA1 (3508 downstream)																							ctccttgaaaacCTTGCTTAGT	0.198													4	2	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	77630481	77630481	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77630481delC	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					TGTCTACTCTCCCCATTCACT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	78487807	78487807	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78487807delT								C10orf11 (170683 upstream) : KCNMA1 (141552 downstream)																							CTTTTTGTCATTTTCTCAAGC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	78595981	78595981	+	IGR	DEL	G	-	-	rs11322830		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78595981delG								C10orf11 (278857 upstream) : KCNMA1 (33378 downstream)																							tatattttctggctatgtgtt	0.040													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	83510346	83510346	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83510346delT								None (None upstream) : NRG3 (124724 downstream)																							TATAAAATGGTTTTTAATTTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	87181338	87181339	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87181338_87181339insG								FAM190B (903062 upstream) : GRID1 (177973 downstream)																							TTAATAGGCTCGGGGGGGTGCT	0.510													4	2	---	---	---	---	
WAPAL	23063	broad.mit.edu	37	10	88235004	88235004	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88235004delA	uc001kdo.2	-						WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_Intron	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog						cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1						ATAGAAAGGTAACACCTCATC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	90634764	90634764	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90634764delT								ANKRD22 (23032 upstream) : STAMBPL1 (5262 downstream)																							AGACGAGAGATTACTCCAAGC	0.423													4	2	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91480732	91480732	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91480732delG	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_5'Flank	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						ccaaagtgctgggattatagg	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91666322	91666322	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91666322delT								KIF20B (131622 upstream) : HTR7 (834256 downstream)																							gatgttgagctttttttcaca	0.000													4	2	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93278596	93278596	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93278596delT	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						tgtttttttgttttttttttt	0.174													2	4	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93691945	93691945	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93691945delA	uc001khr.2	+						BTAF1_uc009xua.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				GCAGAGGACCAAAGGAAAAGT	0.438													4	2	---	---	---	---	
CUEDC2	79004	broad.mit.edu	37	10	104191369	104191369	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104191369delC	uc001kvn.2	-							NM_024040	NP_076945	Q9H467	CUED2_HUMAN	CUE domain containing 2							cytoplasm|nucleus	protein binding				0		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AATTGTGTGGCCCCATCCTAT	0.318													4	2	---	---	---	---	
SH3PXD2A	9644	broad.mit.edu	37	10	105449842	105449842	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105449842delG	uc001kxj.1	-						SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqt.1_Intron|SH3PXD2A_uc009xxn.1_Intron|SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		gactgtgtgtgggcagtcacc	0.159													4	2	---	---	---	---	
SLK	9748	broad.mit.edu	37	10	105777729	105777730	+	Intron	INS	-	T	T	rs145780598	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105777729_105777730insT	uc001kxo.1	+						SLK_uc001kxp.1_Intron	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2						apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TATTCTAATGCTTTTTTCTTAG	0.302													5	8	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108488673	108488674	+	Intron	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108488673_108488674delGA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CTCTACATCTGAGACCTCTTCC	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109803712	109803712	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109803712delG								SORCS1 (879420 upstream) : None (None downstream)																							agctaaagatggggttctttg	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	110959714	110959714	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110959714delA								None (None upstream) : XPNPEP1 (664810 downstream)																							TCACAAAGTCAAAAAAAAGTT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111007515	111007515	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111007515delC								None (None upstream) : XPNPEP1 (617009 downstream)																							GTACAGCTGACCCCCTTGTGA	0.413													3	6	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112333836	112333836	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112333836delC	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		gctttttaaacttgaatgtaa	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116682987	116682988	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116682987_116682988delAC								FAM160B1 (23402 upstream) : TRUB1 (14927 downstream)																							gtacagtggtacgatctcagct	0.089													4	2	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	120966192	120966192	+	5'Flank	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120966192delC	uc001led.2	+						GRK5_uc009xzh.2_5'Flank|GRK5_uc010qta.1_5'Flank	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		CATTAACGCTCCCCACGGCGG	0.542													4	2	---	---	---	---	
FLJ46361	375940	broad.mit.edu	37	10	124536955	124536956	+	Intron	INS	-	ACA	ACA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124536955_124536956insACA	uc001lgo.1	+							NR_003570				Homo sapiens cDNA FLJ46361 fis, clone TESTI4049899, weakly  similar to Homo sapiens deleted in malignant brain tumors 1 (DMBT1).												0						GAGGTGAacacacacacacaca	0.158													4	2	---	---	---	---	
MGMT	4255	broad.mit.edu	37	10	131300142	131300143	+	Intron	INS	-	T	T	rs148851700	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131300142_131300143insT	uc001lkh.2	+							NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)		CGTTCCACTCCTTCAAGGGTGG	0.559								Direct_reversal_of_damage					5	7	---	---	---	---	
GPR123	84435	broad.mit.edu	37	10	134906312	134906312	+	Intron	DEL	A	-	-	rs7476195		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134906312delA	uc001llx.3	+						GPR123_uc001llw.2_Intron	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		agagggagggaagggagggaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	783078	783078	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:783078delT								PDDC1 (5591 upstream) : CEND1 (4032 downstream)																							GCTTTCCTGCTTTTTTCCCGT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1961137	1961138	+	IGR	DEL	TC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1961137_1961138delTC								TNNT3 (1202 upstream) : MRPL23 (7364 downstream)																							TGAGGCCCTGTCTCTCTCTCAC	0.267													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	3227981	3227983	+	IGR	DEL	TGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3227981_3227983delTGA								OSBPL5 (40012 upstream) : C11orf36 (11579 downstream)																							gtggtgatggtgatgatggtggt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	5207753	5207754	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5207753_5207754insT								OR52A1 (34154 upstream) : OR51V1 (13212 downstream)																							TAATTTGTGCATTTTTTTTCTT	0.396													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11460375	11460375	+	Intron	DEL	A	-	-	rs66487564		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11460375delA	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		CAACATGGACAAATACGATCA	0.507													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	12587259	12587260	+	IGR	INS	-	A	A	rs148170557	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12587259_12587260insA								PARVA (35849 upstream) : TEAD1 (108709 downstream)																							gatcctgtcttaaaaaaaataa	0.000													2	4	---	---	---	---	
TEAD1	7003	broad.mit.edu	37	11	12918995	12918998	+	Intron	DEL	ACCC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12918995_12918998delACCC	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TTCCTGACCTACCCAGGTTGAATG	0.441													5	9	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14833829	14833829	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14833829delA	uc001mln.2	+						PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						aaggctgtttaaaaaACACGT	0.015													4	2	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14856992	14856992	+	Intron	DEL	T	-	-	rs36116790	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14856992delT	uc001mln.2	+						PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						ttAAAAAAAATTTTTTTTTTG	0.124													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16624580	16624580	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16624580delA	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron			P35712	SOX6_HUMAN	Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						ataaaaaaagaaaaaaaaaag	0.149													4	2	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	18016652	18016653	+	Intron	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18016652_18016653delAG	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron|SERGEF_uc001mno.1_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						agagaaagaaagagagagagag	0.347													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20816239	20816239	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20816239delG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						tgatgatactgataatgacga	0.234													5	4	---	---	---	---	
SLC17A6	57084	broad.mit.edu	37	11	22383574	22383574	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22383574delT	uc001mqk.2	+							NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent						sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						GTCTAAGACCTTTTTTTTTTT	0.294													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25533935	25533937	+	IGR	DEL	GTT	-	-	rs143893432		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25533935_25533937delGTT								LUZP2 (429753 upstream) : ANO3 (676892 downstream)																							gatctggtacgttgttgttgttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30102755	30102755	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30102755delA								KCNA4 (64267 upstream) : FSHB (149808 downstream)																							agctagggagaaaaaaaaaag	0.000													4	2	---	---	---	---	
ABTB2	25841	broad.mit.edu	37	11	34218677	34218678	+	Intron	INS	-	A	A	rs148675830	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34218677_34218678insA	uc001mvl.1	-							NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CAGCTCAGAGGAAAAAAAAATC	0.540													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37045363	37045363	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37045363delT								C11orf74 (348973 upstream) : None (None downstream)																							ATCAAAGGTATAAAGGCCAGt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37798769	37798770	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37798769_37798770insA								None (None upstream) : None (None downstream)																							CTTGAGAAGTTAAAAAAAAGAA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39614763	39614763	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39614763delA								None (None upstream) : LRRC4C (520990 downstream)																							CTTGATTAATAAGGCTGAGTA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	40107113	40107114	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40107113_40107114delCA								None (None upstream) : LRRC4C (28639 downstream)																							TATAACACCTCACACACACACA	0.366													4	3	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40394474	40394475	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40394474_40394475insT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				ATAATTTGGGATTTTTTTTTAA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42969518	42969518	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42969518delA								None (None upstream) : API5 (363987 downstream)																							ggttataagcaaaaaaaagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44360112	44360113	+	IGR	INS	-	A	A	rs148893697	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44360112_44360113insA								ALX4 (28396 upstream) : CD82 (227028 downstream)																							CCCTTACAAGGAAAAAAAAAAG	0.322													4	4	---	---	---	---	
TP53I11	9537	broad.mit.edu	37	11	44956846	44956847	+	Intron	INS	-	G	G	rs143756531	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44956846_44956847insG	uc001myi.2	-						TP53I11_uc001myf.1_Intron|TP53I11_uc001myj.2_Intron|TP53I11_uc001myk.2_Intron|TP53I11_uc001myl.2_Intron|TP53I11_uc001mym.2_Intron	NM_006034	NP_006025	O14683	P5I11_HUMAN	p53-induced protein						negative regulation of cell proliferation|response to stress	integral to membrane				ovary(1)	1						GCAGTGGGTGTGGGGGGGCCGC	0.550													4	3	---	---	---	---	
KIAA0652	9776	broad.mit.edu	37	11	46666136	46666136	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666136delT	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)		aaaaaaaaaattttttttttt	0.403													9	4	---	---	---	---	
LOC440040	440040	broad.mit.edu	37	11	49786241	49786241	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49786241delT	uc010rhy.1	+						LOC440040_uc009ymb.2_Intron	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						CAGTGTAGTCTTACTTGCAGT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50541462	50541462	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50541462delA								LOC646813 (161659 upstream) : OR4A5 (869986 downstream)																							gattaaaactaaaaaaaagcg	0.000													4	2	---	---	---	---	
MS4A8B	83661	broad.mit.edu	37	11	60474783	60474784	+	Intron	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60474783_60474784delGA	uc001npv.2	+						MS4A8B_uc009yne.1_Intron	NM_031457	NP_113645	Q9BY19	M4A8B_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0						TATGgagagcgagagagagaga	0.470													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60936316	60936316	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60936316delG								VPS37C (7400 upstream) : PGA3 (34668 downstream)																							tttggagggtgGAAACCAGCT	0.114													4	2	---	---	---	---	
PLCB3	5331	broad.mit.edu	37	11	64031076	64031076	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64031076delC	uc001nzb.2	+						PLCB3_uc009ypg.1_Intron|PLCB3_uc009yph.1_Intron|PLCB3_uc009ypi.2_Intron	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3						intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2						TCCGGTGAGGCCTTGGTGGGC	0.642													35	25	---	---	---	---	
PPP2R5B	5526	broad.mit.edu	37	11	64689974	64689974	+	5'Flank	DEL	C	-	-	rs631018		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64689974delC	uc001oby.2	+						PPP2R5B_uc001obz.2_5'Flank	NM_006244	NP_006235	Q15173	2A5B_HUMAN	beta isoform of regulatory subunit B56, protein						signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2						aacaaacaaacaaaaaaTGTT	0.174													4	2	---	---	---	---	
SNX15	29907	broad.mit.edu	37	11	64799369	64799369	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64799369delA	uc001oci.3	+						SNX15_uc009ypy.2_Intron|SNX15_uc001ocj.2_Intron|SNX15_uc001ock.2_Intron	NM_013306	NP_037438	Q9NRS6	SNX15_HUMAN	sorting nexin 15 isoform A						cell communication|intracellular protein transport	cytoplasmic vesicle membrane|cytosol	phosphatidylinositol binding|protein transporter activity			ovary(1)	1						actccatctcaaaaaaaaaaa	0.209													6	3	---	---	---	---	
PACS1	55690	broad.mit.edu	37	11	65842163	65842163	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65842163delT	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6						TTAGGTCACATTTTTTTTAAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67679066	67679066	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67679066delT								LOC645332 (106259 upstream) : UNC93B1 (79509 downstream)																							caaacctcgattttttacttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69224933	69224934	+	IGR	INS	-	GAAT	GAAT	rs139710880	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69224933_69224934insGAAT								MYEOV (68484 upstream) : CCND1 (230939 downstream)																							CTTGGCACTGGgaatgaatgaa	0.376													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71042458	71042458	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71042458delG								SHANK2 (106650 upstream) : DHCR7 (103001 downstream)																							tgATCTAACTGGAGAGAAAAG	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	75954233	75954234	+	IGR	INS	-	A	A	rs145996582	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75954233_75954234insA								WNT11 (32430 upstream) : PRKRIR (106770 downstream)																							GATGCAGGTGGCAGAGCCCAGG	0.609													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76387137	76387137	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76387137delG								LRRC32 (5346 upstream) : GUCY2E (4074 downstream)																							gaagcaacctgggtttaggag	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79870774	79870774	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79870774delA								ODZ4 (719079 upstream) : None (None downstream)																							CAAAGACAACAAAAAATAATA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81406168	81406168	+	IGR	DEL	A	-	-	rs7928035	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81406168delA								None (None upstream) : None (None downstream)																							aggacccatgaaaaaaaaaat	0.000													4	2	---	---	---	---	
TMEM135	65084	broad.mit.edu	37	11	86797516	86797516	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86797516delG	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069	Q86UB9	TM135_HUMAN	transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				agggtgaagagggcagagaag	0.000													4	2	---	---	---	---	
AMOTL1	154810	broad.mit.edu	37	11	94600075	94600075	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94600075delG	uc001pfb.2	+						AMOTL1_uc001pfc.2_Intron	NM_130847	NP_570899	Q8IY63	AMOL1_HUMAN	angiomotin like 1							cytoplasm|tight junction	identical protein binding			ovary(1)|breast(1)	2		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				TAGGTTTCTTGGGGGCAGGCA	0.557													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95962138	95962139	+	Intron	INS	-	C	C	rs149010933		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95962138_95962139insC	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TAGTTGAACAAAAAAAAAATGC	0.332			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	96024192	96024192	+	Intron	DEL	A	-	-	rs72247789		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96024192delA	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				AAAAAACTTGAAAAAAAGTTG	0.194			T	MECT1|CRTC3	salivary gland mucoepidermoid								5	3	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99524318	99524319	+	Intron	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99524318_99524319insG	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		GTAAAATGTGAGGGGGGAAAAT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101577680	101577681	+	IGR	INS	-	T	T	rs72519094		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101577680_101577681insT								TRPC6 (123021 upstream) : ANGPTL5 (183725 downstream)																							CCACAAAAAAAATGCCAGTTTC	0.173													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102557559	102557560	+	IGR	DEL	TA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102557559_102557560delTA								MMP20 (61496 upstream) : MMP27 (4855 downstream)																							ttgcacagcctatatatatata	0.050													4	2	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103096684	103096685	+	Intron	INS	-	T	T	rs35928432		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103096684_103096685insT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		attcctaagtattttttttttt	0.000													4	2	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105675080	105675081	+	Intron	INS	-	CA	CA	rs147192018	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105675080_105675081insCA	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	aaacacacatgcacacacacac	0.272													3	4	---	---	---	---	
RAB39	54734	broad.mit.edu	37	11	107824132	107824132	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107824132delG	uc001pjt.2	+							NM_017516	NP_059986	Q14964	RB39A_HUMAN	RAB39, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0				BRCA - Breast invasive adenocarcinoma(274;3.04e-05)|Epithelial(105;8.56e-05)|all cancers(92;0.00179)		atgggaaagtggaggccaggc	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109042219	109042219	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109042219delC								DDX10 (230573 upstream) : C11orf87 (250656 downstream)																							GTTTCACCATCCCCTATCTAC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109127813	109127813	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109127813delT								DDX10 (316167 upstream) : C11orf87 (165062 downstream)																							TGCTTACCTCTGGATGACCTG	0.373													4	2	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	114041744	114041744	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114041744delG	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GAGCACTGCTGGGGGGCCAGT	0.522													4	2	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	114090383	114090383	+	Intron	DEL	A	-	-	rs35501585		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114090383delA	uc001pop.2	+						ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		AAAAAAGCTTAAAAAAAAAAA	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115019022	115019023	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115019022_115019023delGT								FAM55B (441370 upstream) : CADM1 (20930 downstream)																							tgggagggtggtgtgtgtgtgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115584791	115584791	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115584791delT								CADM1 (209550 upstream) : None (None downstream)																							tactcttaagtttagagccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115964859	115964859	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115964859delT								CADM1 (589618 upstream) : BUD13 (654029 downstream)																							gaatggaaggtttttttaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116568114	116568114	+	IGR	DEL	T	-	-	rs5795049		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116568114delT								None (None upstream) : BUD13 (50774 downstream)																							ttttgttttgtttttgttttg	0.050													4	3	---	---	---	---	
ZNF259	8882	broad.mit.edu	37	11	116650256	116650256	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116650256delA	uc001ppp.2	-						ZNF259_uc009yzd.2_Intron|ZNF259_uc001ppq.2_Intron	NM_003904	NP_003895	O75312	ZPR1_HUMAN	zinc finger protein 259						cell proliferation|signal transduction	cytoplasm|nucleolus					0	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		TTGACTACAGAAAAAAAAGGG	0.403													4	2	---	---	---	---	
GRIK4	2900	broad.mit.edu	37	11	120766588	120766588	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120766588delC	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	CTTAACAGCTCATCCCTCACC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121124996	121124999	+	IGR	DEL	AAAC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121124996_121124999delAAAC								TECTA (63483 upstream) : SC5DL (38389 downstream)																							tctcaaagcaaaacaaacaaaCAA	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123663934	123663934	+	IGR	DEL	A	-	-	rs79249159		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123663934delA								OR6X1 (38708 upstream) : OR6M1 (12183 downstream)																							acttttgctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
OR10G9	219870	broad.mit.edu	37	11	123893481	123893504	+	5'Flank	DEL	AGAGAGAGAGAGAGAGAGAGAGAG	-	-	rs72075895		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123893481_123893504delAGAGAGAGAGAGAGAGAGAGAGAG	uc010sad.1	+							NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGTATGTGACagagagagagagagagagagagagagagagagag	0.210													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124566377	124566378	+	IGR	DEL	AC	-	-	rs72412549		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124566377_124566378delAC								SPA17 (1692 upstream) : NRGN (43451 downstream)																							TGCATTCcatacacacacacac	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	126879621	126879626	+	IGR	DEL	GCAAAA	-	-	rs112199631		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126879621_126879626delGCAAAA								KIRREL3 (6266 upstream) : None (None downstream)																							TGAGACCCTGGCAAAATAATGTATGC	0.316													13	6	---	---	---	---	
LOC100288778	100288778	broad.mit.edu	37	12	84447	84448	+	Intron	INS	-	GTT	GTT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84447_84448insGTT	uc010scy.1	+						uc010scx.1_Intron|LOC100288778_uc010scz.1_Intron|LOC100288778_uc010sdb.1_Intron					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						AAAGTGATGCAGTTTAtggaat	0.282													4	4	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3223473	3223473	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3223473delT	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			ctgcttttgattttttttcaa	0.000													4	2	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6183130	6183130	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6183130delG	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	AAGACCCATCGGGGGCACCCA	0.582													4	2	---	---	---	---	
DPPA3	359787	broad.mit.edu	37	12	7869200	7869200	+	Intron	DEL	C	-	-	rs58184520		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7869200delC	uc001qtf.2	+							NM_199286	NP_954980	Q6W0C5	DPPA3_HUMAN	stella							cytoplasm|nucleus					0				Kidney(36;0.0887)		tAGGTTGATACTTTCACGTGC	0.224													5	4	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11116864	11116864	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11116864delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						ATATAGATACTTTTTAGACTA	0.264										HNSCC(22;0.051)			2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13654224	13654225	+	IGR	INS	-	GC	GC	rs146969284	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13654224_13654225insGC								C12orf36 (124579 upstream) : GRIN2B (60185 downstream)																							CCCTGGCACCGATACTAACTTA	0.312													6	5	---	---	---	---	
PLEKHA5	54477	broad.mit.edu	37	12	19511620	19511620	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19511620delC	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTCAACTTTACAGTGATGATA	0.393													4	2	---	---	---	---	
PDE3A	5139	broad.mit.edu	37	12	20609734	20609734	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20609734delA	uc001reh.1	+							NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A						lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	GATGACTGGTAAAAAGAATTA	0.398													4	2	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21458676	21458676	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21458676delC	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_Intron|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Intron|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						TCCTTTGTTTCCCCCATGGGG	0.443													4	2	---	---	---	---	
ST8SIA1	6489	broad.mit.edu	37	12	22437108	22437109	+	Intron	INS	-	A	A	rs151328984	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22437108_22437109insA	uc001rfo.3	-						ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025	Q92185	SIA8A_HUMAN	alpha-2,8-sialyltransferase 1						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3						GTACCAACGACAAAAAAACAAA	0.421													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	23063647	23063647	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23063647delA								ETNK1 (220040 upstream) : SOX5 (621585 downstream)																							acacaaacagaaaaaaaaaac	0.000													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26522258	26522258	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26522258delG	uc001rhg.2	-							NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					agtcagtagaggggcaagtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30713346	30713347	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30713346_30713347insA								TMTC1 (775654 upstream) : IPO8 (68576 downstream)																							caagaaaccccaaatggtgttc	0.000													4	2	---	---	---	---	
CAPRIN2	65981	broad.mit.edu	37	12	30874289	30874290	+	Intron	DEL	TA	-	-	rs138684084		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30874289_30874290delTA	uc001rji.1	-						CAPRIN2_uc001rjf.1_Intron|CAPRIN2_uc001rjg.1_Intron|CAPRIN2_uc001rjh.1_Intron|CAPRIN2_uc001rjj.1_Intron|CAPRIN2_uc001rjk.3_Intron|CAPRIN2_uc001rjl.3_Intron|CAPRIN2_uc001rjm.1_Intron	NM_001002259	NP_001002259	Q6IMN6	CAPR2_HUMAN	C1q domain containing 1 isoform 1						negative regulation of cell growth|negative regulation of translation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of transcription from RNA polymerase II promoter	mitochondrion|receptor complex	receptor binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GAGATCATAGTATAACTGTGCT	0.431													4	3	---	---	---	---	
CPNE8	144402	broad.mit.edu	37	12	39204290	39204290	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39204290delG	uc001rls.1	-							NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				tcggccatttgggtaagctga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39363810	39363811	+	IGR	INS	-	A	A	rs138985814	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39363810_39363811insA								CPNE8 (64390 upstream) : KIF21A (323220 downstream)																							ATTTCTCACAGAAAAAAAAAGA	0.322													4	2	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40446518	40446518	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40446518delG	uc010skm.1	-						SLC2A13_uc001rmf.2_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				ACTGACATTCGGCCAGGTAGG	0.403										HNSCC(50;0.14)			4	2	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40495629	40495629	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40495629delT	uc010skm.1	-						SLC2A13_uc001rmf.2_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				AGGTTGTTTGTTTTTTTTTTT	0.368										HNSCC(50;0.14)			4	2	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41786331	41786331	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41786331delC	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CTCCATATTACCAGAGTATGA	0.393													4	2	---	---	---	---	
TMEM117	84216	broad.mit.edu	37	12	44499300	44499301	+	Intron	INS	-	T	T	rs147968285	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44499300_44499301insT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		ttcaaagtgtgtttttttttgc	0.000													3	5	---	---	---	---	
NELL2	4753	broad.mit.edu	37	12	44959617	44959617	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44959617delA	uc001rog.2	-						NELL2_uc001rof.3_Intron|NELL2_uc001roh.2_Intron|NELL2_uc009zkd.2_Intron|NELL2_uc010skz.1_Intron|NELL2_uc010sla.1_Intron|NELL2_uc001roi.1_Intron|NELL2_uc010slb.1_Intron	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor						cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		gtggggaaggaatgggaaacg	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47040324	47040324	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47040324delT								SLC38A2 (273679 upstream) : SLC38A4 (118220 downstream)																							tgtccatctctttttgcatgc	0.000													4	2	---	---	---	---	
RHEBL1	121268	broad.mit.edu	37	12	49463362	49463374	+	Intron	DEL	CCTCCACTCTTCC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49463362_49463374delCCTCCACTCTTCC	uc001rtc.1	-						RHEBL1_uc001rtd.1_Intron|RHEBL1_uc009zlc.1_Intron	NM_144593	NP_653194	Q8TAI7	REBL1_HUMAN	Ras homolog enriched in brain like 1 precursor						positive regulation of NF-kappaB transcription factor activity|small GTPase mediated signal transduction|TOR signaling cascade	cytoplasm|plasma membrane	GTP binding|GTPase activity|protein binding			lung(1)|breast(1)	2						CTCTTCCAATCCTCCACTCTTCCATTCCTCCAC	0.573													6	4	---	---	---	---	
BIN2	51411	broad.mit.edu	37	12	51691187	51691188	+	Intron	INS	-	A	A	rs34375896		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51691187_51691188insA	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2							cytoplasm	protein binding			ovary(1)	1						ccgtctctactaaaaaaaaaaa	0.000													6	3	---	---	---	---	
KRT71	112802	broad.mit.edu	37	12	52944238	52944238	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52944238delC	uc001sao.2	-							NM_033448	NP_258259	Q3SY84	K2C71_HUMAN	keratin 71								structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.194)		agcggtggagcccggaactga	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54134558	54134558	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54134558delG								CALCOCO1 (13251 upstream) : HOXC13 (198018 downstream)																							CTGTAAAtgtgggtgagttta	0.025													4	2	---	---	---	---	
PDE1B	5153	broad.mit.edu	37	12	54955632	54955633	+	Intron	INS	-	C	C	rs149849996	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54955632_54955633insC	uc001sgd.1	+						PDE1B_uc010soz.1_Intron|PDE1B_uc010spa.1_Intron|PDE1B_uc001sgf.2_Intron|PDE1B_uc001sge.2_Intron|PDE1B_uc009znq.2_Intron	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1						activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						CCCATTTCCATCCCCCCCCACC	0.356													4	2	---	---	---	---	
KIF5A	3798	broad.mit.edu	37	12	57965358	57965358	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57965358delT	uc001sor.1	+						KIF5A_uc010srr.1_Intron	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						ttttcttttcttttttttttt	0.204													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61884365	61884365	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61884365delT								None (None upstream) : FAM19A2 (217678 downstream)																							gctaaacagatttttttTTCT	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	62042044	62042045	+	IGR	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62042044_62042045delGA								None (None upstream) : FAM19A2 (59998 downstream)																							GGATTTTATTGAGAGAGAAGGA	0.421													2	6	---	---	---	---	
FAM19A2	338811	broad.mit.edu	37	12	62396811	62396811	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62396811delC	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		tggaattactcccttgcatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	62802107	62802108	+	IGR	INS	-	T	T	rs146940964	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62802107_62802108insT								USP15 (2209 upstream) : MON2 (58489 downstream)																							acttccAACTCTCCCTATGTAG	0.193													2	4	---	---	---	---	
TMEM5	10329	broad.mit.edu	37	12	64195604	64195604	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64195604delA	uc001srq.1	+						TMEM5_uc001srr.1_Intron|TMEM5_uc001srs.1_Intron	NM_014254	NP_055069	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5							integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		accctgcctcaaaaaaaaaac	0.139													6	3	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65722027	65722027	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65722027delT	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		AACTACAGGCTTTTTTTTTTA	0.308													4	2	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65849521	65849521	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65849521delT	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		TAGTTTGGGGttttttttgtt	0.174													4	2	---	---	---	---	
HMGA2	8091	broad.mit.edu	37	12	66344719	66344719	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66344719delT	uc001ssx.2	+						HMGA2_uc001ssw.1_Intron	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		GACAtttttgttttttttgag	0.149			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								4	2	---	---	---	---	
PTPRR	5801	broad.mit.edu	37	12	71061131	71061131	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71061131delT	uc001swi.1	-						PTPRR_uc001swf.1_5'Flank|PTPRR_uc001swg.1_5'Flank|PTPRR_uc001swh.1_Intron|PTPRR_uc009zrs.2_Intron|PTPRR_uc010stq.1_Intron|PTPRR_uc010str.1_Intron	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		AACATTAAGGTGCAAAGTTAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76331777	76331778	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76331777_76331778insG								KRR1 (426359 upstream) : PHLDA1 (87450 downstream)																							ttaagaaagtagaaaaaaaatg	0.000													4	2	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76861195	76861195	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76861195delT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						TACCTATATGTTTGGACATTA	0.318													4	2	---	---	---	---	
E2F7	144455	broad.mit.edu	37	12	77458037	77458040	+	Intron	DEL	ACTG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77458037_77458040delACTG	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						ACCCTTGACAACTGTATTATAAAC	0.377													6	3	---	---	---	---	
PAWR	5074	broad.mit.edu	37	12	79989034	79989034	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79989034delT	uc001syx.2	-							NM_002583	NP_002574	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0						TGATTTTTAATTTTTTTTTTC	0.358													4	2	---	---	---	---	
PPP1R12A	4659	broad.mit.edu	37	12	80200369	80200369	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80200369delT	uc001syz.2	-						PPP1R12A_uc010suc.1_Intron|PPP1R12A_uc001sza.2_Intron|PPP1R12A_uc010sud.1_Intron|PPP1R12A_uc001szb.2_Intron|PPP1R12A_uc001szc.2_Intron	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)							contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7						ATATTTCATATTTTTGAAACT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80757261	80757261	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80757261delA	uc009zsg.1	+						uc001szd.2_Intron					RecName: Full=Uncharacterized protein C12orf64;																		TTAGGAGGGCAAAATGAAAGA	0.348													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	82103272	82103273	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82103272_82103273delAC	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						AATGGTTGGTacacacacacac	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82174257	82174258	+	IGR	INS	-	T	T	rs140472831	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82174257_82174258insT								PPFIA2 (21148 upstream) : CCDC59 (571832 downstream)																							atgaaaaaaaacatcatcagta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	83664811	83664811	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83664811delA								TMTC2 (136748 upstream) : None (None downstream)																							TACAGGTTAGAAAAAAAAAGT	0.299													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	87138950	87138951	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87138950_87138951insT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						GCAAAATAAAGTTTTTTTTTTA	0.381													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	87170142	87170142	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87170142delT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						CTTATAACAGTTTTTTTTTTC	0.194													3	3	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	87195079	87195079	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87195079delT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						agggagaacattttttaagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87444562	87444562	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87444562delT								MGAT4C (211881 upstream) : C12orf50 (929254 downstream)																							TGCAAATCTGTTTTTTTTTTG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90655276	90655276	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90655276delG								LOC338758 (549548 upstream) : C12orf12 (690717 downstream)																							gtgtcaacctggggagataca	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94359266	94359268	+	IGR	DEL	CAT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94359266_94359268delCAT								CRADD (70650 upstream) : PLXNC1 (183231 downstream)																							atgtccaagccatcatcatcatc	0.108													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	95699388	95699388	+	5'Flank	DEL	T	-	-	rs7966212		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95699388delT	uc001tea.1	+						MIR331_hsa-mir-331|MI0000812_5'Flank|uc001teb.2_5'Flank					DM119494																		TTTCTTTGGCtttttttttgt	0.164													4	3	---	---	---	---	
CCDC38	120935	broad.mit.edu	37	12	96268954	96268954	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96268954delG	uc001tek.1	-							NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38											skin(1)	1						gctgattgatggcatgagacg	0.000													5	3	---	---	---	---	
CDK17	5128	broad.mit.edu	37	12	96690069	96690069	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96690069delA	uc001tep.1	-						CDK17_uc009ztk.2_Intron|CDK17_uc010svb.1_Intron	NM_002595	NP_002586	Q00537	CDK17_HUMAN	PCTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7						AATTAAAACCAAAAAAATACA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97771666	97771671	+	IGR	DEL	TGTGTC	-	-	rs67037451		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97771666_97771671delTGTGTC								NEDD1 (424205 upstream) : RMST (87128 downstream)																							tgtgtgtgtgtgtgtctgtgtgtgta	0.029													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99840491	99840491	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99840491delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACTCTACTTCAAAATATAGTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102267494	102267495	+	IGR	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102267494_102267495delTT								GNPTAB (42862 upstream) : DRAM1 (3610 downstream)																							CAGACAACTCtttttttatttg	0.218													5	8	---	---	---	---	
PAH	5053	broad.mit.edu	37	12	103295684	103295684	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103295684delA	uc001tjq.1	-						PAH_uc010swc.1_Intron	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase						catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	ggaaaagcagaaaaaaaaatc	0.035													4	2	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103800622	103800623	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103800622_103800623insA	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923	Q96LP6	CL042_HUMAN	hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2						agagcaaaaagaaaaaaaaaat	0.040													4	2	---	---	---	---	
C12orf75	387882	broad.mit.edu	37	12	105748759	105748759	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105748759delT	uc001tlh.3	+						C12orf75_uc001tli.3_Intron	NM_001145199	NP_001138671	Q8TAD7	OCC1_HUMAN	hypothetical protein LOC387882												0						GAAAGGAGGATTTTTTTTTCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105774308	105774311	+	IGR	DEL	TCTG	-	-	rs112376370		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105774308_105774311delTCTG								C12orf75 (9013 upstream) : NUAK1 (682814 downstream)																							ttcttgcctctctgtctgctcgtc	0.000													1	5	---	---	---	---	
BTBD11	121551	broad.mit.edu	37	12	107783624	107783631	+	Intron	DEL	TGTGTGTG	-	-	rs67656571		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107783624_107783631delTGTGTGTG	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3						tgtgtgtgtttgtgtgtgtgtgtgtgtg	0.159													3	4	---	---	---	---	
RAD9B	144715	broad.mit.edu	37	12	110948757	110948757	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110948757delA	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2						agaccctgtcaaaaaaaaaag	0.090													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112985590	112985590	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112985590delT								PTPN11 (37874 upstream) : RPH3A (27311 downstream)																							CTGTTTGATGttttttttttt	0.159													4	2	---	---	---	---	
SDS	10993	broad.mit.edu	37	12	113843550	113843550	+	5'Flank	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113843550delG	uc001tvg.2	-						SDS_uc001tvh.1_5'Flank	NM_006843	NP_006834	P20132	SDHL_HUMAN	serine dehydratase						gluconeogenesis|L-serine catabolic process|pyruvate biosynthetic process	cytoplasm	L-serine ammonia-lyase activity|L-threonine ammonia-lyase activity|protein homodimerization activity|pyridoxal phosphate binding			pancreas(1)	1					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	aaaaaaaaaaggaaaaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114906401	114906401	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114906401delA								TBX5 (60154 upstream) : TBX3 (201658 downstream)																							CAGAAGAAGCAAACAAATTCA	0.229													4	2	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116705152	116705152	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116705152delC	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ACAATTTAATCCTCTGCTCCC	0.328													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	118264325	118264325	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118264325delA	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGAACAAACAAAAAAAAACC	0.393													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119462924	119462925	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119462924_119462925delGT	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						gtgcattagggtgtgtgtgtgt	0.000													4	4	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119568214	119568215	+	Intron	INS	-	GATG	GATG	rs140884648	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119568214_119568215insGATG	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						ttgcttagacagatggatggat	0.030													5	3	---	---	---	---	
KNTC1	9735	broad.mit.edu	37	12	123070613	123070616	+	Intron	DEL	TGTG	-	-	rs7137722		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123070613_123070616delTGTG	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		gtttcttttttgtgtgtttgtttt	0.000													4	2	---	---	---	---	
ZNF664	144348	broad.mit.edu	37	12	124483374	124483375	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124483374_124483375delTG	uc001ufz.2	+						ZNF664_uc001uga.2_Intron|ZNF664_uc001ugb.2_Intron	NM_152437	NP_689650	Q8N3J9	ZN664_HUMAN	zinc finger protein 664						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		AATATGTGCCTGTGTGTGTGCA	0.312													6	3	---	---	---	---	
FAM101A	144347	broad.mit.edu	37	12	124785107	124785108	+	Intron	INS	-	GGAT	GGAT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124785107_124785108insGGAT	uc001ugd.1	+						FAM101A_uc001uge.1_Intron	NM_181709	NP_859060	Q6ZTI6	F101A_HUMAN	hypothetical protein LOC144347												0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		GGGGTTGggaaggatggatgga	0.233													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126650817	126650818	+	IGR	INS	-	TGG	TGG	rs72522601		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126650817_126650818insTGG								TMEM132B (507228 upstream) : LOC100128554 (276209 downstream)																							GGAGCAGGTGATCCTTGGACGC	0.490													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129776555	129776555	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129776555delC	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TCATATGAGTCCACAGCCCCC	0.468													4	2	---	---	---	---	
DKFZp686A1627	266695	broad.mit.edu	37	13	19661249	19661253	+	Intron	DEL	AAAAC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19661249_19661253delAAAAC	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0						cttgtctcaaaaaacaaaacaaaat	0.024													3	3	---	---	---	---	
ZMYM5	9205	broad.mit.edu	37	13	20425258	20425258	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20425258delA	uc010tcn.1	-						ZMYM5_uc001umm.1_Intron|ZMYM5_uc001umn.2_Intron|ZMYM5_uc001umo.2_Intron	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3							nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ctcaggcaggaaaaaaaaaat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22306028	22306028	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22306028delA								FGF9 (27388 upstream) : None (None downstream)																							gttaaggcccaaatagaacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22642552	22642552	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22642552delT	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		CTGCTATTTCTTACCAAATTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	25775124	25775124	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25775124delA								FAM123A (28819 upstream) : MTMR6 (27183 downstream)																							acataccagtaaagtgatgca	0.000													4	2	---	---	---	---	
SHISA2	387914	broad.mit.edu	37	13	26624159	26624159	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26624159delA	uc001uqm.1	-							NM_001007538	NP_001007539	Q6UWI4	SHSA2_HUMAN	shisa homolog 2 precursor						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2						AATTTGAAAGAAAAAAAAAAT	0.468													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31964856	31964856	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31964856delT								B3GALTL (58447 upstream) : RXFP2 (348823 downstream)																							tacccatcccttttttttccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35303587	35303587	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35303587delG								RFC3 (762893 upstream) : NBEA (212869 downstream)																							tctgtctcctggattattaca	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37953749	37953749	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37953749delG								CSNK1A1L (273948 upstream) : POSTN (182971 downstream)																							tcatgtaactggatggacggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40886862	40886863	+	IGR	INS	-	GC	GC	rs35967008		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40886862_40886863insGC								COG6 (521060 upstream) : LOC646982 (34410 downstream)																							tgtgtgtgtgtgCACTCTTCAT	0.277													3	4	---	---	---	---	
WBP4	11193	broad.mit.edu	37	13	41646620	41646620	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41646620delT	uc001uxt.2	+						WBP4_uc010tfd.1_Intron	NM_007187	NP_009118	O75554	WBP4_HUMAN	WW domain-containing binding protein 4						nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		caaagggaggtgccacacact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	50438551	50438551	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50438551delT								KPNA3 (71494 upstream) : LOC220429 (25994 downstream)																							TATGTGTGACTTTTTTTTCTT	0.323													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	52140535	52140535	+	IGR	DEL	A	-	-	rs79711212		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52140535delA								INTS6 (113260 upstream) : WDFY2 (17949 downstream)																							gaggaataagaaaaaaaaaac	0.000													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52753378	52753378	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52753378delT	uc001vgk.2	-						THSD1P1_uc001vgm.1_Intron|THSD1P1_uc010adx.1_Intron|THSD1P1_uc010ady.1_Intron|THSD1P1_uc001vgl.1_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						acgtacaacatttttttttct	0.075													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	56253882	56253882	+	IGR	DEL	G	-	-	rs662309	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56253882delG								None (None upstream) : None (None downstream)																							CTTTTTTTTTGGGGGGGGCAG	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	62365239	62365239	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62365239delA								PCDH20 (363160 upstream) : None (None downstream)																							agcctgtaggagttacataat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71586061	71586062	+	IGR	INS	-	A	A	rs145878161	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71586061_71586062insA								ATXN8OS (872176 upstream) : DACH1 (426036 downstream)																							tacttgtcaatagcccagtgtg	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72668594	72668594	+	IGR	DEL	A	-	-	rs79305788		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72668594delA								DACH1 (227264 upstream) : C13orf37 (613901 downstream)																							AGTACATTTGAAAAAAAAAAG	0.249											OREG0002712	type=REGULATORY REGION|Gene=DACH1-FLJ22624|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72917957	72917957	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72917957delT								DACH1 (476627 upstream) : C13orf37 (364538 downstream)																							TCATGACAGGTTTTTTTTTCC	0.428													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81099330	81099330	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81099330delA								SPRY2 (184244 upstream) : None (None downstream)																							atgaCAGCTTAAAAAAAAAAA	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85550049	85550050	+	IGR	INS	-	AAA	AAA	rs150353834	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85550049_85550050insAAA								None (None upstream) : SLITRK6 (816872 downstream)																							TTTTAAAAAGTAGAAGAAAGGG	0.257													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85670065	85670065	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85670065delT								None (None upstream) : SLITRK6 (696857 downstream)																							tttttcTCTCTTTTTTTTTTC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	86356038	86356038	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86356038delC								None (None upstream) : SLITRK6 (10884 downstream)																							TCTTTCATATCCCCCAACTGA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87710976	87710976	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87710976delA								None (None upstream) : SLITRK5 (613894 downstream)																							TATTTCAAAGAAAGATTTAAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87906269	87906269	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87906269delT								None (None upstream) : SLITRK5 (418601 downstream)																							TGAAAAAGGATAACATATGCT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88162098	88162098	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88162098delT	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																		TCAGGAAAAATTTTTTTTTTG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90994284	90994284	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90994284delG								MIR622 (110753 upstream) : LOC144776 (548924 downstream)																							tctctttgtaggtctctaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	91763440	91763440	+	IGR	DEL	A	-	-	rs11322457		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91763440delA								LOC144776 (184589 upstream) : MIR17HG (236634 downstream)																							CCTTTATTCCaaaaaaaaaaa	0.254													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92572826	92572827	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92572826_92572827delAC	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				acacgtgcctacacacacacag	0.000													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94023383	94023383	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94023383delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GTTGAAATGTAACATAGTTCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	100569504	100569504	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100569504delC								CLYBL (24681 upstream) : ZIC5 (45771 downstream)																							TCTTGGAAGTCCGTGCAAGAG	0.527											OREG0022489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PCCA	5095	broad.mit.edu	37	13	101122034	101122034	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101122034delA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	gctctgtctcaaaaaaaaaca	0.124													4	2	---	---	---	---	
TPP2	7174	broad.mit.edu	37	13	103257477	103257478	+	Intron	INS	-	CAGTAGTTCA	CAGTAGTTCA	rs145083043	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103257477_103257478insCAGTAGTTCA	uc001vpi.3	+							NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					taacggggttccagtcgccctg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103551441	103551441	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103551441delT								LOC121952 (3058 upstream) : SLC10A2 (144909 downstream)																							TACTTTTTTCTTTTTTTTTGG	0.308													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104285969	104285970	+	IGR	INS	-	G	G	rs72569753		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104285969_104285970insG								SLC10A2 (566773 upstream) : None (None downstream)																							AGTTAAAAAAAATTGTATTGCT	0.317													4	2	---	---	---	---	
RAB20	55647	broad.mit.edu	37	13	111216844	111216845	+	5'Flank	INS	-	CA	CA	rs140956522	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111216844_111216845insCA	uc001vqy.2	-							NM_017817	NP_060287	Q9NX57	RAB20_HUMAN	RAB20, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	all_cancers(4;1.54e-11)|all_epithelial(4;1.22e-06)|all_lung(23;1e-05)|Lung NSC(43;0.000453)|Colorectal(4;0.00323)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.197)			CTGCCCCCCGCCACACACACAC	0.470													4	5	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114778098	114778100	+	Intron	DEL	CTC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114778098_114778100delCTC	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			tccccactcactcctcattccac	0.236													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19040400	19040400	+	IGR	DEL	T	-	-	rs113500961		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19040400delT								None (None upstream) : OR11H12 (337194 downstream)																							ggttcaactctgtgagttgaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19438402	19438405	+	IGR	DEL	TTTC	-	-	rs142638829		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19438402_19438405delTTTC								OR11H12 (59830 upstream) : POTEG (114960 downstream)																							TTTGGGTGAATTTCTTTATTTTTC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20718783	20718783	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20718783delT								OR11H4 (6859 upstream) : TTC5 (38520 downstream)																							aggaacaatatttacaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22189413	22189415	+	5'Flank	DEL	AGG	-	-	rs112881923		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22189413_22189415delAGG	uc001wbn.2	+											Homo sapiens mRNA for T cell receptor alpha variable 3, partial cds, clone: SEB 36.																		aagaataagaaggaggaggagga	0.212													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23219055	23219055	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23219055delA								ABHD4 (137798 upstream) : OXA1L (16676 downstream)																							gaCACCTTTCAAAAAAAACAC	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25554176	25554176	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25554176delT								STXBP6 (35005 upstream) : None (None downstream)																							GCCTTAGGAGTAGGGTCTATG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27682233	27682234	+	IGR	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27682233_27682234delTT								NOVA1 (615273 upstream) : None (None downstream)																							GAGATCATGATTAACAATAGAC	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27814901	27814901	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27814901delT	uc010amc.1	-											Homo sapiens cDNA clone IMAGE:40107853.																		taatcagttattttttaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29677787	29677787	+	IGR	DEL	T	-	-	rs11320065		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29677787delT								C14orf23 (413788 upstream) : PRKD1 (367902 downstream)																							agaatgatggtttttcagctt	0.174													3	3	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	33438285	33438285	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33438285delT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		aagccactgctttctaaaatg	0.000													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	33616259	33616259	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33616259delT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GTATGTCAGGTTTTTTTTTTC	0.269													5	3	---	---	---	---	
MIPOL1	145282	broad.mit.edu	37	14	37665320	37665321	+	5'Flank	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37665320_37665321delAG	uc001wuc.2	+						MIPOL1_uc010amr.2_5'Flank|MIPOL1_uc001wub.3_5'Flank|MIPOL1_uc001wud.2_5'Flank|MIPOL1_uc010ams.2_5'Flank|MIPOL1_uc001wue.2_5'Flank|MIPOL1_uc010amt.2_5'Flank	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		TGCATAAAACAGAGAGAGAGAG	0.347													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38365281	38365282	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38365281_38365282delCA	uc001wug.2	+						uc001wuk.1_RNA					Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		CTCATTTATTCACTTTATCAGG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	43790520	43790521	+	IGR	INS	-	T	T	rs76685656	byFrequency	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43790520_43790521insT								None (None upstream) : None (None downstream)																							ttagttttttgtttttttttta	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46080680	46080681	+	IGR	INS	-	AT	AT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46080680_46080681insAT								C14orf106 (358075 upstream) : None (None downstream)																							aatgagctaacatatatatagt	0.109													4	2	---	---	---	---	
FRMD6	122786	broad.mit.edu	37	14	52046845	52046846	+	Intron	INS	-	GT	GT	rs142320784	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52046845_52046846insGT	uc001wzb.2	+							NM_001042481	NP_001035946	Q96NE9	FRMD6_HUMAN	FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					TTGTGTGCACCgtgtgtgtgtg	0.391													5	3	---	---	---	---	
WDHD1	11169	broad.mit.edu	37	14	55410807	55410807	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55410807delT	uc001xbm.1	-						WDHD1_uc010aom.1_Intron|WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1						AGGCTTTTCCTTTTTTTTTTA	0.189													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55981566	55981566	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55981566delA								TBPL2 (74303 upstream) : C14orf33 (43124 downstream)																							GGATCTGACTAATCTATCTCC	0.149													4	2	---	---	---	---	
RTN1	6252	broad.mit.edu	37	14	60177977	60177977	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60177977delC	uc001xen.1	-						RTN1_uc001xem.1_Intron|uc001xeo.2_5'Flank	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A						neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TGAACACAGGCCCACAGTGAT	0.443													4	2	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	69129520	69129520	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69129520delA	uc001xkg.1	+							NM_133510	NP_598194	O15315	RA51B_HUMAN	RAD51-like 1 isoform 2						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		GAGAGAAATTAACCCTGAGTT	0.144			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	69177486	69177486	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69177486delA	uc001xkg.1	+							NM_133510	NP_598194	O15315	RA51B_HUMAN	RAD51-like 1 isoform 2						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		AACCGGGAGGAAAAAAACTGG	0.428			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	69277267	69277267	+	IGR	DEL	T	-	-	rs35110169		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69277267delT								C14orf181 (14077 upstream) : ACTN1 (63574 downstream)																							AAAAGTAACATTTTTTTTTTC	0.393													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	74062614	74062614	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74062614delT								ACOT4 (146 upstream) : ACOT6 (20934 downstream)																							TCCTTCTAGATTTTTTTAGTT	0.333													4	2	---	---	---	---	
FAM161B	145483	broad.mit.edu	37	14	74409633	74409634	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74409633_74409634insT	uc001xpd.1	-							NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1						tacaaaccagcttccttttttt	0.213													4	2	---	---	---	---	
LIN52	91750	broad.mit.edu	37	14	74608755	74608755	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74608755delT	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845	Q52LA3	LIN52_HUMAN	lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)		TCCAGGAGCATTTCAGGTCAG	0.393													4	2	---	---	---	---	
LTBP2	4053	broad.mit.edu	37	14	74998850	74998850	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74998850delA	uc001xqa.2	-							NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding						protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		ATTAGAAAGGAAAAAAAATAA	0.458													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79043152	79043152	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79043152delC	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		tttgcgaCTTCCTAtactggg	0.015													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79283307	79283307	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79283307delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGGTGACAACTTATATCAGAA	0.308													4	2	---	---	---	---	
TSHR	7253	broad.mit.edu	37	14	81494014	81494014	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81494014delA	uc001xvd.1	+						TSHR_uc001xvb.1_Intron|TSHR_uc001xvc.2_Intron|TSHR_uc010tvs.1_Intron	NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1						cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	aacgtaggggaaaaaaaccta	0.000			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						4	2	---	---	---	---	
STON2	85439	broad.mit.edu	37	14	81830444	81830445	+	Intron	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81830444_81830445insG	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)		AGACACCCTTTGGGAAATGCTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82400216	82400216	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82400216delT								SEL1L (400011 upstream) : None (None downstream)																							CAATGAATACTTTTTTGGAGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88067970	88067970	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88067970delA								None (None upstream) : GALC (236194 downstream)																							TACCCTAAAGAAAAAAAAATG	0.219													4	2	---	---	---	---	
GALC	2581	broad.mit.edu	37	14	88371017	88371017	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88371017delA	uc010tvw.1	-							NM_000153		P54803	GALC_HUMAN	galactosylceramidase isoform a precursor						carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0						GGAACTTTCTAAAAATGGGGA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88613602	88613602	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88613602delT								GPR65 (135188 upstream) : KCNK10 (32852 downstream)																							gggaaggccctccccactgat	0.000													4	2	---	---	---	---	
KCNK10	54207	broad.mit.edu	37	14	88732923	88732925	+	Intron	DEL	GTG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88732923_88732925delGTG	uc001xwo.2	-						KCNK10_uc001xwm.2_Intron|KCNK10_uc001xwn.2_Intron	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10						signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5						ttGTTTTCCAgtggtggtggtgg	0.118													7	4	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89830606	89830607	+	Intron	INS	-	A	A	rs139986652	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89830606_89830607insA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						GATTAAAAAAGAAAAAAAAAAG	0.243													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	91911965	91911965	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91911965delA								CCDC88C (27832 upstream) : SMEK1 (11993 downstream)																							gcagaaatagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94364370	94364370	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94364370delT								PRIMA1 (109604 upstream) : C14orf86 (6706 downstream)																							GTTGTGACTCTCCCCAGCCAT	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97523968	97523968	+	IGR	DEL	A	-	-	rs67907111		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97523968delA								VRK1 (176018 upstream) : C14orf64 (867979 downstream)																							ACACTCATGGAAAAAAAAATC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100660773	100660773	+	IGR	DEL	T	-	-	rs36018069		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100660773delT								DEGS2 (34761 upstream) : YY1 (44329 downstream)																							TGCCGCTGACTTAGACAACAC	0.512													2	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101278018	101278018	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101278018delT								DLK1 (76544 upstream) : MEG3 (14427 downstream)																							CCCAGCCTCATTCTCATTCCA	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101634830	101634831	+	IGR	INS	-	T	T	rs34351957		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101634830_101634831insT								MIR656 (101692 upstream) : DIO3OS (383729 downstream)																							catctagtgagttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102105700	102105701	+	IGR	INS	-	A	A	rs138348141	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102105700_102105701insA								DIO3 (75911 upstream) : C14orf72 (91073 downstream)																							AATGTTATGTGAAAAAAAAAAG	0.406													2	5	---	---	---	---	
AHNAK2	113146	broad.mit.edu	37	14	105418731	105418731	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105418731delG	uc010axc.1	-	7	3177	c.3057delC	c.(3055-3057)GCCfs	p.A1019fs	AHNAK2_uc001ypx.2_Frame_Shift_Del_p.A919fs	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1019						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CATCCACCAAGGCCTTGATGG	0.577													100	47	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106768449	106768450	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106768449_106768450delAC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						taatttgtaaacacacacacac	0.015													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106810588	106810588	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106810588delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TGGTTATGATGGGGAATCCAG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20573875	20573875	+	IGR	DEL	A	-	-	rs150151593		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20573875delA								None (None upstream) : GOLGA6L6 (163219 downstream)																							AGAAAAGTGGAAAAAAAAGTC	0.308													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20578717	20578718	+	IGR	DEL	AA	-	-	rs146862453		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20578717_20578718delAA								None (None upstream) : GOLGA6L6 (158376 downstream)																							tgacagagcgaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BCL8	606	broad.mit.edu	37	15	20874552	20874552	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20874552delA	uc010tzd.1	-											Homo sapiens mRNA; cDNA DKFZp686P1536 (from clone DKFZp686P1536).												0						TCCTGAATGGAAAAAGGCATA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21914867	21914867	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21914867delT								NF1P1 (780242 upstream) : LOC646214 (17647 downstream)																							TAAATGATACTTTCTTTTCTC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22464122	22464125	+	IGR	DEL	AATT	-	-	rs78529461		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22464122_22464125delAATT								OR4N3P (49737 upstream) : MIR1268 (49104 downstream)																							tgcttagacaaattaattgtgtca	0.000													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	26106310	26106311	+	Intron	INS	-	A	A	rs146650709	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26106310_26106311insA	uc010ayu.2	-						ATP10A_uc001zax.2_Intron	NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGGTGTTTCTGAAAGTGTGGGC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39037722	39037722	+	IGR	DEL	A	-	-	rs5812051		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39037722delA								C15orf53 (45483 upstream) : C15orf54 (505163 downstream)																							TGGTATAGTTAAAAATCTTGA	0.388													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	43231441	43231442	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43231441_43231442insT								TTBK2 (18434 upstream) : UBR1 (3661 downstream)																							tttatttttaatttttttttaa	0.252													4	2	---	---	---	---	
SPG11	80208	broad.mit.edu	37	15	44905926	44905926	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44905926delA	uc001ztx.2	-						SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTTTAGAGATAGAGATTTTAG	0.259													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	47934638	47934639	+	Intron	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47934638_47934639delCA	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GAAACAGATGCACACACACACA	0.223													4	2	---	---	---	---	
FBN1	2200	broad.mit.edu	37	15	48908669	48908669	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48908669delA	uc001zwx.1	-							NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTATACACAGAAAAAAAACAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53368035	53368036	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53368035_53368036delGT								ONECUT1 (285826 upstream) : WDR72 (437902 downstream)																							gtatgtgtgagtgtgtgtgtgt	0.347													4	3	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54444683	54444683	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54444683delT	uc002ack.2	+							NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AGGGCTTAAATTTATGAGGAA	0.303													4	2	---	---	---	---	
NEDD4	4734	broad.mit.edu	37	15	56126729	56126730	+	Intron	INS	-	C	C	rs144235710	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56126729_56126730insC	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		agtggctcattctgtaatccca	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	59153166	59153167	+	RNA	INS	-	A	A	rs138888947	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59153166_59153167insA	uc002afm.2	+	1		c.185_186insA								Homo sapiens cDNA clone IMAGE:4797580.																		GACAGCTTGTTACAGATTCACA	0.342													4	4	---	---	---	---	
RNF111	54778	broad.mit.edu	37	15	59325089	59325090	+	Intron	DEL	CT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59325089_59325090delCT	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		TGCGTGCTGACTCTCTCTCTCT	0.391													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61087530	61087532	+	Intron	DEL	AGC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61087530_61087532delAGC	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						AAACAACAAGAGCAGCAGCAGCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61999240	61999240	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61999240delA								RORA (477738 upstream) : VPS13C (145352 downstream)																							tggcccatagaaaaaacaagt	0.000													4	2	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62182074	62182075	+	Intron	DEL	AC	-	-	rs72490391		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62182074_62182075delAC	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						AACTCATTAAacacacacacac	0.223													4	2	---	---	---	---	
HERC1	8925	broad.mit.edu	37	15	64028691	64028691	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64028691delA	uc002amp.2	-						HERC1_uc010uil.1_Intron	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						gacagacatgaaatattacct	0.000													4	2	---	---	---	---	
ZNF609	23060	broad.mit.edu	37	15	64891492	64891493	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64891492_64891493insT	uc002ann.2	+							NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						AACCAAACCTGTTTTTTTTCTT	0.208													4	2	---	---	---	---	
MTFMT	123263	broad.mit.edu	37	15	65298717	65298717	+	Intron	DEL	T	-	-	rs72003727		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65298717delT	uc002aof.3	-							NM_139242	NP_640335	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)	TTATAAGATCttttttttttt	0.184													6	3	---	---	---	---	
AAGAB	79719	broad.mit.edu	37	15	67494910	67494910	+	3'UTR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67494910delA	uc002aqk.3	-	10					AAGAB_uc002aql.2_3'UTR|AAGAB_uc010uju.1_3'UTR	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0						TTCCTAGAACAAAAAAAAAGT	0.363													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	69414036	69414036	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69414036delT								TMEM84 (25875 upstream) : GLCE (38937 downstream)																							ccctctccccttccctctcTT	0.234													4	2	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	77154363	77154363	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77154363delG	uc002bby.2	-						SCAPER_uc002bbx.2_5'Flank|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						agaacagcatgggggaaacca	0.000													4	2	---	---	---	---	
KIAA1024	23251	broad.mit.edu	37	15	79757192	79757193	+	Intron	INS	-	A	A	rs144345752	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79757192_79757193insA	uc002bew.1	+						KIAA1024_uc010unk.1_Intron	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251							integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4						TGCGGGCAAGGAGGCTAGACAG	0.480													2	4	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	85945038	85945038	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85945038delT	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TTCTGTGCAGTTTTTCTGGGA	0.348													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86279656	86279656	+	Intron	DEL	G	-	-	rs66738511		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86279656delG	uc002blv.1	+						AKAP13_uc002blu.1_Intron|AKAP13_uc002blw.1_Intron|AKAP13_uc002blx.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						Ctgtttttttgtttgtttgtt	0.259													5	3	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87053762	87053762	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87053762delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CTTTATCAACTTTTTTGCAGT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96755826	96755826	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96755826delC								LOC145820 (704752 upstream) : NR2F2 (113331 downstream)																							ACCAATTACACCATGTTTATT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97083572	97083572	+	IGR	DEL	A	-	-	rs35690247		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97083572delA								NR2F2 (200082 upstream) : SPATA8 (243107 downstream)																							TTCAACTAGTAAAAAAAAAAA	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98923332	98923332	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98923332delA								ARRDC4 (406265 upstream) : FAM169B (57059 downstream)																							aacagtaattaagactgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5004790	5004790	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5004790delC								PPL (17654 upstream) : SEC14L5 (3528 downstream)																							TCAGAGCCATCCCAGGGCCCA	0.393													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7085884	7085885	+	Intron	INS	-	AC	AC	rs148918227	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7085884_7085885insAC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TGTGAacacagacacacacaca	0.361													6	5	---	---	---	---	
C16orf72	29035	broad.mit.edu	37	16	9189736	9189739	+	Intron	DEL	ACTG	-	-	rs140269942		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9189736_9189739delACTG	uc002czm.2	+							NM_014117	NP_054836	Q14CZ0	CP072_HUMAN	hypothetical protein LOC29035											large_intestine(1)	1						AAGCCAAAATACTGACTGCTGGTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9744244	9744244	+	IGR	DEL	A	-	-	rs184354	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9744244delA								C16orf72 (530699 upstream) : GRIN2A (103023 downstream)																							AGTCTGTGGGAAAAAAAAAAA	0.403													4	2	---	---	---	---	
CLEC16A	23274	broad.mit.edu	37	16	11039333	11039333	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11039333delG	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2						CTACAGCTCTGGGGGAGGACA	0.408													4	2	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12756049	12756049	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12756049delT	uc002dca.3	-	4					CPPED1_uc002dcb.3_3'UTR|CPPED1_uc002dbz.3_RNA	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						AAGGCACTTATTTTTTGATAT	0.318													4	2	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14589928	14589928	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14589928delC	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						ctcttttcctcctcaaaacca	0.234													4	2	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15939580	15939581	+	Intron	INS	-	G	G	rs147112836		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15939580_15939581insG	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						agagagagagaaaaagaaggag	0.277			T	CBFB	AML								3	3	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15939581	15939582	+	Intron	INS	-	G	G	rs67298798		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15939581_15939582insG	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						gagagagagaaaaagaaggaga	0.277			T	CBFB	AML								3	3	---	---	---	---	
ABCC1	4363	broad.mit.edu	37	16	16047191	16047191	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16047191delA	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	gtctcaaaagaaaaaaaaaaT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18226908	18226908	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18226908delG								XYLT1 (662170 upstream) : NOMO2 (284275 downstream)																							ttagccatcagggaaatgcaa	0.124													4	2	---	---	---	---	
LOC81691	81691	broad.mit.edu	37	16	20843816	20843817	+	Intron	DEL	AA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20843816_20843817delAA	uc002dhv.2	+						ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Intron|LOC81691_uc002dhw.2_Intron|LOC81691_uc002dhy.3_Intron	NM_030941	NP_112203	Q96IC2	REXON_HUMAN	exonuclease NEF-sp isoform 1							nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2						ATCCTTGATCAAAAAAAAAAAA	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21584660	21584660	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21584660delA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		GTCTCAAAAGAAAAAAAAAAT	0.045													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22203003	22203003	+	IGR	DEL	T	-	-	rs117589939		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22203003delT								VWA3A (34723 upstream) : EEF2K (14589 downstream)																							GCATGAAAAATTTAAAAAAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24431361	24431361	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24431361delA								CACNG3 (57625 upstream) : RBBP6 (117653 downstream)																							gcccaaatagaaaaaaaaggc	0.060													4	2	---	---	---	---	
LCMT1	51451	broad.mit.edu	37	16	25161552	25161555	+	Intron	DEL	AAAG	-	-	rs34073458		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25161552_25161555delAAAG	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron|uc002dob.1_5'Flank	NM_016309	NP_057393	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	actgaggcttaaagaagttaattt	0.088													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26158146	26158146	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26158146delT								HS3ST4 (9138 upstream) : C16orf82 (920073 downstream)																							ctcttcttcatttttttttga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26386144	26386147	+	IGR	DEL	TGGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26386144_26386147delTGGA								HS3ST4 (237136 upstream) : C16orf82 (692072 downstream)																							GGTAgatggttggatggatggatg	0.103													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29209389	29209390	+	Intron	INS	-	ATGG	ATGG	rs149563932	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29209389_29209390insATGG	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		tacatagatgaatggatggatg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29318956	29318957	+	Intron	DEL	AT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29318956_29318957delAT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		GTCAGCACTCATAATGTGGCTG	0.554													0	7	---	---	---	---	
ZNF720	124411	broad.mit.edu	37	16	31749205	31749205	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31749205delA	uc002ecn.3	+						ZNF720_uc010vfs.1_Intron|ZNF720_uc002eco.2_Intron|ZNF720_uc002ecp.1_Intron|ZNF720_uc002ecq.2_Intron	NM_001130913	NP_001124385	Q7Z2F6	ZN720_HUMAN	zinc finger protein 720						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0						attttgatggagagtacattg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32212321	32212321	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32212321delC								HERC2P4 (48447 upstream) : TP53TG3B (472520 downstream)																							GCTTCCTGGGCCCCCTCCTGT	0.672													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32539797	32539798	+	IGR	INS	-	A	A	rs138179239		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32539797_32539798insA								HERC2P4 (375923 upstream) : TP53TG3B (145043 downstream)																							caagatcctacaaaaatgcgtt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33045409	33045411	+	IGR	DEL	AAC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33045409_33045411delAAC								SLC6A10P (148946 upstream) : MIR1826 (920097 downstream)																							GAAGAATGAAAACAAGAAATAAT	0.217													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33504025	33504026	+	IGR	INS	-	T	T	rs151049869	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33504025_33504026insT								SLC6A10P (607562 upstream) : MIR1826 (461482 downstream)																							ACAACACAACCTTTTTCTCTGA	0.292													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33997732	33997733	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33997732_33997733delCA								MIR1826 (32140 upstream) : UBE2MP1 (406069 downstream)																							gagatgaatgcacacatcaaaa	0.000													3	3	---	---	---	---	
ITFG1	81533	broad.mit.edu	37	16	47190712	47190712	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47190712delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				AGCAACTGGTAAAAAATACGA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47965744	47965745	+	IGR	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47965744_47965745delAG								PHKB (230311 upstream) : ABCC12 (151139 downstream)																							acacacacacagacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51557721	51557724	+	IGR	DEL	TATC	-	-	rs145646378		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51557721_51557724delTATC								SALL1 (372538 upstream) : TOX3 (914194 downstream)																							ATTCCTTGAATATCTATCCATTAC	0.451													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58836022	58836022	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58836022delT								GOT2 (67776 upstream) : None (None downstream)																							ttgtctttcctttttagcagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59325985	59325985	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59325985delG								GOT2 (557739 upstream) : None (None downstream)																							AACCTACTATGGTGTTTTGTA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62910138	62910138	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62910138delA								CDH8 (840102 upstream) : None (None downstream)																							agaagctggcaatgtttctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65674549	65674549	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65674549delG								LOC283867 (64346 upstream) : CDH5 (725976 downstream)																							tctattgcctggggttcctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65902824	65902824	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65902824delG								LOC283867 (292621 upstream) : CDH5 (497701 downstream)																							ACAAGAATGTGGATGGTGGCT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66053828	66053828	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66053828delT								LOC283867 (443625 upstream) : CDH5 (346697 downstream)																							tttgcacaactttttttattt	0.015													4	2	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71018828	71018829	+	Intron	INS	-	A	A	rs112227827		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71018828_71018829insA	uc002ezr.2	-							NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CATTATCATGGAAAAAAAATCc	0.238													9	9	---	---	---	---	
CFDP1	10428	broad.mit.edu	37	16	75359586	75359586	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75359586delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1						gtaggcactcaaaaaatattt	0.129													4	2	---	---	---	---	
CHST6	4166	broad.mit.edu	37	16	75512296	75512297	+	3'UTR	INS	-	C	C	rs146724437	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75512296_75512297insC	uc002fef.2	-	3					CHST6_uc002feg.1_RNA|CHST6_uc002feh.1_3'UTR	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)						keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0						CCCAGAGGAGGAGGGGCAAGAG	0.515													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76648988	76648988	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76648988delA								CNTNAP4 (55853 upstream) : MON1B (575848 downstream)																							CCAAAAAAAGAAAAAAAAAAA	0.199													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76830265	76830266	+	IGR	DEL	TT	-	-	rs142654713		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76830265_76830266delTT								CNTNAP4 (237130 upstream) : MON1B (394570 downstream)																							TGAGTGAGTCTTTTTTTTTTTT	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76917180	76917181	+	IGR	INS	-	A	A	rs141294543	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76917180_76917181insA								CNTNAP4 (324045 upstream) : MON1B (307655 downstream)																							TGCCTCTCCATATACTCTCTGG	0.436													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79493476	79493476	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79493476delT								WWOX (246913 upstream) : MAF (134270 downstream)																							TTATTCTCACttttttttttt	0.159													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	82782125	82782127	+	Intron	DEL	TGG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82782125_82782127delTGG	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TCTGTTCTGTTGGTGGTGGTGGT	0.256													4	3	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984579	83984580	+	Intron	DEL	CA	-	-	rs71392792		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984579_83984580delCA	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						tacatactggcacacacgtaca	0.000													8	4	---	---	---	---	
MBTPS1	8720	broad.mit.edu	37	16	84112449	84112449	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84112449delG	uc002fhi.2	-							NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1						cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2						ggtgggggcagggggaaggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85217973	85217974	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85217973_85217974insG								FAM92B (71859 upstream) : KIAA0182 (427055 downstream)																							TGTATTCCCTAGGGGAAAAGAG	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86748832	86748833	+	IGR	INS	-	T	T	rs140779535	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86748832_86748833insT								FOXL1 (133529 upstream) : FBXO31 (614111 downstream)																							TCCTACTTAGGTTTTTTTTTTC	0.416													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86774753	86774754	+	IGR	DEL	AC	-	-	rs147082163		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86774753_86774754delAC								FOXL1 (159450 upstream) : FBXO31 (588190 downstream)																							CAAAACAAAAACACACACACAA	0.441													3	3	---	---	---	---	
ZC3H18	124245	broad.mit.edu	37	16	88683110	88683110	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88683110delA	uc002fky.2	+						ZC3H18_uc010voz.1_Intron|ZC3H18_uc010chw.2_Intron	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GGGAGTTTGTAATCATTAGGT	0.453													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89502209	89502210	+	Intron	INS	-	AA	AA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89502209_89502210insAA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron|uc002fnh.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GCTCTTcacacacacacacaca	0.406													4	2	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	822308	822308	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:822308delA	uc002fsa.2	-							NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		ctattgctttaaaaaaaaaaa	0.010													3	3	---	---	---	---	
ABR	29	broad.mit.edu	37	17	950547	950547	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:950547delA	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		GGCCGGAGTGAAGGCAGAGAC	0.632													4	2	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2934618	2934619	+	Intron	INS	-	T	T	rs138961407	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2934618_2934619insT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						AGGTGGGAAGGGCTGGTTCCTG	0.624													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6844526	6844526	+	IGR	DEL	A	-	-	rs67032989		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6844526delA								ALOX12P2 (40859 upstream) : ALOX12 (54858 downstream)																							ATATACAGTCAAAAAAAACAA	0.219													4	2	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11857309	11857309	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11857309delA	uc002gne.2	+						DNAH9_uc010coo.2_Intron|DNAH9_uc002gnf.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		gaggattcacagctgagtagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14138249	14138249	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14138249delA								COX10 (26257 upstream) : CDRT15 (926 downstream)																							TTTCTTAAAGAAaaaaaattc	0.184													4	2	---	---	---	---	
ALKBH5	54890	broad.mit.edu	37	17	18104323	18104324	+	Intron	DEL	CA	-	-	rs35844584		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18104323_18104324delCA	uc010cpw.2	+						ALKBH5_uc010cpx.2_Intron	NM_017758	NP_060228	Q6P6C2	ALKB5_HUMAN	alkB, alkylation repair homolog 5							integral to membrane	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_neural(463;0.228)					TCATTAGATCCACAGAGTTCGA	0.525													7	4	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21195701	21195702	+	Intron	INS	-	TT	TT	rs141502124		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21195701_21195702insTT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		tcttcttctcattttttttttt	0.188													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21231493	21231494	+	IGR	INS	-	TCTC	TCTC	rs138596924		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21231493_21231494insTCTC								MAP2K3 (12944 upstream) : KCNJ12 (48205 downstream)																							tccctttcctttcccacagcac	0.000													3	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21305663	21305663	+	Intron	DEL	T	-	-	rs33926742		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21305663delT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	CCTCAGCCTGTTTTTTTTTGG	0.522										Prostate(3;0.18)			5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25274265	25274265	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25274265delA								None (None upstream) : WSB1 (346841 downstream)																							ataaacaaataggcattgtaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25291422	25291422	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25291422delC								None (None upstream) : WSB1 (329684 downstream)																							acataaaatacactaatgcta	0.060													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25305226	25305226	+	IGR	DEL	G	-	-	rs137889546	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25305226delG								None (None upstream) : WSB1 (315880 downstream)																							cagtaatgtagtacacaggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25328464	25328464	+	IGR	DEL	T	-	-	rs112373547		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25328464delT								None (None upstream) : WSB1 (292642 downstream)																							gaagagaatctttttttctga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25648890	25648890	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25648890delT								WSB1 (8245 upstream) : KSR1 (150146 downstream)																							CGTGAGCCCCttttttttttt	0.239													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	26034509	26034509	+	IGR	DEL	T	-	-	rs72232254		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26034509delT								LGALS9 (57924 upstream) : NOS2 (49284 downstream)																							CCTTAATATGTTTTTTTTATT	0.294													7	4	---	---	---	---	
C17orf63	55731	broad.mit.edu	37	17	27107295	27107295	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27107295delT	uc002hct.1	-						C17orf63_uc010wax.1_Intron|C17orf63_uc010way.1_Intron|C17orf63_uc002hcw.2_Intron	NM_018182	NP_060652	Q8WU58	CQ063_HUMAN	hypothetical protein LOC55731											ovary(1)	1	all_epithelial(6;5.06e-20)|Lung NSC(42;0.01)		Epithelial(11;3.38e-06)|all cancers(11;2.46e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.104)			gacagagcaattaggcaagaa	0.000													4	2	---	---	---	---	
C17orf75	64149	broad.mit.edu	37	17	30658518	30658518	+	3'UTR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30658518delA	uc002hhg.2	-	10						NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			GAAATTTTTTAAGCAACAACT	0.363													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32486415	32486416	+	5'Flank	INS	-	C	C	rs139581882	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32486415_32486416insC	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	TCCGCCCTCCTCCCCAGCAGCC	0.525													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32615559	32615560	+	IGR	INS	-	AGGTTTAGGTGC	AGGTTTAGGTGC	rs143014241	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32615559_32615560insAGGTTTAGGTGC								CCL11 (360 upstream) : CCL8 (30506 downstream)																							CCTTTGACCAGAGGTTTAGGTG	0.515													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34825862	34825865	+	IGR	DEL	ACAG	-	-	rs148707495		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34825862_34825865delACAG								TBC1D3G (17759 upstream) : ZNHIT3 (16608 downstream)																							ctgttaggatacagacaatgaccg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	37748174	37748175	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37748174_37748175delTG								CDK12 (57375 upstream) : NEUROD2 (11847 downstream)																							TCTCAGGATATGTGTGTGTGAA	0.470													4	2	---	---	---	---	
CASC3	22794	broad.mit.edu	37	17	38319330	38319330	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38319330delA	uc010cwt.1	+						CASC3_uc010cws.1_Intron|CASC3_uc002hue.2_Intron	NM_007359	NP_031385	O15234	CASC3_HUMAN	metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1						gaaaaaaaggaaaaaAAAAAT	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38590317	38590318	+	IGR	DEL	TG	-	-	rs35269070		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38590317_38590318delTG								TOP2A (16148 upstream) : IGFBP4 (9358 downstream)																							tgccaggcactgtgtttagtgc	0.114													4	2	---	---	---	---	
C17orf57	124989	broad.mit.edu	37	17	45419565	45419565	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45419565delA	uc002iln.2	+						ITGB3_uc010wkr.1_Intron|C17orf57_uc002ilm.2_Intron|C17orf57_uc002ill.1_Intron|C17orf57_uc010daz.1_Intron	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989								calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						TCTTCTCCTTAAAAAAAAAAT	0.269													15	7	---	---	---	---	
NGFR	4804	broad.mit.edu	37	17	47571768	47571769	+	5'Flank	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47571768_47571769delGT	uc002ioz.3	+							NM_002507	NP_002498	P08138	TNR16_HUMAN	nerve growth factor receptor precursor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					atgggtgtcagtgtgtgtgtgc	0.084													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51043234	51043235	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51043234_51043235delGT								CA10 (805857 upstream) : KIF2B (857004 downstream)																							gcaggctccagtgtgtgttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51482628	51482629	+	IGR	DEL	TC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51482628_51482629delTC								None (None upstream) : KIF2B (417610 downstream)																							caccttgttttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51556566	51556567	+	IGR	INS	-	A	A	rs149375608	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51556566_51556567insA								None (None upstream) : KIF2B (343672 downstream)																							CCCTTTACCCCGTAATTTTCAT	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51973835	51973836	+	IGR	DEL	AG	-	-	rs35917422		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51973835_51973836delAG								KIF2B (71262 upstream) : None (None downstream)																							tgagaggacaagagagagagag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55799878	55799881	+	IGR	DEL	TGAA	-	-	rs139568751		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55799878_55799881delTGAA								MSI2 (42579 upstream) : MRPS23 (116963 downstream)																							aagtgtttgttgaatgaatgaatg	0.127													3	3	---	---	---	---	
CLTC	1213	broad.mit.edu	37	17	57738541	57738541	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57738541delT	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TTCTGGATAATTTTTTTTTTT	0.274			T	ALK|TFE3	ALCL|renal 								4	2	---	---	---	---	
ERN1	2081	broad.mit.edu	37	17	62161891	62161891	+	Intron	DEL	A	-	-	rs11305629		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62161891delA	uc002jdz.2	-							NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9						atcagtaaggaaaaaaaaaat	0.010													0	6	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	64013246	64013246	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64013246delA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			gtgaacacccaaaatcacaat	0.030													4	2	---	---	---	---	
APOH	350	broad.mit.edu	37	17	64219480	64219480	+	Intron	DEL	A	-	-	rs8178840		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64219480delA	uc002jfn.3	-							NM_000042	NP_000033	P02749	APOH_HUMAN	apolipoprotein H precursor						blood coagulation, intrinsic pathway|negative regulation of angiogenesis|negative regulation of blood coagulation|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of myeloid cell apoptosis|negative regulation of smooth muscle cell apoptosis|plasminogen activation|positive regulation of lipoprotein lipase activity|triglyceride metabolic process|triglyceride transport	cell surface|chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	eukaryotic cell surface binding|glycoprotein binding|heparin binding|lipoprotein lipase activator activity|phospholipid binding				0			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TTAAGTGGTGACAGTCCCTGA	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67696720	67696720	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67696720delC								MAP2K6 (158258 upstream) : KCNJ16 (374706 downstream)																							TCACCTGTATCCCACCAAGCT	0.413													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70905696	70905696	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70905696delA	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						aatcctaaggaaaaaaaagaa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72648876	72648877	+	IGR	INS	-	TCCTA	TCCTA	rs138996111	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72648876_72648877insTCCTA								CD300E (29075 upstream) : RAB37 (18379 downstream)																							TCTTCTTCAGTTCCCTCTATTA	0.223													5	3	---	---	---	---	
SAP30BP	29115	broad.mit.edu	37	17	73682028	73682029	+	Intron	INS	-	T	T	rs146641606	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73682028_73682029insT	uc002jpe.2	+						SAP30BP_uc010dgm.1_Intron|SAP30BP_uc002jpc.1_Intron|SAP30BP_uc010wsf.1_Intron|SAP30BP_uc010wsg.1_Intron|SAP30BP_uc002jpf.2_Intron	NM_013260	NP_037392	Q9UHR5	S30BP_HUMAN	transcriptional regulator protein						apoptosis|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTTGAATCAAATGTAGATTGTA	0.396													3	3	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75368005	75368005	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75368005delT	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_5'Flank	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			ACCTAGAACATTTTCCGCAAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76536299	76536300	+	IGR	INS	-	TTTGA	TTTGA	rs71676692		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76536299_76536300insTTTGA								DNAH17 (67443 upstream) : CYTH1 (133831 downstream)																							ttttatttgtctttgtctttgg	0.000													3	3	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78880013	78880014	+	Intron	DEL	AA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78880013_78880014delAA	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						CACCCACTCTAAAAAAAAAAAA	0.579													4	2	---	---	---	---	
HEXDC	284004	broad.mit.edu	37	17	80377960	80377960	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80377960delA	uc002kew.2	+						C17orf101_uc002ket.1_5'Flank|C17orf101_uc002keu.1_5'Flank|C17orf101_uc010dip.1_5'Flank|HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron			Q8WVB3	HEXDC_HUMAN	SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GACAAAAGGGAAAAAAAAAAA	0.299													5	3	---	---	---	---	
THOC1	9984	broad.mit.edu	37	18	261055	261055	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:261055delA	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GATTATCTTCAAAAAATAACA	0.254													4	2	---	---	---	---	
LPIN2	9663	broad.mit.edu	37	18	3004525	3004526	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3004525_3004526insT	uc002klo.2	-							NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		CTCTGAAACTGTTTAACTTAAG	0.243													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	6574947	6574947	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6574947delC								L3MBTL4 (160037 upstream) : ARHGAP28 (213546 downstream)																							TTCTAAAATTCCAGGATAATT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	7441213	7441213	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7441213delA								LRRC30 (209172 upstream) : PTPRM (126101 downstream)																							CAACTAATGCAAAAAAAATAA	0.299													4	2	---	---	---	---	
ANKRD12	23253	broad.mit.edu	37	18	9191477	9191478	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9191477_9191478insT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3						TATCACATAGGTTTTTTTTTTA	0.322													4	3	---	---	---	---	
FAM38B	63895	broad.mit.edu	37	18	10755830	10755832	+	Intron	DEL	GAG	-	-	rs74794516		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10755830_10755832delGAG	uc002kos.1	-									Q9H5I5	PIEZ2_HUMAN	SubName: Full=cDNA FLJ45725 fis, clone HCHON2009766; Flags: Fragment;							integral to membrane	ion channel activity			ovary(1)	1						accaagggatgaggaggagagat	0.222													1	5	---	---	---	---	
SLMO1	10650	broad.mit.edu	37	18	12430368	12430369	+	Intron	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12430368_12430369delGT	uc002kra.2	+						SLMO1_uc010wzu.1_Intron|SLMO1_uc010wzv.1_Intron	NM_001142405	NP_001135877	Q96N28	SLMO1_HUMAN	slowmo homolog 1 isoform 1												0						tgtgtgtgtggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13159838	13159838	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13159838delA								CEP192 (34789 upstream) : C18orf1 (58948 downstream)																							gcagcccctgaaaattagact	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14391221	14391221	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14391221delT								LOC284233 (48699 upstream) : CXADRP3 (86735 downstream)																							AACAACTTTCTTTAAAAAAAA	0.388													4	2	---	---	---	---	
ZNF271	10778	broad.mit.edu	37	18	32881933	32881933	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32881933delG	uc002kyq.3	+						ZNF271_uc002kyp.3_Intron|ZNF271_uc002kyr.3_Intron	NR_024565				SubName: Full=cDNA FLJ13394 fis, clone PLACE1001304, highly similar to Homo sapiens zinc finger protein 271 (ZNF271), mRNA;												0						gggctcttgtgggtctgcaca	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	33859753	33859753	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33859753delA								MOCOS (11069 upstream) : FHOD3 (17949 downstream)																							ggccctgtccaaaaaaaaatg	0.000													4	4	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34041705	34041705	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34041705delG	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				ttggaaTGTAGGGCAGGTAGC	0.244													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35009272	35009273	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35009272_35009273delTG	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						tgtgtaagtctgtgtgtgtgtg	0.233													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39765800	39765800	+	5'Flank	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39765800delG	uc002las.1	+						uc002lat.2_5'Flank|uc002lau.2_5'Flank					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TTTGCTGGAAGGGGGGAAGTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39862661	39862662	+	Intron	INS	-	C	C	rs72539919	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39862661_39862662insC	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TGTGTTTTTTTTTAACCTTGCA	0.312													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45060069	45060070	+	Intron	INS	-	AG	AG	rs142066124	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45060069_45060070insAG	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		TTTAAATGACCAGAGAGAGAGA	0.252													2	4	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45929138	45929138	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45929138delG	uc010dnw.2	-						ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						GCTGGTTCcagaaaaaaaaga	0.159													4	2	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46728017	46728017	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46728017delA	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron|DYM_uc010dov.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						TATCACAGATAAATCTGTTTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	47955964	47955965	+	IGR	INS	-	GT	GT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47955964_47955965insGT								SKA1 (35430 upstream) : MAPK4 (130519 downstream)																							ccaatgtttcagtgtaggaaat	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48067065	48067065	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48067065delT								SKA1 (146531 upstream) : MAPK4 (19419 downstream)																							tcctcattacttttttttaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49142937	49142937	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49142937delT								MEX3C (419247 upstream) : DCC (723634 downstream)																							tgttgtttagttttttttttt	0.169													3	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	49981128	49981128	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49981128delT	uc002lfe.1	+							NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GAAGGTGACATTTTAATTTCA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53322959	53322959	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53322959delA								TCF4 (19774 upstream) : TXNL1 (947096 downstream)																							CCAAAGGAATAAGGTCCCCAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53460223	53460224	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53460223_53460224delTG								TCF4 (157038 upstream) : TXNL1 (809831 downstream)																							tgtatatgcctgtgtgtgtgtg	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57370731	57370732	+	IGR	DEL	CT	-	-	rs10580362		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57370731_57370732delCT								CCBE1 (6087 upstream) : PMAIP1 (196460 downstream)																							GCAAAAATAACTCTCTTCAAAT	0.277													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57376869	57376879	+	IGR	DEL	GATTTCTTTTG	-	-	rs35444869		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57376869_57376879delGATTTCTTTTG								CCBE1 (12225 upstream) : PMAIP1 (190313 downstream)																							gctcacattagatttcttttggacagtgctg	0.213													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61607060	61607060	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61607060delA								SERPINB10 (4586 upstream) : HMSD (9528 downstream)																							TCTGTGGTTTAAAAAATACAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63878607	63878607	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63878607delG								CDH7 (330433 upstream) : CDH19 (292714 downstream)																							GATGTTTTGTGGAACCCATAA	0.244													4	2	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67351716	67351717	+	Intron	INS	-	T	T	rs143189425	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67351716_67351717insT	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				AAAGATGCAGATTTTGAAAGTA	0.411													6	3	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67450768	67450768	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67450768delG	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				gcattgTTCTGGTATGatcca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70092506	70092506	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70092506delT								None (None upstream) : CBLN2 (111409 downstream)																							TAAATGCTCATTTTTTTTTTG	0.284													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70695105	70695105	+	IGR	DEL	T	-	-	rs146499545		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70695105delT								NETO1 (160295 upstream) : None (None downstream)																							caataaaaaataataaaatcc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71410916	71410916	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71410916delC								NETO1 (876106 upstream) : FBXO15 (329672 downstream)																							ATTTCCGGCTCCCCATCCCAC	0.502													4	2	---	---	---	---	
ZNF407	55628	broad.mit.edu	37	18	72630001	72630001	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72630001delA	uc002llw.2	+						ZNF407_uc010dqu.1_Intron	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TGAAGAATTCAAAAAAAAATT	0.378													2	4	---	---	---	---	
ZADH2	284273	broad.mit.edu	37	18	72913186	72913186	+	3'UTR	DEL	T	-	-	rs67264905		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72913186delT	uc002llx.2	-	2					ZADH2_uc010dqv.2_3'UTR	NM_175907	NP_787103	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain							peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TATTAGCACATTTTTTTTTTT	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75717155	75717155	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75717155delT								GALR1 (735061 upstream) : None (None downstream)																							TTTCATTTTCTTTTTTTTAAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75838683	75838684	+	IGR	DEL	TC	-	-	rs144824392		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75838683_75838684delTC								GALR1 (856589 upstream) : SALL3 (901591 downstream)																							GTTTTTTTTTTCTTTCTTTCTC	0.391													4	2	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	76835730	76835730	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76835730delT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmu.2_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		cggttggttctttttttttac	0.000													4	2	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77444926	77444927	+	Intron	DEL	GG	-	-	rs113059721		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77444926_77444927delGG	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CTGGTGAGGAGGACGGTGCAGG	0.589													5	3	---	---	---	---	
C18orf22	79863	broad.mit.edu	37	18	77818586	77818586	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77818586delT	uc010dri.1	+						uc002lnu.2_Intron			Q8N0V3	RBFA_HUMAN	Homo sapiens hypothetical p38 protein mRNA, complete cds.						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)		tgggaagagattcggagttat	0.000													4	2	---	---	---	---	
PARD6G	84552	broad.mit.edu	37	18	77962937	77962937	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77962937delG	uc002lny.2	-						PARD6G_uc010xfp.1_Intron	NM_032510	NP_115899	Q9BYG4	PAR6G_HUMAN	PAR-6 gamma protein						cell cycle|cell division|tight junction assembly	cytosol|tight junction	protein binding				0		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		GGGAAGAAGTGGGACCCCAGA	0.323													4	2	---	---	---	---	
ZNF555	148254	broad.mit.edu	37	19	2851297	2851297	+	Intron	DEL	A	-	-	rs10713166		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2851297delA	uc002lwo.2	+						ZNF555_uc002lwn.3_Intron	NM_152791	NP_690004	Q8NEP9	ZN555_HUMAN	zinc finger protein 555						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cctggccGTGaattttttttt	0.144													8	4	---	---	---	---	
GNA15	2769	broad.mit.edu	37	19	3156162	3156163	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3156162_3156163delAC	uc002lxf.2	+							NM_002068	NP_002059	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		AGGACCCCAGacacacacacac	0.257													8	4	---	---	---	---	
SAFB	6294	broad.mit.edu	37	19	5642481	5642481	+	Intron	DEL	A	-	-	rs66503750		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5642481delA	uc002mcf.2	+						SAFB_uc010xiq.1_Intron|SAFB_uc002mcg.2_Intron|SAFB_uc002mce.3_Intron|SAFB_uc010xir.1_Intron|SAFB_uc010xis.1_Intron|SAFB_uc010xit.1_Intron|SAFB_uc010xiu.1_Intron	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		acaaacaaacaaaaaaaAAAA	0.144													7	4	---	---	---	---	
OR1M1	125963	broad.mit.edu	37	19	9203755	9203756	+	5'Flank	INS	-	AC	AC	rs4804095	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9203755_9203756insAC	uc010xkj.1	+							NM_001004456	NP_001004456	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3						attctatatatacacacacaca	0.213													4	2	---	---	---	---	
AP1M2	10053	broad.mit.edu	37	19	10699510	10699510	+	5'Flank	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10699510delG	uc002mpc.2	-						AP1M2_uc002mpd.2_5'Flank	NM_005498	NP_005489	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit						cellular membrane organization|post-Golgi vesicle-mediated transport|protein targeting|regulation of defense response to virus by virus|vesicle targeting|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(2)	2			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			tcaacttcctgggctcaagcc	0.000													4	2	---	---	---	---	
CNN1	1264	broad.mit.edu	37	19	11650183	11650183	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11650183delC	uc002msc.1	+						CNN1_uc010xmb.1_5'UTR|CNN1_uc010xmc.1_5'UTR	NM_001299	NP_001290	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0						TGCTGGGGTACCTGGGAAGTG	0.562													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13173235	13173235	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13173235delT	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron			Q14938	NFIX_HUMAN	RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GAAGGGTCTCTTTGGAGTCTT	0.328													4	2	---	---	---	---	
ZSWIM4	65249	broad.mit.edu	37	19	13918079	13918079	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13918079delC	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GGATGATGGACCCATGATGGG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14481233	14481234	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14481233_14481234insA								LPHN1 (164236 upstream) : CD97 (10979 downstream)																							TCTTTTTGTTTAAAAAAAAAAA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14916039	14916039	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14916039delA								OR7C1 (5091 upstream) : OR7A5 (21101 downstream)																							TCCTGCCTGCAAAAAAAAATC	0.488													3	3	---	---	---	---	
SLC1A6	6511	broad.mit.edu	37	19	15067809	15067809	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15067809delC	uc002naa.1	-						SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Intron	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity						synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	TGTACCTACTCCCCATTCAAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21088856	21088857	+	IGR	INS	-	A	A	rs7249876	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21088856_21088857insA								ZNF626 (244454 upstream) : ZNF85 (17223 downstream)																							CTAAAAAAAGGAACCTCTTCAC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21149420	21149420	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21149420delT								ZNF85 (15919 upstream) : ZNF430 (54077 downstream)																							CTTGTGCTACTTTGATTGTCT	0.393													4	2	---	---	---	---	
ZNF429	353088	broad.mit.edu	37	19	21691045	21691046	+	Intron	INS	-	A	A	rs112400992		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21691045_21691046insA	uc002nqd.1	+						ZNF429_uc010ecu.1_Intron	NM_001001415	NP_001001415	Q86V71	ZN429_HUMAN	zinc finger protein 429						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						aactccatctgaaaaaaaaaaa	0.188													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31319437	31319437	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31319437delA								ZNF536 (270472 upstream) : DKFZp566F0947 (321346 downstream)																							tgagaagtacaaaaaaaatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32334849	32334849	+	IGR	DEL	T	-	-	rs71335150		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32334849delT								TSHZ3 (494659 upstream) : ZNF507 (501665 downstream)																							tgacaatggattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33684306	33684306	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33684306delT								WDR88 (17605 upstream) : LRP3 (1293 downstream)																							CTTCCCCCCATTTTTTATTAA	0.383													4	3	---	---	---	---	
NPHS1	4868	broad.mit.edu	37	19	36335512	36335512	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36335512delG	uc002oby.2	-							NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor						cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			gctaagctcaggggtaaggtt	0.174													6	3	---	---	---	---	
ZNF529	57711	broad.mit.edu	37	19	37037308	37037309	+	3'UTR	INS	-	AAG	AAG	rs77850123		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37037308_37037309insAAG	uc002oeh.3	-	5					ZNF529_uc010xth.1_3'UTR|ZNF529_uc010xti.1_3'UTR|ZNF529_uc002oeg.3_3'UTR	NM_020951	NP_066002	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					CAAAACAAAACAACATTACACA	0.292													4	2	---	---	---	---	
PSG5	5673	broad.mit.edu	37	19	43676135	43676136	+	Intron	INS	-	A	A	rs71336843		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43676135_43676136insA	uc002ovu.2	-						PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Intron|PSG5_uc002ovv.2_Intron|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5						female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)				tccctctcttcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
KCNN4	3783	broad.mit.edu	37	19	44272893	44272893	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44272893delT	uc002oxl.2	-						KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)	CTTTGTGCAATTTTTTTTTTT	0.308													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50636891	50636891	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50636891delA								SNAR-A4 (15794 upstream) : SNAR-B2 (111 downstream)																							gtctcccaacaaaaaaaaaaa	0.139													6	3	---	---	---	---	
ZNF83	55769	broad.mit.edu	37	19	53159176	53159177	+	Intron	DEL	AT	-	-	rs150719246		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53159176_53159177delAT	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		AATACAAAAAATATATGTctgg	0.158													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	347809	347812	+	IGR	DEL	CGCA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:347809_347812delCGCA								NRSN2 (7465 upstream) : TRIB3 (13496 downstream)																							gagccaagatcgcaccattgcact	0.039													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2143204	2143205	+	IGR	INS	-	TG	TG	rs113823209		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2143204_2143205insTG								STK35 (14008 upstream) : TGM3 (133408 downstream)																							ctgtgtgtgaatgtgtgtgtgt	0.267													4	2	---	---	---	---	
TMC2	117532	broad.mit.edu	37	20	2605655	2605655	+	Intron	DEL	T	-	-	rs148142979		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2605655delT	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3						TCAACAACCATTAGAGAACAA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4808788	4808788	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4808788delG								RASSF2 (4497 upstream) : SLC23A2 (24214 downstream)																							cattaaaggtggggggtttgg	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5386424	5386424	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5386424delC								PROKR2 (89046 upstream) : LOC149837 (92794 downstream)																							agagcctGCTCCCACACAGGC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6429907	6429907	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6429907delG								FERMT1 (325716 upstream) : BMP2 (318838 downstream)																							aagaggtaaagggggcaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7680261	7680263	+	IGR	DEL	AGG	-	-	rs147439928		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7680261_7680263delAGG								BMP2 (919351 upstream) : HAO1 (183368 downstream)																							TGATAACACCAGGAGAAGGCCAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	8917496	8917496	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8917496delT								PLCB1 (51951 upstream) : PLCB4 (132205 downstream)																							TTTTCTTTTCTTTTTTTTTTT	0.388													11	5	---	---	---	---	
JAG1	182	broad.mit.edu	37	20	10645022	10645023	+	Intron	DEL	AC	-	-	rs113252426		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10645022_10645023delAC	uc002wnw.2	-							NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9						GCATGAGGAAacacacacacac	0.317									Alagille_Syndrome				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11223979	11223980	+	IGR	INS	-	T	T	rs139097264	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11223979_11223980insT								JAG1 (569285 upstream) : BTBD3 (647497 downstream)																							AGCCATACCAAtttttttttct	0.267													3	3	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15817675	15817675	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15817675delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TTTTCTTTGCAAAAATATGAG	0.413													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17330306	17330306	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17330306delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ACCTACCAAGAAAAAAAAAAT	0.378													4	2	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19673699	19673699	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19673699delT	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						CAGTGGGTAATTTTTTTTTTA	0.403											OREG0025804	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26132977	26132977	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26132977delT								C20orf191 (38300 upstream) : MIR663 (55845 downstream)																							AAGTGGCAGCTTAGAACAAGA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29583385	29583385	+	IGR	DEL	T	-	-	rs112099758		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29583385delT								None (None upstream) : FRG1B (28494 downstream)																							AATGTTTTAATTTTTGTAAAG	0.279													4	3	---	---	---	---	
XKR7	343702	broad.mit.edu	37	20	30580646	30580646	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30580646delT	uc002wxe.2	+							NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|breast(1)|skin(1)	3			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			aaactgaggctttgagaggGC	0.279													4	2	---	---	---	---	
DNMT3B	1789	broad.mit.edu	37	20	31387738	31387741	+	Intron	DEL	TAGT	-	-	rs145092112		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31387738_31387741delTAGT	uc002wyc.2	+						DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Intron|DNMT3B_uc002wyg.2_Intron|DNMT3B_uc010geg.2_5'Flank|DNMT3B_uc010geh.2_5'Flank	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						GGAGATAAACTAGTTAACAACTAC	0.363													11	11	---	---	---	---	
C20orf70	140683	broad.mit.edu	37	20	31755945	31755947	+	5'Flank	DEL	CCA	-	-	rs11470590		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31755945_31755947delCCA	uc002wyo.1	+							NM_080574	NP_542141	Q96DR5	SPLC2_HUMAN	chromosome 20 open reading frame 70 precursor							extracellular region	lipid binding			ovary(1)|central_nervous_system(1)	2						ATAATAGCCGCCACCATTCAGCA	0.552													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31776104	31776104	+	IGR	DEL	T	-	-	rs67745079		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31776104delT								C20orf70 (6881 upstream) : BASE (5307 downstream)																							TATAAGTGGGTTtttttttgt	0.209													9	4	---	---	---	---	
ZNF341	84905	broad.mit.edu	37	20	32334456	32334457	+	Intron	INS	-	GT	GT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32334456_32334457insGT	uc002wzy.2	+						ZNF341_uc002wzx.2_Intron|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Intron	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						tttgagggagggtgagagagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36182785	36182786	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36182785_36182786delTG								BLCAP (26482 upstream) : CTNNBL1 (139648 downstream)																							tcatgtaacttgtgtgtgtgag	0.000													4	2	---	---	---	---	
DHX35	60625	broad.mit.edu	37	20	37638249	37638250	+	Intron	DEL	CC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37638249_37638250delCC	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				CCTCTTTTTTCCCCACCCTTCC	0.436													4	2	---	---	---	---	
LPIN3	64900	broad.mit.edu	37	20	39970731	39970733	+	Intron	DEL	TGC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39970731_39970733delTGC	uc002xjx.2	+						LPIN3_uc010ggh.2_Intron|LPIN3_uc010zwf.1_Intron	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3						fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)				GCTGTCATGATGCTGCTGCTGAT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47011150	47011150	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47011150delA								LOC284749 (11769 upstream) : PREX1 (229643 downstream)																							gagtgaatgcaaccggggtgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47187518	47187519	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47187518_47187519delAC								LOC284749 (188137 upstream) : PREX1 (53274 downstream)																							GAATACACAAACACACACACAC	0.376													4	2	---	---	---	---	
PTPN1	5770	broad.mit.edu	37	20	49187762	49187762	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49187762delT	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)	AACCTTTCCCTTTGGGTTACT	0.493													4	2	---	---	---	---	
MOCS3	27304	broad.mit.edu	37	20	49575435	49575435	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49575435delA	uc002xvy.1	+	1	73	c.56delA	c.(55-57)GAGfs	p.E19fs	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	19					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			skin(2)|ovary(1)	3						CAACGTGAGGAGGAATTGAAT	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51321256	51321256	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51321256delA								ZFP64 (512732 upstream) : TSHZ2 (267621 downstream)																							GGGAGAAATGAAAAAAAAATG	0.343													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51877679	51877683	+	Intron	DEL	TGATG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51877679_51877683delTGATG	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			CCTCCTTGCCTGATGGTTTCTAGGT	0.293													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52490163	52490163	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52490163delA								ZNF217 (279362 upstream) : SUMO1P1 (879 downstream)																							ATGTAAAAGGAAAAAAAACCC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52996606	52996607	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52996606_52996607delCA								PFDN4 (160115 upstream) : DOK5 (95650 downstream)																							ACCCGCCCCCcacacacacgtg	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56626220	56626220	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56626220delT								PMEPA1 (339679 upstream) : C20orf85 (99763 downstream)																							taactttggatttggcagcag	0.000													4	2	---	---	---	---	
GNAS	2778	broad.mit.edu	37	20	57443599	57443600	+	Intron	INS	-	T	T	rs151220209	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57443599_57443600insT	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GGCATCTGCTCGCCACAAGAAG	0.431			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			6	3	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62052641	62052650	+	Intron	DEL	GAGAGTGAAT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62052641_62052650delGAGAGTGAAT	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	CCTGAGACTCGAGAGTGAATCTCTAACCGT	0.490													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9675173	9675173	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9675173delT								None (None upstream) : None (None downstream)																							ttttttttcctttttttctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9833418	9833418	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9833418delG								None (None upstream) : None (None downstream)																							GGTTGGGTTTGTGAACAAATA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10153144	10153144	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10153144delA								None (None upstream) : TPTE (753599 downstream)																							aggccaacacaacaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10728996	10728999	+	IGR	DEL	AAGT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10728996_10728999delAAGT								None (None upstream) : TPTE (177744 downstream)																							gctcaaagcaaagtaagtttcaac	0.000													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11045983	11045983	+	Intron	DEL	A	-	-	rs111961463		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11045983delA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTCAAGTATCAAAACATTTAT	0.244													4	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11069158	11069158	+	Intron	DEL	T	-	-	rs148402445		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11069158delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gaataatatattaaaaaaaac	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11114232	11114232	+	IGR	DEL	T	-	-	rs71914052		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11114232delT								BAGE (15295 upstream) : None (None downstream)																							aaaaaaaaaaTATCACAGTCA	0.159													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	16271891	16271891	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16271891delA								SAMSN1 (316168 upstream) : NRIP1 (61665 downstream)																							TGGTTTTGGTAATCCATTCAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18819547	18819547	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18819547delT	uc011abz.1	+						uc002ykg.1_Intron					Homo sapiens cDNA clone IMAGE:40146531.																		ttctttctagtttttttttct	0.164													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25790065	25790065	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25790065delT								None (None upstream) : NCRNA00158 (968069 downstream)																							ttcatatgtgttgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26381979	26381980	+	IGR	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26381979_26381980insT								None (None upstream) : NCRNA00158 (376154 downstream)																							TTATGTTCAAATTTTTTTCATT	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26746376	26746376	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26746376delC								None (None upstream) : NCRNA00158 (11758 downstream)																							TCTGCTTTTTCCCCCTACTTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28185913	28185914	+	IGR	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28185913_28185914delAG								CYYR1 (240332 upstream) : ADAMTS1 (22694 downstream)																							gtgtggaggcagagagagagag	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34319674	34319675	+	IGR	INS	-	A	A	rs148823758	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34319674_34319675insA								C21orf62 (133621 upstream) : OLIG2 (78564 downstream)																							CAGAGAAGCCCAATCAAGGCAG	0.545													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35413157	35413157	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35413157delA								ATP5O (124999 upstream) : MRPS6 (32666 downstream)																							ttagttcaggaaagtcaccaa	0.000													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36337499	36337500	+	Intron	INS	-	CACACACACAGCCT	CACACACACAGCCT	rs146467174	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36337499_36337500insCACACACACAGCCT	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tcccgcacgtgcacacacacag	0.069			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				6	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37123927	37123927	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37123927delA	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						acaatttactaagtggcctac	0.055			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37315053	37315054	+	Intron	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37315053_37315054delAC	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tacacatcatacacacacacac	0.045			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37858152	37858152	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37858152delT	uc002yvn.1	-						CLDN14_uc002yvo.1_Intron	NM_001146078	NP_001139550	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						TTCCATTTCCTTTTTTTTTTT	0.393													9	6	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37937719	37937720	+	Intron	INS	-	T	T	rs141515495		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37937719_37937720insT	uc002yvo.1	-							NM_001146077	NP_001139549	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						TTTCCCAAATCTTTTTTTTTTT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39329810	39329810	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39329810delA								KCNJ6 (41114 upstream) : DSCR4 (96504 downstream)																							TCCCCAATGTAAACCTATCTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40261429	40261429	+	IGR	DEL	A	-	-	rs74455252		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40261429delA								ETS2 (64553 upstream) : PSMG1 (285961 downstream)																							atatttggacaaaactttcta	0.000													3	4	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42107462	42107462	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42107462delC	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CAAATATTtaccatttgtgca	0.030													4	2	---	---	---	---	
RIPK4	54101	broad.mit.edu	37	21	43165453	43165453	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43165453delA	uc002yzn.1	-							NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7						CAGCCTCATCACCCGAAAAGG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44593847	44593847	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44593847delA								CRYAA (934 upstream) : SIK1 (240551 downstream)																							ccacacacacacaccacacac	0.328													5	3	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46894164	46894165	+	Intron	INS	-	GT	GT	rs142872277	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46894164_46894165insGT	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AGCTCAGCAAAgtgtgtgtgtg	0.223													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	47719587	47719587	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47719587delC								C21orf57 (1923 upstream) : C21orf58 (758 downstream)																							CTGCCTTGGTCCCTGGGTCAT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16955063	16955065	+	IGR	DEL	ATT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16955063_16955065delATT								OR11H1 (505259 upstream) : CCT8L2 (116583 downstream)																							TATGTCTCTCATTATTTTGGTAA	0.187													18	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17236265	17236265	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17236265delT								psiTPTE22 (56744 upstream) : XKR3 (28048 downstream)																							AATTGGCATCTTTATTTTCCA	0.274													4	2	---	---	---	---	
LOC400891	400891	broad.mit.edu	37	22	21406283	21406283	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21406283delC	uc011ahz.1	+						LOC400891_uc002zug.2_Intron|LOC400891_uc002zuh.2_Intron					Homo sapiens cDNA FLJ46805 fis, clone TRACH3033535.												0						ttcctgacttcccccaagaca	0.000													4	2	---	---	---	---	
PPM1F	9647	broad.mit.edu	37	22	22283231	22283232	+	Intron	INS	-	C	C	rs146075500	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22283231_22283232insC	uc002zvp.1	-						PPM1F_uc011aik.1_Intron|PPM1F_uc002zvq.2_Intron	NM_014634	NP_055449	P49593	PPM1F_HUMAN	protein phosphatase 1F						apoptosis|protein dephosphorylation	protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(2)|large_intestine(1)|breast(1)|kidney(1)	5	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GCCTCATCCTGCCAGGTCCTTG	0.342													3	3	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33126823	33126823	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33126823delG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						GCCATGTTTTGGTTTCTAGAG	0.234													4	2	---	---	---	---	
APOL3	80833	broad.mit.edu	37	22	36555015	36555016	+	Intron	DEL	GT	-	-	rs113377904		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36555015_36555016delGT	uc003aot.2	-						APOL3_uc003aoq.2_Intron|APOL3_uc003aor.2_Intron|APOL3_uc003aos.2_Intron|APOL3_uc003aou.2_Intron|APOL3_uc003aov.2_Intron	NM_145640	NP_663615	O95236	APOL3_HUMAN	apolipoprotein L3 isoform 1						inflammatory response|lipoprotein metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	lipid binding|lipid transporter activity|signal transducer activity				0						gtgagtgtgcgtgtgtgtgtgt	0.327													4	2	---	---	---	---	
TRIOBP	11078	broad.mit.edu	37	22	38161835	38161836	+	Intron	INS	-	G	G	rs138412450	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38161835_38161836insG	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atw.2_Intron|TRIOBP_uc003atx.1_Intron|TRIOBP_uc010gxh.2_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GTATGGACCCTGGGGGGGGCAC	0.629													6	4	---	---	---	---	
ADSL	158	broad.mit.edu	37	22	40753780	40753780	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40753780delT	uc003ayp.3	+						ADSL_uc003ays.3_Intron|ADSL_uc003ayq.3_Intron|ADSL_uc003ayr.3_Intron|ADSL_uc003ayt.3_Intron|ADSL_uc010gyb.1_5'Flank	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a						AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1						ATCttgtttcttttttttcat	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41044265	41044265	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41044265delT								MKL1 (11575 upstream) : MCHR1 (30917 downstream)																							GAAGTGATTATTTTTTTCTTG	0.348													4	2	---	---	---	---	
MEI1	150365	broad.mit.edu	37	22	42159534	42159535	+	Intron	INS	-	ATT	ATT	rs142590476	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42159534_42159535insATT	uc003baz.1	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_Intron|MEI1_uc003bbb.1_Intron|MEI1_uc003bbc.1_Intron|MEI1_uc010gym.1_Intron|MEI1_uc003bbd.1_Intron	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2						gggaggaagagattatttgcat	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46244233	46244233	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46244233delC								ATXN10 (3404 upstream) : WNT7B (72015 downstream)																							cccacatgatccagtcacctc	0.040													4	2	---	---	---	---	
GRAMD4	23151	broad.mit.edu	37	22	47048870	47048870	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47048870delG	uc003bhx.2	+						GRAMD4_uc010had.2_Intron	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		ATGGAGTCGTGGGGCGTGTGA	0.582													4	2	---	---	---	---	
C22orf34	348645	broad.mit.edu	37	22	49980236	49980237	+	Intron	DEL	CA	-	-	rs71762244		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49980236_49980237delCA	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0						GCATGTTTAGCACAGAGTCACT	0.510													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1370101	1370102	+	IGR	INS	-	AGAC	AGAC			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1370101_1370102insAGAC								CRLF2 (38571 upstream) : CSF2RA (17591 downstream)																							tagaGGGACATAGATAATAAAT	0.079													10	12	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536654	1536655	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536654_1536655insA	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				cagacatgctccatgtcacagg	0.045													10	6	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536657	1536659	+	Intron	DEL	TGT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536657_1536659delTGT	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				acatgctccatgtcacaggtatg	0.054													6	6	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536664	1536665	+	Intron	DEL	GG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536664_1536665delGG	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ccatgtcacaggtatgctccag	0.054													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	4768620	4768620	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4768620delA								None (None upstream) : None (None downstream)																							CAtggaactcagagaattgga	0.224													4	2	---	---	---	---	
STS	412	broad.mit.edu	37	X	7254837	7254837	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7254837delA	uc004cry.3	+							NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	TGAACCTTGCAAAATTGTATT	0.398									Ichthyosis				4	2	---	---	---	---	
FAM9B	171483	broad.mit.edu	37	X	9088932	9088933	+	Intron	INS	-	GT	GT			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9088932_9088933insGT	uc011mhv.1	-									Q8IZU0	FAM9B_HUMAN	Homo sapiens family with sequence similarity 9, member B (FAM9B) mRNA, complete cds.							nucleus					0		Hepatocellular(5;0.219)				atctatttgaagtgtccagaag	0.000													4	2	---	---	---	---	
FRMPD4	9758	broad.mit.edu	37	X	12307200	12307200	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12307200delT	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						GTCTTCTTCCTTTTTTTCTGG	0.393													4	2	---	---	---	---	
EGFL6	25975	broad.mit.edu	37	X	13593231	13593242	+	Intron	DEL	AAACAAACAAAC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13593231_13593242delAAACAAACAAAC	uc004cvi.2	+						EGFL6_uc004cvj.2_Intron|EGFL6_uc011mik.1_Intron	NM_015507	NP_056322	Q8IUX8	EGFL6_HUMAN	epidermal growth factor-like protein 6						cell adhesion|cell cycle|cell differentiation|multicellular organismal development	basement membrane|extracellular space|membrane	calcium ion binding|integrin binding			breast(2)	2						AGCTTATTTAaaacaaacaaacaaacaaacaa	0.160													5	4	---	---	---	---	
GPM6B	2824	broad.mit.edu	37	X	13858934	13858935	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13858934_13858935delTG	uc004cvx.2	-						GPM6B_uc011min.1_Intron|GPM6B_uc004cwa.2_Intron	NM_001001994	NP_001001994	Q13491	GPM6B_HUMAN	glycoprotein M6B isoform 4						cell differentiation|nervous system development	integral to membrane					0						GACACACAAatgtgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	15179873	15179873	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15179873delT								MOSPD2 (240418 upstream) : ASB9 (82238 downstream)																							GGCTTTTGGATTTTTTTTTTT	0.353													4	2	---	---	---	---	
GPR64	10149	broad.mit.edu	37	X	19009395	19009395	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19009395delT	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					TCTATGGCAGTTTTTTTTTTG	0.323													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	19927884	19927884	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19927884delA								SH3KBP1 (22140 upstream) : CXorf23 (3320 downstream)																							aaaagaaaagaaaaaaaaaag	0.050													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	23000416	23000416	+	IGR	DEL	C	-	-	rs66861809		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23000416delC								ZNF645 (707842 upstream) : DDX53 (17671 downstream)																							tctcatatggccccctgctca	0.144													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	23013547	23013548	+	IGR	INS	-	AT	AT	rs142361754		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23013547_23013548insAT								ZNF645 (720973 upstream) : DDX53 (4539 downstream)																							aaaactaaaacaattttctcat	0.079													3	5	---	---	---	---	
PCYT1B	9468	broad.mit.edu	37	X	24577570	24577570	+	3'UTR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24577570delG	uc004dbi.2	-	8					PCYT1B_uc004dbk.3_3'UTR|PCYT1B_uc004dbj.2_3'UTR	NM_004845	NP_004836	Q9Y5K3	PCY1B_HUMAN	choline phosphate cytidylyltransferase 1 beta							endoplasmic reticulum	choline-phosphate cytidylyltransferase activity				0					Choline(DB00122)	gagagagagagagaaagaaag	0.144													4	2	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24850264	24850264	+	Intron	DEL	G	-	-	rs59523232		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24850264delG	uc004dbl.2	+							NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	GTTTATAAAAGTAGAGGCATT	0.458													4	3	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24850266	24850269	+	Intron	DEL	AGAG	-	-	rs61279220	by1000genomes	TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24850266_24850269delAGAG	uc004dbl.2	+							NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	TTATAAAAGTAGAGGCATTTTGAG	0.456													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	25769158	25769159	+	IGR	DEL	TT	-	-	rs10711679		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25769158_25769159delTT								ARX (735093 upstream) : MAGEB18 (387304 downstream)																							TTGCTCAGAGTTTTTTTTTTTT	0.332													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	26829642	26829643	+	IGR	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26829642_26829643delTT								VENTXP1 (250474 upstream) : SMEK3P (648685 downstream)																							tgtctctctcttgaattctaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	27050733	27050734	+	IGR	INS	-	AA	AA			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27050733_27050734insAA								VENTXP1 (471565 upstream) : SMEK3P (427594 downstream)																							tgatttaaaacaaaaaaaaagt	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	28243641	28243641	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28243641delA								DCAF8L1 (244075 upstream) : IL1RAPL1 (362040 downstream)																							TGTAGGTTGGAATTCTGTTAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	28514333	28514333	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28514333delT								DCAF8L1 (514767 upstream) : IL1RAPL1 (91348 downstream)																							gccaaaaaggttttttttatt	0.104													4	2	---	---	---	---	
IL1RAPL1	11141	broad.mit.edu	37	X	29439725	29439725	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29439725delA	uc004dby.2	+							NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						AGAGAGAGAGAAAAAAAAAAT	0.358													2	4	---	---	---	---	
IL1RAPL1	11141	broad.mit.edu	37	X	29876679	29876679	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29876679delA	uc004dby.2	+							NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						TTCATCTTCTAACCTCAATCT	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	30665047	30665047	+	IGR	DEL	A	-	-	rs62662262		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30665047delA								CXorf21 (69133 upstream) : GK (6429 downstream)																							atctctacccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	30668859	30668860	+	IGR	DEL	CA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30668859_30668860delCA								CXorf21 (72945 upstream) : GK (2616 downstream)																							CCGCCCTCACCACACACACTCA	0.342													4	2	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	32081304	32081305	+	Intron	INS	-	ACACACACACACAC	ACACACACACACAC	rs113943502		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32081304_32081305insACACACACACACAC	uc004dda.1	-						DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc010ngn.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AAGTATGTCTAacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	37366174	37366174	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37366174delA								PRRG1 (49627 upstream) : LANCL3 (64648 downstream)																							AAGCTGGTTTAAAAAAAAAAA	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	37613071	37613071	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37613071delT								XK (21689 upstream) : CYBB (26199 downstream)																							gctcaaggtcttatagcttgt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	38400749	38400750	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38400749_38400750delGT								OTC (120047 upstream) : TSPAN7 (19981 downstream)																							ataaacaagagtgatgagattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	43501948	43501949	+	IGR	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43501948_43501949delTT								PPP1R2P9 (864462 upstream) : MAOA (13460 downstream)																							CTGCTCCCTCTTCTCTCTCACT	0.347													4	2	---	---	---	---	
PHF16	9767	broad.mit.edu	37	X	46824849	46824850	+	Intron	INS	-	TATC	TATC	rs66778564		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46824849_46824850insTATC	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						TATATCGTTTAtatctatctat	0.243													3	3	---	---	---	---	
GRIPAP1	56850	broad.mit.edu	37	X	48844012	48844012	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48844012delA	uc004dly.1	-						GRIPAP1_uc004dlz.2_Intron|GRIPAP1_uc004dma.2_Intron	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1 isoform 1							early endosome				breast(2)|kidney(1)	3						tttaaaagttaaaaaaaaaaa	0.234													9	4	---	---	---	---	
DGKK	139189	broad.mit.edu	37	X	50143186	50143186	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50143186delT	uc010njr.1	-							NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)					ctagctctTGTTTTTTTTCCT	0.159													4	2	---	---	---	---	
SHROOM4	57477	broad.mit.edu	37	X	50520961	50520961	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50520961delT	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					CATGTGCTGATTTTTTTGGTG	0.194													4	2	---	---	---	---	
FAM156A	29057	broad.mit.edu	37	X	52963336	52963337	+	Intron	INS	-	AC	AC			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52963336_52963337insAC	uc004drm.2	-							NM_014138		Q8NDB6	FA156_HUMAN	family with sequence similarity 156, member A							integral to membrane|nuclear envelope					0						aaaagactgaaacacacacaca	0.149													4	2	---	---	---	---	
MAGED2	10916	broad.mit.edu	37	X	54831519	54831519	+	5'Flank	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54831519delT	uc004dtk.1	+							NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2											ovary(2)|breast(1)	3						ctttctccggttttttttttt	0.000													4	3	---	---	---	---	
PFKFB1	5207	broad.mit.edu	37	X	54975858	54975859	+	Intron	DEL	AG	-	-	rs151303090		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54975858_54975859delAG	uc004dty.1	-						PFKFB1_uc010nkd.1_Intron|PFKFB1_uc011mol.1_Intron	NM_002625	NP_002616	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,						energy reserve metabolic process|fructose 2,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|intracellular protein kinase cascade	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(1)	1						AGAGCATGACagagagagagag	0.307													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56640088	56640088	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56640088delT								UBQLN2 (46719 upstream) : LOC550643 (115630 downstream)																							aacttcgggatttttttttca	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61956542	61956542	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61956542delA								None (None upstream) : SPIN4 (610566 downstream)																							cctgctgaataaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	66043390	66043390	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66043390delA								EDA2R (184282 upstream) : AR (720484 downstream)																							CCCTCAATTCAAAAAAAAATT	0.373													4	3	---	---	---	---	
AR	367	broad.mit.edu	37	X	66915981	66915982	+	Intron	INS	-	T	T			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66915981_66915982insT	uc004dwu.1	+						AR_uc004dwv.1_Intron	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1						cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)	GATCttttttcttttttttttt	0.292									Androgen_Insensitivity_Syndrome				2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	67802944	67802944	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67802944delT								YIPF6 (50644 upstream) : STARD8 (64567 downstream)																							CAGACTTATCTTTTTTTTTTC	0.279													3	3	---	---	---	---	
STARD8	9754	broad.mit.edu	37	X	67870104	67870104	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67870104delA	uc004dxa.2	+						STARD8_uc004dxb.2_Intron	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						tatgaaaaataaaaaaaattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68700532	68700533	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68700532_68700533delAC								PJA1 (315192 upstream) : FAM155B (24545 downstream)																							gtgctaacggacacacacacac	0.000													3	3	---	---	---	---	
ACRC	93953	broad.mit.edu	37	X	70821386	70821386	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70821386delT	uc004eae.2	+						BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein							nucleus				ovary(3)	3	Renal(35;0.156)					cattcatctgtttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	72607939	72607940	+	IGR	DEL	GA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72607939_72607940delGA								NAP1L2 (173255 upstream) : CDX4 (59150 downstream)																							tgcatattctgaggaatctaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	72756141	72756141	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72756141delA								CDX4 (81721 upstream) : CHIC1 (26843 downstream)																							TTTCAAATTGAaaaaaaaaat	0.204													4	2	---	---	---	---	
XIST	7503	broad.mit.edu	37	X	73071846	73071846	+	RNA	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73071846delA	uc004ebm.1	-	1		c.743delT				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						ATGGGCGATGAAAAAAAAAAA	0.413													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	74973336	74973336	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74973336delA								ZDHHC15 (229999 upstream) : MAGEE2 (29487 downstream)																							TTCCCTTTGGAAAAAAAAAAC	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	76577269	76577269	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76577269delA								MIR325 (351343 upstream) : FGF16 (132378 downstream)																							GTAGATCTGGAAAAAAAAATC	0.214													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	77843541	77843541	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77843541delT								CYSLTR1 (260454 upstream) : ZCCHC5 (68025 downstream)																							tgtttttttcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	81280741	81280741	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81280741delA								SH3BGRL (726699 upstream) : None (None downstream)																							aagcaaattcaaaaaattgga	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	83147308	83147308	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83147308delT								CYLC1 (5682 upstream) : RPS6KA6 (171676 downstream)																							tctacattgattttTTTTCTC	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	84666234	84666234	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84666234delG								POF1B (31486 upstream) : MIR1321 (424551 downstream)																							caaggtacatggggtacccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	87055808	87055808	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87055808delT								KLHL4 (130758 upstream) : CPXCR1 (946418 downstream)																							tgttttgttcttttttttcta	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	90966242	90966242	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:90966242delG								PABPC5 (272660 upstream) : PCDH11X (68062 downstream)																							AGTTGAGGATGGAGACATTTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	95872361	95872362	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95872361_95872362delAC								LOC643486 (279460 upstream) : DIAPH2 (67300 downstream)																							TGTGATcacaacacacacacac	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	96941959	96941961	+	IGR	DEL	ATC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96941959_96941961delATC								DIAPH2 (86363 upstream) : None (None downstream)																							ATatcatcatatcatcatcatca	0.172													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	98065567	98065567	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:98065567delT								None (None upstream) : LOC442459 (651033 downstream)																							acatgggtcattttttttttg	0.000													3	3	---	---	---	---	
SYTL4	94121	broad.mit.edu	37	X	99964651	99964651	+	Intron	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99964651delC	uc004egd.3	-						SYTL4_uc010nnc.2_Intron|SYTL4_uc004ege.3_Intron|SYTL4_uc004egf.3_Intron|SYTL4_uc004egg.3_Intron	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	aaaaattgtacctatcctttg	0.000													4	2	---	---	---	---	
TCEAL7	56849	broad.mit.edu	37	X	102587009	102587009	+	3'UTR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102587009delT	uc004ekc.1	+	3						NM_152278	NP_689491	Q9BRU2	TCAL7_HUMAN	transcription elongation factor A (SII)-like 7						negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				upper_aerodigestive_tract(1)	1						gtgtgatctctttttttttct	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	103780069	103780069	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103780069delT								ESX1 (280481 upstream) : IL1RAPL2 (30927 downstream)																							gggctcaccctttcttgttct	0.000													4	2	---	---	---	---	
NRK	203447	broad.mit.edu	37	X	105147234	105147234	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105147234delT	uc004emd.2	+						NRK_uc010npc.1_Intron	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase								ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14						TTTTCCCCTATTTTTGCATTC	0.398										HNSCC(51;0.14)			4	2	---	---	---	---	
COL4A5	1287	broad.mit.edu	37	X	107758014	107758015	+	Intron	DEL	TT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107758014_107758015delTT	uc004enz.1	+						COL4A5_uc011mso.1_Intron	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						ACACCTCCTCTTTTATCACCCA	0.351									Alport_syndrome_with_Diffuse_Leiomyomatosis				4	2	---	---	---	---	
COL4A5	1287	broad.mit.edu	37	X	107858701	107858701	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107858701delT	uc004enz.1	+						COL4A5_uc011mso.1_Intron|COL4A5_uc004eob.1_Intron	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						TCCCATTTTCTTTTTTTTTCA	0.328									Alport_syndrome_with_Diffuse_Leiomyomatosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	108110400	108110401	+	IGR	INS	-	T	T	rs35641112		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108110400_108110401insT								IRS4 (130793 upstream) : GUCY2F (505735 downstream)																							caaaataataaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ACSL4	2182	broad.mit.edu	37	X	108927132	108927132	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108927132delT	uc004eoi.2	-						ACSL4_uc004eoj.2_Intron|ACSL4_uc004eok.2_Intron|ACSL4_uc010npp.1_Intron	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4						fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)	TCTGAATTTATTTTTTTCTAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	109787063	109787063	+	IGR	DEL	C	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109787063delC								TDGF3 (20814 upstream) : CHRDL1 (130022 downstream)																							ctataaatttccagctgtctt	0.070													4	2	---	---	---	---	
PAK3	5063	broad.mit.edu	37	X	110223522	110223522	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110223522delA	uc010npt.1	+						PAK3_uc010npu.1_Intron	NM_001128166	NP_001121638	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform a						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						ctcagaggggaggggattata	0.045										TSP Lung(19;0.15)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	113504093	113504093	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113504093delA								None (None upstream) : HTR2C (314458 downstream)																							cccttaacctaaggtcttcca	0.005													4	2	---	---	---	---	
HTR2C	3358	broad.mit.edu	37	X	114116064	114116064	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114116064delT	uc004epu.1	+						HTR2C_uc010nqc.1_Intron|HTR2C_uc004epv.1_Intron	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C						cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)	attttgagggttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115282217	115282218	+	IGR	INS	-	G	G			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115282217_115282218insG								PLS3 (397227 upstream) : AGTR2 (19740 downstream)																							ccacacttaatggggaaaaact	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115820469	115820470	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115820469_115820470insA								CXorf61 (226332 upstream) : None (None downstream)																							aatggctttggaaaaaaaaatg	0.000													4	2	---	---	---	---	
SLC25A43	203427	broad.mit.edu	37	X	118556453	118556454	+	Intron	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118556453_118556454delAG	uc004erd.2	+						SLC25A43_uc004erc.1_Intron|SLC25A43_uc011mtt.1_Intron	NM_145305	NP_660348	Q8WUT9	S2543_HUMAN	mitochondrial solute carrier protein						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			skin(1)	1						tatttcctctagattgcaaact	0.000													4	2	---	---	---	---	
SEPT6	23157	broad.mit.edu	37	X	118826071	118826071	+	Intron	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118826071delT	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc011mtv.1_Intron|SEPT6_uc011mtw.1_Intron	NM_015129	NP_055944	Q14141	SEPT6_HUMAN	septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4						TAAATGAAGATTTTTTTTTTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	120777109	120777110	+	IGR	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120777109_120777110delTG								GLUD2 (593315 upstream) : None (None downstream)																							AAGGAgtgtttgtgtgtgtgtg	0.203													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	120885221	120885222	+	IGR	DEL	GT	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120885221_120885222delGT								GLUD2 (701427 upstream) : None (None downstream)																							AATTTTTTGAGTGTGTGTGTGT	0.243													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	121841307	121841307	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121841307delG								None (None upstream) : GRIA3 (476789 downstream)																							acaaatatatgccaacaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	123265102	123265102	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123265102delT								STAG2 (28599 upstream) : SH2D1A (215046 downstream)																							TGATTTTGGATTTTTTTCCTC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125065045	125065046	+	IGR	DEL	AC	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125065045_125065046delAC								ODZ1 (967379 upstream) : DCAF12L2 (233468 downstream)																							cacacaaactacacacacacac	0.243													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	127701173	127701173	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127701173delA								ACTRT1 (514791 upstream) : SMARCA1 (879307 downstream)																							TTTTCAATATAAAAAATGACC	0.353													4	2	---	---	---	---	
SMARCA1	6594	broad.mit.edu	37	X	128598445	128598446	+	Intron	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128598445_128598446insA	uc004eun.3	-						SMARCA1_uc004eup.3_Intron|SMARCA1_uc011muk.1_Intron|SMARCA1_uc011mul.1_Intron	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated						ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						ATGCCAACATTAAAAATGTGTT	0.322													4	2	---	---	---	---	
UTP14A	10813	broad.mit.edu	37	X	129052864	129052864	+	Intron	DEL	A	-	-	rs11315972		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129052864delA	uc004euz.2	+						UTP14A_uc011mup.1_Intron|UTP14A_uc011muq.1_Intron|UTP14A_uc004eva.1_5'Flank	NM_006649	NP_006640	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,						rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2						aagaaaaaagaaaaaaaaaaa	0.199													4	2	---	---	---	---	
ZNF280C	55609	broad.mit.edu	37	X	129372925	129372925	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129372925delA	uc004evm.2	-						ZNF280C_uc010nrf.1_Intron	NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						TCAATGAGACAAAATTCCTTT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	130369354	130369354	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130369354delT								ARHGAP36 (145498 upstream) : IGSF1 (38129 downstream)																							CCAGTTGTCCTTCATTTCTGG	0.284													4	2	---	---	---	---	
GPC3	2719	broad.mit.edu	37	X	132745740	132745740	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132745740delA	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					TCAAAACTTCAAATATGTTGC	0.308			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				4	2	---	---	---	---	
PLAC1	10761	broad.mit.edu	37	X	133725254	133725255	+	Intron	DEL	TG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133725254_133725255delTG	uc004exo.1	-						PLAC1_uc004exp.1_Intron	NM_021796	NP_068568	Q9HBJ0	PLAC1_HUMAN	placenta-specific 1 precursor						placenta development	extracellular region				pancreas(1)	1	Acute lymphoblastic leukemia(192;0.000127)					ATCTTGGAAAtgtgtgtgtgtg	0.287													4	2	---	---	---	---	
FHL1	2273	broad.mit.edu	37	X	135240531	135240531	+	Intron	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135240531delA	uc010nrz.2	+						FHL1_uc004ezm.2_Intron|FHL1_uc004ezl.2_Intron|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Intron	NM_001449	NP_001440	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 2						cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)					TCCAAGTGTCAAAAAATATCT	0.398													4	2	---	---	---	---	
GPR112	139378	broad.mit.edu	37	X	135495904	135495905	+	Intron	DEL	TG	-	-	rs143438843		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135495904_135495905delTG	uc004ezu.1	+						GPR112_uc010nsb.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)					tttttgtttttgtttttttttt	0.158													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	136064479	136064479	+	Intron	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136064479delG	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																		tgtcctttctgtttgttagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	136532293	136532293	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136532293delA								GPR101 (418460 upstream) : ZIC3 (116053 downstream)																							tctttcattgaaaggagatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	137362434	137362434	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137362434delA								ZIC3 (708177 upstream) : LOC158696 (334458 downstream)																							ttttgttattaggataatgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	138993914	138993915	+	IGR	INS	-	A	A			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138993914_138993915insA								ATP11C (79467 upstream) : MIR505 (12392 downstream)																							gccaggaaaataaaaaatcctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139548614	139548615	+	IGR	DEL	AA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139548614_139548615delAA								CXorf66 (500937 upstream) : SOX3 (36537 downstream)																							TATTAagaagaaagaggaggag	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	141172600	141172600	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141172600delG								MAGEC1 (175418 upstream) : MAGEC2 (117530 downstream)																							aaagttagttggacctatgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142899588	142899588	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142899588delA								SPANXN2 (95072 upstream) : UBE2NL (67585 downstream)																							CAATGAGCATAAAGATTTGTA	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144120082	144120082	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144120082delA								None (None upstream) : SPANXN1 (209025 downstream)																							atgttagagtaaaaattcaca	0.000													4	2	---	---	---	---	
AFF2	2334	broad.mit.edu	37	X	148080912	148080912	+	3'UTR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148080912delA	uc004fcp.2	+	21					AFF2_uc004fcq.2_3'UTR|AFF2_uc004fcr.2_3'UTR|AFF2_uc011mxb.1_3'UTR|AFF2_uc004fcs.2_3'UTR|AFF2_uc011mxc.1_3'UTR	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					TTCTTCCTGGAAAAAAAAGGA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	148649908	148649908	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148649908delT								CXorf40A (17853 upstream) : MAGEA9B (13403 downstream)																							tgacaagtcctttccactagg	0.030													4	2	---	---	---	---	
MTM1	4534	broad.mit.edu	37	X	149826093	149826093	+	Intron	DEL	A	-	-	rs222408		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149826093delA	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243	Q13496	MTM1_HUMAN	myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					agtataatttaaaaaaaaaag	0.174													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150588914	150588914	+	IGR	DEL	G	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150588914delG								VMA21 (11079 upstream) : PASD1 (143093 downstream)																							CATGGGTCCTGGCATATTGAA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150948341	150948341	+	IGR	DEL	T	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150948341delT								CNGA2 (34305 upstream) : MAGEA4 (132655 downstream)																							ACATCTTGGCTTTTTTCTTAA	0.408													4	2	---	---	---	---	
MAGEA3	4102	broad.mit.edu	37	X	151939271	151939284	+	5'Flank	DEL	TTTTGTTGCGTAGA	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151939271_151939284delTTTTGTTGCGTAGA	uc004fgp.2	-							NM_005362	NP_005353	P43357	MAGA3_HUMAN	melanoma antigen family A, 3												0	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTTCCCTGTTTTGTTGCGTAGATTTTGTTGCT	0.449													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9954147	9954147	+	IGR	DEL	A	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9954147delA								TTTY22 (303293 upstream) : None (None downstream)																							caaaaaaaataaaaataaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9962422	9962422	+	IGR	DEL	G	-	-	rs141716206		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9962422delG								TTTY22 (311568 upstream) : None (None downstream)																							ctcagtagatggaatatacaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9992165	9992167	+	IGR	DEL	CTC	-	-	rs112314725		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992165_9992167delCTC								TTTY22 (341311 upstream) : None (None downstream)																							ttttcttctactcctccccacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59009271	59009272	+	IGR	DEL	AG	-	-			TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59009271_59009272delAG								None (None upstream) : None (None downstream)																							taacacaaacagagaatacaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59011712	59011715	+	IGR	DEL	CAAT	-	-	rs71268707		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59011712_59011715delCAAT								None (None upstream) : None (None downstream)																							CTGCCAAAAACAATCACTTGCACT	0.314													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59013019	59013019	+	IGR	DEL	A	-	-	rs148494923		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59013019delA								None (None upstream) : None (None downstream)																							gtctcaaaagaaaaaaaaaaT	0.189													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59016409	59016409	+	IGR	DEL	T	-	-	rs146809444		TCGA-CW-5583-01A-02D-1534-10	TCGA-CW-5583-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59016409delT								None (None upstream) : None (None downstream)																							ttttggaaactttttttgtag	0.000													3	3	---	---	---	---	
