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
SPEN	23013	broad.mit.edu	37	1	16256690	16256690	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256690C>T	uc001axk.1	+	11	4159	c.3955C>T	c.(3955-3957)CAG>TAG	p.Q1319*	SPEN_uc010obp.1_Nonsense_Mutation_p.Q1278*	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1319					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CAGGAGAGAACAGATGGCAGA	0.383													11	40	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22166424	22166424	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22166424C>T	uc001bfj.2	-	72	9640	c.9600G>A	c.(9598-9600)GTG>GTA	p.V3200V	HSPG2_uc009vqd.2_Silent_p.V3201V	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3200	Ig-like C2-type 17.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	TGTCCACGATCACCTCCACCT	0.582													34	64	---	---	---	---	PASS
TCEB3	6924	broad.mit.edu	37	1	24083468	24083468	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24083468G>T	uc001bho.2	+	10	2248	c.2188G>T	c.(2188-2190)GGA>TGA	p.G730*		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	730					positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		GTACCCCATGGGAAGCAGCCA	0.587													5	107	---	---	---	---	PASS
TMEM54	113452	broad.mit.edu	37	1	33363913	33363913	+	Silent	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33363913C>G	uc001bwi.1	-	2	138	c.24G>C	c.(22-24)CTG>CTC	p.L8L	TMEM54_uc001bwj.1_Silent_p.L8L|TMEM54_uc001bwk.1_Silent_p.L8L	NM_033504	NP_277039	Q969K7	TMM54_HUMAN	transmembrane protein 54	8						integral to membrane					0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CGCCCACACTCAGGCCTCCTG	0.617													6	27	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38197177	38197177	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38197177G>A	uc009vvi.2	-	7	1655	c.1569C>T	c.(1567-1569)ACC>ACT	p.T523T	EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	523	Fibronectin type-III 2.|Extracellular (Potential).					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)				AGACGTAGCGGGTAGCCGGCT	0.587													26	46	---	---	---	---	PASS
PPT1	5538	broad.mit.edu	37	1	40555127	40555127	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40555127C>T	uc001cfb.2	-	5	723	c.491G>A	c.(490-492)CGA>CAA	p.R164Q	PPT1_uc010ojf.1_Missense_Mutation_p.R114Q|PPT1_uc010ojg.1_Missense_Mutation_p.R61Q|PPT1_uc009vwa.2_RNA	NM_000310	NP_000301	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1 isoform 1	164					brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGTGTTTTTCGGATGAAGTC	0.403													5	65	---	---	---	---	PASS
BEND5	79656	broad.mit.edu	37	1	49224681	49224681	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49224681T>C	uc001crx.3	-	3	680	c.636A>G	c.(634-636)GTA>GTG	p.V212V	AGBL4_uc001cru.2_Intron|AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron|BEND5_uc001crw.3_Silent_p.V43V	NM_024603	NP_078879	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	212	Potential.									skin(1)	1						TGGCCTGTTGTACCAGCTGCC	0.612													19	31	---	---	---	---	PASS
OMA1	115209	broad.mit.edu	37	1	58999665	58999665	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58999665A>C	uc001cyy.2	-	5	1059	c.971T>G	c.(970-972)CTT>CGT	p.L324R	DAB1_uc001cyt.1_Intron|OMA1_uc001cyx.1_Missense_Mutation_p.L324R|OMA1_uc009vzz.2_Missense_Mutation_p.L324R	NM_145243	NP_660286	Q96E52	OMA1_HUMAN	OMA1 homolog, zinc metallopeptidase precursor	324					proteolysis	integral to membrane|mitochondrial membrane	metal ion binding|metalloendopeptidase activity			large_intestine(1)	1	all_cancers(7;6.54e-05)					ATGGCCCAGAAGGAAAGAAAG	0.343													5	97	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74648474	74648474	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74648474A>G	uc001dfy.3	-	3	513	c.321T>C	c.(319-321)AAT>AAC	p.N107N	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	107	LRR 3.									ovary(2)	2						TTGCAAACCCATTGTCATGAA	0.308													5	28	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94577027	94577027	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94577027G>C	uc001dqh.2	-	3	373	c.269C>G	c.(268-270)TCT>TGT	p.S90C	ABCA4_uc010otn.1_Missense_Mutation_p.S90C	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	90	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AATTCCAGGAGATTCTCCTGG	0.517													3	16	---	---	---	---	PASS
GATAD2B	57459	broad.mit.edu	37	1	153790506	153790506	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153790506G>T	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TCCCACTATGGGTCACATACC	0.493													8	392	---	---	---	---	PASS
UBQLN4	56893	broad.mit.edu	37	1	156020106	156020106	+	Silent	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156020106G>C	uc001fna.2	-	4	741	c.717C>G	c.(715-717)CTC>CTG	p.L239L	UBQLN4_uc010pgx.1_Silent_p.L219L	NM_020131	NP_064516	Q9NRR5	UBQL4_HUMAN	ataxin-1 ubiquitin-like interacting protein	239						cytosol|endoplasmic reticulum membrane|nucleus	identical protein binding			pancreas(1)|skin(1)	2	Hepatocellular(266;0.133)|all_neural(408;0.195)					CAGGGTTATTGAGCATGTGGC	0.547													13	58	---	---	---	---	PASS
SLAMF8	56833	broad.mit.edu	37	1	159799840	159799840	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159799840C>T	uc001fue.3	+	2	435	c.225C>T	c.(223-225)CGC>CGT	p.R75R		NM_020125	NP_064510	Q9P0V8	SLAF8_HUMAN	SLAM family member 8 precursor	75	Extracellular (Potential).					integral to membrane					0	all_hematologic(112;0.0597)					ACCATTCCCGCTTCCTGGGCC	0.602													31	83	---	---	---	---	PASS
NCSTN	23385	broad.mit.edu	37	1	160325486	160325486	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160325486T>G	uc001fvx.2	+	12	1518	c.1394T>G	c.(1393-1395)GTG>GGG	p.V465G	NCSTN_uc001fvy.2_Missense_Mutation_p.V445G|NCSTN_uc010pjf.1_Missense_Mutation_p.V327G|NCSTN_uc001fvz.2_Missense_Mutation_p.V245G|NCSTN_uc010pjg.1_Missense_Mutation_p.V207G	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor	465	Extracellular (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AACATTAATGTGAGCTATCCC	0.537													16	76	---	---	---	---	PASS
RXRG	6258	broad.mit.edu	37	1	165397950	165397950	+	Intron	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165397950A>T	uc001gda.2	-							NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)	GAGGAAGAACACTTACCTGAG	0.567													11	60	---	---	---	---	PASS
SERPINC1	462	broad.mit.edu	37	1	173880967	173880967	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173880967A>G	uc001gjt.2	-	3	713	c.594T>C	c.(592-594)TAT>TAC	p.Y198Y		NM_000488	NP_000479	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C, member 1	198			Y -> C (in AT3D; type-I and -II; Whitechapel).|Y -> H (in AT3D; type-I).		blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)	GCTTGGCTCCATATACCAACT	0.488													11	84	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175360549	175360549	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175360549T>G	uc001gkp.1	-	5	1463	c.1382A>C	c.(1381-1383)CAG>CCG	p.Q461P	TNR_uc009wwu.1_Missense_Mutation_p.Q461P	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	461	Fibronectin type-III 2.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GCTGGGGACCTGAGCAATCAC	0.502													3	27	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176738877	176738877	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176738877G>A	uc001gkz.2	+	16	5622	c.4458G>A	c.(4456-4458)CTG>CTA	p.L1486L	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1486	Sushi 2.				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						CCAAATTTCTGAAACGCTGCT	0.527													31	83	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177250597	177250597	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177250597C>A	uc001glf.2	+	8	2597	c.2285C>A	c.(2284-2286)TCC>TAC	p.S762Y	FAM5B_uc001glg.2_Missense_Mutation_p.S657Y	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	762						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						ATCCAGTCCTCCCTGAGGGCT	0.557													18	63	---	---	---	---	PASS
NPHS2	7827	broad.mit.edu	37	1	179526328	179526328	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179526328G>T	uc001gmq.3	-	5	657	c.572C>A	c.(571-573)GCC>GAC	p.A191D	NPHS2_uc009wxi.2_Intron	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin	191	Cytoplasmic (Potential).				excretion	integral to plasma membrane	protein binding				0						GTAGCAAATGGCATCTATCTC	0.428													8	32	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179604999	179604999	+	Silent	SNP	C	A	A	rs147568109	byFrequency	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179604999C>A	uc001gnf.1	+	9	1747	c.1497C>A	c.(1495-1497)CTC>CTA	p.L499L	TDRD5_uc010pnp.1_Silent_p.L499L|TDRD5_uc001gnh.1_Silent_p.L54L	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	499					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						CAGAGTTACTCGAAGACATGA	0.343													4	55	---	---	---	---	PASS
QSOX1	5768	broad.mit.edu	37	1	180163472	180163472	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180163472C>T	uc001gnz.2	+	11	1488	c.1413C>T	c.(1411-1413)AAC>AAT	p.N471N	QSOX1_uc001gny.2_Silent_p.N471N|QSOX1_uc001goa.2_Silent_p.N471N|QSOX1_uc001goc.2_Silent_p.N13N	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a	471	ERV/ALR sulfhydryl oxidase.				cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						GGAGTCCCAACGCCGCTGTCC	0.622													6	30	---	---	---	---	PASS
RNASEL	6041	broad.mit.edu	37	1	182544528	182544528	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182544528C>T	uc001gpj.1	-	6	2392	c.2225G>A	c.(2224-2226)TGA>TAA	p.*742*	RNASEL_uc009wxz.1_Silent_p.*742*	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	742					mRNA processing|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)|stomach(1)	5						ATCAGTCCATCAGCACCCAGG	0.393									Hereditary_Prostate_Cancer				14	65	---	---	---	---	PASS
RGS16	6004	broad.mit.edu	37	1	182572472	182572472	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182572472G>A	uc001gpl.3	-	2	201	c.47C>T	c.(46-48)GCC>GTC	p.A16V	RGS16_uc010pnv.1_Missense_Mutation_p.A16V	NM_002928	NP_002919	O15492	RGS16_HUMAN	regulator of G-protein signalling 16	16					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(1)	1						GAACTCTTTGGCTCTGAAAAA	0.502													12	60	---	---	---	---	PASS
RGL1	23179	broad.mit.edu	37	1	183857654	183857654	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183857654C>T	uc001gqo.2	+	8	1155	c.998C>T	c.(997-999)TCG>TTG	p.S333L	RGL1_uc010pof.1_Missense_Mutation_p.S138L|RGL1_uc001gqm.2_Missense_Mutation_p.S368L|RGL1_uc010pog.1_Missense_Mutation_p.S331L|RGL1_uc010poh.1_Missense_Mutation_p.S331L|RGL1_uc010poi.1_Missense_Mutation_p.S333L	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation	333	Ras-GEF.				cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11						GCCATCGTTTCGGCACTGCAG	0.428													20	106	---	---	---	---	PASS
RGS21	431704	broad.mit.edu	37	1	192335237	192335237	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192335237T>C	uc001gsh.2	+	5	616	c.442T>C	c.(442-444)TGG>CGG	p.W148R		NM_001039152	NP_001034241	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	148					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2						TCATAAAAAATGGCTCCCTTT	0.333													16	24	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197404369	197404369	+	Missense_Mutation	SNP	C	A	A	rs149390998		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197404369C>A	uc001gtz.2	+	9	3511	c.3376C>A	c.(3376-3378)CTC>ATC	p.L1126I	CRB1_uc010poz.1_Missense_Mutation_p.L1102I|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.L1014I|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.L607I|CRB1_uc001gub.1_Missense_Mutation_p.L775I	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1126	Extracellular (Potential).|Laminin G-like 3.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding	p.L1126F(1)		ovary(5)|skin(3)|large_intestine(1)	9						AGAGCAATTTCTCAAAATCTC	0.398													26	46	---	---	---	---	PASS
CDK18	5129	broad.mit.edu	37	1	205495521	205495521	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205495521G>T	uc001hcr.2	+	7	907	c.688G>T	c.(688-690)GCC>TCC	p.A230S	CDK18_uc010pri.1_Missense_Mutation_p.R220L|CDK18_uc001hcp.2_Missense_Mutation_p.A200S|CDK18_uc001hcq.2_Missense_Mutation_p.A200S|CDK18_uc010prj.1_Missense_Mutation_p.A111S|CDK18_uc001hcs.2_Missense_Mutation_p.A111S|CDK18_uc009xbm.1_Missense_Mutation_p.A111S|CDK18_uc001hct.2_5'Flank	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a	198	Protein kinase.						ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						CCTGAAGCACGCCAATATTGT	0.587													7	55	---	---	---	---	PASS
IL10	3586	broad.mit.edu	37	1	206944254	206944254	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206944254A>G	uc001hen.1	-	3	435	c.376T>C	c.(376-378)TGT>CGT	p.C126R		NM_000572	NP_000563	P22301	IL10_HUMAN	interleukin 10 precursor	126					anti-apoptosis|B cell differentiation|B cell proliferation|cytoplasmic sequestering of NF-kappaB|inflammatory response|leukocyte chemotaxis|negative regulation of B cell proliferation|negative regulation of cytokine secretion involved in immune response|negative regulation of interferon-alpha biosynthetic process|negative regulation of interleukin-6 production|negative regulation of membrane protein ectodomain proteolysis|negative regulation of MHC class II biosynthetic process|negative regulation of T cell proliferation|positive regulation of B cell apoptosis|positive regulation of cytokine secretion|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|receptor biosynthetic process|regulation of isotype switching|response to glucocorticoid stimulus|type 2 immune response	extracellular space	cytokine activity|growth factor activity|interleukin-10 receptor binding				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			CTACTTACACAGCGCCGTAGC	0.547													8	66	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207649608	207649608	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207649608A>G	uc001hfw.2	+	14	2663	c.2569A>G	c.(2569-2571)ACC>GCC	p.T857A	CR2_uc001hfv.2_Missense_Mutation_p.T916A|CR2_uc009xch.2_Intron	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	857	Sushi 14.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						TCCGCCTAAGACCCCTAACGG	0.507													23	45	---	---	---	---	PASS
FAM71A	149647	broad.mit.edu	37	1	212799258	212799258	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212799258G>C	uc001hjk.2	+	1	1443	c.1039G>C	c.(1039-1041)GCT>CCT	p.A347P	uc010pth.1_RNA	NM_153606	NP_705834	Q8IYT1	FA71A_HUMAN	hypothetical protein LOC149647	347	Ala-rich.									skin(3)|ovary(1)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		TGTGGCAGGGGCTGCAGGCAA	0.607													7	15	---	---	---	---	PASS
MIA3	375056	broad.mit.edu	37	1	222833078	222833078	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222833078C>A	uc001hnl.2	+	22	4818	c.4809C>A	c.(4807-4809)CTC>CTA	p.L1603L	MIA3_uc001hnm.2_Silent_p.L481L	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1603	Cytoplasmic (Potential).|Potential.				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		TTCAATAGCTCAAAGCTCGTG	0.383													22	36	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226550831	226550831	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226550831G>A	uc001hqd.3	-	21	2988	c.2817C>T	c.(2815-2817)AGC>AGT	p.S939S		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1	939	PARP catalytic.				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)		TGGGTAACTTGCTGATATGTG	0.502								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					12	65	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229577773	229577773	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229577773C>T	uc001htn.2	-	26	3441	c.3349G>A	c.(3349-3351)GAG>AAG	p.E1117K		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	1117					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)				GGTAAGTACTCACTGAGCTGA	0.363													12	104	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229599292	229599292	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229599292G>A	uc001htn.2	-	19	2775	c.2683C>T	c.(2683-2685)CAG>TAG	p.Q895*		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	895					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)				CTCATCACCTGATCAGCAAAC	0.443													5	57	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233161104	233161104	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233161104C>A	uc001hvl.2	-	26	4628	c.4393G>T	c.(4393-4395)GGC>TGC	p.G1465C	PCNXL2_uc001hvk.1_Missense_Mutation_p.G117C|PCNXL2_uc001hvm.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1465						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				TCCTCGTCGCCCTCCATGATG	0.572											OREG0014326	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	17	33	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419658	247419658	+	Silent	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419658C>G	uc010pyu.1	+	2	285	c.285C>G	c.(283-285)CTC>CTG	p.L95L		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	95	Helical; Name=3; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			TACTGCTGCTCTTCACCCAGG	0.398													6	115	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247420096	247420096	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247420096T>A	uc010pyu.1	+	2	723	c.723T>A	c.(721-723)TAT>TAA	p.Y241*		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	241	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			ATGGTGATTATTTTATACAGA	0.473													33	69	---	---	---	---	PASS
OR2G3	81469	broad.mit.edu	37	1	247769158	247769158	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247769158A>G	uc010pyz.1	+	1	271	c.271A>G	c.(271-273)ACG>GCG	p.T91A		NM_001001914	NP_001001914	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACCAAAGAAGACGATCACTTA	0.468													55	120	---	---	---	---	PASS
OR2M2	391194	broad.mit.edu	37	1	248344097	248344097	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248344097G>A	uc010pzf.1	+	1	810	c.810G>A	c.(808-810)CAG>CAA	p.Q270Q		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	270	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CCCCAACGCAGGACAAGATGG	0.502													33	140	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525076	248525076	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525076T>G	uc001ieh.1	+	1	194	c.194T>G	c.(193-195)GTG>GGG	p.V65G		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	65	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTCATTTTTGTGGTTTTCCTG	0.478													7	150	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11767139	11767139	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11767139C>T	uc002rbk.1	+	25	4658	c.4358C>T	c.(4357-4359)GCA>GTA	p.A1453V	GREB1_uc002rbp.1_Missense_Mutation_p.A451V	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1453						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CGTCAGACGGCACGGATGAGA	0.572													5	24	---	---	---	---	PASS
FAM98A	25940	broad.mit.edu	37	2	33817136	33817136	+	Intron	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33817136C>A	uc002rpa.1	-						FAM98A_uc010yne.1_Intron	NM_015475	NP_056290	Q8NCA5	FA98A_HUMAN	hypothetical protein LOC25940											ovary(1)	1	all_hematologic(175;0.115)					TTCTAGTAGCCATGAACTTAC	0.378													19	78	---	---	---	---	PASS
SOS1	6654	broad.mit.edu	37	2	39294858	39294858	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294858C>G	uc002rrk.3	-	2	165	c.124G>C	c.(124-126)GAT>CAT	p.D42H	SOS1_uc010ynr.1_RNA	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1	42					apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)				AGAGCATCATCATTAGACTCG	0.343									Noonan_syndrome				32	158	---	---	---	---	PASS
PEX13	5194	broad.mit.edu	37	2	61258651	61258651	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61258651G>T	uc002sau.3	+	2	273	c.190G>T	c.(190-192)GGA>TGA	p.G64*		NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	64	Lumenal (Potential).				cerebral cortex cell migration|fatty acid alpha-oxidation|locomotory behavior|microtubule-based peroxisome localization|neuron migration|protein import into peroxisome matrix, docking|suckling behavior	integral to peroxisomal membrane|membrane fraction	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			ACAGCAGACAGGAAGTAGCAG	0.438													5	79	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61415429	61415429	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61415429C>G	uc002sbe.2	-	80	10471	c.10449G>C	c.(10447-10449)TTG>TTC	p.L3483F	USP34_uc002sbd.2_Missense_Mutation_p.L285F	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3483					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CACAGCTTCTCAAGTCAGCTA	0.478													30	61	---	---	---	---	PASS
REG1B	5968	broad.mit.edu	37	2	79314668	79314668	+	Intron	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79314668A>T	uc002sny.2	-						REG1B_uc010ffv.1_Intron|REG1B_uc010ffw.2_Intron	NM_006507	NP_006498	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta precursor						cell proliferation	extracellular region	sugar binding			central_nervous_system(1)|skin(1)	2						GTGGGGGAAAATCTCACCTTG	0.468													11	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89384783	89384783	+	RNA	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89384783G>C	uc010ytr.1	-	50		c.5357C>G			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		AACCTGGCTGGGATACCAGTG	0.532													42	48	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90260185	90260185	+	RNA	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90260185C>G	uc010fhm.2	+	30		c.4168C>G								Parts of antibodies, mostly variable regions.																		TCACTCTCACCATCAGTTGCC	0.488													37	180	---	---	---	---	PASS
ACTR1B	10120	broad.mit.edu	37	2	98274880	98274880	+	Intron	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98274880C>T	uc002syb.2	-							NM_005735	NP_005726	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B,							centrosome|dynactin complex	ATP binding|protein binding			skin(1)	1						ACCCTCTCGCCCCTTGTCACC	0.617													7	31	---	---	---	---	PASS
TSGA10	80705	broad.mit.edu	37	2	99634803	99634803	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99634803G>A	uc002szg.3	-	18	2560	c.1932C>T	c.(1930-1932)GCC>GCT	p.A644A	TSGA10_uc002szh.3_Silent_p.A644A|TSGA10_uc002szi.3_Silent_p.A644A|TSGA10_uc010fin.1_Silent_p.A644A	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	644	Interaction with HIF1A (By similarity).				spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2						GTTCTTGTACGGCCCTCTCCC	0.333													12	49	---	---	---	---	PASS
GCC2	9648	broad.mit.edu	37	2	109086257	109086257	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109086257G>A	uc002tec.2	+	6	626	c.472G>A	c.(472-474)GAA>AAA	p.E158K	GCC2_uc002ted.2_Missense_Mutation_p.E57K	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	158	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						GCAGCTGGAAGAAGCAATGAA	0.303													48	87	---	---	---	---	PASS
TUBA3E	112714	broad.mit.edu	37	2	130951676	130951676	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130951676C>T	uc002tqv.2	-	4	840	c.739G>A	c.(739-741)GCC>ACC	p.A247T		NM_207312	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	247					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			skin(1)	1	Colorectal(110;0.1)					ACATTCAGGGCCCCATCAAAT	0.592													36	126	---	---	---	---	PASS
PKP4	8502	broad.mit.edu	37	2	159535159	159535159	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159535159G>A	uc002tzv.2	+	21	3583	c.3323G>A	c.(3322-3324)CGG>CAG	p.R1108Q	PKP4_uc002tzw.2_Missense_Mutation_p.R1065Q|PKP4_uc002tzx.2_Missense_Mutation_p.R765Q|PKP4_uc002uaa.2_Missense_Mutation_p.R917Q|uc002uab.1_Intron|PKP4_uc002uac.2_Missense_Mutation_p.R289Q|PKP4_uc002uad.2_RNA	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	1108					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						CAAAATAGACGGCTACAGGTG	0.398										HNSCC(62;0.18)			8	20	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166901684	166901684	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166901684C>T	uc010zcz.1	-	10	1549	c.1531G>A	c.(1531-1533)GGT>AGT	p.G511S	SCN1A_uc002udo.3_Missense_Mutation_p.G380S|SCN1A_uc010fpk.2_Missense_Mutation_p.G380S	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	511						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	TCTTCCCCACCAGACTGCTCT	0.448													32	71	---	---	---	---	PASS
DLX1	1745	broad.mit.edu	37	2	172951530	172951530	+	Silent	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172951530T>G	uc002uhl.2	+	2	660	c.462T>G	c.(460-462)GCT>GCG	p.A154A	DLX1_uc010fqj.1_Silent_p.A154A|DLX1_uc002uhm.2_Intron	NM_178120	NP_835221	P56177	DLX1_HUMAN	distal-less homeobox 1 isoform 1	154	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)			AGTACCTAGCTCTGCCGGAGA	0.582													35	95	---	---	---	---	PASS
ATP5G3	518	broad.mit.edu	37	2	176043809	176043809	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176043809C>A	uc002ujz.3	-	3	560	c.290G>T	c.(289-291)GGC>GTC	p.G97V	ATP5G3_uc002uka.3_Missense_Mutation_p.G97V|ATP5G3_uc002ukb.1_Missense_Mutation_p.G97V	NM_001002258	NP_001002258	P48201	AT5G3_HUMAN	ATP synthase, H+ transporting, mitochondrial F0	97	Helical; (Potential).				ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.147)			GATAAGGCTGCCAAAGACTGT	0.413													10	47	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179596503	179596503	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179596503A>G	uc010zfg.1	-	55	13591	c.13367T>C	c.(13366-13368)GTA>GCA	p.V4456A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.V1117A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5383							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)			ATCTGCAGCTACAAACTTGAG	0.478													17	115	---	---	---	---	PASS
ZNF385B	151126	broad.mit.edu	37	2	180634369	180634369	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180634369C>T	uc002unn.3	-	3	718	c.114G>A	c.(112-114)GTG>GTA	p.V38V		NM_152520	NP_689733	Q569K4	Z385B_HUMAN	zinc finger protein 385B isoform 1	38	Matrin-type 1.					nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GGATGTTGCACACCTCACAGA	0.507													15	36	---	---	---	---	PASS
CERKL	375298	broad.mit.edu	37	2	182438605	182438605	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182438605G>A	uc002unx.2	-	3	589	c.488C>T	c.(487-489)CCA>CTA	p.P163L	CERKL_uc002uny.2_Missense_Mutation_p.P163L|CERKL_uc010zfm.1_Intron|CERKL_uc002unz.2_5'UTR|CERKL_uc002uoa.2_Missense_Mutation_p.P163L|CERKL_uc002uob.2_Intron|CERKL_uc002uoc.2_Intron|CERKL_uc010frk.2_Intron|CERKL_uc002uod.1_5'UTR|CERKL_uc002uoe.2_Missense_Mutation_p.P163L	NM_001030311	NP_001025482	Q49MI3	CERKL_HUMAN	ceramide kinase-like isoform b	163					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CGGTCTGTTTGGAAAGCCTAA	0.338													14	60	---	---	---	---	PASS
FAM171B	165215	broad.mit.edu	37	2	187615909	187615909	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187615909T>A	uc002ups.2	+	5	885	c.773T>A	c.(772-774)ATA>AAA	p.I258K	FAM171B_uc002upr.1_Missense_Mutation_p.I258K	NM_177454	NP_803237	Q6P995	F171B_HUMAN	KIAA1946	258	Extracellular (Potential).					integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10						TGTGTGAAAATATATTCTGGA	0.353													33	88	---	---	---	---	PASS
MYO1B	4430	broad.mit.edu	37	2	192273764	192273764	+	Intron	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192273764A>G	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002usu.2_Intron|MYO1B_uc002usv.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)			TGTCAACCCAACACAGGTGCA	0.328													9	36	---	---	---	---	PASS
IKZF2	22807	broad.mit.edu	37	2	213921675	213921675	+	Silent	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213921675G>C	uc002vem.2	-	4	457	c.288C>G	c.(286-288)GTC>GTG	p.V96V	IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Silent_p.V43V|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Silent_p.V96V|IKZF2_uc002vel.2_Silent_p.V43V|IKZF2_uc010fuw.2_5'UTR|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Silent_p.V96V|IKZF2_uc002ven.2_Silent_p.V96V	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	96					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GAAGCTCCTGGACTTTCCTGT	0.532													21	38	---	---	---	---	PASS
PNKD	25953	broad.mit.edu	37	2	219204777	219204777	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219204777C>A	uc002vhn.2	+	4	522	c.378C>A	c.(376-378)GTC>GTA	p.V126V	PNKD_uc002vhq.2_Silent_p.V102V	NM_015488	NP_056303	Q8N490	PNKD_HUMAN	myofibrillogenesis regulator 1 isoform 1	126						membrane|mitochondrion|nucleus	hydroxyacylglutathione hydrolase activity|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCATCCCTGTCCTCTCGGACA	0.647													4	37	---	---	---	---	PASS
C2orf24	27013	broad.mit.edu	37	2	220039778	220039778	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220039778G>A	uc002vju.3	-	4	465	c.313C>T	c.(313-315)CGG>TGG	p.R105W	C2orf24_uc002vjv.2_Missense_Mutation_p.R105W	NM_015680	NP_056495	Q9BV87	CNPD1_HUMAN	hypothetical protein LOC27013	105					regulation of cyclin-dependent protein kinase activity	integral to membrane	protein kinase binding				0		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCCGGAGCCGTTCAATGTAC	0.527													29	52	---	---	---	---	PASS
KIAA1486	57624	broad.mit.edu	37	2	226516205	226516205	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226516205C>T	uc002voe.2	+	6	2061	c.1886C>T	c.(1885-1887)CCA>CTA	p.P629L	KIAA1486_uc010fxa.1_3'UTR|KIAA1486_uc002vof.1_Missense_Mutation_p.P399L	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	629										ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		GTGCCTCCTCCATCAGTCACT	0.493													76	122	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228881839	228881839	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228881839G>T	uc002vpq.2	-	7	3778	c.3731C>A	c.(3730-3732)TCC>TAC	p.S1244Y	SPHKAP_uc002vpp.2_Missense_Mutation_p.S1244Y|SPHKAP_uc010zlx.1_Missense_Mutation_p.S1244Y	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1244						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GGAGCATGGGGATCTGCTGTC	0.572													27	40	---	---	---	---	PASS
GIGYF2	26058	broad.mit.edu	37	2	233704607	233704607	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233704607C>G	uc002vti.3	+	25	3152	c.2815C>G	c.(2815-2817)CAG>GAG	p.Q939E	GIGYF2_uc002vtj.3_Missense_Mutation_p.Q960E|GIGYF2_uc002vtk.3_Missense_Mutation_p.Q939E|GIGYF2_uc002vth.3_Missense_Mutation_p.Q933E|GIGYF2_uc010zmk.1_RNA|GIGYF2_uc010zml.1_Missense_Mutation_p.Q770E|GIGYF2_uc002vtq.3_Missense_Mutation_p.Q272E	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b	939	Gln-rich.				cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AACAGCATGTCAGTCCCAGGC	0.458													21	27	---	---	---	---	PASS
RPL32	6161	broad.mit.edu	37	3	12880933	12880933	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12880933T>C	uc003bxl.2	-	2	406	c.193A>G	c.(193-195)AAA>GAA	p.K65E	RPL32_uc003bxm.2_Missense_Mutation_p.K65E|RPL32_uc003bxn.2_Missense_Mutation_p.K65E	NM_001007074	NP_001007075	P62910	RL32_HUMAN	ribosomal protein L32	65					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome			ovary(1)	1						TGCTTTGTTTTTTTGTTGCTT	0.507													7	214	---	---	---	---	PASS
EFHB	151651	broad.mit.edu	37	3	19956850	19956850	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19956850T>C	uc003cbl.3	-	5	1429	c.1233A>G	c.(1231-1233)AAA>AAG	p.K411K	EFHB_uc003cbm.2_Silent_p.K281K	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	411					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0						CATTTCCTTCTTTAAATACTT	0.363													4	14	---	---	---	---	PASS
TGFBR2	7048	broad.mit.edu	37	3	30713559	30713559	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30713559C>G	uc003ceo.2	+	4	1266	c.884C>G	c.(883-885)TCA>TGA	p.S295*	TGFBR2_uc003cen.2_Nonsense_Mutation_p.S320*	NM_003242	NP_003233	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II	295	Protein kinase.|Cytoplasmic (Potential).				activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1)	26						GACATCTTCTCAGACATCAAT	0.493													25	39	---	---	---	---	PASS
XYLB	9942	broad.mit.edu	37	3	38406756	38406756	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38406756C>T	uc003cic.2	+	5	467	c.358C>T	c.(358-360)CGG>TGG	p.R120W	XYLB_uc011ayp.1_5'UTR|XYLB_uc003cid.1_Missense_Mutation_p.R42W	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase	120					D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		ACCAGACCTCCGGCTACACCA	0.542													12	36	---	---	---	---	PASS
MST1R	4486	broad.mit.edu	37	3	49928037	49928037	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49928037G>A	uc003cxy.3	-	18	3955	c.3691C>T	c.(3691-3693)CGC>TGC	p.R1231C	MST1R_uc011bdc.1_Missense_Mutation_p.R110C	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1231	Cytoplasmic (Potential).|Protein kinase.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		AGGATGTCGCGGGCCAAACCA	0.557													13	16	---	---	---	---	PASS
RBM6	10180	broad.mit.edu	37	3	50114516	50114516	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50114516C>T	uc003cyc.2	+	21	3455	c.3322C>T	c.(3322-3324)CGA>TGA	p.R1108*	RBM6_uc003cyd.2_Nonsense_Mutation_p.R586*|RBM6_uc003cye.2_Nonsense_Mutation_p.R586*|RBM6_uc011bdi.1_Nonsense_Mutation_p.R450*|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	1108					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		CGAGACTTACCGAGATGCTGT	0.458													8	21	---	---	---	---	PASS
PRKCD	5580	broad.mit.edu	37	3	53212538	53212538	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53212538G>C	uc003dgl.2	+	3	453	c.100G>C	c.(100-102)GAG>CAG	p.E34Q	PRKCD_uc003dgm.2_Missense_Mutation_p.E34Q|PRKCD_uc003dgn.2_Missense_Mutation_p.E34Q	NM_006254	NP_006245	Q05655	KPCD_HUMAN	protein kinase C, delta	34	C2.				activation of phospholipase C activity|cellular component disassembly involved in apoptosis|cellular senescence|interferon-gamma-mediated signaling pathway|intracellular signal transduction|mRNA metabolic process|negative regulation of insulin receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein binding|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of ceramide biosynthetic process|positive regulation of glucosylceramide catabolic process|positive regulation of protein dephosphorylation|positive regulation of sphingomyelin catabolic process|protein stabilization|regulation of receptor activity|termination of signal transduction	cytosol|endoplasmic reticulum|nucleoplasm	ATP binding|calcium-independent protein kinase C activity|enzyme activator activity|enzyme binding|insulin receptor substrate binding|metal ion binding|protein C-terminus binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)		GAAGATGAAGGAGGCGCTCAG	0.657													11	8	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73433611	73433611	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73433611G>A	uc003dpl.1	-	10	2202	c.2106C>T	c.(2104-2106)ATC>ATT	p.I702I	PDZRN3_uc011bgh.1_Silent_p.I359I|PDZRN3_uc010hoe.1_Silent_p.I400I|PDZRN3_uc011bgf.1_Silent_p.I419I|PDZRN3_uc011bgg.1_Silent_p.I422I	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	702	Potential.						ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGGCGCGCACGATGCTCAGGC	0.627													7	15	---	---	---	---	PASS
GPR128	84873	broad.mit.edu	37	3	100362185	100362185	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100362185G>A	uc003duc.2	+	7	1042	c.774G>A	c.(772-774)CAG>CAA	p.Q258Q	GPR128_uc011bhc.1_Intron	NM_032787	NP_116176	Q96K78	GP128_HUMAN	G protein-coupled receptor 128 precursor	258	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4						TAGCAATACAGTCAGCAAATT	0.388													22	91	---	---	---	---	PASS
CD200	4345	broad.mit.edu	37	3	112066467	112066467	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112066467G>T	uc003dyw.2	+	5	703	c.559G>T	c.(559-561)GCC>TCC	p.A187S	CD200_uc010hqd.1_Missense_Mutation_p.A46S|CD200_uc003dyx.2_Missense_Mutation_p.A162S|CD200_uc003dyy.2_Missense_Mutation_p.A46S|CD200_uc003dyz.2_Missense_Mutation_p.A88S	NM_001004196	NP_001004196	P41217	OX2G_HUMAN	CD200 antigen isoform b	162	Ig-like C2-type.|Extracellular (Potential).				regulation of immune response	integral to plasma membrane					0		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				CACTTGCTCTGCCACTGCCCG	0.468													31	83	---	---	---	---	PASS
C3orf17	25871	broad.mit.edu	37	3	112724646	112724646	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112724646T>C	uc003dzr.2	-	9	1502	c.1441A>G	c.(1441-1443)ACA>GCA	p.T481A	GTPBP8_uc011bhy.1_Intron|C3orf17_uc003dzq.2_Missense_Mutation_p.T106A|C3orf17_uc011bhz.1_Missense_Mutation_p.T106A|C3orf17_uc010hqh.2_Missense_Mutation_p.T106A|C3orf17_uc003dzt.2_Missense_Mutation_p.T384A|C3orf17_uc003dzs.2_Missense_Mutation_p.T345A|C3orf17_uc010hqg.2_Missense_Mutation_p.T306A|C3orf17_uc011bia.1_Missense_Mutation_p.T278A|C3orf17_uc003dzu.2_Missense_Mutation_p.T410A|C3orf17_uc011bib.1_Missense_Mutation_p.T370A|C3orf17_uc011bic.1_Missense_Mutation_p.T314A|C3orf17_uc011bid.1_RNA	NM_015412	NP_056227	Q6NW34	CC017_HUMAN	hypothetical protein LOC25871	481						integral to membrane					0						CTGGTATCTGTAGCACTCTTC	0.433													17	33	---	---	---	---	PASS
ZNF80	7634	broad.mit.edu	37	3	113955426	113955426	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113955426A>G	uc010hqo.2	-	1	1000	c.496T>C	c.(496-498)TGT>CGT	p.C166R	ZNF80_uc003ebf.2_RNA	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	166	C2H2-type 5.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				GTTTTTCCACATTCTTTGCAC	0.483													14	63	---	---	---	---	PASS
TOPBP1	11073	broad.mit.edu	37	3	133337159	133337159	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133337159G>C	uc003eps.2	-	21	3622	c.3490C>G	c.(3490-3492)CCT>GCT	p.P1164A	TOPBP1_uc003ept.1_Missense_Mutation_p.P168A	NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1164					DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						GGACAACTAGGCCACTGCAAA	0.443								Other_conserved_DNA_damage_response_genes					29	76	---	---	---	---	PASS
AADACL2	344752	broad.mit.edu	37	3	151451952	151451952	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151451952T>C	uc003ezc.2	+	1	249	c.129T>C	c.(127-129)TGT>TGC	p.C43C	AADACL2_uc010hvn.2_5'UTR	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	43						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CTAAAACTTGTACATTTACGG	0.333													7	29	---	---	---	---	PASS
MIR15B	406949	broad.mit.edu	37	3	160122461	160122461	+	RNA	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160122461T>C	hsa-mir-15b|MI0000438	+			c.86T>C			IFT80_uc003fda.2_Intron|SMC4_uc003fdf.1_Intron|SMC4_uc003fdg.1_Intron|SMC4_uc010hwc.1_Intron|SMC4_uc003fdh.2_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|uc011boz.1_RNA|uc003fdk.2_5'Flank|MIR16-2_hsa-mir-16-2|MI0000115_5'Flank																	0						TCTAGAAATTTAAGGAAATTC	0.353													5	29	---	---	---	---	PASS
PEX5L	51555	broad.mit.edu	37	3	179529630	179529630	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179529630C>T	uc003fki.1	-	11	1243	c.1113G>A	c.(1111-1113)GCG>GCA	p.A371A	PEX5L_uc011bqd.1_Silent_p.A328A|PEX5L_uc011bqe.1_Silent_p.A179A|PEX5L_uc011bqf.1_Silent_p.A263A|PEX5L_uc003fkj.1_Silent_p.A336A|PEX5L_uc010hxd.1_Silent_p.A369A|PEX5L_uc011bqg.1_Silent_p.A347A|PEX5L_uc011bqh.1_Silent_p.A312A	NM_016559	NP_057643	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	371	TPR 1.				protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			TTTCATTCTCCGCCTGGGTTA	0.448													60	74	---	---	---	---	PASS
EVC2	132884	broad.mit.edu	37	4	5642280	5642280	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5642280C>A	uc003gij.2	-	10	1485	c.1431G>T	c.(1429-1431)ATG>ATT	p.M477I	EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_Missense_Mutation_p.M397I	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	477	Potential.					integral to membrane				large_intestine(3)|ovary(2)	5						CTGCTTCCTCCATTGCCATCA	0.468													6	162	---	---	---	---	PASS
ACOX3	8310	broad.mit.edu	37	4	8383231	8383231	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8383231C>G	uc010idk.2	-	14	1786	c.1641G>C	c.(1639-1641)AGG>AGC	p.R547S	ACOX3_uc003glc.3_Missense_Mutation_p.R547S|ACOX3_uc003gld.3_Missense_Mutation_p.R547S|ACOX3_uc003gle.1_Missense_Mutation_p.R452S	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	547					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						GGCATTTGTTCCTTGCTTCAA	0.368													24	56	---	---	---	---	PASS
CLRN2	645104	broad.mit.edu	37	4	17528651	17528651	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17528651G>C	uc003gpg.1	+	3	747	c.645G>C	c.(643-645)GAG>GAC	p.E215D		NM_001079827	NP_001073296	A0PK11	CLRN2_HUMAN	clarin 2	215						integral to membrane					0						CCCTCCCTGAGATTAAGACCA	0.502													30	63	---	---	---	---	PASS
MED28	80306	broad.mit.edu	37	4	17616413	17616413	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17616413G>C	uc003gpi.1	+	1	148	c.136G>C	c.(136-138)GAC>CAC	p.D46H	MED28_uc003gpj.2_RNA	NM_025205	NP_079481	Q9H204	MED28_HUMAN	mediator complex subunit 28	46					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0						TACTTTGGTGGACGAGTTGGA	0.582													27	60	---	---	---	---	PASS
STIM2	57620	broad.mit.edu	37	4	26921165	26921165	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26921165A>G	uc003gsh.3	+	2	668	c.452A>G	c.(451-453)GAA>GGA	p.E151G	STIM2_uc003gsg.3_Missense_Mutation_p.E151G|STIM2_uc010iex.2_Missense_Mutation_p.E151G	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	64	Extracellular (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TTTACAGAAGAAGACAGATTT	0.393													24	53	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42618096	42618096	+	Splice_Site	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42618096C>T	uc003gwr.2	-	5	596	c.364_splice	c.e5-1	p.K122_splice	ATP8A1_uc003gws.2_Splice_Site_p.K122_splice|ATP8A1_uc011byz.1_Splice_Site_p.K122_splice	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma 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			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	TATGTCGTTTCTAAAGTTTAA	0.303													6	27	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55981484	55981484	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55981484G>T	uc003has.2	-	4	755	c.453C>A	c.(451-453)CTC>CTA	p.L151L	KDR_uc003hat.1_Silent_p.L151L|KDR_uc011bzx.1_Silent_p.L151L	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	151	Ig-like C2-type 2.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	AAATGGACCCGAGACATGGAA	0.368			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			11	20	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55981485	55981485	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55981485A>C	uc003has.2	-	4	754	c.452T>G	c.(451-453)CTC>CGC	p.L151R	KDR_uc003hat.1_Missense_Mutation_p.L151R|KDR_uc011bzx.1_Missense_Mutation_p.L151R	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	151	Ig-like C2-type 2.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	AATGGACCCGAGACATGGAAT	0.368			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			11	20	---	---	---	---	PASS
ADAMTS3	9508	broad.mit.edu	37	4	73154571	73154571	+	Silent	SNP	G	A	A	rs112565530		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73154571G>A	uc003hgk.1	-	21	2983	c.2946C>T	c.(2944-2946)TGC>TGT	p.C982C		NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	982	TSP type-1 4.				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCCTTCACCGCAGGTCACTG	0.448													13	17	---	---	---	---	PASS
LARP7	51574	broad.mit.edu	37	4	113568634	113568634	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113568634G>T	uc003iay.2	+	7	1204	c.926G>T	c.(925-927)CGA>CTA	p.R309L	LARP7_uc003iaz.2_Missense_Mutation_p.R316L|LARP7_uc003iba.2_Missense_Mutation_p.R230L|LARP7_uc003ibb.2_Missense_Mutation_p.R309L	NM_016648	NP_057732	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	309	Lys-rich.				RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CTAGCTCCCCGATCAAAAGTA	0.378													36	112	---	---	---	---	PASS
ACCN5	51802	broad.mit.edu	37	4	156757901	156757901	+	Missense_Mutation	SNP	G	T	T	rs139903903		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156757901G>T	uc003ipe.1	-	8	1222	c.1175C>A	c.(1174-1176)CCA>CAA	p.P392Q		NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,	392	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)		TTTTTGACTTGGAAAAGAGGA	0.338													4	43	---	---	---	---	PASS
ETFDH	2110	broad.mit.edu	37	4	159620142	159620142	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159620142G>A	uc003iqb.2	+	9	1308	c.976G>A	c.(976-978)GGT>AGT	p.G326S	ETFDH_uc011cjg.1_Missense_Mutation_p.G279S|ETFDH_uc010iqr.2_Intron|ETFDH_uc011cjh.1_Missense_Mutation_p.G265S|ETFDH_uc010iqs.2_Missense_Mutation_p.G248S	NM_004453	NP_004444	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	326					fatty acid beta-oxidation using acyl-CoA dehydrogenase|respiratory electron transport chain|response to oxidative stress|transport	integral to mitochondrial inner membrane|mitochondrial matrix	4 iron, 4 sulfur cluster binding|electron carrier activity|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity, oxidizing metal ions with flavin as acceptor|ubiquinone binding			large_intestine(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		TTTTAAGGTTGGTCTAGACTA	0.328													13	31	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897673	175897673	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175897673C>A	uc003iuc.2	+	5	1667	c.997C>A	c.(997-999)CAT>AAT	p.H333N	ADAM29_uc003iud.2_Missense_Mutation_p.H333N|ADAM29_uc010irr.2_Missense_Mutation_p.H333N|ADAM29_uc011cki.1_Missense_Mutation_p.H333N	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	333	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AGTGGCTCATCATCTAGGTCA	0.398													30	70	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175898265	175898265	+	Missense_Mutation	SNP	G	C	C	rs148692882		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175898265G>C	uc003iuc.2	+	5	2259	c.1589G>C	c.(1588-1590)CGT>CCT	p.R530P	ADAM29_uc003iud.2_Missense_Mutation_p.R530P|ADAM29_uc010irr.2_Missense_Mutation_p.R530P|ADAM29_uc011cki.1_Missense_Mutation_p.R530P	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	530	Cys-rich.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TTAGGTGACCGTGTTGGTCAC	0.418													25	28	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187540391	187540391	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187540391G>C	uc003izf.2	-	10	7537	c.7349C>G	c.(7348-7350)TCA>TGA	p.S2450*		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2450	Extracellular (Potential).|Cadherin 22.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						GTGCAGGTTTGAGAGGGTGAT	0.433										HNSCC(5;0.00058)			34	112	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187540705	187540705	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187540705G>A	uc003izf.2	-	10	7223	c.7035C>T	c.(7033-7035)CTC>CTT	p.L2345L		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2345	Extracellular (Potential).|Cadherin 21.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						CCAGGGTTCTGAGTAGTGAGA	0.493										HNSCC(5;0.00058)			31	81	---	---	---	---	PASS
SLC12A7	10723	broad.mit.edu	37	5	1085507	1085507	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1085507C>A	uc003jbu.2	-	7	823	c.757G>T	c.(757-759)GTG>TTG	p.V253L		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	253	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GTGCCGTACACACGCATGTTG	0.647													3	5	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14297283	14297283	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14297283G>C	uc003jff.2	+	7	1285	c.1279G>C	c.(1279-1281)GAG>CAG	p.E427Q	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.E378Q|TRIO_uc003jfh.1_Missense_Mutation_p.E76Q	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	427					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					GAGTCAGCTGGAGCAGGAGTG	0.562													11	22	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14378141	14378141	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14378141C>A	uc003jff.2	+	20	3358	c.3352C>A	c.(3352-3354)CAA>AAA	p.Q1118K	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.Q1069K|TRIO_uc003jfh.1_Missense_Mutation_p.Q767K	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1118	Spectrin 4.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					TGAACTCTTCCAACGGGAGAA	0.423													4	27	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24488226	24488226	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24488226C>A	uc003jgr.1	-	12	2245	c.1913G>T	c.(1912-1914)CGA>CTA	p.R638L	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	638	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	p.R638Q(1)		ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		CTCTTTTTTTCGCTGTCTTTT	0.398										HNSCC(23;0.051)			23	39	---	---	---	---	PASS
RNASEN	29102	broad.mit.edu	37	5	31429647	31429647	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31429647C>T	uc003jhg.2	-	26	3510	c.3151G>A	c.(3151-3153)GTT>ATT	p.V1051I	RNASEN_uc003jhh.2_Missense_Mutation_p.V1014I|RNASEN_uc003jhi.2_Missense_Mutation_p.V1014I	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	1051	Necessary for interaction with DGCR8 and pri-miRNA processing activity.|RNase III 1.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						TCCAAGTAAACAGCTCCTAGA	0.368													18	44	---	---	---	---	PASS
RANBP3L	202151	broad.mit.edu	37	5	36257555	36257555	+	Splice_Site	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36257555C>T	uc003jkh.2	-	9	1265	c.772_splice	c.e9+1	p.R258_splice	RANBP3L_uc011cow.1_Splice_Site_p.R283_splice	NM_145000	NP_659437	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like isoform 2						intracellular transport					ovary(1)	1	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			AGAATTCTTACTTGAACTTAA	0.254													6	23	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41181632	41181632	+	Silent	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41181632T>A	uc003jmk.2	-	7	966	c.756A>T	c.(754-756)ACA>ACT	p.T252T	C6_uc003jml.1_Silent_p.T252T	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	252	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGTAGAAATCTGTTTTCAAGT	0.348													15	37	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41181633	41181633	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41181633G>C	uc003jmk.2	-	7	965	c.755C>G	c.(754-756)ACA>AGA	p.T252R	C6_uc003jml.1_Missense_Mutation_p.T252R	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	252	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GTAGAAATCTGTTTTCAAGTC	0.348													15	38	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45262388	45262388	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262388T>C	uc003jok.2	-	8	2333	c.2308A>G	c.(2308-2310)AGC>GGC	p.S770G		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	770	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						GCCTGCGTGCTCTTGTGCACT	0.488													9	33	---	---	---	---	PASS
APC	324	broad.mit.edu	37	5	112155052	112155052	+	Intron	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112155052T>C	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron|APC_uc010jca.2_5'Flank	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTATGTTCTCTATAGTGTACA	0.378		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			8	30	---	---	---	---	PASS
ALDH7A1	501	broad.mit.edu	37	5	125896775	125896775	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125896775C>A	uc003ktx.2	-	10	1105	c.913G>T	c.(913-915)GCC>TCC	p.A305S	ALDH7A1_uc003ktv.2_5'UTR|ALDH7A1_uc003kty.2_RNA|ALDH7A1_uc011cxa.1_Missense_Mutation_p.A332S	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	305					cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	GCAGCCTTACCAATAATGGCA	0.358													5	140	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	129001218	129001218	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129001218G>T	uc003kvb.1	+	16	2434	c.2434G>T	c.(2434-2436)GCT>TCT	p.A812S	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	812	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GGTGATACCTGCTGGAGCAAG	0.398													5	24	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131008511	131008511	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008511A>G	uc003kvs.1	-	14	1768	c.1626T>C	c.(1624-1626)TTT>TTC	p.F542F	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Silent_p.F514F|FNIP1_uc010jdm.1_Silent_p.F497F	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	542					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		AGCATCTTATAAAATAAGTAA	0.413													15	25	---	---	---	---	PASS
WNT8A	7478	broad.mit.edu	37	5	137420286	137420286	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137420286A>T	uc003lcd.1	+	3	207	c.202A>T	c.(202-204)AAT>TAT	p.N68Y	BRD8_uc003lcc.1_Intron|WNT8A_uc011cyj.1_Missense_Mutation_p.N86Y|WNT8A_uc011cyk.1_Missense_Mutation_p.N86Y	NM_058244	NP_490645	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family,	68					brain segmentation|canonical Wnt receptor signaling pathway involved in neural crest cell differentiation|cell migration involved in gastrulation|dorsal/ventral pattern formation|ectoderm development|endoderm development|eye development|hindbrain development|mesodermal cell fate commitment|negative regulation of Wnt receptor signaling pathway|neural crest cell fate commitment|neural plate pattern specification|notochord development|palate development|polarity specification of anterior/posterior axis|polarity specification of proximal/distal axis|positive regulation of fibroblast growth factor receptor signaling pathway|regulation of transcription involved in anterior/posterior axis specification|response to retinoic acid|somitogenesis|spinal cord anterior/posterior patterning|tail morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled binding|signal transducer activity			ovary(1)|lung(1)|breast(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTGCCCTGAAAATGCTCTTCA	0.532													14	31	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140175262	140175262	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140175262A>G	uc003lhd.2	+	1	819	c.713A>G	c.(712-714)AAT>AGT	p.N238S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.N238S|PCDHA2_uc011czy.1_Missense_Mutation_p.N238S	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	238	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAAATGACAATGAACCAACT	0.398													10	51	---	---	---	---	PASS
PCDHB4	56131	broad.mit.edu	37	5	140502911	140502911	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140502911A>G	uc003lip.1	+	1	1331	c.1331A>G	c.(1330-1332)AAT>AGT	p.N444S		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	444	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCGACGTCAATGACAACGCC	0.597													25	69	---	---	---	---	PASS
PCDHB8	56128	broad.mit.edu	37	5	140558610	140558610	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140558610G>A	uc011dai.1	+	1	1181	c.995G>A	c.(994-996)TGC>TAC	p.C332Y	PCDHB16_uc003liv.2_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	332	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCTGGAAAATGCACCGTTCTG	0.433													36	219	---	---	---	---	PASS
PCDHGB2	56103	broad.mit.edu	37	5	140741324	140741324	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140741324C>T	uc003ljs.1	+	1	1622	c.1622C>T	c.(1621-1623)GCG>GTG	p.A541V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGA5_uc003lju.1_5'Flank|PCDHGB2_uc011dar.1_Missense_Mutation_p.A541V|PCDHGA5_uc011das.1_5'Flank	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	541	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTCGCCCGCGCTCAGCGCC	0.701													9	17	---	---	---	---	PASS
KCTD16	57528	broad.mit.edu	37	5	143587013	143587013	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143587013C>A	uc003lnm.1	+	3	1365	c.736C>A	c.(736-738)CAC>AAC	p.H246N	KCTD16_uc003lnn.1_Missense_Mutation_p.H246N	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain	246						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			GTGTGGATTCCACATGGTGGC	0.438													28	45	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167673804	167673804	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167673804G>C	uc010jjd.2	+	27	5833	c.5833G>C	c.(5833-5835)GAG>CAG	p.E1945Q	ODZ2_uc003lzr.3_Missense_Mutation_p.E1715Q|ODZ2_uc003lzt.3_Missense_Mutation_p.E1318Q|ODZ2_uc010jje.2_Missense_Mutation_p.E1209Q	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)		GTATATATTTGAGTATGACTC	0.512													8	259	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167674284	167674284	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167674284G>T	uc010jjd.2	+	27	6313	c.6313G>T	c.(6313-6315)GTT>TTT	p.V2105F	ODZ2_uc003lzr.3_Missense_Mutation_p.V1875F|ODZ2_uc003lzt.3_Missense_Mutation_p.V1478F|ODZ2_uc010jje.2_Missense_Mutation_p.V1369F	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)		TCCCCTCCCCGTTGACCTCTA	0.493													36	114	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169685177	169685177	+	Intron	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169685177A>T	uc003man.1	-						LCP2_uc011des.1_Intron|LCP2_uc011det.1_Intron	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2						immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGCACTGTGCAGAAGTAGAAA	0.478													22	88	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170610401	170610401	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170610401A>G	uc003mba.2	+	18	2021	c.2005A>G	c.(2005-2007)ACA>GCA	p.T669A	RANBP17_uc003mbb.2_5'UTR|RANBP17_uc003mbd.2_Missense_Mutation_p.T32A|RANBP17_uc010jjs.2_RNA|RANBP17_uc003mbc.2_Missense_Mutation_p.T32A	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	669					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AACCTTCTACACAGCGCTCAC	0.408			T	TRD@	ALL								12	58	---	---	---	---	PASS
FLT4	2324	broad.mit.edu	37	5	180046468	180046468	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180046468G>T	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc003mmb.1_Silent_p.V481V	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	GGGCCCCCAGGACATCCTGCC	0.692									Congenital_Hereditary_Lymphedema				3	4	---	---	---	---	PASS
BTNL9	153579	broad.mit.edu	37	5	180486679	180486679	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180486679C>T	uc003mmt.2	+	11	1656	c.1425C>T	c.(1423-1425)CAC>CAT	p.H475H		NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	475	Cytoplasmic (Potential).|B30.2/SPRY.					integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCACCTTCCACGACACCTTCT	0.672													6	9	---	---	---	---	PASS
EXOC2	55770	broad.mit.edu	37	6	633008	633008	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:633008G>T	uc003mtd.2	-	3	362	c.228C>A	c.(226-228)GTC>GTA	p.V76V	EXOC2_uc003mte.2_Silent_p.V76V|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	76	IPT/TIG.				exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		ACTTAGTGGTGACAATAATGT	0.408													9	34	---	---	---	---	PASS
ALDH5A1	7915	broad.mit.edu	37	6	24523060	24523060	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24523060C>T	uc003neg.2	+	7	1108	c.1080C>T	c.(1078-1080)TTC>TTT	p.F360F	ALDH5A1_uc003nef.2_Silent_p.F373F	NM_001080	NP_001071	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 2 precursor	360					acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)	TAAAAGCATTCGCCGAGGCCA	0.448													9	95	---	---	---	---	PASS
HIST1H2BD	3017	broad.mit.edu	37	6	26158772	26158772	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26158772C>A	uc003ngr.2	+	1	424	c.375C>A	c.(373-375)TCC>TCA	p.S125S	HIST1H2BD_uc003ngs.2_Silent_p.S125S	NM_021063	NP_066407	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	125					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|pancreas(1)	2						ACACCAGTTCCAAGTAACTTT	0.512													5	70	---	---	---	---	PASS
ZNF391	346157	broad.mit.edu	37	6	27368656	27368656	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27368656A>G	uc003njf.1	+	3	1025	c.507A>G	c.(505-507)GAA>GAG	p.E169E		NM_001076781	NP_001070249	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	169	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(2)|skin(1)	3						AATGCAATGAATGTGGAAAAG	0.383													18	81	---	---	---	---	PASS
OR2B2	81697	broad.mit.edu	37	6	27879341	27879341	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27879341C>A	uc011dkw.1	-	1	757	c.757G>T	c.(757-759)GGT>TGT	p.G253C		NM_033057	NP_149046	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ATAGCTGTACCATAAAAAAGT	0.463													5	73	---	---	---	---	PASS
GPX6	257202	broad.mit.edu	37	6	28472214	28472214	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28472214A>G	uc011dlj.1	-	6	571	c.521T>C	c.(520-522)ATG>ACG	p.M174T	GPX6_uc010jrg.1_RNA	NM_182701	NP_874360	P59796	GPX6_HUMAN	glutathione peroxidase 6 precursor	174					response to oxidative stress	extracellular region	glutathione peroxidase activity			ovary(3)|pancreas(1)|skin(1)	5					Glutathione(DB00143)	ATGGACCTTCATGGGCTCCCA	0.498													6	34	---	---	---	---	PASS
OR5V1	81696	broad.mit.edu	37	6	29323727	29323727	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29323727C>T	uc011dlo.1	-	1	328	c.246G>A	c.(244-246)ATG>ATA	p.M82I		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4						GGAGGTGCACCATCATCTGGG	0.433													16	97	---	---	---	---	PASS
TRIM39	56658	broad.mit.edu	37	6	30309968	30309968	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30309968C>T	uc010jrz.2	+	9	1801	c.1489C>T	c.(1489-1491)CCA>TCA	p.P497S	TRIM39_uc003npz.2_Missense_Mutation_p.P467S|TRIM39_uc003nqb.2_Missense_Mutation_p.P467S|TRIM39_uc003nqc.2_Missense_Mutation_p.P467S|TRIM39_uc010jsa.1_Intron|RPP21_uc003nqd.1_5'Flank|RPP21_uc003nqe.1_5'Flank|RPP21_uc003nqf.1_5'Flank	NM_021253	NP_067076	Q9HCM9	TRI39_HUMAN	tripartite motif-containing 39 isoform 1	497	B30.2/SPRY.				apoptosis	cytosol|mitochondrion	identical protein binding|zinc ion binding			ovary(3)	3						CCTCTTCTACCCAGGCATCCG	0.527													14	40	---	---	---	---	PASS
C6orf136	221545	broad.mit.edu	37	6	30619146	30619146	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30619146G>A	uc003nqw.3	+	4	860	c.667G>A	c.(667-669)GAG>AAG	p.E223K	C6orf136_uc003nqx.3_Missense_Mutation_p.E404K|C6orf136_uc011dmn.1_Missense_Mutation_p.E89K	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1	223											0						CCGCCACCCTGAGAACTGGAC	0.552													60	170	---	---	---	---	PASS
CCHCR1	54535	broad.mit.edu	37	6	31112669	31112669	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31112669G>T	uc003nsr.3	-	14	1914	c.1791C>A	c.(1789-1791)TAC>TAA	p.Y597*	CCHCR1_uc011dne.1_Nonsense_Mutation_p.Y597*|CCHCR1_uc003nsq.3_Nonsense_Mutation_p.Y650*|CCHCR1_uc003nsp.3_Nonsense_Mutation_p.Y686*|CCHCR1_uc010jsk.1_Nonsense_Mutation_p.Y597*	NM_019052	NP_061925	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1 isoform	597	Potential.				cell differentiation|multicellular organismal development	cytoplasm|nucleus	protein binding			skin(1)	1						CACCTTGCCCGTAGAGTTCCT	0.627													4	98	---	---	---	---	PASS
SKIV2L	6499	broad.mit.edu	37	6	31936487	31936487	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31936487C>T	uc003nyn.1	+	25	3483	c.3094C>T	c.(3094-3096)CAG>TAG	p.Q1032*	SKIV2L_uc011dou.1_Nonsense_Mutation_p.Q874*|SKIV2L_uc011dov.1_Nonsense_Mutation_p.Q839*|STK19_uc003nyt.2_5'Flank	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	1032						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						GGAGCGAATGCAGATACAGAA	0.597													7	57	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32032739	32032739	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32032739G>T	uc003nzl.2	-	19	6902	c.6700C>A	c.(6700-6702)CAG>AAG	p.Q2234K		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	2306	Fibronectin type-III 15.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						GCCTTGGGCTGCCCGTCCCCA	0.607													6	27	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32037522	32037522	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32037522G>A	uc003nzl.2	-	15	5597	c.5395C>T	c.(5395-5397)CCT>TCT	p.P1799S		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1881	Fibronectin type-III 11.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						TGGCCCTCAGGGACTGTCCAG	0.637													10	21	---	---	---	---	PASS
C6orf10	10665	broad.mit.edu	37	6	32260883	32260883	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32260883C>A	uc011dpy.1	-	12	1740	c.1567G>T	c.(1567-1569)GGT>TGT	p.G523C	C6orf10_uc011dpx.1_Intron	NM_006781	NP_006772	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	523	Lys-rich.					integral to membrane				skin(1)	1						cctttgtcaccttttgtgttt	0.154													4	33	---	---	---	---	PASS
KIAA0240	23506	broad.mit.edu	37	6	42797822	42797822	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42797822C>A	uc003osn.1	+	6	1902	c.1751C>A	c.(1750-1752)TCT>TAT	p.S584Y	KIAA0240_uc003osm.1_Missense_Mutation_p.S584Y|KIAA0240_uc011duw.1_Missense_Mutation_p.S584Y|KIAA0240_uc003oso.1_Missense_Mutation_p.S584Y|KIAA0240_uc003osp.1_Missense_Mutation_p.S584Y	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	584										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			GTCAGTGTGTCTCATCGTCTT	0.488													16	49	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43400305	43400305	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43400305G>T	uc003ouy.1	+	3	802	c.587G>T	c.(586-588)CGA>CTA	p.R196L	ABCC10_uc003ouz.1_Missense_Mutation_p.R153L	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	196						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GGGGGACCACGAGAACCCTGG	0.627													5	62	---	---	---	---	PASS
SUPT3H	8464	broad.mit.edu	37	6	45290659	45290659	+	5'UTR	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45290659C>A	uc003oxo.2	-	3					SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						ACCATGAGTCCATGGAGAAAA	0.413													4	57	---	---	---	---	PASS
GPR115	221393	broad.mit.edu	37	6	47682138	47682138	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47682138C>A	uc003oza.1	+	6	1415	c.1157C>A	c.(1156-1158)TCT>TAT	p.S386Y	GPR115_uc003oyz.1_Missense_Mutation_p.S443Y|GPR115_uc003ozb.1_Missense_Mutation_p.S384Y	NM_153838	NP_722580	Q8IZF3	GP115_HUMAN	G-protein coupled receptor 115 precursor	386	GPS.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8						GTGGTGATGTCTTTTTCCATT	0.463													13	45	---	---	---	---	PASS
CRISP1	167	broad.mit.edu	37	6	49803029	49803029	+	Nonstop_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49803029C>A	uc003ozw.2	-	8	829	c.750G>T	c.(748-750)TAG>TAT	p.*250Y	CRISP1_uc003ozx.2_3'UTR	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	250					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					TAACAAAGACCTATTTTATCT	0.393													6	124	---	---	---	---	PASS
C6orf142	90523	broad.mit.edu	37	6	54095515	54095515	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54095515G>T	uc003pcg.3	+	11	1230	c.1117G>T	c.(1117-1119)GTA>TTA	p.V373L	C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Missense_Mutation_p.V908L	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523	373						nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)					CCACCAGGATGTAACAGTCCC	0.458													53	181	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55739374	55739374	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55739374G>T	uc003pcq.2	-	1	1002	c.290C>A	c.(289-291)TCG>TAG	p.S97*	BMP5_uc011dxf.1_Nonsense_Mutation_p.S97*	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	97					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGAGTACTCCGACTCTTCAGG	0.493													30	73	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56506733	56506733	+	Intron	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56506733T>C	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Intron|DST_uc003pdd.3_Intron|DST_uc003pde.2_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)			AAAGAATAAGTAGCACTCTTA	0.333													5	19	---	---	---	---	PASS
ZNF451	26036	broad.mit.edu	37	6	57012894	57012894	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57012894C>A	uc003pdm.1	+	10	2235	c.2011C>A	c.(2011-2013)CTT>ATT	p.L671I	ZNF451_uc003pdl.2_Missense_Mutation_p.L671I|ZNF451_uc003pdn.1_Missense_Mutation_p.L671I|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Missense_Mutation_p.L671I	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1	671	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			CTTCTGTGGGCTTTGTGATCT	0.368													10	53	---	---	---	---	PASS
ZNF451	26036	broad.mit.edu	37	6	57012976	57012976	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57012976C>G	uc003pdm.1	+	10	2317	c.2093C>G	c.(2092-2094)TCA>TGA	p.S698*	ZNF451_uc003pdl.2_Nonsense_Mutation_p.S698*|ZNF451_uc003pdn.1_Nonsense_Mutation_p.S698*|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Nonsense_Mutation_p.S698*	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1	698					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GTATTTGTGTCAGAAAAAACT	0.353													5	31	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70847580	70847580	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70847580G>A	uc003pfc.1	+	19	1504	c.1387G>A	c.(1387-1389)GAA>AAA	p.E463K	COL19A1_uc010kam.1_Missense_Mutation_p.E359K	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	463	Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TTGAAAGGGTGAAACTGGACT	0.408													46	119	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70850836	70850836	+	Intron	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70850836T>A	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TTTCTACCCCTTCTCCTTAGG	0.383													45	132	---	---	---	---	PASS
IMPG1	3617	broad.mit.edu	37	6	76728524	76728524	+	Missense_Mutation	SNP	C	A	A	rs139136879	byFrequency	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76728524C>A	uc003pik.1	-	7	848	c.718G>T	c.(718-720)GTC>TTC	p.V240F		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	240	SEA 1.				visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				ACCAGAGAGACGCTGAGCTCC	0.463													17	49	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83839921	83839921	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83839921G>C	uc003pjs.1	+	17	2681	c.2421G>C	c.(2419-2421)CAG>CAC	p.Q807H	DOPEY1_uc011dyy.1_Missense_Mutation_p.Q798H|DOPEY1_uc010kbl.1_Missense_Mutation_p.Q798H	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	807					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCAGTGTTCAGAGTGTTGCTA	0.493													14	37	---	---	---	---	PASS
SNAP91	9892	broad.mit.edu	37	6	84417613	84417613	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84417613C>A	uc011dze.1	-	2	351	c.34G>T	c.(34-36)GCC>TCC	p.A12S	SNAP91_uc003pkb.2_5'UTR|SNAP91_uc003pkc.2_Missense_Mutation_p.A12S|SNAP91_uc003pkd.2_Missense_Mutation_p.A12S|SNAP91_uc003pka.2_Missense_Mutation_p.A12S|SNAP91_uc011dzf.1_5'UTR	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog	12					clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TACTGAGCGGCGGCGATCCGA	0.562													9	26	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85472385	85472385	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85472385G>A	uc003pkl.1	-	2	374	c.374C>T	c.(373-375)TCC>TTC	p.S125F	TBX18_uc010kbq.1_5'UTR	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	125					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CCGGGCCAGGGAGCGCGCCGG	0.701													7	26	---	---	---	---	PASS
RRAGD	58528	broad.mit.edu	37	6	90097269	90097269	+	Silent	SNP	C	A	A	rs142842793	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90097269C>A	uc003pnd.3	-	2	472	c.189G>T	c.(187-189)CCG>CCT	p.P63P	RRAGD_uc010kcc.2_Intron	NM_021244	NP_067067	Q9NQL2	RRAGD_HUMAN	Ras-related GTP binding D	63					cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosome|nucleus	GTP binding|protein heterodimerization activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)		GCAGGATTCTCGGCTTCACTT	0.463													73	224	---	---	---	---	PASS
FUT9	10690	broad.mit.edu	37	6	96651208	96651208	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96651208T>G	uc003pop.3	+	3	518	c.177T>G	c.(175-177)GAT>GAG	p.D59E		NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)	59	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		CCAAAACTGATTATTTTAATG	0.418													15	35	---	---	---	---	PASS
MCHR2	84539	broad.mit.edu	37	6	100403844	100403844	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100403844T>C	uc003pqh.1	-	2	495	c.180A>G	c.(178-180)ATA>ATG	p.I60M	MCHR2_uc003pqi.1_Missense_Mutation_p.I60M	NM_001040179	NP_001035269	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	60	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TTCCTTACCTTATTATAGTGA	0.403													4	24	---	---	---	---	PASS
QRSL1	55278	broad.mit.edu	37	6	107103556	107103556	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107103556A>G	uc003prm.2	+	9	1225	c.1109A>G	c.(1108-1110)AAT>AGT	p.N370S		NM_018292	NP_060762	Q9H0R6	QRSL1_HUMAN	glutaminyl-tRNA synthase	370					translation		ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		GAAGGGTTTAATGATGTGGTG	0.363													12	50	---	---	---	---	PASS
PDSS2	57107	broad.mit.edu	37	6	107475972	107475972	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107475972T>A	uc003prt.2	-	8	1341	c.1051A>T	c.(1051-1053)AGA>TGA	p.R351*	PDSS2_uc011eak.1_Nonsense_Mutation_p.R215*|PDSS2_uc011eal.1_Nonsense_Mutation_p.R249*	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2	351					isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		GCTTTGATTCTTTCTCGCAAC	0.453													6	36	---	---	---	---	PASS
C6orf182	285753	broad.mit.edu	37	6	109484003	109484003	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109484003G>T	uc010kdk.2	+	13	1790	c.1213G>T	c.(1213-1215)GGT>TGT	p.G405C	C6orf182_uc003psx.3_3'UTR|C6orf182_uc010kdl.2_Missense_Mutation_p.G405C|C6orf182_uc003psy.3_Missense_Mutation_p.G405C	NM_001083535	NP_001077004	Q8IYX8	CE57L_HUMAN	hypothetical protein LOC285753	405						microtubule|microtubule organizing center					0		all_cancers(87;4.45e-07)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(75;3.25e-08)|all_epithelial(87;0.000254)|Colorectal(196;0.0293)|all_lung(197;0.11)		BRCA - Breast invasive adenocarcinoma(108;0.00123)|Epithelial(106;0.0022)|all cancers(137;0.00405)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)		TGAAGCTTCAGGTATTCAGCA	0.333													5	71	---	---	---	---	PASS
CDK19	23097	broad.mit.edu	37	6	110953347	110953347	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110953347T>A	uc003puh.1	-	6	605	c.532A>T	c.(532-534)AGA>TGA	p.R178*	CDK19_uc003pui.1_Nonsense_Mutation_p.R118*|CDK19_uc011eax.1_Nonsense_Mutation_p.R54*	NM_015076	NP_055891	Q9BWU1	CDK19_HUMAN	cell division cycle 2-like 6 (CDK8-like)	178	Protein kinase.						ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						TTGAATAATCTGGCAAAACCC	0.284													11	27	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112496574	112496574	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112496574C>A	uc003pvu.2	-	11	1607	c.1298G>T	c.(1297-1299)CGT>CTT	p.R433L	LAMA4_uc003pvv.2_Missense_Mutation_p.R426L|LAMA4_uc003pvt.2_Missense_Mutation_p.R426L	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	433	Domain II and I.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AAATGGTTGACGGCTTCTAAT	0.488													14	82	---	---	---	---	PASS
FAM184A	79632	broad.mit.edu	37	6	119327317	119327317	+	Intron	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119327317C>T	uc003pyj.2	-						FAM184A_uc003pyk.3_Intron|FAM184A_uc003pyl.3_Intron	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						tgccgaatgccaagaatgcct	0.000													14	83	---	---	---	---	PASS
RSPO3	84870	broad.mit.edu	37	6	127517050	127517050	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127517050A>C	uc003qar.2	+	5	1007	c.717A>C	c.(715-717)GAA>GAC	p.E239D	RSPO3_uc003qas.1_Missense_Mutation_p.E239D	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor	239						extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		AAAGTCTGGAATCCAGCAAAG	0.299													9	58	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129785527	129785527	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129785527C>G	uc003qbn.2	+	49	7190	c.7085C>G	c.(7084-7086)TCC>TGC	p.S2362C	LAMA2_uc003qbo.2_Missense_Mutation_p.S2362C	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2362	Laminin G-like 2.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCCAACATCTCCACTGTCATG	0.463													22	94	---	---	---	---	PASS
TCF21	6943	broad.mit.edu	37	6	134210701	134210701	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134210701C>A	uc003qei.3	+	1	442	c.166C>A	c.(166-168)CTG>ATG	p.L56M	uc003qeg.1_5'Flank|TCF21_uc003qej.2_Missense_Mutation_p.L56M	NM_003206	NP_003197	O43680	TCF21_HUMAN	transcription factor 21	56					branching involved in ureteric bud morphogenesis|mesoderm development|negative regulation of androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus	androgen receptor binding|E-box binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity				0	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)		CCGCGGCGGCCTGGGCAAGAG	0.632													4	25	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144769802	144769802	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144769802C>T	uc003qkt.2	+	16	2061	c.1969C>T	c.(1969-1971)CGT>TGT	p.R657C	UTRN_uc010khq.1_Missense_Mutation_p.R657C	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	657	Interaction with SYNM.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GGAGACTGTTCGTGTAAGAGA	0.423													30	49	---	---	---	---	PASS
CCR6	1235	broad.mit.edu	37	6	167549917	167549917	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167549917G>T	uc003qvl.2	+	13	2675	c.199G>T	c.(199-201)GTG>TTG	p.V67L	CCR6_uc010kkm.2_Missense_Mutation_p.V67L|CCR6_uc003qvn.3_Missense_Mutation_p.V67L|CCR6_uc003qvm.3_Missense_Mutation_p.V67L	NM_031409	NP_113597	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	67	Helical; Name=1; (Potential).				cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		GAATATTCTGGTGGTGATCAC	0.478													26	52	---	---	---	---	PASS
HDAC9	9734	broad.mit.edu	37	7	18631171	18631171	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18631171C>A	uc003suh.2	+	4	480	c.439C>A	c.(439-441)CTT>ATT	p.L147I	HDAC9_uc003sue.2_Missense_Mutation_p.L147I|HDAC9_uc011jyd.1_Missense_Mutation_p.L147I|HDAC9_uc003sui.2_Missense_Mutation_p.L150I|HDAC9_uc003suj.2_Missense_Mutation_p.L150I|HDAC9_uc011jya.1_Missense_Mutation_p.L188I|HDAC9_uc003sua.1_Missense_Mutation_p.L169I|HDAC9_uc011jyb.1_Missense_Mutation_p.L147I|HDAC9_uc003sud.1_Missense_Mutation_p.L147I|HDAC9_uc011jyc.1_Missense_Mutation_p.L150I|HDAC9_uc003suf.1_Missense_Mutation_p.L178I|HDAC9_uc010kud.1_Missense_Mutation_p.L150I|HDAC9_uc011jye.1_Missense_Mutation_p.L119I|HDAC9_uc011jyf.1_Missense_Mutation_p.L116I|HDAC9_uc010kue.1_5'UTR	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1	147	Interaction with MEF2 (By similarity).				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|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)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	AAAGCAGAAGCTTCAAGAGTT	0.348													10	20	---	---	---	---	PASS
AMPH	273	broad.mit.edu	37	7	38471795	38471795	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38471795T>C	uc003tgu.2	-	13	1221	c.1152A>G	c.(1150-1152)CTA>CTG	p.L384L	AMPH_uc003tgv.2_Silent_p.L384L|AMPH_uc003tgt.2_Silent_p.L137L|AMPH_uc003tgw.1_5'Flank|AMPH_uc010kxl.1_5'Flank	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	384					endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						TTACCGTCCATAGGTCCCAGG	0.318													12	70	---	---	---	---	PASS
URGCP	55665	broad.mit.edu	37	7	43916608	43916608	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43916608T>C	uc003tiw.2	-	6	2511	c.2454A>G	c.(2452-2454)GTA>GTG	p.V818V	URGCP_uc003tiu.2_Silent_p.V775V|URGCP_uc003tiv.2_Silent_p.V743V|URGCP_uc003tix.2_Silent_p.V809V|URGCP_uc003tiy.2_Silent_p.V775V|URGCP_uc003tiz.2_Silent_p.V775V|URGCP_uc011kbj.1_Silent_p.V775V	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	818					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4						GGTTCTGGTATACAAACTGGT	0.522													11	44	---	---	---	---	PASS
NUDCD3	23386	broad.mit.edu	37	7	44507678	44507678	+	Intron	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507678G>A	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						TTGGTTATGGGAGCAACAAAA	0.478													6	235	---	---	---	---	PASS
NUDCD3	23386	broad.mit.edu	37	7	44507688	44507688	+	Intron	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507688A>G	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						GAGCAACAAAAAAACAAAGCA	0.498													6	218	---	---	---	---	PASS
NUDCD3	23386	broad.mit.edu	37	7	44507739	44507739	+	Intron	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507739A>G	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						GGTCCACAACATCAAGGAGCT	0.493													14	169	---	---	---	---	PASS
NUDCD3	23386	broad.mit.edu	37	7	44507904	44507904	+	Intron	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507904A>G	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						AAATGAGTAGACAGCTCGTGT	0.353													3	63	---	---	---	---	PASS
ZNF680	340252	broad.mit.edu	37	7	64004166	64004166	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64004166T>C	uc003tta.2	-	3	345	c.172A>G	c.(172-174)AAG>GAG	p.K58E	ZNF680_uc010kzr.2_Intron|ZNF680_uc003ttb.2_Missense_Mutation_p.K58E	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	58	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)				AGGTGAGGCTTAGAGACAGCA	0.403													28	60	---	---	---	---	PASS
C7orf42	55069	broad.mit.edu	37	7	66410077	66410077	+	Missense_Mutation	SNP	G	A	A	rs56128303		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66410077G>A	uc003tvk.2	+	3	538	c.274G>A	c.(274-276)GGG>AGG	p.G92R	C7orf42_uc010lah.2_RNA|C7orf42_uc003tvl.2_Missense_Mutation_p.G92R	NM_017994	NP_060464	Q9NWD8	CG042_HUMAN	hypothetical protein LOC55069	92						integral to membrane				ovary(1)	1						AATGACCAGCGGGCAGGCCCG	0.547													8	26	---	---	---	---	PASS
ELN	2006	broad.mit.edu	37	7	73474756	73474756	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73474756G>A	uc003tzw.2	+	25	1781	c.1690G>A	c.(1690-1692)GGC>AGC	p.G564S	RFC2_uc011kfa.1_Intron|ELN_uc003tzn.2_Missense_Mutation_p.G558S|ELN_uc003tzz.2_Missense_Mutation_p.G477S|ELN_uc003tzo.2_Missense_Mutation_p.G510S|ELN_uc003tzp.2_Missense_Mutation_p.G469S|ELN_uc003tzq.2_Missense_Mutation_p.G422S|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Missense_Mutation_p.G539S|ELN_uc003tzt.2_Missense_Mutation_p.G563S|ELN_uc003tzu.2_Missense_Mutation_p.G544S|ELN_uc003tzv.2_Missense_Mutation_p.G529S|ELN_uc003tzx.2_Missense_Mutation_p.G548S|ELN_uc011kff.1_Missense_Mutation_p.G558S|ELN_uc003tzy.2_Missense_Mutation_p.G534S	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	587	Ala-rich.				blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)	AGTTGGTGTCGGCGTCCCTGG	0.627			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						13	63	---	---	---	---	PASS
PTPN12	5782	broad.mit.edu	37	7	77256840	77256840	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77256840G>T	uc003ugh.2	+	13	1935	c.1844G>T	c.(1843-1845)GGT>GTT	p.G615V	PTPN12_uc011kgp.1_Missense_Mutation_p.G496V|PTPN12_uc011kgq.1_Missense_Mutation_p.G485V|PTPN12_uc010lds.2_Missense_Mutation_p.G347V	NM_002835	NP_002826	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type	615						soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3						AACTCTGATGGTGCTGTGACC	0.413													18	80	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87760755	87760755	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87760755G>T	uc003ujn.2	+						ADAM22_uc003ujj.1_Missense_Mutation_p.V333L|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TTTTTCGTACGTAACTTCTGT	0.328													8	40	---	---	---	---	PASS
ANKIB1	54467	broad.mit.edu	37	7	92027804	92027804	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92027804G>A	uc003ulw.2	+	20	3187	c.2811G>A	c.(2809-2811)CTG>CTA	p.L937L	ANKIB1_uc010lew.1_Silent_p.L206L	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	937							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)			CTGACACCCTGAGCTCACACC	0.512													19	52	---	---	---	---	PASS
CALCR	799	broad.mit.edu	37	7	93055874	93055874	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93055874C>A	uc003umv.1	-	15	1582	c.1321G>T	c.(1321-1323)GCC>TCC	p.A441S	CALCR_uc011kia.1_Missense_Mutation_p.A221S|CALCR_uc003ums.1_RNA|CALCR_uc003umt.1_RNA|CALCR_uc003umu.1_Missense_Mutation_p.A407S|CALCR_uc003umw.2_Missense_Mutation_p.A407S	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor	423	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)	TTGAATTGGGCCCATTGGCGC	0.537													5	31	---	---	---	---	PASS
SLC25A13	10165	broad.mit.edu	37	7	95822420	95822420	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95822420C>A	uc003uof.3	-	6	735	c.544G>T	c.(544-546)GAC>TAC	p.D182Y	SLC25A13_uc003uog.3_Missense_Mutation_p.D182Y|SLC25A13_uc011kik.1_Missense_Mutation_p.D74Y	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	182	3.|EF-hand 4.				ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	TCTCGGAAGTCGATGGCTGTG	0.453													12	45	---	---	---	---	PASS
PTCD1	26024	broad.mit.edu	37	7	99022669	99022669	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99022669C>G	uc003uqh.2	-	6	1617	c.1486G>C	c.(1486-1488)GTG>CTG	p.V496L	PTCD1_uc011kiw.1_Missense_Mutation_p.V545L	NM_015545	NP_056360	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	496										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)			GACTCCACCACCTCGGCCAGT	0.617													7	29	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100372950	100372950	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100372950G>T	uc003uwj.2	+	33	5945	c.5780G>T	c.(5779-5781)GGT>GTT	p.G1927V	ZAN_uc003uwk.2_Missense_Mutation_p.G1927V|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kke.1_Missense_Mutation_p.G14V	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	1927	Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GTCCTCCCAGGTGTGGGAGTG	0.567													4	17	---	---	---	---	PASS
MYL10	93408	broad.mit.edu	37	7	101267539	101267539	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101267539C>A	uc003uyr.2	-	2	262	c.84G>T	c.(82-84)CCG>CCT	p.P28P		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	28						mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						GAGCTCTTCTCGGTGCCTGCG	0.602													4	41	---	---	---	---	PASS
SRPK2	6733	broad.mit.edu	37	7	104783528	104783528	+	Intron	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104783528G>A	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						AGGCCCCACTGACCATTGTCC	0.542													23	80	---	---	---	---	PASS
CPA4	51200	broad.mit.edu	37	7	129950677	129950677	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129950677G>C	uc003vpr.2	+	9	891	c.844G>C	c.(844-846)GCC>CCC	p.A282P	CPA4_uc011kpd.1_Missense_Mutation_p.A249P|CPA4_uc011kpe.1_Missense_Mutation_p.A178P	NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein	282					histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)					TGGACCCCACGCCAATTCGGA	0.493													16	71	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700338	136700338	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700338G>T	uc003vtf.1	+	4	1349	c.726G>T	c.(724-726)AAG>AAT	p.K242N	CHRM2_uc003vtg.1_Missense_Mutation_p.K242N|CHRM2_uc003vtj.1_Missense_Mutation_p.K242N|CHRM2_uc003vtk.1_Missense_Mutation_p.K242N|CHRM2_uc003vtl.1_Missense_Mutation_p.K242N|CHRM2_uc003vtm.1_Missense_Mutation_p.K242N|CHRM2_uc003vti.1_Missense_Mutation_p.K242N|CHRM2_uc003vto.1_Missense_Mutation_p.K242N|CHRM2_uc003vtn.1_Missense_Mutation_p.K242N|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	242	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	GGATAGTGAAGCCAAACAATA	0.502													7	23	---	---	---	---	PASS
UBN2	254048	broad.mit.edu	37	7	138978162	138978162	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138978162C>T	uc011kqr.1	+	16	3854	c.3854C>T	c.(3853-3855)ACC>ATC	p.T1285I		NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	1285										ovary(1)|skin(1)	2						GGAGTGACAACCACCTCGGGA	0.517													14	52	---	---	---	---	PASS
WEE2	494551	broad.mit.edu	37	7	141408804	141408804	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141408804G>A	uc003vwn.2	+	1	652	c.246G>A	c.(244-246)AGG>AGA	p.R82R	FLJ40852_uc011krh.1_Intron|FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron	NM_001105558	NP_001099028	P0C1S8	WEE2_HUMAN	WEE1 homolog 2	82					egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I	centrosome|nucleus	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2	Melanoma(164;0.0171)					AGATTTTGAGGACTCCAGTGT	0.522													43	150	---	---	---	---	PASS
PDIA4	9601	broad.mit.edu	37	7	148716232	148716232	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148716232C>A	uc003wff.2	-	3	609	c.327G>T	c.(325-327)AAG>AAT	p.K109N		NM_004911	NP_004902	P13667	PDIA4_HUMAN	protein disulfide isomerase A4 precursor	109	Thioredoxin 1.				cell redox homeostasis|glycerol ether metabolic process|protein secretion	endoplasmic reticulum lumen|melanosome	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			lung(5)|ovary(1)	6	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			GATCTTTATCCTTTAATATGT	0.448													5	66	---	---	---	---	PASS
ABCF2	10061	broad.mit.edu	37	7	150921066	150921066	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150921066C>G	uc003wjp.2	-	4	613	c.502G>C	c.(502-504)GAG>CAG	p.E168Q	ABCF2_uc003wjo.1_Missense_Mutation_p.E168Q	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	168	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGGCCCGCTCTGTGTCGACT	0.592													8	56	---	---	---	---	PASS
ABCF2	10061	broad.mit.edu	37	7	150921083	150921083	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150921083A>T	uc003wjp.2	-	4	596	c.485T>A	c.(484-486)GTG>GAG	p.V162E	ABCF2_uc003wjo.1_Missense_Mutation_p.V162E	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	162	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GACTTCCATCACACAATGCAA	0.577													8	58	---	---	---	---	PASS
HTR5A	3361	broad.mit.edu	37	7	154876035	154876035	+	Silent	SNP	C	G	G	rs140450324		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154876035C>G	uc003wlu.1	+	2	976	c.912C>G	c.(910-912)ACC>ACG	p.T304T		NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	304	Extracellular (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		TCTTTCTCACCGAGCTCATCA	0.587													20	73	---	---	---	---	PASS
SGK223	157285	broad.mit.edu	37	8	8233763	8233763	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8233763C>T	uc003wsh.3	-	2	2156	c.2156G>A	c.(2155-2157)CGG>CAG	p.R719Q		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	719							ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TGGTACTCACCGCGACTTTGG	0.552													9	28	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	14181717	14181717	+	Intron	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14181717C>A	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TACCATCCTACAAGCAATGAA	0.358													10	33	---	---	---	---	PASS
KIF13B	23303	broad.mit.edu	37	8	28989937	28989937	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28989937C>T	uc003xhh.3	-	23	2889	c.2830G>A	c.(2830-2832)GAA>AAA	p.E944K	uc003xhi.1_Intron	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	944					microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AATGCTCCTTCGGAAAGATGC	0.413													13	22	---	---	---	---	PASS
TEX15	56154	broad.mit.edu	37	8	30702390	30702390	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30702390C>G	uc003xil.2	-	1	4144	c.4144G>C	c.(4144-4146)GAG>CAG	p.E1382Q		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1382										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TTTAGAAGCTCTTTTTCTCTA	0.398													17	37	---	---	---	---	PASS
SLC20A2	6575	broad.mit.edu	37	8	42329912	42329912	+	5'UTR	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42329912G>T	uc010lxl.2	-	2					SLC20A2_uc010lxm.2_5'UTR|SLC20A2_uc003xpe.2_5'UTR	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			TGGCCATTTTGGAAAGTGGGT	0.398													5	46	---	---	---	---	PASS
SOX17	64321	broad.mit.edu	37	8	55372456	55372456	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55372456T>C	uc003xsb.3	+	2	1350	c.1146T>C	c.(1144-1146)CAT>CAC	p.H382H		NM_022454	NP_071899	Q9H6I2	SOX17_HUMAN	SRY-box 17	382	Sox C-terminal.				angiogenesis|cardiac cell fate determination|endocardial cell differentiation|endocardium formation|endoderm formation|heart formation|heart looping|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell growth|outflow tract morphogenesis|positive regulation of transcription, DNA-dependent|protein destabilization|protein stabilization|regulation of embryonic development|renal system development|vasculogenesis|Wnt receptor signaling pathway	transcription factor complex	beta-catenin binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			lung(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			ACCAGGGGCATGACTCCGGTG	0.612													5	20	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55541069	55541069	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55541069G>C	uc003xsd.1	+	4	4775	c.4627G>C	c.(4627-4629)GAT>CAT	p.D1543H	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1543					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTTTTGCTATGATTCTAAGCA	0.333													11	31	---	---	---	---	PASS
YTHDF3	253943	broad.mit.edu	37	8	64099372	64099372	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64099372C>T	uc003xuy.2	+	5	1119	c.803C>T	c.(802-804)CCT>CTT	p.P268L	YTHDF3_uc010lys.2_Missense_Mutation_p.P212L|YTHDF3_uc003xuz.2_Missense_Mutation_p.P212L|YTHDF3_uc003xva.2_Missense_Mutation_p.P212L|YTHDF3_uc011len.1_Missense_Mutation_p.P212L	NM_152758	NP_689971	Q7Z739	YTHD3_HUMAN	YTH domain family, member 3	268											0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)			GTACCACCACCTCCTATAAAA	0.488													20	84	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77776502	77776502	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77776502C>T	uc003yav.2	+	11	10804	c.10417C>T	c.(10417-10419)CTT>TTT	p.L3473F		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3469	Ser-rich.					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)			CTATCCTCATCTTTCTTGCTT	0.483										HNSCC(33;0.089)			23	51	---	---	---	---	PASS
CNBD1	168975	broad.mit.edu	37	8	88365862	88365862	+	Splice_Site	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88365862A>T	uc003ydy.2	+	10	1201	c.1153_splice	c.e10-2	p.K385_splice		NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1											ovary(3)	3						TTTTTTTAACAGAAAAGATCT	0.318													8	24	---	---	---	---	PASS
SMARCA2	6595	broad.mit.edu	37	9	2116022	2116022	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2116022C>T	uc003zhc.2	+	25	3756	c.3657C>T	c.(3655-3657)GCC>GCT	p.A1219A	SMARCA2_uc003zhd.2_Silent_p.A1219A|SMARCA2_uc010mha.2_Silent_p.A1152A	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	1219					chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		TCCTGCAGGCCATCTTGGAGC	0.478											OREG0019074	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	30	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5753220	5753220	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5753220G>T	uc003zji.2	+	12	1329	c.1236G>T	c.(1234-1236)GAG>GAT	p.E412D	KIAA1432_uc003zjh.2_Missense_Mutation_p.E412D|KIAA1432_uc003zjl.3_Missense_Mutation_p.E412D|KIAA1432_uc003zjj.1_Intron	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	491						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		CCTATCTAGAGAGCAATTGGC	0.363													28	32	---	---	---	---	PASS
C9orf85	138241	broad.mit.edu	37	9	74526683	74526683	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74526683C>A	uc004ain.2	+	1	261	c.33C>A	c.(31-33)TCC>TCA	p.S11S	C9orf85_uc004aio.2_RNA|C9orf85_uc010mou.2_RNA|C9orf85_uc010mov.2_RNA|FAM108B1_uc004ail.2_5'Flank|FAM108B1_uc004aim.1_5'Flank	NM_182505	NP_872311	Q96MD7	CI085_HUMAN	hypothetical protein LOC138241	11											0						TGGCTCGTTCCAGACCTCAGA	0.507													6	202	---	---	---	---	PASS
SHC3	53358	broad.mit.edu	37	9	91661806	91661806	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91661806G>A	uc004aqg.2	-	8	1373	c.1066C>T	c.(1066-1068)CTT>TTT	p.L356F		NM_016848	NP_058544	Q92529	SHC3_HUMAN	src homology 2 domain-containing transforming	356	CH1.				central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4						CTAGTATCAAGAAAGCCCCCT	0.488													17	60	---	---	---	---	PASS
SPTLC1	10558	broad.mit.edu	37	9	94812283	94812283	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94812283C>A	uc004arl.1	-	9	885	c.847G>T	c.(847-849)GGA>TGA	p.G283*	SPTLC1_uc011ltv.1_Nonsense_Mutation_p.G283*	NM_006415	NP_006406	O15269	SPTC1_HUMAN	serine palmitoyltransferase subunit 1 isoform a	283	Cytoplasmic (Potential).					integral to membrane|SPOTS complex	protein binding|pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			ovary(1)|breast(1)	2					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	CCATGCTCTCCTAGGACTCCA	0.368													5	113	---	---	---	---	PASS
ZNF367	195828	broad.mit.edu	37	9	99160542	99160542	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99160542C>T	uc004awf.2	-	2	830	c.475G>A	c.(475-477)GAA>AAA	p.E159K	ZNF367_uc004awg.2_Missense_Mutation_p.E159K	NM_153695	NP_710162	Q7RTV3	ZN367_HUMAN	zinc finger protein 367	159					regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0167)				TGCTCTCCTTCATTTATTAAA	0.398													25	92	---	---	---	---	PASS
PAPPA	5069	broad.mit.edu	37	9	119109373	119109373	+	Silent	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119109373C>G	uc004bjn.2	+	15	4230	c.3849C>G	c.(3847-3849)GTC>GTG	p.V1283V	PAPPA_uc011lxq.1_Silent_p.V658V	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	1283	Sushi 2.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						GTGAGCCAGTCGACTGCAGCA	0.572													15	33	---	---	---	---	PASS
DBC1	1620	broad.mit.edu	37	9	122075433	122075433	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122075433G>T	uc004bkc.2	-	2	657	c.201C>A	c.(199-201)ACC>ACA	p.T67T	DBC1_uc004bkd.2_Silent_p.T67T	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	67					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						TTTTATATCTGGTTGTAAATC	0.448													9	30	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131345357	131345357	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131345357A>G	uc004bvl.3	+	15	1921	c.1808A>G	c.(1807-1809)GAT>GGT	p.D603G	SPTAN1_uc011mbg.1_Missense_Mutation_p.D603G|SPTAN1_uc011mbh.1_Missense_Mutation_p.D615G|SPTAN1_uc004bvm.3_Missense_Mutation_p.D603G|SPTAN1_uc004bvn.3_Missense_Mutation_p.D603G	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	603	Spectrin 7.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						TATTCACAGGATCCATCCAAC	0.433													12	33	---	---	---	---	PASS
TTF1	7270	broad.mit.edu	37	9	135273587	135273587	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135273587G>T	uc004cbl.2	-	4	1770	c.1718C>A	c.(1717-1719)CCT>CAT	p.P573H	TTF1_uc011mcp.1_RNA|TTF1_uc004cbm.2_Missense_Mutation_p.P58H	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	573					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		TTTTTCCTCAGGATATCTGTC	0.403													4	45	---	---	---	---	PASS
ADAMTS13	11093	broad.mit.edu	37	9	136319552	136319552	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136319552C>A	uc004cdv.3	+	24	3504	c.3060C>A	c.(3058-3060)TCC>TCA	p.S1020S	ADAMTS13_uc004cdp.3_Silent_p.S247S|ADAMTS13_uc004cdt.1_Silent_p.S1020S|ADAMTS13_uc004cdu.1_Silent_p.S989S|ADAMTS13_uc004cdw.3_Silent_p.S1020S|ADAMTS13_uc004cdx.3_Silent_p.S989S|ADAMTS13_uc004cdz.3_Silent_p.S690S|ADAMTS13_uc004cea.1_5'Flank|ADAMTS13_uc004ceb.3_5'Flank	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1020	TSP type-1 7.				cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AAGTCATGTCCCTTGGCCCAT	0.637													11	48	---	---	---	---	PASS
MLLT10	8028	broad.mit.edu	37	10	21959505	21959505	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21959505C>G	uc001iqs.2	+	10	1271	c.923C>G	c.(922-924)TCA>TGA	p.S308*	MLLT10_uc001iqt.2_Nonsense_Mutation_p.S308*|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Nonsense_Mutation_p.S308*|MLLT10_uc001ira.2_5'UTR|MLLT10_uc001iqz.2_Nonsense_Mutation_p.S63*	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	308					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						AAAGATGTTTCAGAGACTAGA	0.453			T	MLL|PICALM|CDK6	AL								14	32	---	---	---	---	PASS
C10orf67	256815	broad.mit.edu	37	10	23622020	23622020	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23622020A>T	uc010qcx.1	-	2	367	c.301T>A	c.(301-303)TTG>ATG	p.L101M		NM_153714	NP_714925	Q8IYJ2	CJ067_HUMAN	hypothetical protein LOC256815	101											0						GATGAACTCAATTCTTTTACT	0.343													5	17	---	---	---	---	PASS
ARID5B	84159	broad.mit.edu	37	10	63852295	63852295	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63852295G>A	uc001jlt.1	+	10	3099	c.3073G>A	c.(3073-3075)GGG>AGG	p.G1025R		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1025					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					TGTGATTGCAGGGAAAAAGGC	0.597													22	40	---	---	---	---	PASS
CDHR1	92211	broad.mit.edu	37	10	85972907	85972907	+	Missense_Mutation	SNP	G	A	A	rs144856473		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85972907G>A	uc001kcv.2	+	16	1843	c.1843G>A	c.(1843-1845)GAG>AAG	p.E615K	CDHR1_uc001kcw.2_Missense_Mutation_p.E615K|CDHR1_uc009xst.2_Missense_Mutation_p.E319K|CDHR1_uc001kcx.2_5'UTR	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	615	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1						CACCCATGCAGAGCCCGCCAA	0.572													11	47	---	---	---	---	PASS
DNMBP	23268	broad.mit.edu	37	10	101636941	101636941	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101636941G>A	uc001kqj.2	-	17	4793	c.4701C>T	c.(4699-4701)CCC>CCT	p.P1567P	DNMBP_uc010qpl.1_Silent_p.P503P|DNMBP_uc001kqg.2_Silent_p.P855P|DNMBP_uc001kqh.2_Silent_p.P1199P	NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1567	SH3 6.				intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TATAATTGGAGGGAACGTAGC	0.522													19	25	---	---	---	---	PASS
POLL	27343	broad.mit.edu	37	10	103343256	103343256	+	Intron	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103343256G>A	uc001ktg.1	-						DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_5'Flank|POLL_uc001kte.1_Intron|POLL_uc001kth.1_Intron|POLL_uc001kti.1_Intron|POLL_uc001ktj.1_Intron|POLL_uc001ktf.2_Intron|POLL_uc001ktk.1_Intron|POLL_uc010qqa.1_Intron|POLL_uc010qqb.1_Intron|POLL_uc001ktm.2_Intron|POLL_uc001ktl.2_Intron|POLL_uc010qqc.1_Intron|POLL_uc010qqd.1_3'UTR	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda						DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		GGCTGAGCCAGGGTGTGACCT	0.557								DNA_polymerases_(catalytic_subunits)					15	33	---	---	---	---	PASS
PPRC1	23082	broad.mit.edu	37	10	103901552	103901552	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103901552C>T	uc001kum.2	+	5	3326	c.3287C>T	c.(3286-3288)GCA>GTA	p.A1096V	PPRC1_uc001kun.2_Missense_Mutation_p.A976V|PPRC1_uc010qqj.1_Missense_Mutation_p.A1096V|PPRC1_uc009xxa.2_RNA	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	1096	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		GAGGAGCCTGCATCAGAGAGG	0.577													8	11	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108447979	108447979	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108447979G>T	uc001kym.2	-	10	1539	c.1531C>A	c.(1531-1533)CTA>ATA	p.L511I	SORCS1_uc001kyl.2_Missense_Mutation_p.L511I|SORCS1_uc009xxs.2_Missense_Mutation_p.L511I|SORCS1_uc001kyn.1_Missense_Mutation_p.L511I|SORCS1_uc001kyo.2_Missense_Mutation_p.L511I	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	511	Lumenal (Potential).					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)		TCCCCCCTTAGATCCGTGTCC	0.483													17	35	---	---	---	---	PASS
C10orf81	79949	broad.mit.edu	37	10	115534730	115534730	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115534730C>A	uc001lat.1	+	9	1469	c.907C>A	c.(907-909)CAG>AAG	p.Q303K	C10orf81_uc001lar.1_Missense_Mutation_p.Q309K|C10orf81_uc009xyc.1_Missense_Mutation_p.Q221K|C10orf81_uc001las.1_Missense_Mutation_p.Q221K|C10orf81_uc001lau.1_Missense_Mutation_p.Q123K	NM_024889	NP_079165	Q5SXH7	CJ081_HUMAN	hypothetical protein LOC79949	303										central_nervous_system(1)	1		Colorectal(252;0.175)		Epithelial(162;0.0181)|all cancers(201;0.0204)		TGTGGAAGCACAGACCACAAA	0.483													19	34	---	---	---	---	PASS
OAT	4942	broad.mit.edu	37	10	126094046	126094046	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126094046C>A	uc001lhp.2	-	5	714	c.607G>T	c.(607-609)GGA>TGA	p.G203*	OAT_uc001lhq.2_RNA|OAT_uc001lhr.2_Nonsense_Mutation_p.G65*	NM_000274	NP_000265	P04181	OAT_HUMAN	ornithine aminotransferase precursor	203					cellular amino acid biosynthetic process|visual perception	mitochondrial matrix	ornithine-oxo-acid transaminase activity|protein binding|pyridoxal phosphate binding				0		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)|Pyridoxal Phosphate(DB00114)	ATGTCGAATCCCGGCATAAAT	0.458													13	34	---	---	---	---	PASS
STIM1	6786	broad.mit.edu	37	11	4104625	4104625	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4104625C>G	uc001lyv.2	+	10	1939	c.1371C>G	c.(1369-1371)GAC>GAG	p.D457E	STIM1_uc009yef.2_Missense_Mutation_p.D457E|STIM1_uc009yeg.2_Missense_Mutation_p.D284E	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	457	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		TCAACATAGACCCCAGCTGGA	0.572													10	38	---	---	---	---	PASS
TRIM68	55128	broad.mit.edu	37	11	4621770	4621770	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4621770C>T	uc001lzf.1	-	7	1432	c.1194G>A	c.(1192-1194)CTG>CTA	p.L398L	TRIM68_uc001lzg.1_Silent_p.L175L|TRIM68_uc010qyj.1_RNA	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137	398	B30.2/SPRY.				protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		TTCCCTTCCTCAGCCTTATCA	0.557													13	52	---	---	---	---	PASS
OR51L1	119682	broad.mit.edu	37	11	5021116	5021116	+	Missense_Mutation	SNP	C	T	T	rs139272622	byFrequency	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5021116C>T	uc010qyu.1	+	1	904	c.904C>T	c.(904-906)CGT>TGT	p.R302C		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	302	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAAGCAGATTCGTCTAGGAAT	0.433													6	47	---	---	---	---	PASS
HPX	3263	broad.mit.edu	37	11	6453010	6453010	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6453010C>A	uc001mdg.2	-	9	1051	c.990G>T	c.(988-990)CTG>CTT	p.L330L	HPX_uc001mdf.2_Silent_p.L76L|HPX_uc009yfc.2_RNA	NM_000613	NP_000604	P02790	HEMO_HUMAN	hemopexin precursor	330	Hemopexin-like 5.				cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		CTCCCTTTGTCAGGAAGACAT	0.522													7	119	---	---	---	---	PASS
SCUBE2	57758	broad.mit.edu	37	11	9111341	9111341	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9111341G>T	uc001mhh.1	-	2	249	c.169C>A	c.(169-171)CAT>AAT	p.H57N	SCUBE2_uc001mhi.1_Missense_Mutation_p.H57N|SCUBE2_uc001mhj.1_Missense_Mutation_p.H57N	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	57	EGF-like 1; calcium-binding (Potential).					extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GCGTCGGCATGGCAGTCATCT	0.532													6	91	---	---	---	---	PASS
NUCB2	4925	broad.mit.edu	37	11	17332502	17332502	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17332502C>T	uc001mmw.2	+	7	859	c.614C>T	c.(613-615)TCT>TTT	p.S205F	NUCB2_uc001mms.1_Missense_Mutation_p.S206F|NUCB2_uc001mmt.1_Missense_Mutation_p.S205F|NUCB2_uc001mmv.1_Missense_Mutation_p.S205F|NUCB2_uc009ygz.2_Missense_Mutation_p.S205F	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor	205	By similarity.					cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0						GAAGAAGAGTCTAAATTTGAA	0.279													6	65	---	---	---	---	PASS
NUCB2	4925	broad.mit.edu	37	11	17332538	17332538	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17332538A>C	uc001mmw.2	+	7	895	c.650A>C	c.(649-651)CAC>CCC	p.H217P	NUCB2_uc001mms.1_Missense_Mutation_p.H218P|NUCB2_uc001mmt.1_Missense_Mutation_p.H217P|NUCB2_uc001mmv.1_Missense_Mutation_p.H217P|NUCB2_uc009ygz.2_Missense_Mutation_p.H217P	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor	217	By similarity.|Binds to necdin (By similarity).					cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0						CATGAAAATCACCCTAAAGTT	0.294													9	67	---	---	---	---	PASS
NELL1	4745	broad.mit.edu	37	11	20691260	20691260	+	5'UTR	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20691260C>A	uc001mqe.2	+	1					NELL1_uc001mqf.2_5'UTR|NELL1_uc009yid.2_5'UTR|NELL1_uc010rdo.1_5'UTR|NELL1_uc010rdp.1_5'UTR	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						GGCGGGGACCCTCGAGAGCGA	0.597													5	23	---	---	---	---	PASS
LUZP2	338645	broad.mit.edu	37	11	24753661	24753661	+	Intron	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24753661C>A	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2						CTTTTCTTATCAGTCCTTAAA	0.353													10	25	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32975556	32975556	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32975556C>G	uc001mty.2	+	5	4211	c.3944C>G	c.(3943-3945)TCA>TGA	p.S1315*	QSER1_uc001mtz.1_Nonsense_Mutation_p.S1076*|QSER1_uc001mua.2_Nonsense_Mutation_p.S820*	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1315										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TCAGAATCCTCAAAGCCCATT	0.318													14	35	---	---	---	---	PASS
EHF	26298	broad.mit.edu	37	11	34680084	34680084	+	Silent	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34680084G>C	uc001mvr.1	+	8	723	c.612G>C	c.(610-612)CCG>CCC	p.P204P	EHF_uc009yke.1_Silent_p.P181P|EHF_uc009ykf.1_Silent_p.P207P	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor	204					cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			CATCAGACCCGAGAGGGACTC	0.468													14	59	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55135797	55135797	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55135797G>T	uc010rif.1	+	1	438	c.438G>T	c.(436-438)ATG>ATT	p.M146I		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	146	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TGGTGGTAATGGCCTATGATC	0.438													22	118	---	---	---	---	PASS
OR4S2	219431	broad.mit.edu	37	11	55418439	55418439	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55418439G>T	uc001nhs.1	+	1	60	c.60G>T	c.(58-60)GAG>GAT	p.E20D		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.0748)				AGAGCCCAGAGATTGAGAAAG	0.373													17	68	---	---	---	---	PASS
OR5D13	390142	broad.mit.edu	37	11	55541234	55541234	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55541234C>A	uc010ril.1	+	1	321	c.321C>A	c.(319-321)TGC>TGA	p.C107*		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3		all_epithelial(135;0.196)				GTTTTGCTTGCATTTTTGGAG	0.398													25	93	---	---	---	---	PASS
OR5L1	219437	broad.mit.edu	37	11	55579243	55579243	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55579243T>C	uc001nhw.1	+	1	301	c.301T>C	c.(301-303)TTC>CTC	p.F101L		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	101	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				CATGGTGCAATTCTACTTGTT	0.453													29	93	---	---	---	---	PASS
SERPING1	710	broad.mit.edu	37	11	57367679	57367679	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57367679G>A	uc001nkp.1	+	3	570	c.379G>A	c.(379-381)GTT>ATT	p.V127I	SERPING1_uc001nkq.1_Missense_Mutation_p.V127I|SERPING1_uc010rju.1_Missense_Mutation_p.V75I|SERPING1_uc010rjv.1_Missense_Mutation_p.V132I|SERPING1_uc001nkr.1_Missense_Mutation_p.V127I|SERPING1_uc009ymi.1_Missense_Mutation_p.V127I|SERPING1_uc009ymj.1_Missense_Mutation_p.V127I|SERPING1_uc001nks.1_Intron	NM_000062	NP_000053	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	127			Missing (in HAE; type 2).		blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1						CCCAGGACCTGTTACTCTCTG	0.328									Hereditary_Angioedema				37	126	---	---	---	---	PASS
OR10W1	81341	broad.mit.edu	37	11	58034512	58034512	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58034512G>T	uc001nmq.1	-	1	1221	c.819C>A	c.(817-819)ACC>ACA	p.T273T		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	273	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)				TGAGCAGTGGGGTTCCCAATG	0.537													15	49	---	---	---	---	PASS
OR10W1	81341	broad.mit.edu	37	11	58034871	58034871	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58034871T>A	uc001nmq.1	-	1	862	c.460A>T	c.(460-462)ATC>TTC	p.I154F		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	154	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)				AGAGAGAAGATGAAGGCCACC	0.488													6	29	---	---	---	---	PASS
OR10W1	81341	broad.mit.edu	37	11	58034879	58034879	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58034879A>C	uc001nmq.1	-	1	854	c.452T>G	c.(451-453)GTG>GGG	p.V151G		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)				GATGAAGGCCACCAGTTGTAA	0.507													11	24	---	---	---	---	PASS
OR4D9	390199	broad.mit.edu	37	11	59282787	59282787	+	Silent	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59282787C>G	uc010rkv.1	+	1	402	c.402C>G	c.(400-402)ACC>ACG	p.T134T		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	134	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ACTATATGACCATCATGAGTA	0.537													10	42	---	---	---	---	PASS
TCN1	6947	broad.mit.edu	37	11	59623397	59623397	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59623397C>A	uc001noj.2	-	6	980	c.882G>T	c.(880-882)CTG>CTT	p.L294L		NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor	294					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(2)	2		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCTTTCCCATCAGGGCAGGTA	0.448													11	67	---	---	---	---	PASS
FERMT3	83706	broad.mit.edu	37	11	63978760	63978760	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63978760A>G	uc001nyl.2	+	5	677	c.528A>G	c.(526-528)GCA>GCG	p.A176A	FERMT3_uc001nym.2_Silent_p.A176A	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form	176					integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1						TGGCACCTGCACTGTTCCGGG	0.716													3	11	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65269052	65269052	+	RNA	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65269052G>C	uc010roh.1	+	1		c.3820G>C			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TTTTTTCTAAGATTTTCCACA	0.423													5	64	---	---	---	---	PASS
PC	5091	broad.mit.edu	37	11	66619899	66619899	+	Intron	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66619899T>C	uc001ojn.1	-						PC_uc001ojo.1_Intron|PC_uc001ojp.1_Intron|PC_uc001ojm.1_5'Flank	NM_022172	NP_071504	P11498	PYC_HUMAN	pyruvate carboxylase precursor						gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CTGCGCAGCATGCCAGCCTAC	0.602													10	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	67372302	67372302	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67372302G>T	uc001omi.1	-	2	395	c.239C>A	c.(238-240)GCC>GAC	p.A80D	NDUFV1_uc001omj.2_5'Flank|NDUFV1_uc010rpv.1_5'Flank|NDUFV1_uc001oml.2_5'Flank|NDUFV1_uc001omk.3_5'Flank					RecName: Full=Uncharacterized protein C11orf72;																		atacctcttggcttgtggcct	0.264													8	17	---	---	---	---	PASS
MRGPRD	116512	broad.mit.edu	37	11	68748108	68748108	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68748108C>T	uc010rqf.1	-	1	348	c.348G>A	c.(346-348)CTG>CTA	p.L116L		NM_198923	NP_944605	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	116	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(1)	1			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGATGGCCGTCAGCAGGCTCA	0.587													7	20	---	---	---	---	PASS
MRGPRD	116512	broad.mit.edu	37	11	68748447	68748447	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68748447C>G	uc010rqf.1	-	1	9	c.9G>C	c.(7-9)CAG>CAC	p.Q3H		NM_198923	NP_944605	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	3	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(1)	1			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TATTCAAAGTCTGGTTCATCC	0.557													9	61	---	---	---	---	PASS
MRGPRD	116512	broad.mit.edu	37	11	68748456	68748456	+	5'Flank	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68748456C>T	uc010rqf.1	-							NM_198923	NP_944605	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D							integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(1)	1			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCTGGTTCATCCCTACGAGAG	0.567													10	60	---	---	---	---	PASS
P2RY2	5029	broad.mit.edu	37	11	72945520	72945520	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72945520T>A	uc001otj.2	+	3	649	c.316T>A	c.(316-318)TGC>AGC	p.C106S	P2RY2_uc001otk.2_Missense_Mutation_p.C106S|P2RY2_uc001otl.2_Missense_Mutation_p.C106S	NM_002564	NP_002555	P41231	P2RY2_HUMAN	purinergic receptor P2Y2	106	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(1)|skin(1)	4					Suramin(DB04786)	CACGGTGCTCTGCAAGCTGGT	0.602													14	50	---	---	---	---	PASS
MED17	9440	broad.mit.edu	37	11	93545108	93545108	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93545108G>T	uc001pem.3	+	12	2109	c.1834G>T	c.(1834-1836)GAT>TAT	p.D612Y		NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	612					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGTTTTACAAGATAACAAATG	0.383													17	73	---	---	---	---	PASS
DLAT	1737	broad.mit.edu	37	11	111908010	111908010	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111908010G>T	uc001pmo.2	+	6	1460	c.801G>T	c.(799-801)CAG>CAT	p.Q267H	DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Missense_Mutation_p.Q140H	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	267	Lipoyl-binding 2.				glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	TTGAAGTACAGGAAGAAGGTT	0.383													5	62	---	---	---	---	PASS
TTC12	54970	broad.mit.edu	37	11	113222836	113222836	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113222836C>T	uc001pnu.2	+	16	1458	c.1353C>T	c.(1351-1353)TGC>TGT	p.C451C	TTC12_uc001pnv.2_Silent_p.C457C|TTC12_uc001pnw.2_RNA|TTC12_uc001pnx.2_Silent_p.C301C	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	451							binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		TGTGCCAGTGCATTGCCATCA	0.542													15	38	---	---	---	---	PASS
FOXRED1	55572	broad.mit.edu	37	11	126146370	126146370	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126146370C>A	uc001qdi.2	+	9	1100	c.1053C>A	c.(1051-1053)CGC>CGA	p.R351R	FOXRED1_uc010sbn.1_Silent_p.R181R|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_Silent_p.R164R|FOXRED1_uc010sbq.1_Silent_p.R218R|FOXRED1_uc001qdj.2_Silent_p.R140R|FOXRED1_uc010sbr.1_Silent_p.R337R|FOXRED1_uc001qdk.2_Silent_p.R140R	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	351						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		CCTATTTTCGCCGGGAAGGAT	0.552													18	114	---	---	---	---	PASS
NFRKB	4798	broad.mit.edu	37	11	129762615	129762615	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129762615C>A	uc001qfi.2	-	3	331	c.130G>T	c.(130-132)GAG>TAG	p.E44*	NFRKB_uc001qfg.2_Nonsense_Mutation_p.E57*|NFRKB_uc001qfh.2_Nonsense_Mutation_p.E67*|NFRKB_uc010sbw.1_Nonsense_Mutation_p.E44*	NM_001143835	NP_001137307	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	44					DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CTCACATCCTCCAGAAGGTCC	0.522													12	71	---	---	---	---	PASS
KCNA1	3736	broad.mit.edu	37	12	5021036	5021036	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5021036G>T	uc001qnh.2	+	2	1597	c.492G>T	c.(490-492)GGG>GGT	p.G164G		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	164					synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)|skin(1)	2					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AGAGCTCGGGGCCCGCCAGGG	0.622													9	16	---	---	---	---	PASS
KCNA5	3741	broad.mit.edu	37	12	5153731	5153731	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5153731C>G	uc001qni.2	+	1	647	c.418C>G	c.(418-420)CAG>GAG	p.Q140E		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	140						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4						CACCCTGGCGCAGTTCCCCAA	0.667													7	35	---	---	---	---	PASS
TAS2R8	50836	broad.mit.edu	37	12	10958656	10958656	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10958656C>T	uc010shh.1	-	1	924	c.924G>A	c.(922-924)ATG>ATA	p.M308I		NM_023918	NP_076407	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	308	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	taste receptor activity			ovary(2)	2						GATTTCATATCATGCAGGCAA	0.303													8	22	---	---	---	---	PASS
TAS2R20	259295	broad.mit.edu	37	12	11150207	11150207	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11150207C>T	uc001qzm.2	-	1	268	c.268G>A	c.(268-270)GTA>ATA	p.V90I	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176889	NP_795370	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	90	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0						TGATTGGTTACTGCCCAGGCA	0.328													18	64	---	---	---	---	PASS
PIK3C2G	5288	broad.mit.edu	37	12	18491356	18491356	+	Intron	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18491356A>G	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				CTTGTTATCTACAGGAAAACG	0.308													14	46	---	---	---	---	PASS
SLCO1C1	53919	broad.mit.edu	37	12	20893149	20893149	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20893149C>A	uc001rej.3	+	13	1935	c.1580C>A	c.(1579-1581)GCA>GAA	p.A527E	SLCO1C1_uc010sii.1_Missense_Mutation_p.A527E|SLCO1C1_uc010sij.1_Missense_Mutation_p.A478E|SLCO1C1_uc009zip.2_Missense_Mutation_p.A361E|SLCO1C1_uc001rei.2_Missense_Mutation_p.A527E|SLCO1C1_uc010sik.1_Missense_Mutation_p.A409E	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,	527	Extracellular (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)					GTGGGAATTGCAGCTTCTAAA	0.353													6	54	---	---	---	---	PASS
ST8SIA1	6489	broad.mit.edu	37	12	22354570	22354570	+	Silent	SNP	G	T	T	rs113763889		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22354570G>T	uc001rfo.3	-	5	1469	c.987C>A	c.(985-987)CTC>CTA	p.L329L	ST8SIA1_uc009zix.2_Silent_p.L186L	NM_003034	NP_003025	Q92185	SIA8A_HUMAN	alpha-2,8-sialyltransferase 1	329	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3						ACCAGAGTTGGAGAAATTCCT	0.493													5	110	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32145370	32145370	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32145370A>G	uc001rks.2	+	6	5559	c.5145A>G	c.(5143-5145)CTA>CTG	p.L1715L	C12orf35_uc001rkt.2_RNA	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1715										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			TTGAGATGCTACAAAACCCAG	0.343													55	157	---	---	---	---	PASS
SLC38A1	81539	broad.mit.edu	37	12	46582748	46582748	+	3'UTR	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46582748G>A	uc001rpa.2	-	17					SLC38A1_uc001rpb.2_3'UTR|SLC38A1_uc001rpc.2_3'UTR|SLC38A1_uc001rpd.2_3'UTR|SLC38A1_uc001rpe.2_3'UTR	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1						cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			TTTTCTCGGCGGGTTTCAGTG	0.493													14	70	---	---	---	---	PASS
NCKAP5L	57701	broad.mit.edu	37	12	50195633	50195633	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50195633G>T	uc009zlk.2	-	6	551	c.349C>A	c.(349-351)CAG>AAG	p.Q117K		NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	113	Pro-rich.									central_nervous_system(1)	1						ATGCCTACCTGAGGGAGCGAG	0.582													4	47	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56713650	56713650	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56713650C>T	uc001skx.2	-	21	3329	c.2956G>A	c.(2956-2958)GAG>AAG	p.E986K	PAN2_uc001skw.2_Missense_Mutation_p.E134K|PAN2_uc001skz.2_Missense_Mutation_p.E985K|PAN2_uc001sky.2_Missense_Mutation_p.E982K	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	986	Exonuclease.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						TTGGTTACCTCATTAAGGGTG	0.448													10	40	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57569263	57569263	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57569263G>T	uc001snd.2	+	23	4034	c.3568G>T	c.(3568-3570)GGT>TGT	p.G1190C		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1190	EGF-like 5.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TCTGAATAACGGTGGCTGCAG	0.627											OREG0021937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	13	---	---	---	---	PASS
LRRC10	376132	broad.mit.edu	37	12	70004494	70004494	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70004494C>A	uc001svc.2	-	1	449	c.125G>T	c.(124-126)CGC>CTC	p.R42L		NM_201550	NP_963844	Q5BKY1	LRC10_HUMAN	leucine rich repeat containing 10	42						nucleus					0	all_cancers(2;2.83e-105)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;1.98e-18)|GBM - Glioblastoma multiforme(2;7.43e-12)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GGGGAAGCGGCGTAACTGGCT	0.607													3	27	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78522538	78522538	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78522538C>T	uc001syp.2	+	18	4506	c.4333C>T	c.(4333-4335)CGT>TGT	p.R1445C	NAV3_uc001syo.2_Missense_Mutation_p.R1445C|NAV3_uc010sub.1_Missense_Mutation_p.R931C|NAV3_uc009zsf.2_Missense_Mutation_p.R276C	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1445	Ser-rich.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						AGAGTGGTTGCGTTCTCATTC	0.498										HNSCC(70;0.22)			20	55	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	80650165	80650165	+	IGR	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80650165G>C								PPP1R12A (320930 upstream) : PTPRQ (187961 downstream)																							TCTGGAGGATGATTTTAACAA	0.378													3	18	---	---	---	---	PASS
HAL	3034	broad.mit.edu	37	12	96387243	96387243	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96387243C>A	uc001tem.1	-	8	872	c.575G>T	c.(574-576)CGC>CTC	p.R192L	HAL_uc009zti.1_RNA|HAL_uc010suw.1_5'UTR|HAL_uc010sux.1_Missense_Mutation_p.R192L	NM_002108	NP_002099	P42357	HUTH_HUMAN	histidine ammonia-lyase	192					biosynthetic process|histidine catabolic process	cytosol	histidine ammonia-lyase activity			ovary(2)|skin(1)	3					L-Histidine(DB00117)	AGAATGTGAGCGTACTAAGTT	0.428													14	55	---	---	---	---	PASS
ASCL4	121549	broad.mit.edu	37	12	108169032	108169032	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108169032C>A	uc001tmr.2	+	1	871	c.40C>A	c.(40-42)CCA>ACA	p.P14T		NM_203436	NP_982260	Q6XD76	ASCL4_HUMAN	achaete-scute complex-like 4	13					regulation of transcription from RNA polymerase II promoter|skin development|transcription, DNA-dependent	nucleus	DNA binding			central_nervous_system(1)	1						GCTGGCCTTGCCATACTCGCT	0.637													14	40	---	---	---	---	PASS
CORO1C	23603	broad.mit.edu	37	12	109052593	109052593	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109052593C>T	uc001tnj.2	-	5	647	c.551G>A	c.(550-552)CGG>CAG	p.R184Q	CORO1C_uc009zva.2_Missense_Mutation_p.R237Q|CORO1C_uc010sxf.1_Missense_Mutation_p.R147Q	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1	184	WD 3.				actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3						ACTGCCATTCCGGTTCCAGCT	0.428													16	51	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109698427	109698427	+	Silent	SNP	G	T	T	rs61753862		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109698427G>T	uc001tob.2	+	48	6758	c.6639G>T	c.(6637-6639)CCG>CCT	p.P2213P	ACACB_uc001toc.2_Silent_p.P2213P|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Silent_p.P879P	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	2213	Carboxyltransferase.				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	CCATCAACCCGCTGTGCATAG	0.542													21	90	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112694272	112694272	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112694272G>T	uc009zwc.2	-	14	1901	c.1883C>A	c.(1882-1884)CCT>CAT	p.P628H	C12orf51_uc010syk.1_Missense_Mutation_p.P451H|C12orf51_uc001tts.2_Missense_Mutation_p.P451H|C12orf51_uc001ttt.3_Missense_Mutation_p.P449H	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						CCATGGGGCAGGAATCTTTAA	0.448													4	30	---	---	---	---	PASS
MSI1	4440	broad.mit.edu	37	12	120789151	120789151	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120789151A>G	uc001tye.1	-	11	850	c.786T>C	c.(784-786)CTT>CTC	p.L262L		NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1	262					nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACTGACCTGTAAGCTCGGGGA	0.557													11	10	---	---	---	---	PASS
TCTN2	79867	broad.mit.edu	37	12	124163813	124163813	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124163813G>A	uc001ufp.2	+	5	669	c.541G>A	c.(541-543)GAT>AAT	p.D181N	TCTN2_uc009zya.2_Missense_Mutation_p.D180N	NM_024809	NP_079085	Q96GX1	TECT2_HUMAN	tectonic family member 2 isoform 1	181	Extracellular (Potential).|Cys-rich.				cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		TGGAGCCTGTGATGTTCGCTG	0.453													24	56	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124257441	124257441	+	Nonsense_Mutation	SNP	G	T	T	rs142898915	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124257441G>T	uc001uft.3	+	4	299	c.274G>T	c.(274-276)GAG>TAG	p.E92*		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	92	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CCCTCTTCCCGAGGAGTTCCT	0.468													5	162	---	---	---	---	PASS
ZDHHC20	253832	broad.mit.edu	37	13	21976986	21976986	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21976986T>C	uc001uob.2	-	5	503	c.390A>G	c.(388-390)AAA>AAG	p.K130K	ZDHHC20_uc001uod.2_RNA|ZDHHC20_uc001uoc.2_RNA|ZDHHC20_uc001uoe.2_RNA|ZDHHC20_uc010tcs.1_Silent_p.K67K	NM_153251	NP_694983	Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	130	DHHC-type.					integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		TCAGCTGACATTTTTCACAAT	0.358													6	19	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23906130	23906130	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23906130A>G	uc001uon.2	-	10	12474	c.11885T>C	c.(11884-11886)ATA>ACA	p.I3962T	SACS_uc001uoo.2_Missense_Mutation_p.I3815T|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	3962					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AAAGAGCATTATCAACTTAGT	0.383													31	69	---	---	---	---	PASS
N4BP2L2	10443	broad.mit.edu	37	13	33110164	33110164	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33110164T>C	uc001uuk.3	-	2	1179	c.1001A>G	c.(1000-1002)AAC>AGC	p.N334S	N4BP2L2_uc010abe.1_Intron|N4BP2L2_uc010tdz.1_Intron|N4BP2L2_uc001uul.1_Missense_Mutation_p.N334S|N4BP2L2_uc001uum.2_5'Flank	NM_014887	NP_055702	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	334											0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ATATTCATTGTTCTGATCAAA	0.358													10	30	---	---	---	---	PASS
CSNK1A1L	122011	broad.mit.edu	37	13	37679333	37679333	+	Missense_Mutation	SNP	G	C	C	rs56158728	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37679333G>C	uc001uwm.1	-	1	469	c.61C>G	c.(61-63)CGG>GGG	p.R21G		NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	21	Protein kinase.		R -> W.		Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity	p.R21Q(1)		large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		CCGATCTTCCGCACCAGTTTG	0.557													17	31	---	---	---	---	PASS
UFM1	51569	broad.mit.edu	37	13	38934882	38934882	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38934882G>A	uc001uwu.2	+	6	340	c.225G>A	c.(223-225)CGG>CGA	p.R75R	UFM1_uc010aca.2_3'UTR	NM_016617	NP_057701	P61960	UFM1_HUMAN	ubiquitin-fold modifier 1 precursor	75					protein ufmylation	cytoplasm|nucleus	protein binding				0		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)		CAGAACTGCGGATTATTCCTA	0.284													7	28	---	---	---	---	PASS
PCDH20	64881	broad.mit.edu	37	13	61986832	61986832	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61986832C>A	uc001vid.3	-	2	1764	c.1400G>T	c.(1399-1401)TGC>TTC	p.C467F	PCDH20_uc010thj.1_Missense_Mutation_p.C467F	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	440	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		ATCCAGGTAGCAGTTAACCTT	0.403													6	45	---	---	---	---	PASS
DACH1	1602	broad.mit.edu	37	13	72014822	72014822	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72014822C>A	uc010thn.1	-	12	2509	c.2086G>T	c.(2086-2088)GGA>TGA	p.G696*	DACH1_uc010tho.1_Nonsense_Mutation_p.G548*|DACH1_uc010thp.1_Nonsense_Mutation_p.G494*	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a	748					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TACAGTCTTCCATCTAGAAAT	0.313													4	55	---	---	---	---	PASS
EDNRB	1910	broad.mit.edu	37	13	78492262	78492262	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78492262C>A	uc001vko.2	-	1	705	c.447G>T	c.(445-447)CTG>CTT	p.L149L	uc001vks.2_5'Flank|EDNRB_uc001vkq.1_Silent_p.L149L|EDNRB_uc010aez.1_Silent_p.L149L|EDNRB_uc001vkp.1_Silent_p.L232L|EDNRB_uc010afa.1_Silent_p.L149L	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	149	Helical; Name=2; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)	TGACGATGTGCAGCAGGTCTC	0.517													32	89	---	---	---	---	PASS
CLDN10	9071	broad.mit.edu	37	13	96086145	96086145	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96086145G>A	uc001vmg.2	+	1	293	c.58G>A	c.(58-60)GTT>ATT	p.V20I	CLDN10_uc010tii.1_Missense_Mutation_p.V20I	NM_182848	NP_878268	P78369	CLD10_HUMAN	claudin 10 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			TGGAGCTCTCGTTGCTGCTAC	0.592													14	23	---	---	---	---	PASS
DOCK9	23348	broad.mit.edu	37	13	99452707	99452707	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99452707C>G	uc001vnt.2	-	52	5851	c.5796G>C	c.(5794-5796)AAG>AAC	p.K1932N	DOCK9_uc001vnw.2_Missense_Mutation_p.K1931N|DOCK9_uc001vnq.2_Missense_Mutation_p.K479N|DOCK9_uc001vnr.2_Missense_Mutation_p.K561N|DOCK9_uc010tin.1_Missense_Mutation_p.K550N|DOCK9_uc001vns.2_Missense_Mutation_p.K467N|DOCK9_uc010tio.1_Missense_Mutation_p.K587N|DOCK9_uc010tip.1_Missense_Mutation_p.K628N	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1932	DHR-2.				blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GGATGCGCTTCTTCACATAAG	0.507													8	33	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101753194	101753194	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101753194C>T	uc001vox.1	-	27	3292	c.3103G>A	c.(3103-3105)GGA>AGA	p.G1035R		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1035	Helical; Name=S5 of repeat III; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGCTGAACTCCAAAGCTTGCA	0.318													13	37	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103518976	103518976	+	Intron	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103518976C>T	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjc.1_Intron|ERCC5_uc010tjd.1_Intron	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					ACCCCTCACTCTGCAGGAACT	0.607			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				10	24	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103528079	103528079	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103528079G>T	uc001vpw.2	+	15	3830	c.3387G>T	c.(3385-3387)TCG>TCT	p.S1129S		NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	1129					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CTTCAGATTCGCAGAACTCAG	0.468			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				22	33	---	---	---	---	PASS
FAM155A	728215	broad.mit.edu	37	13	108518186	108518186	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108518186C>A	uc001vql.2	-	1	1275	c.759G>T	c.(757-759)AAG>AAT	p.K253N		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	253						integral to membrane	binding			skin(1)	1						CGCCGCCTTCCTTGAGCACCA	0.498													7	154	---	---	---	---	PASS
LIG4	3981	broad.mit.edu	37	13	108861558	108861558	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108861558C>A	uc001vqn.2	-	2	2332	c.2059G>T	c.(2059-2061)GGT>TGT	p.G687C	LIG4_uc001vqo.2_Missense_Mutation_p.G687C|LIG4_uc010agg.1_Missense_Mutation_p.G620C|LIG4_uc010agf.2_Missense_Mutation_p.G687C|LIG4_uc001vqp.2_Missense_Mutation_p.G687C	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	687	BRCT 1.				cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ACTATATAACCACCAAATTCT	0.368								NHEJ					25	34	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20216032	20216032	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20216032G>C	uc010tkt.1	+	1	446	c.446G>C	c.(445-447)TGC>TCC	p.C149S		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GTTCTTGCCTGCTGGTGTGGG	0.498													15	108	---	---	---	---	PASS
OR4M1	441670	broad.mit.edu	37	14	20248958	20248958	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20248958G>C	uc010tku.1	+	1	477	c.477G>C	c.(475-477)CAG>CAC	p.Q159H		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	159	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTATAATACAGGTGGCTCTCA	0.507													26	329	---	---	---	---	PASS
OR4K15	81127	broad.mit.edu	37	14	20444613	20444613	+	Silent	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20444613G>C	uc010tkx.1	+	1	936	c.936G>C	c.(934-936)ACG>ACC	p.T312T		NM_001005486	NP_001005486	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K,	312	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TAATCTACACGCTAAGAAACA	0.398													25	62	---	---	---	---	PASS
NGDN	25983	broad.mit.edu	37	14	23945346	23945346	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23945346G>T	uc001wjy.2	+	7	556	c.529G>T	c.(529-531)GTT>TTT	p.V177F	NGDN_uc001wjz.2_Missense_Mutation_p.V177F|NGDN_uc001wka.2_5'Flank	NM_001042635	NP_001036100	Q8NEJ9	NGDN_HUMAN	neuroguidin isoform 1	177					regulation of translation	axon|cytoplasm|dendrite|filopodium|nucleus					0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TCCACGCTTGGTTCCAGTACA	0.433													15	60	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33291286	33291286	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33291286C>T	uc001wrq.2	+	13	4437	c.4267C>T	c.(4267-4269)CCA>TCA	p.P1423S		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1423					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		CATTAAGCTTCCAAATAGCTC	0.413													15	51	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36219896	36219896	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36219896T>A	uc001wti.2	-	9	1194	c.803A>T	c.(802-804)GAC>GTC	p.D268V	RALGAPA1_uc001wtj.2_Missense_Mutation_p.D268V|RALGAPA1_uc010tpv.1_Missense_Mutation_p.D268V|RALGAPA1_uc010tpw.1_Missense_Mutation_p.D268V|RALGAPA1_uc001wtk.1_Missense_Mutation_p.D119V	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	268					activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						CTGCGGGATGTCTGTGCAAAA	0.323													11	45	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42356584	42356584	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356584G>C	uc001wvm.2	+	3	1954	c.756G>C	c.(754-756)AGG>AGC	p.R252S	LRFN5_uc010ana.2_Missense_Mutation_p.R252S	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	252	Extracellular (Potential).|LRRCT.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGTGGTTGAGGCGTCTGTCCA	0.443										HNSCC(30;0.082)			26	101	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44973864	44973864	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44973864A>T	uc001wvn.2	-	1	2636	c.2327T>A	c.(2326-2328)GTT>GAT	p.V776D		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	776						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TTCCAAAACAACCGATCCTAA	0.413													25	82	---	---	---	---	PASS
ERO1L	30001	broad.mit.edu	37	14	53120022	53120022	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53120022C>G	uc001wzv.2	-	12	1046	c.820G>C	c.(820-822)GAA>CAA	p.E274Q	ERO1L_uc001wzw.2_RNA|ERO1L_uc010aof.2_RNA	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor	274					chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					CATTTCTTTTCTAACCAGGTC	0.303													31	81	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64692225	64692225	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64692225A>G	uc001xgm.2	+	115	20869	c.20639A>G	c.(20638-20640)AAT>AGT	p.N6880S	SYNE2_uc001xgl.2_Missense_Mutation_p.N6902S|SYNE2_uc010apy.2_Missense_Mutation_p.N3265S|SYNE2_uc001xgn.2_Missense_Mutation_p.N1841S|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Missense_Mutation_p.N850S|SYNE2_uc001xgq.2_Missense_Mutation_p.N1259S|SYNE2_uc001xgr.2_Missense_Mutation_p.N663S|SYNE2_uc010tsi.1_Missense_Mutation_p.N537S|SYNE2_uc001xgs.2_Missense_Mutation_p.N551S|SYNE2_uc001xgt.2_Missense_Mutation_p.N424S	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6880	Perinuclear space (Potential).|KASH.				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGGTACACCAATGGGCCACCC	0.527													7	31	---	---	---	---	PASS
KIAA0247	9766	broad.mit.edu	37	14	70171368	70171368	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70171368G>A	uc001xlk.2	+	4	683	c.367G>A	c.(367-369)GCT>ACT	p.A123T	KIAA0247_uc010aqz.2_Missense_Mutation_p.A98T	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor	123	Helical; (Potential).					integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		GTCTATAGTGGCTTCTACTGC	0.493													8	20	---	---	---	---	PASS
DPF3	8110	broad.mit.edu	37	14	73238469	73238469	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73238469G>C	uc001xnc.2	-	2	178	c.165C>G	c.(163-165)ATC>ATG	p.I55M	DPF3_uc001xnf.2_RNA|DPF3_uc010ari.1_Missense_Mutation_p.I55M|DPF3_uc010ttq.1_Missense_Mutation_p.I65M	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	55					chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCTCCATCCAGATGTAGCAGT	0.627													13	51	---	---	---	---	PASS
NEK9	91754	broad.mit.edu	37	14	75590749	75590749	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75590749C>A	uc001xrl.2	-	2	551	c.397G>T	c.(397-399)GGA>TGA	p.G133*		NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	133	Protein kinase.				cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)		TCTATCTTACCATTACAATAT	0.383													5	80	---	---	---	---	PASS
SPTLC2	9517	broad.mit.edu	37	14	77987879	77987879	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77987879C>T	uc001xub.2	-	10	1537	c.1349G>A	c.(1348-1350)AGG>AAG	p.R450K		NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base	450				KECVQQLAENTRYFRRRLKEMGFIIYGNEDSPVV -> NGI TIHEVVQTRNTYHRFSPLSPVFSHQCLWIML (in Ref. 5).		integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups	p.R450R(1)		upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	CAGGCGTCTCCTGAAATACCT	0.413													8	48	---	---	---	---	PASS
SPATA7	55812	broad.mit.edu	37	14	88857754	88857754	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88857754G>T	uc001xwq.2	+	2	200	c.49G>T	c.(49-51)GGT>TGT	p.G17C	SPATA7_uc001xwr.2_Missense_Mutation_p.G17C	NM_018418	NP_060888	Q9P0W8	SPAT7_HUMAN	spermatogenesis-associated protein 7 isoform a	17					response to stimulus|visual perception					ovary(1)	1						TCCCAGATATGGTCCACCGTG	0.358													4	14	---	---	---	---	PASS
ASB2	51676	broad.mit.edu	37	14	94420769	94420769	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94420769C>A	uc001ycc.1	-	2	717	c.228G>T	c.(226-228)ATG>ATT	p.M76I	ASB2_uc001ycd.2_Missense_Mutation_p.M124I|ASB2_uc001yce.1_Missense_Mutation_p.M22I	NM_016150	NP_057234	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box-containing protein	76	ANK 1.				intracellular signal transduction					ovary(1)|pancreas(1)	2		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CTTCCTTGATCATGGTCTTCA	0.592													6	28	---	---	---	---	PASS
TNFAIP2	7127	broad.mit.edu	37	14	103598002	103598002	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103598002T>G	uc001ymm.1	+	7	1456	c.1325T>G	c.(1324-1326)GTA>GGA	p.V442G	TNFAIP2_uc010awo.1_Missense_Mutation_p.V154G|TNFAIP2_uc010txz.1_Missense_Mutation_p.V111G|TNFAIP2_uc010tya.1_5'Flank	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	442					angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)			AATTGGCAGGTACCCCAGGAC	0.622													4	4	---	---	---	---	PASS
OR4M2	390538	broad.mit.edu	37	15	22369360	22369360	+	Missense_Mutation	SNP	G	T	T	rs138137222	byFrequency	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22369360G>T	uc010tzu.1	+	1	785	c.785G>T	c.(784-786)CGC>CTC	p.R262L	LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron	NM_001004719	NP_001004719	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M,	262	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		ATTTATGCTCGCCCATTTGAC	0.418													22	89	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22382912	22382912	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22382912C>A	uc001yuc.1	+	7	1421	c.440C>A	c.(439-441)GCT>GAT	p.A147D	LOC727924_uc001yub.1_Intron|OR4N4_uc010tzv.1_Missense_Mutation_p.A147D	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		ATGATGTTGGCTCTGTGGCTT	0.527													16	75	---	---	---	---	PASS
C15orf2	23742	broad.mit.edu	37	15	24924184	24924184	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24924184C>G	uc001ywo.2	+	1	3644	c.3170C>G	c.(3169-3171)GCA>GGA	p.A1057G		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	1057					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)		TTTGGTCAGGCAGCCTGGGAC	0.547													9	25	---	---	---	---	PASS
PPIP5K1	9677	broad.mit.edu	37	15	43827208	43827208	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43827208C>A	uc001zrw.2	-	31	4149	c.3966G>T	c.(3964-3966)GAG>GAT	p.E1322D	PPIP5K1_uc001zrx.1_Missense_Mutation_p.E1295D|PPIP5K1_uc001zru.2_Missense_Mutation_p.E1297D|PPIP5K1_uc001zry.3_Missense_Mutation_p.E1297D|PPIP5K1_uc001zrv.2_Missense_Mutation_p.E1083D	NM_001130858	NP_001124330	Q6PFW1	VIP1_HUMAN	histidine acid phosphatase domain containing 2A	1322					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity				0						GGCAAACTTCCTCAGAGACTT	0.557													23	44	---	---	---	---	PASS
STRC	161497	broad.mit.edu	37	15	43903132	43903132	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43903132C>T	uc001zsf.2	-	14	3435	c.3357G>A	c.(3355-3357)GTG>GTA	p.V1119V	STRC_uc010bdl.2_Intron|STRC_uc001zse.2_Translation_Start_Site	NM_153700	NP_714544	Q7RTU9	STRC_HUMAN	stereocilin precursor	1119					sensory perception of sound	cell surface					0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGGGATACACACAGCTGGAC	0.418													16	69	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45443357	45443357	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45443357C>A	uc001zus.1	+	24	3271	c.2925C>A	c.(2923-2925)AGC>AGA	p.S975R	DUOX1_uc001zut.1_Missense_Mutation_p.S975R|DUOX1_uc010bee.1_Missense_Mutation_p.S355R|DUOX1_uc001zuu.2_Missense_Mutation_p.S117R	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	975	Cytoplasmic (Potential).|Interaction with TXNDC11 (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GTTCCCGCAGCGACATTGAGA	0.547													4	57	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62219377	62219377	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62219377G>T	uc002agz.2	-	52	6503	c.6429C>A	c.(6427-6429)CTC>CTA	p.L2143L	VPS13C_uc002aha.2_Silent_p.L2100L|VPS13C_uc002ahb.1_Silent_p.L2143L|VPS13C_uc002ahc.1_Silent_p.L2100L	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	2143					protein localization					ovary(2)	2						TCATCTGTTCGAGTTTGGATG	0.458													5	224	---	---	---	---	PASS
MPI	4351	broad.mit.edu	37	15	75189482	75189482	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75189482C>A	uc002azc.1	+	7	980	c.975C>A	c.(973-975)CTC>CTA	p.L325L	MPI_uc002azd.1_Intron|MPI_uc010ulx.1_Silent_p.L275L|MPI_uc002aze.1_Silent_p.L264L	NM_002435	NP_002426	P34949	MPI_HUMAN	mannose-6- phosphate isomerase	325					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	mannose-6-phosphate isomerase activity|zinc ion binding			ovary(2)	2						GGCTCTTTCTCCCAACACGGA	0.532													24	77	---	---	---	---	PASS
C16orf90	646174	broad.mit.edu	37	16	3544563	3544563	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3544563G>A	uc002cvi.2	-	2	361	c.361C>T	c.(361-363)CTG>TTG	p.L121L		NM_001080524	NP_001073993	A8MZG2	CP090_HUMAN	hypothetical protein LOC646174	111											0						CGGGCTTCCAGAAGGGCTGAA	0.662													7	36	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7383002	7383002	+	Intron	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7383002C>G	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|A2BP1_uc002cyw.2_5'UTR|A2BP1_uc002cyy.2_5'UTR|A2BP1_uc002cyx.2_5'UTR|A2BP1_uc010uyc.1_5'UTR	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)		CTACGTAAAGCATGCTGGCGT	0.478													22	100	---	---	---	---	PASS
XYLT1	64131	broad.mit.edu	37	16	17211579	17211579	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17211579G>T	uc002dfa.2	-	11	2566	c.2481C>A	c.(2479-2481)CAC>CAA	p.H827Q		NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	827	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						GCACCCAGTGGTGGAGAATTT	0.537													8	50	---	---	---	---	PASS
ACSM1	116285	broad.mit.edu	37	16	20651905	20651905	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20651905T>C	uc002dhm.1	-	7	1062	c.994A>G	c.(994-996)ATC>GTC	p.I332V	ACSM1_uc002dhn.1_Intron|ACSM1_uc010bwg.1_Missense_Mutation_p.I332V	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member	332					benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2						GGGAACCTGATGCTTAGAGGA	0.552													11	31	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24135245	24135245	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24135245G>A	uc002dmd.2	+	9	1205	c.1008G>A	c.(1006-1008)CGG>CGA	p.R336R	PRKCB_uc002dme.2_Silent_p.R336R	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	336					apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	ACAGAGACCGGATGAAACTGA	0.483													23	92	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28842045	28842045	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28842045C>T	uc002drc.2	+	9	1312	c.1144C>T	c.(1144-1146)CGT>TGT	p.R382C	uc010vct.1_Intron|ATXN2L_uc010byl.1_Missense_Mutation_p.R382C|ATXN2L_uc002drb.2_Missense_Mutation_p.R382C|ATXN2L_uc002dqy.2_Missense_Mutation_p.R382C|ATXN2L_uc002dra.2_Missense_Mutation_p.R382C|ATXN2L_uc002dqz.2_Missense_Mutation_p.R382C|ATXN2L_uc010vdb.1_Missense_Mutation_p.R382C|ATXN2L_uc002dre.2_Missense_Mutation_p.R382C|ATXN2L_uc002drf.2_5'UTR	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	382						membrane				upper_aerodigestive_tract(1)|ovary(1)	2						TTTGCCACCTCGTGGCCCTCA	0.612													11	24	---	---	---	---	PASS
SPNS1	83985	broad.mit.edu	37	16	28994515	28994515	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28994515C>T	uc010vdi.1	+	11	1364	c.1224C>T	c.(1222-1224)TAC>TAT	p.Y408Y	uc010vct.1_Intron|SPNS1_uc002drx.2_Silent_p.Y335Y|SPNS1_uc002dsa.2_Silent_p.Y408Y|SPNS1_uc002drz.2_Silent_p.Y356Y|SPNS1_uc010byp.2_Silent_p.Y334Y|SPNS1_uc010byq.1_Silent_p.Y340Y|LAT_uc010vdj.1_5'Flank|LAT_uc002dsb.2_5'Flank|LAT_uc002dsd.2_5'Flank|LAT_uc002dsc.2_5'Flank|LAT_uc010vdk.1_5'Flank|LAT_uc010vdl.1_5'Flank	NM_001142448	NP_001135920	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 isoform 1	408					lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding				0						CTCCACAGTACGTGGTGATCC	0.662													6	15	---	---	---	---	PASS
ITFG1	81533	broad.mit.edu	37	16	47196508	47196508	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47196508C>T	uc002eet.2	-	15	1583	c.1521G>A	c.(1519-1521)CGG>CGA	p.R507R	ITFG1_uc010vgg.1_Silent_p.R252R|ITFG1_uc010vgh.1_Silent_p.R394R	NM_030790	NP_110417	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	507						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)				AATTTGCGCTCCGACCTAAAC	0.363													20	80	---	---	---	---	PASS
CES1	1066	broad.mit.edu	37	16	55855441	55855441	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55855441G>T	uc002eim.2	-						CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	GTGCTGTGAGGAAGAGAACAG	0.587													8	38	---	---	---	---	PASS
CES1	1066	broad.mit.edu	37	16	55855442	55855442	+	Intron	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55855442A>T	uc002eim.2	-						CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	TGCTGTGAGGAAGAGAACAGG	0.587													7	39	---	---	---	---	PASS
GPR97	222487	broad.mit.edu	37	16	57712152	57712152	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57712152G>A	uc002emh.2	+	4	519	c.416G>A	c.(415-417)CGA>CAA	p.R139Q	GPR97_uc010cdc.2_Missense_Mutation_p.R139Q|GPR97_uc010vhv.1_Missense_Mutation_p.R19Q|GPR97_uc010cdd.2_RNA|GPR97_uc010cde.2_5'Flank	NM_170776	NP_740746	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97 precursor	139	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1						AGCCTTTTTCGATCCCTGCCA	0.572													12	55	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61851395	61851395	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61851395G>T	uc002eog.1	-	7	1517	c.1265C>A	c.(1264-1266)TCC>TAC	p.S422Y	CDH8_uc002eoh.2_Missense_Mutation_p.S191Y	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	422	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TATAGGACTGGAAGTGATATC	0.433													8	52	---	---	---	---	PASS
C16orf86	388284	broad.mit.edu	37	16	67701881	67701881	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67701881G>A	uc002ety.2	+	3	590	c.433G>A	c.(433-435)GAG>AAG	p.E145K	C16orf48_uc002etw.1_5'Flank|C16orf48_uc010cem.1_5'Flank|C16orf86_uc002etx.1_Missense_Mutation_p.E160K|C16orf86_uc002etz.2_RNA	NM_001012984	NP_001013002	Q6ZW13	CP086_HUMAN	hypothetical protein LOC388284	145											0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CAGCCAGAGTGAGCCCTCACC	0.622											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	24	---	---	---	---	PASS
ZFP90	146198	broad.mit.edu	37	16	68598587	68598587	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68598587C>A	uc010cff.2	+	5	2189	c.1897C>A	c.(1897-1899)CGA>AGA	p.R633R	ZFP90_uc002ewb.2_3'UTR|ZFP90_uc002ewc.2_3'UTR|ZFP90_uc002ewd.2_Silent_p.R633R|ZFP90_uc002ewe.2_Silent_p.R633R	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90	633					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		AATTCATACTCGAAATAAACT	0.378													4	61	---	---	---	---	PASS
ZNF19	7567	broad.mit.edu	37	16	71510125	71510125	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71510125C>G	uc010cgc.1	-	6	831	c.325G>C	c.(325-327)GAA>CAA	p.E109Q	ZNF23_uc002fai.2_Intron|ZNF19_uc002fak.1_Missense_Mutation_p.E97Q|ZNF19_uc002fal.1_Missense_Mutation_p.E97Q|ZNF19_uc002fam.1_Missense_Mutation_p.E109Q	NM_006961	NP_008892	P17023	ZNF19_HUMAN	zinc finger protein 19	109						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		TCTCTTTCTTCAGAAATTCCC	0.428													7	40	---	---	---	---	PASS
PMFBP1	83449	broad.mit.edu	37	16	72166752	72166752	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72166752C>G	uc002fcc.3	-	10	1514	c.1342G>C	c.(1342-1344)GCT>CCT	p.A448P	PMFBP1_uc002fcd.2_Missense_Mutation_p.A448P|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Missense_Mutation_p.A303P	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	448	Potential.									ovary(2)	2		Ovarian(137;0.179)				TCCTGCTTAGCCTCCTTGACT	0.542													12	61	---	---	---	---	PASS
CHST5	23563	broad.mit.edu	37	16	75563809	75563809	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75563809G>T	uc002fei.2	-	3	1869	c.474C>A	c.(472-474)AGC>AGA	p.S158R	CHST5_uc002fej.1_Missense_Mutation_p.S164R	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	158	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0						GGGGAAAGGCGCTGCAGGCGG	0.642													15	74	---	---	---	---	PASS
C16orf7	9605	broad.mit.edu	37	16	89777102	89777102	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89777102C>G	uc002fom.1	-	10	1275	c.1150G>C	c.(1150-1152)GAG>CAG	p.E384Q	C16orf7_uc002fol.1_Missense_Mutation_p.E314Q|uc002fon.1_5'Flank	NM_004913	NP_004904	Q9Y2B5	CP007_HUMAN	chromosome 16 open reading frame 7	384					ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		AGGAACTGCTCCAGGTCCTCG	0.692													3	3	---	---	---	---	PASS
OR1D2	4991	broad.mit.edu	37	17	2996205	2996205	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2996205C>A	uc010vrb.1	-	1	86	c.86G>T	c.(85-87)TGG>TTG	p.W29L		NM_002548	NP_002539	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D,	29	Helical; Name=1; (Potential).				cellular component movement|chemotaxis|protein import into nucleus, translocation|sensory perception of smell|single fertilization	integral to plasma membrane	olfactory receptor activity			ovary(1)	1						CAGGAACATCCAAAACAGGAT	0.542													5	91	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577547	7577547	+	Missense_Mutation	SNP	C	A	A	rs121912656		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577547C>A	uc002gim.2	-	7	928	c.734G>T	c.(733-735)GGC>GTC	p.G245V	TP53_uc002gig.1_Missense_Mutation_p.G245V|TP53_uc002gih.2_Missense_Mutation_p.G245V|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.G113V|TP53_uc010cng.1_Missense_Mutation_p.G113V|TP53_uc002gii.1_Missense_Mutation_p.G113V|TP53_uc010cnh.1_Missense_Mutation_p.G245V|TP53_uc010cni.1_Missense_Mutation_p.G245V|TP53_uc002gij.2_Missense_Mutation_p.G245V|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.G152V|TP53_uc002gio.2_Missense_Mutation_p.G113V	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	245	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> A (in sporadic cancers; somatic mutation).|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.G245S(274)|p.G245D(93)|p.G245V(50)|p.G245C(47)|p.G245R(10)|p.G245A(8)|p.0?(7)|p.G245G(3)|p.G245fs*2(3)|p.G245N(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.G245E(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245del(1)|p.C242fs*98(1)|p.G245fs*22(1)|p.M243fs*18(1)|p.S241_G245delSCMGG(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CCGGTTCATGCCGCCCATGCA	0.582		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			9	26	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8051027	8051027	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8051027C>T	uc002gkd.2	-	11	1591	c.1353G>A	c.(1351-1353)AAG>AAA	p.K451K	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Silent_p.K435K	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	451	PAC.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						CGAAGGCTACCTTGCGGCTCC	0.647			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					3	11	---	---	---	---	PASS
KRBA2	124751	broad.mit.edu	37	17	8272809	8272809	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8272809G>T	uc002glf.1	-	2	1128	c.1122C>A	c.(1120-1122)ACC>ACA	p.T374T	KRBA2_uc002glg.1_Silent_p.T291T	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	374	Integrase catalytic.				DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0						TCTGCATCCAGGTACTTATCA	0.507													5	52	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10427107	10427107	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10427107G>A	uc010coi.2	-	36	5398	c.5270C>T	c.(5269-5271)GCA>GTA	p.A1757V	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.A1757V|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1757	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						CTTTTCTTCTGCATTGCGGGC	0.458													18	44	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18022930	18022930	+	Silent	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18022930A>G	uc010vxh.1	+	2	1154	c.816A>G	c.(814-816)CCA>CCG	p.P272P		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	272	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					CGGCCTGGCCACCCTACGGCG	0.662													5	15	---	---	---	---	PASS
ABHD15	116236	broad.mit.edu	37	17	27890113	27890113	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27890113G>T	uc002hed.1	-							NM_198147	NP_937790	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15 precursor							extracellular region	carboxylesterase activity				0						ACCTGGCAGCGAGGTGTTTAG	0.458													4	39	---	---	---	---	PASS
AP2B1	163	broad.mit.edu	37	17	33953725	33953725	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33953725G>C	uc002hjr.2	+	7	991	c.802G>C	c.(802-804)GAA>CAA	p.E268Q	AP2B1_uc002hjq.2_Missense_Mutation_p.E268Q|AP2B1_uc010wci.1_Missense_Mutation_p.E230Q|AP2B1_uc002hjs.2_Missense_Mutation_p.E211Q|AP2B1_uc002hjt.2_Missense_Mutation_p.E268Q|AP2B1_uc010ctv.2_Missense_Mutation_p.E268Q|AP2B1_uc010wcj.1_Missense_Mutation_p.E5Q	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1	268					axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GAAGTTTCTAGAATTGTTACC	0.483													46	141	---	---	---	---	PASS
MED24	9862	broad.mit.edu	37	17	38183201	38183201	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38183201G>A	uc002htt.2	-	17	1930	c.1617C>T	c.(1615-1617)ATC>ATT	p.I539I	MED24_uc010wes.1_Silent_p.I399I|MED24_uc010wet.1_Intron|MED24_uc002hts.2_Silent_p.I564I|MED24_uc002htu.2_Silent_p.I526I|MED24_uc010cwn.2_Silent_p.I526I|MED24_uc010weu.1_Silent_p.I449I|MED24_uc010wev.1_Silent_p.I489I|MED24_uc010wew.1_Silent_p.I480I|MED24_uc010wex.1_Silent_p.I244I|SNORD124_uc010wey.1_5'Flank	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1	539					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)					CAGGGTTCAGGATCTTGCCCT	0.602											OREG0024386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	24	---	---	---	---	PASS
KRTAP9-4	85280	broad.mit.edu	37	17	39405965	39405965	+	5'UTR	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39405965C>T	uc002hwi.2	+	1					KRTAP9-9_uc010wfq.1_Intron	NM_033191	NP_149461	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4							keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCCTCTACCCCTGACACCATG	0.562													39	119	---	---	---	---	PASS
UBTF	7343	broad.mit.edu	37	17	42289033	42289033	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42289033G>A	uc002igb.2	-	9	1055	c.988C>T	c.(988-990)CAG>TAG	p.Q330*	UBTF_uc002igc.2_Nonsense_Mutation_p.Q293*|UBTF_uc010czs.2_Nonsense_Mutation_p.Q330*|UBTF_uc002igd.2_Nonsense_Mutation_p.Q293*|UBTF_uc010czt.2_Nonsense_Mutation_p.Q330*|UBTF_uc002ige.2_Nonsense_Mutation_p.Q293*	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA	330	HMG box 3.				positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TTCCACTGCTGGCTGCACAGC	0.592													24	58	---	---	---	---	PASS
UBTF	7343	broad.mit.edu	37	17	42293285	42293285	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42293285T>G	uc002igb.2	-	3	374	c.307A>C	c.(307-309)AAA>CAA	p.K103Q	UBTF_uc002igc.2_Missense_Mutation_p.K103Q|UBTF_uc010czs.2_Missense_Mutation_p.K103Q|UBTF_uc002igd.2_Missense_Mutation_p.K103Q|UBTF_uc010czt.2_Missense_Mutation_p.K103Q|UBTF_uc002ige.2_Missense_Mutation_p.K103Q	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA	103					positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TTGAGTTTTTTGCCTTTGTAA	0.478													15	62	---	---	---	---	PASS
SGCA	6442	broad.mit.edu	37	17	48244818	48244818	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48244818G>A	uc002iqi.2	+	2	163	c.127G>A	c.(127-129)GAG>AAG	p.E43K	SGCA_uc010wmh.1_5'UTR|SGCA_uc002iqj.2_Missense_Mutation_p.E43K|SGCA_uc010wmi.1_RNA	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	43	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2						CTTGGACCATGAGACGTTTCT	0.657													16	38	---	---	---	---	PASS
USP32	84669	broad.mit.edu	37	17	58260692	58260692	+	Silent	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58260692G>C	uc002iyo.1	-	31	4243	c.3957C>G	c.(3955-3957)CTC>CTG	p.L1319L	USP32_uc002iyn.1_Silent_p.L989L	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	1319					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TATGCTGGCAGAGAGCCGGGT	0.493													34	76	---	---	---	---	PASS
FTSJ3	117246	broad.mit.edu	37	17	61902623	61902623	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61902623C>G	uc002jbz.2	-	6	652	c.574G>C	c.(574-576)GAG>CAG	p.E192Q	FTSJ3_uc002jca.2_Missense_Mutation_p.E192Q|PSMC5_uc002jcb.2_5'Flank|PSMC5_uc010ddy.2_5'Flank|PSMC5_uc010ddz.2_5'Flank|PSMC5_uc002jcc.2_5'Flank|PSMC5_uc002jcd.2_5'Flank	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3	192					RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						ACAAAGATCTCTGCAGATTCA	0.493													20	34	---	---	---	---	PASS
PSMC5	5705	broad.mit.edu	37	17	61908527	61908527	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61908527C>G	uc002jcb.2	+	8	852	c.811C>G	c.(811-813)CGC>GGC	p.R271G	PSMC5_uc010ddy.2_Missense_Mutation_p.R248G|PSMC5_uc010ddz.2_Missense_Mutation_p.R192G|PSMC5_uc002jcc.2_Missense_Mutation_p.R263G|PSMC5_uc002jcd.2_Missense_Mutation_p.R263G	NM_002805	NP_002796	P62195	PRS8_HUMAN	proteasome 26S ATPase subunit 5	271					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of programmed cell death|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|thyrotropin-releasing hormone receptor binding|transcription cofactor activity|transcription factor binding			large_intestine(1)	1						TGAAGTGCAGCGCACGATGCT	0.587													19	72	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	62385870	62385870	+	IGR	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62385870C>A								TEX2 (45217 upstream) : PECAM1 (13994 downstream)																							AAGTGTGCATCTGGAGTTCCC	0.473													6	17	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65822267	65822267	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65822267G>T	uc002jgf.2	+	1	488	c.427G>T	c.(427-429)GAG>TAG	p.E143*	BPTF_uc002jge.2_Nonsense_Mutation_p.E143*|BPTF_uc010wqm.1_Nonsense_Mutation_p.E143*	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	143	Glu-rich.				brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			catggtctccgaggaggagga	0.468													3	35	---	---	---	---	PASS
WIPI1	55062	broad.mit.edu	37	17	66425064	66425064	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66425064G>A	uc010dey.2	-	10	1070	c.979C>T	c.(979-981)CCA>TCA	p.P327S	WIPI1_uc002jhd.3_RNA|WIPI1_uc010wqo.1_Missense_Mutation_p.P245S|WIPI1_uc002jhe.3_RNA	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting	327	WD 3.				macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						AGCAGCCGTGGCAACTTCTGG	0.493													7	23	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66881394	66881394	+	Silent	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66881394G>T	uc002jhp.2	-	25	3551	c.3372C>A	c.(3370-3372)ATC>ATA	p.I1124I	ABCA8_uc002jhq.2_Silent_p.I1164I|ABCA8_uc010wqq.1_Silent_p.I1164I	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1124	Helical; (Potential).					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					AAAAAGTGAAGATAAATGGAA	0.373													13	50	---	---	---	---	PASS
SLC16A5	9121	broad.mit.edu	37	17	73096607	73096607	+	Silent	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73096607C>T	uc002jmr.2	+	5	1221	c.849C>T	c.(847-849)AGC>AGT	p.S283S	SLC16A5_uc002jms.1_Silent_p.S283S|SLC16A5_uc002jmt.2_Silent_p.S283S|SLC16A5_uc002jmu.2_Silent_p.S283S|SLC16A5_uc010wrt.1_Silent_p.S323S	NM_004695	NP_004686	O15375	MOT6_HUMAN	solute carrier family 16, member 5	283	Helical; (Potential).				organic anion transport	integral to plasma membrane|membrane fraction	secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	TCGGCTTCAGCAACATCTTCC	0.617													84	220	---	---	---	---	PASS
RPTOR	57521	broad.mit.edu	37	17	78921039	78921039	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78921039G>A	uc002jyt.1	+	27	3958	c.3153G>A	c.(3151-3153)TGG>TGA	p.W1051*	RPTOR_uc010wug.1_Nonsense_Mutation_p.W893*|RPTOR_uc002jyu.1_5'Flank	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	1051	WD 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						TTTGGGACTGGGAGAAAGGGG	0.353													8	24	---	---	---	---	PASS
AATK	9625	broad.mit.edu	37	17	79093228	79093228	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79093228G>T	uc010dia.2	-	13	4116	c.4036C>A	c.(4036-4038)CGC>AGC	p.R1346S	AATK_uc010dhz.2_RNA	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1346						integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ATGGAGAAGCGGGACGTGGGC	0.736													3	15	---	---	---	---	PASS
FAM38B	63895	broad.mit.edu	37	18	10696076	10696076	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10696076C>T	uc002kor.3	-	5	858	c.718G>A	c.(718-720)GAG>AAG	p.E240K	FAM38B_uc002koq.2_Missense_Mutation_p.E138K	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2283						integral to membrane	ion channel activity			ovary(1)	1						CCTTACCTCTCAGTCACACCA	0.502													25	62	---	---	---	---	PASS
UHRF1	29128	broad.mit.edu	37	19	4932748	4932748	+	Intron	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4932748C>G	uc002mbo.2	+						UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_Intron|UHRF1_uc002mbp.2_Intron	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains						cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		GGGCTTTCCTCCCAGCTACCC	0.657													13	37	---	---	---	---	PASS
KHSRP	8570	broad.mit.edu	37	19	6422370	6422370	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6422370C>A	uc002mer.3	-	2	437	c.327G>T	c.(325-327)AAG>AAT	p.K109N		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	109	Gly-rich.				mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1						CCAACTGTCTCTTTTGGCCCC	0.488													19	75	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9068085	9068085	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9068085G>T	uc002mkp.2	-	3	19565	c.19361C>A	c.(19360-19362)GCG>GAG	p.A6454E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6456	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CTGTGATGTCGCCCTATGAGG	0.498													25	128	---	---	---	---	PASS
ZNF560	147741	broad.mit.edu	37	19	9578918	9578918	+	Silent	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9578918A>T	uc002mlp.1	-	10	915	c.705T>A	c.(703-705)ACT>ACA	p.T235T	ZNF560_uc010dwr.1_Silent_p.T129T	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	235					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						CTCTATTTTGAGTACTCATGT	0.378													13	53	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10472640	10472640	+	Intron	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10472640T>C	uc002moc.3	-						TYK2_uc010dxe.2_Intron|TYK2_uc002mod.2_Intron	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2						intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			AGCTGCGGGATCATGTGGCAC	0.662													6	33	---	---	---	---	PASS
CCDC151	115948	broad.mit.edu	37	19	11545644	11545644	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11545644G>T	uc002mrs.2	-	1	337	c.194C>A	c.(193-195)CCC>CAC	p.P65H	CCDC151_uc010dxz.2_Missense_Mutation_p.P65H|PRKCSH_uc002mrt.2_5'Flank|PRKCSH_uc002mru.2_5'Flank|PRKCSH_uc010xlz.1_5'Flank|PRKCSH_uc010dya.2_5'Flank|PRKCSH_uc002mrv.1_5'Flank|PRKCSH_uc010dyb.2_5'Flank	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	65										ovary(1)	1						GTGCACAGAGGGCTTCCCTGC	0.587											OREG0025257	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	79	---	---	---	---	PASS
HOOK2	29911	broad.mit.edu	37	19	12876760	12876760	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12876760T>A	uc002muy.2	-	16	1751	c.1580A>T	c.(1579-1581)CAG>CTG	p.Q527L	HOOK2_uc010xmq.1_5'UTR|HOOK2_uc002muz.2_Missense_Mutation_p.Q527L	NM_013312	NP_037444	Q96ED9	HOOK2_HUMAN	hook homolog 2 isoform 1	527	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)|skin(1)	3						CTTGCCCCCCTGCTCCTGCAG	0.652											OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	34	---	---	---	---	PASS
CACNA1A	773	broad.mit.edu	37	19	13476130	13476130	+	Splice_Site	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13476130C>T	uc010dze.2	-	5	1020	c.784_splice	c.e5+1	p.D262_splice	CACNA1A_uc002mwy.3_Splice_Site_p.D262_splice	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	CGTGGACCTACCTGTCCCCTC	0.463													22	86	---	---	---	---	PASS
EPHX3	79852	broad.mit.edu	37	19	15341907	15341907	+	Intron	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15341907G>T	uc002nap.2	-						EPHX3_uc002naq.2_Intron	NM_024794	NP_079070	Q9H6B9	EPHX3_HUMAN	abhydrolase domain containing 9 precursor							extracellular region	hydrolase activity				0						GTAACCTGTGGGAATTCAAGG	0.567													4	29	---	---	---	---	PASS
ZNF14	7561	broad.mit.edu	37	19	19823724	19823724	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19823724C>G	uc002nnk.1	-	4	520	c.366G>C	c.(364-366)ATG>ATC	p.M122I		NM_021030	NP_066358	P17017	ZNF14_HUMAN	zinc finger protein 14	122	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Renal(1328;0.0474)				TGTGAGATCTCATGTGCCTAT	0.383													13	82	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22157371	22157371	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22157371A>T	uc002nqp.2	-	4	614	c.465T>A	c.(463-465)CAT>CAA	p.H155Q	ZNF208_uc002nqo.1_Intron|ZNF208_uc010ecw.1_5'Flank	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTGAACATTTATGAAAGACAT	0.333													11	62	---	---	---	---	PASS
ZNF681	148213	broad.mit.edu	37	19	23927115	23927115	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23927115T>C	uc002nrk.3	-	4	1379	c.1237A>G	c.(1237-1239)AAG>GAG	p.K413E	ZNF681_uc002nrl.3_Missense_Mutation_p.K344E|ZNF681_uc002nrj.3_Missense_Mutation_p.K344E	NM_138286	NP_612143	Q96N22	ZN681_HUMAN	zinc finger protein 681	413	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TGAATGCTCTTATGTCTAGTA	0.368													20	50	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31039116	31039116	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039116C>A	uc002nsu.1	+	4	2728	c.2590C>A	c.(2590-2592)CTC>ATC	p.L864I	ZNF536_uc010edd.1_Missense_Mutation_p.L864I	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	864					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					ATCAGGGGTTCTCTCCTCTGG	0.582													5	83	---	---	---	---	PASS
ZNF790	388536	broad.mit.edu	37	19	37310031	37310031	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37310031C>G	uc002oew.2	-	5	1334	c.1215G>C	c.(1213-1215)TGG>TGC	p.W405C	uc002oev.1_Intron	NM_206894	NP_996777	Q6PG37	ZN790_HUMAN	zinc finger protein 790	405	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			GGTGTGAGCTCCAAATATAGG	0.413													11	69	---	---	---	---	PASS
TMEM145	284339	broad.mit.edu	37	19	42818838	42818838	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42818838G>T	uc002otk.1	+	4	399	c.347G>T	c.(346-348)TGG>TTG	p.W116L		NM_173633	NP_775904	Q8NBT3	TM145_HUMAN	transmembrane protein 145	116						integral to membrane					0		Prostate(69;0.00682)				CAGTATGCCTGGTCCGGCTGT	0.617													9	76	---	---	---	---	PASS
PSG1	5669	broad.mit.edu	37	19	43382240	43382240	+	Missense_Mutation	SNP	G	T	T	rs1058959		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43382240G>T	uc002ovb.2	-	2	393	c.255C>A	c.(253-255)GAC>GAA	p.D85E	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.D85E|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Missense_Mutation_p.D85E|PSG1_uc010eio.1_Missense_Mutation_p.D85E|PSG1_uc002oux.1_Missense_Mutation_p.D14E|PSG1_uc002ouy.1_Missense_Mutation_p.D85E|PSG1_uc002ouz.1_Missense_Mutation_p.D85E|PSG1_uc002ova.1_Missense_Mutation_p.D85E|PSG1_uc002ovc.2_Missense_Mutation_p.D85E|PSG1_uc002ovd.1_Missense_Mutation_p.D85E	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	85	Ig-like V-type.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				TTATTTCACCGTCTACTACAT	0.448													53	186	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43414888	43414888	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43414888G>C	uc002ovj.1	-	3	602	c.550C>G	c.(550-552)CAG>GAG	p.Q184E	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Missense_Mutation_p.Q191E|PSG6_uc002ovi.2_Missense_Mutation_p.Q185E|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG6_uc002ove.1_5'UTR|PSG6_uc002ovf.1_Missense_Mutation_p.Q184E|PSG6_uc002ovg.1_Missense_Mutation_p.Q184E	NM_002782	NP_002773	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6 isoform	184	Ig-like C2-type 1.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				GGGAGGTTCTGACCATTCAGC	0.498													49	156	---	---	---	---	PASS
PSG4	5672	broad.mit.edu	37	19	43699169	43699169	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43699169G>A	uc002ovy.2	-	4	1068	c.966C>T	c.(964-966)GAC>GAT	p.D322D	PSG6_uc010xwk.1_Intron|PSG4_uc002owa.2_RNA|PSG4_uc002owb.2_Silent_p.D229D|PSG4_uc002ovz.2_Intron	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	322	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)				GGGTGACTGGGTCACTGCGGA	0.488													36	123	---	---	---	---	PASS
TEX101	83639	broad.mit.edu	37	19	43922108	43922108	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43922108G>T	uc010xwo.1	+	5	665	c.470G>T	c.(469-471)TGT>TTT	p.C157F	TEX101_uc002owk.2_Missense_Mutation_p.C175F	NM_001130011	NP_001123483	Q9BY14	TX101_HUMAN	testis expressed 101 isoform 2	157				C -> Y (in Ref. 1; AAK28327).		anchored to membrane|plasma membrane				ovary(1)	1		Prostate(69;0.0199)				TCTCTTCCCTGTCCCAATGGT	0.463													20	85	---	---	---	---	PASS
MARK4	57787	broad.mit.edu	37	19	45781203	45781203	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45781203G>C	uc002pbb.1	+	9	814	c.809G>C	c.(808-810)AGA>ACA	p.R270T	MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Missense_Mutation_p.R270T|MARK4_uc002pbc.1_Missense_Mutation_p.R136T			Q96L34	MARK4_HUMAN	RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;	270	Protein kinase.				microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CGAGTACTCAGAGGGAAGTAC	0.507													4	35	---	---	---	---	PASS
IGFL3	388555	broad.mit.edu	37	19	46627176	46627176	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46627176C>T	uc002pea.1	-	3	342	c.317G>A	c.(316-318)TGT>TAT	p.C106Y		NM_207393	NP_997276	Q6UXB1	IGFL3_HUMAN	IGF-like family member 3 precursor	106						extracellular region	protein binding				0		Ovarian(192;0.0175)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00473)|GBM - Glioblastoma multiforme(486;0.0149)|Epithelial(262;0.239)		AGATAAGTGACACTGAGACTT	0.517													73	196	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46811522	46811522	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46811522T>A	uc002peh.2	+	4	437	c.408T>A	c.(406-408)TGT>TGA	p.C136*	HIF3A_uc002pef.1_Nonsense_Mutation_p.C136*|HIF3A_uc002peg.3_Nonsense_Mutation_p.C136*|HIF3A_uc010xxx.1_RNA|HIF3A_uc002pei.3_Nonsense_Mutation_p.C80*|HIF3A_uc002pej.1_Nonsense_Mutation_p.C67*|HIF3A_uc002pek.2_Nonsense_Mutation_p.C80*|HIF3A_uc010xxy.1_Nonsense_Mutation_p.C67*|HIF3A_uc002pel.2_Nonsense_Mutation_p.C134*|HIF3A_uc010xxz.1_Nonsense_Mutation_p.C85*	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	136	PAS 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		TCCACCCCTGTGACCAAGAGG	0.502													26	76	---	---	---	---	PASS
TEAD2	8463	broad.mit.edu	37	19	49846557	49846557	+	Silent	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49846557C>G	uc002pnj.2	-	10	1099	c.1008G>C	c.(1006-1008)CTG>CTC	p.L336L	uc002pnb.1_5'Flank|TEAD2_uc002png.2_Silent_p.L339L|TEAD2_uc002pnh.2_Silent_p.L340L|TEAD2_uc002pni.2_Silent_p.L339L|TEAD2_uc010yao.1_Silent_p.L208L|TEAD2_uc010emw.2_Silent_p.L339L	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	336	Transcriptional activation (Potential).				hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TCATGTGTTCCAGGCTCTCAT	0.617													10	46	---	---	---	---	PASS
SIGLEC9	27180	broad.mit.edu	37	19	51628650	51628650	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51628650C>A	uc002pvu.2	+	1	486	c.419C>A	c.(418-420)ACA>AAA	p.T140K	SIGLEC9_uc010yct.1_Missense_Mutation_p.T140K	NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9 precursor	140	Extracellular (Potential).|Ig-like V-type.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GTGAATGTGACAGGTAAGGCA	0.532													7	24	---	---	---	---	PASS
ZNF28	7576	broad.mit.edu	37	19	53303738	53303738	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53303738G>A	uc002qad.2	-	4	1480	c.1360C>T	c.(1360-1362)CTT>TTT	p.L454F	ZNF28_uc002qac.2_Missense_Mutation_p.L401F|ZNF28_uc010eqe.2_Missense_Mutation_p.L400F	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	454	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TGGCGTGCAAGAGTTGATTGT	0.373													25	83	---	---	---	---	PASS
CNOT3	4849	broad.mit.edu	37	19	54649754	54649754	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54649754C>T	uc002qdj.1	+	9	1123	c.812C>T	c.(811-813)CCG>CTG	p.P271L	CNOT3_uc010yel.1_Missense_Mutation_p.P271L|CNOT3_uc002qdi.2_Missense_Mutation_p.P184L|CNOT3_uc002qdk.1_Missense_Mutation_p.P271L|CNOT3_uc010ere.1_RNA	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	271					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCTCCCATCCCGCCCAGCCCA	0.622													12	32	---	---	---	---	PASS
TTYH1	57348	broad.mit.edu	37	19	54930341	54930341	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54930341G>T	uc002qfq.2	+	2	258	c.166G>T	c.(166-168)GGC>TGC	p.G56C	TTYH1_uc010yey.1_Missense_Mutation_p.G105C|TTYH1_uc002qfr.2_Missense_Mutation_p.G56C|TTYH1_uc002qft.2_Missense_Mutation_p.G56C|TTYH1_uc002qfu.1_5'Flank	NM_020659	NP_065710	Q9H313	TTYH1_HUMAN	tweety 1 isoform 1	56	Helical; Name=1; (Potential).				cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CCTGGGCTTGGGCCTGAGCCT	0.682													16	36	---	---	---	---	PASS
KIR2DL3	3804	broad.mit.edu	37	19	55258843	55258843	+	Intron	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55258843T>A	uc002qgv.2	+						KIR2DL3_uc002qgx.2_Intron|KIR2DL3_uc002qgy.2_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron	NM_015868	NP_056952	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)		AACCGGTGAGTACAGAACCCT	0.507													11	17	---	---	---	---	PASS
SYT5	6861	broad.mit.edu	37	19	55687076	55687076	+	Splice_Site	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55687076C>T	uc002qjm.1	-	4	1600	c.540_splice	c.e4+1	p.K180_splice	SYT5_uc002qjp.2_Splice_Site_p.K177_splice|SYT5_uc002qjn.1_Splice_Site_p.K180_splice|SYT5_uc002qjo.1_Splice_Site_p.K180_splice	NM_003180	NP_003171	O00445	SYT5_HUMAN	synaptotagmin V						energy reserve metabolic process|regulation of insulin secretion|synaptic transmission	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane	metal ion binding|transporter activity				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CAGGAGCTCACCTTGAAGGCG	0.627													17	49	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56388478	56388478	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56388478T>C	uc002qmd.3	+	8	3064	c.2642T>C	c.(2641-2643)GTG>GCG	p.V881A	NLRP4_uc002qmf.2_Missense_Mutation_p.V806A|NLRP4_uc010etf.2_Missense_Mutation_p.V656A	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	881	LRR 6.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GATGTGGGTGTGCAGCTGTTG	0.502													22	56	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56490755	56490755	+	Intron	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56490755C>T	uc002qmh.2	+						NLRP8_uc010etg.2_Intron	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8							cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GTTTCTGTGTCACAGGCTGGA	0.507													15	50	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57642755	57642755	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57642755G>T	uc002qny.2	+	4	3068	c.2712G>T	c.(2710-2712)CAG>CAT	p.Q904H		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	904					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CTAGCACACAGGCAGGGGTGA	0.493													17	59	---	---	---	---	PASS
ZIM3	114026	broad.mit.edu	37	19	57646494	57646494	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57646494G>C	uc002qnz.1	-	5	1597	c.1211C>G	c.(1210-1212)TCA>TGA	p.S404*		NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	404	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATGAAGGTTTGACTTCTGAAA	0.378													13	128	---	---	---	---	PASS
ZNF548	147694	broad.mit.edu	37	19	57911091	57911091	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57911091G>A	uc002qom.2	+	3	1686	c.1436G>A	c.(1435-1437)TGC>TAC	p.C479Y	ZNF547_uc002qpm.3_Intron|ZNF548_uc002qon.2_Missense_Mutation_p.C482Y	NM_152909	NP_690873	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	479	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTTATGAGTGCAGCGAATGC	0.468													24	87	---	---	---	---	PASS
ZSCAN4	201516	broad.mit.edu	37	19	58190146	58190146	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58190146G>T	uc002qpu.2	+	5	1872	c.1175G>T	c.(1174-1176)GGA>GTA	p.G392V		NM_152677	NP_689890	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	392					telomere maintenance via telomere lengthening|viral reproduction	nuclear chromosome, telomeric region	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATCCACACAGGAGAAAAGCCT	0.453													40	108	---	---	---	---	PASS
ZNF135	7694	broad.mit.edu	37	19	58578819	58578819	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58578819G>A	uc010yhq.1	+	5	1099	c.1003G>A	c.(1003-1005)GAG>AAG	p.E335K	ZNF135_uc002qre.2_Missense_Mutation_p.E323K|ZNF135_uc002qrd.1_Missense_Mutation_p.E281K|ZNF135_uc002qrf.2_Missense_Mutation_p.E281K|ZNF135_uc002qrg.2_Missense_Mutation_p.E293K|ZNF135_uc010yhr.1_Missense_Mutation_p.E144K	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	335					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TCACACAGGCGAGAAGCCCTA	0.542													13	69	---	---	---	---	PASS
GNAS	2778	broad.mit.edu	37	20	57484238	57484238	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57484238G>A	uc002xzw.2	+	7	2766	c.2481G>A	c.(2479-2481)GTG>GTA	p.V827V	GNAS_uc002xzt.2_3'UTR|GNAS_uc010gjq.2_Silent_p.V125V|GNAS_uc002xzx.2_Silent_p.V125V|GNAS_uc010gjr.2_Silent_p.V75V|GNAS_uc002xzy.2_Silent_p.V110V|GNAS_uc002yaa.2_Silent_p.V170V|GNAS_uc010zzt.1_Silent_p.V185V|GNAS_uc002yab.2_Intron|GNAS_uc002yad.2_Silent_p.V75V|GNAS_uc002yae.2_Silent_p.V109V	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	184					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)			AGATCGACGTGATCAAGCAGG	0.507			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			73	147	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19666726	19666726	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19666726G>A	uc002ykw.2	-	21	2378	c.2347C>T	c.(2347-2349)CCA>TCA	p.P783S		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	783	Extracellular (Potential).				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						ACAATCTTTGGGGTGATGTCT	0.458													18	64	---	---	---	---	PASS
DOPEY2	9980	broad.mit.edu	37	21	37610953	37610953	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37610953G>C	uc002yvg.2	+	17	2909	c.2830G>C	c.(2830-2832)GAG>CAG	p.E944Q	DOPEY2_uc011aeb.1_Missense_Mutation_p.E893Q	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	944					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						TCTGACAAGAGAGATCCAAGG	0.473													8	30	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22707535	22707535	+	Intron	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22707535C>T	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						GACTCACCTGCACCTTGCGCA	0.547													11	93	---	---	---	---	PASS
GGT1	2678	broad.mit.edu	37	22	25007072	25007072	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25007072G>A	uc003aan.1	+	5	511	c.24G>A	c.(22-24)CTG>CTA	p.L8L	GGT1_uc003aas.1_Silent_p.L8L|GGT1_uc003aat.1_Silent_p.L8L|GGT1_uc003aau.1_Silent_p.L8L|GGT1_uc003aav.1_Silent_p.L8L|GGT1_uc003aaw.1_Silent_p.L8L|GGT1_uc003aax.1_Silent_p.L8L	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor	8	Helical; Signal-anchor for type II membrane protein; (Probable).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	TAGTGGTGCTGGGCCTGCTGG	0.617													5	9	---	---	---	---	PASS
MN1	4330	broad.mit.edu	37	22	28195045	28195045	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28195045C>T	uc003adj.2	-	1	2442	c.1487G>A	c.(1486-1488)GGC>GAC	p.G496D		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	496							binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						TGTGAACTCGCCGGGTAGGCC	0.617			T	ETV6	AML|meningioma								4	12	---	---	---	---	PASS
TOM1	10043	broad.mit.edu	37	22	35713920	35713920	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35713920G>C	uc003ann.2	+	2	228	c.103G>C	c.(103-105)GAG>CAG	p.E35Q	TOM1_uc011ami.1_Missense_Mutation_p.E2Q|TOM1_uc011amj.1_5'UTR|TOM1_uc003ans.2_5'UTR|TOM1_uc011amk.1_Missense_Mutation_p.W13C|TOM1_uc003anp.2_Missense_Mutation_p.E35Q|TOM1_uc011aml.1_Missense_Mutation_p.E35Q|TOM1_uc003ano.2_RNA|TOM1_uc003anq.2_Missense_Mutation_p.E35Q|TOM1_uc003anr.2_5'UTR	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1	35	VHS.				endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						CCTCAACATGGAGATCTGCGA	0.582													10	35	---	---	---	---	PASS
ELFN2	114794	broad.mit.edu	37	22	37770023	37770023	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37770023C>T	uc003asq.3	-	3	2338	c.1552G>A	c.(1552-1554)GAG>AAG	p.E518K		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	518	Cytoplasmic (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)					AGGTCATCCTCGGGCCGAGCC	0.627													10	16	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	43972302	43972302	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43972302T>G	uc003bdy.1	-	26	3510	c.3295A>C	c.(3295-3297)AAG>CAG	p.K1099Q	EFCAB6_uc003bdz.1_Missense_Mutation_p.K947Q|EFCAB6_uc010gzi.1_Missense_Mutation_p.K947Q|EFCAB6_uc010gzj.1_Missense_Mutation_p.K325Q	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1099	EF-hand 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				CAGAAATCCTTAAGAACTTGT	0.313													16	30	---	---	---	---	PASS
C22orf9	23313	broad.mit.edu	37	22	45607906	45607906	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45607906G>T	uc003bfx.1	-	2	213	c.147C>A	c.(145-147)GAC>GAA	p.D49E	C22orf9_uc003bfv.1_Missense_Mutation_p.D58E|C22orf9_uc003bfw.1_Missense_Mutation_p.D54E|C22orf9_uc010gzx.2_Missense_Mutation_p.D31E	NM_001009880	NP_001009880	Q6ICG6	K0930_HUMAN	hypothetical protein LOC23313 isoform b	49							protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|READ - Rectum adenocarcinoma(1;0.000617)|Colorectal(1;0.0024)		AAAGCATGTCGTCCTGCCGGG	0.617													10	9	---	---	---	---	PASS
CD99	4267	broad.mit.edu	37	X	2640679	2640679	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2640679G>C	uc004cqm.2	+	6	448	c.274G>C	c.(274-276)GAT>CAT	p.D92H	CD99_uc010nda.2_Missense_Mutation_p.D76H|CD99_uc004cqn.2_RNA|CD99_uc004cqo.2_Missense_Mutation_p.D92H	NM_002414	NP_002405	P14209	CD99_HUMAN	CD99 antigen isoform a precursor	92	Extracellular (Potential).				cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1						TAGCTTTTCAGATGCTGACCT	0.438													30	92	---	---	---	---	PASS
ARSE	415	broad.mit.edu	37	X	2878444	2878444	+	5'UTR	SNP	T	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2878444T>A	uc004crc.3	-	2					ARSE_uc011mhi.1_5'UTR|ARSE_uc011mhh.1_5'UTR	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor						skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2		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)				TGTAACATGTTGTCTCTCTCT	0.274													11	17	---	---	---	---	PASS
PNPLA4	8228	broad.mit.edu	37	X	7894053	7894053	+	Silent	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7894053G>A	uc011mhq.1	-	2	270	c.108C>T	c.(106-108)GTC>GTT	p.V36V	PNPLA4_uc011mhr.1_Silent_p.V36V|PNPLA4_uc011mhs.1_Intron	NM_004650	NP_004641	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	36	Patatin.				lipid catabolic process		triglyceride lipase activity				0		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				CGAAGGCTTTGACATCCTTCA	0.463											OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	13	---	---	---	---	PASS
TAB3	257397	broad.mit.edu	37	X	30872850	30872850	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30872850A>G	uc004dcj.2	-	6	1595	c.932T>C	c.(931-933)GTG>GCG	p.V311A	TAB3_uc004dck.2_Missense_Mutation_p.V311A|TAB3_uc010ngl.2_Missense_Mutation_p.V311A	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	311	Pro-rich.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB 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|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1						GGAAGGTTGCACTTGATGCTG	0.498													8	20	---	---	---	---	PASS
KDM6A	7403	broad.mit.edu	37	X	44936072	44936072	+	Splice_Site	SNP	G	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44936072G>A	uc004dge.3	+	18	3207	c.2832_splice	c.e18+1	p.Y944_splice	KDM6A_uc010nhk.2_Splice_Site_p.Y910_splice|KDM6A_uc011mkz.1_Splice_Site_p.Y996_splice|KDM6A_uc011mla.1_Splice_Site_p.Y899_splice|KDM6A_uc011mlb.1_Splice_Site_p.Y951_splice|KDM6A_uc011mlc.1_Splice_Site_p.Y648_splice|KDM6A_uc011mld.1_Splice_Site_p.Y583_splice	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						TAGTATTTACGTGAGTCTGAA	0.383			D|N|F|S		renal|oesophageal SCC|MM								26	28	---	---	---	---	PASS
RBM10	8241	broad.mit.edu	37	X	47044725	47044725	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47044725A>G	uc004dhf.2	+	19	2504	c.2125A>G	c.(2125-2127)ACC>GCC	p.T709A	RBM10_uc004dhg.2_Missense_Mutation_p.T631A|RBM10_uc004dhh.2_Missense_Mutation_p.T708A|RBM10_uc010nhq.2_Missense_Mutation_p.T632A|RBM10_uc004dhi.2_Missense_Mutation_p.T774A	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	709					mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			ovary(1)|large_intestine(1)|prostate(1)|breast(1)|pancreas(1)	5						GAGACAGCACACCAGCATGGA	0.632													7	4	---	---	---	---	PASS
KDM5C	8242	broad.mit.edu	37	X	53231062	53231062	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53231062C>A	uc004drz.2	-	13	2373	c.1840G>T	c.(1840-1842)GCT>TCT	p.A614S	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Missense_Mutation_p.A547S|KDM5C_uc004dsa.2_Missense_Mutation_p.A613S	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	614	JmjC.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18						AAGTTGACAGCCTCGGCAAAG	0.547			N|F|S		clear cell renal carcinoma								15	18	---	---	---	---	PASS
CYSLTR1	10800	broad.mit.edu	37	X	77528293	77528293	+	Silent	SNP	C	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77528293C>A	uc004edb.2	-	3	1351	c.951G>T	c.(949-951)GTG>GTT	p.V317V	CYSLTR1_uc010nma.2_Silent_p.V317V|CYSLTR1_uc010nmb.2_Silent_p.V317V	NM_006639	NP_006630	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	317	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|respiratory gaseous exchange	integral to plasma membrane|membrane fraction	leukotriene receptor activity			ovary(1)	1					Amlexanox(DB01025)|Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	GTACATAAGTCACGCTGGACA	0.388													5	15	---	---	---	---	PASS
TEX13A	56157	broad.mit.edu	37	X	104464811	104464811	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104464811G>C	uc004ema.2	-	2	383	c.271C>G	c.(271-273)CGG>GGG	p.R91G	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Missense_Mutation_p.R91G	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	91						intracellular	zinc ion binding			ovary(2)	2						TGCAGCCACCGCACCCTGTGC	0.627													4	10	---	---	---	---	PASS
PRPS1	5631	broad.mit.edu	37	X	106885651	106885651	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106885651G>T	uc004ene.3	+	4	666	c.461G>T	c.(460-462)TGG>TTG	p.W154L	PRPS1_uc010npg.2_Missense_Mutation_p.W121L|PRPS1_uc011msj.1_Intron	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	154					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						GTCCTAAAGTGGATAAGGGAG	0.428													4	56	---	---	---	---	PASS
IL13RA1	3597	broad.mit.edu	37	X	117895230	117895230	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117895230C>G	uc004eqs.2	+	6	849	c.806C>G	c.(805-807)ACT>AGT	p.T269S	IL13RA1_uc004eqr.1_Missense_Mutation_p.T269S|IL13RA1_uc004eqt.1_Missense_Mutation_p.T269S	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor	269	Extracellular (Potential).					interleukin-13 receptor complex	cytokine receptor activity				0						AACAGCCAAACTGAGACACAT	0.303													29	52	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118222757	118222757	+	Silent	SNP	T	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118222757T>C	uc004era.3	-	11	2436	c.2436A>G	c.(2434-2436)CAA>CAG	p.Q812Q		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	812										ovary(4)|skin(1)	5						AGAAGACTTCTTGTTCATCTT	0.488													15	12	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130215797	130215797	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130215797A>G	uc004evz.2	+	2	503	c.158A>G	c.(157-159)CAC>CGC	p.H53R	ARHGAP36_uc004ewa.2_Missense_Mutation_p.H41R|ARHGAP36_uc004ewb.2_Missense_Mutation_p.H22R|ARHGAP36_uc004ewc.2_5'Flank	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	53					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						GTATCGATACACAGCCTCTCT	0.532													12	34	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140985615	140985615	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140985615G>T	uc011mwp.1	+	8	1929	c.1929G>T	c.(1927-1929)GAG>GAT	p.E643D	MAGEC3_uc004fbs.2_3'UTR|MAGEC3_uc010nsj.2_3'UTR	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	643	MAGE 2.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TCTGTCCTGAGTGATGTCTGA	0.532													17	23	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140996228	140996228	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140996228A>G	uc004fbt.2	+	4	3324	c.3038A>G	c.(3037-3039)TAT>TGT	p.Y1013C	MAGEC1_uc010nsl.1_Missense_Mutation_p.Y80C	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	1013	MAGE.						protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					AAGGGCACCTATGCCTCTGAG	0.542										HNSCC(15;0.026)			35	39	---	---	---	---	PASS
AGRN	375790	broad.mit.edu	37	1	965876	965877	+	Intron	INS	-	GT	GT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:965876_965877insGT	uc001ack.1	+							NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor						axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-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)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GTGAGATCAGCGTGTGTGTGCA	0.381													4	2	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3097650	3097651	+	Intron	INS	-	CA	CA	rs142664042		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3097650_3097651insCA	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		tcttacacacggccttacacac	0.000			T	EVI1	MDS|AML								4	3	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3097802	3097803	+	Intron	DEL	AC	-	-	rs142437669	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3097802_3097803delAC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		acacggtcttacacacagtctt	0.000			T	EVI1	MDS|AML								10	5	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3098113	3098116	+	Intron	DEL	CACG	-	-	rs143695290	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3098113_3098116delCACG	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		cggtcttacacacgcagtcttaca	0.000			T	EVI1	MDS|AML								8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5386478	5386479	+	IGR	INS	-	GCC	GCC	rs146867562	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5386478_5386479insGCC								AJAP1 (542628 upstream) : NPHP4 (536391 downstream)																							CCAGAGCTGTGGCCGCCTCCTC	0.411													1	5	---	---	---	---	
ESPN	83715	broad.mit.edu	37	1	6496168	6496168	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6496168delA	uc001amy.2	+							NM_031475	NP_113663	B1AK53	ESPN_HUMAN	espin						sensory perception of sound	brush border|cytoplasm|filamentous actin|stereocilium	actin filament binding|SH3 domain binding				0	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GGTCTGCGGGAGAAGGGCAGT	0.443													5	3	---	---	---	---	
NPPB	4879	broad.mit.edu	37	1	11921016	11921017	+	5'Flank	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11921016_11921017delTG	uc001atj.2	-							NM_002521	NP_002512	P16860	ANFB_HUMAN	natriuretic peptide precursor B preproprotein						body fluid secretion|cGMP biosynthetic process|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation	extracellular space	diuretic hormone activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Carvedilol(DB01136)|Nesiritide(DB04899)|Testosterone(DB00624)	GGGGTAGTTTtgtgtgtgtgtg	0.361													3	3	---	---	---	---	
VPS13D	55187	broad.mit.edu	37	1	12378659	12378659	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12378659delG	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc001aty.1_Intron	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CCTGGGCAGTGGTCTTTTTTT	0.537													4	2	---	---	---	---	
HNRNPCL1	343069	broad.mit.edu	37	1	12908384	12908385	+	Intron	INS	-	A	A	rs143606605		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12908384_12908385insA	uc010obf.1	-						LOC649330_uc009vno.2_5'Flank	NM_001013631	NP_001013653	O60812	HNRCL_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleotide binding				0						ATTGCATTTAGAAAAAAAATCA	0.356													4	2	---	---	---	---	
PLEKHM2	23207	broad.mit.edu	37	1	16056542	16056556	+	Intron	DEL	GGGCGGGGCGGGGCG	-	-	rs12729712		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16056542_16056556delGGGCGGGGCGGGGCG	uc010obo.1	+							NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M						Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TCGCCTACCTgggcggggcggggcggggcggggcg	0.465													5	3	---	---	---	---	
CLCNKB	1188	broad.mit.edu	37	1	16372283	16372283	+	Intron	DEL	T	-	-	rs67016480		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16372283delT	uc001axw.3	+						FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_Intron	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TTGGGGGGGGTGCTCTGGGTG	0.358													3	3	---	---	---	---	
FAM131C	348487	broad.mit.edu	37	1	16400993	16400994	+	5'Flank	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16400993_16400994delAC	uc001axz.3	-						FAM131C_uc010obz.1_5'Flank	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487												0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GCTTGCATTTacacacacacac	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16856184	16856184	+	IGR	DEL	T	-	-	rs76459018		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16856184delT								CROCCL2 (36988 upstream) : NBPF1 (34228 downstream)																							accatccagatgggtctccct	0.000													3	4	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17030903	17030905	+	Intron	DEL	GAG	-	-	rs150669528		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17030903_17030905delGAG	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						AGAGATCGACGAGGAGGGGGCCT	0.640													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17051739	17051747	+	IGR	DEL	AGCTTCTGG	-	-	rs4661927		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17051739_17051747delAGCTTCTGG								ESPNP (5087 upstream) : CROCC (15021 downstream)																							CGGCTTCTGCAGCTTCTGGAGCTTCTGGG	0.694													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19387850	19387858	+	IGR	DEL	CATCATCAC	-	-	rs11267789		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19387850_19387858delCATCATCAC								IFFO2 (105024 upstream) : UBR4 (10746 downstream)																							ccaccatcatcatcatcaccaccaccacc	0.000													3	3	---	---	---	---	
KIF17	57576	broad.mit.edu	37	1	21006478	21006479	+	Intron	INS	-	GATT	GATT	rs139833555	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21006478_21006479insGATT	uc001bdr.3	-						KIF17_uc001bdp.3_Intron|KIF17_uc001bdq.3_Intron|KIF17_uc009vpx.2_Intron|KIF17_uc001bds.3_Intron	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		aatCAGAGATCGATTGATTGAT	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25301653	25301654	+	IGR	INS	-	GGAA	GGAA	rs7547501	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25301653_25301654insGGAA								RUNX3 (10041 upstream) : SYF2 (247113 downstream)																							tagaAGCAGATggaaggaagga	0.015													6	4	---	---	---	---	
PIGV	55650	broad.mit.edu	37	1	27120400	27120400	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27120400delT	uc001bmz.2	+						PIGV_uc001bmy.2_Intron|PIGV_uc009vso.2_Intron|PIGV_uc010ofg.1_Intron|PIGV_uc001bna.2_Intron	NM_017837	NP_060307	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan class V						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	glycolipid mannosyltransferase activity			ovary(1)	1		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		gtgctcagACtttttttttta	0.005													4	2	---	---	---	---	
EYA3	2140	broad.mit.edu	37	1	28357834	28357834	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28357834delT	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_Intron	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		GATCCAATGGTTTGACTCCAC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31580927	31580928	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31580927_31580928insT								PUM1 (42164 upstream) : NKAIN1 (71665 downstream)																							TTTTCATTTCCTTTTTTTTTTT	0.337													4	2	---	---	---	---	
KIAA0319L	79932	broad.mit.edu	37	1	35976509	35976510	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35976509_35976510insA	uc001byx.2	-						KIAA0319L_uc010ohw.1_Intron|KIAA0319L_uc001byz.2_Intron|KIAA0319L_uc010ohx.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)				gcgcctggcTGAAAAAAAAAAG	0.163													4	2	---	---	---	---	
RIMS3	9783	broad.mit.edu	37	1	41091998	41091999	+	3'UTR	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41091998_41091999delAC	uc001cfu.1	-	8					RIMS3_uc001cfv.1_3'UTR	NM_014747	NP_055562	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GTGGTcacgtacacacacacac	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	42589898	42589903	+	IGR	DEL	TGTGTG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42589898_42589903delTGTGTG								HIVEP3 (88302 upstream) : GUCA2B (29189 downstream)																							tgtgtgtgtatgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
KDM4A	9682	broad.mit.edu	37	1	44160187	44160187	+	Intron	DEL	A	-	-	rs71897447		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44160187delA	uc001cjx.2	+						KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						actccgtctcaaaaaaaaaaa	0.199													4	3	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49171457	49171457	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49171457delG	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)		cagaatttgaggcaaaattat	0.000													4	2	---	---	---	---	
EPS15	2060	broad.mit.edu	37	1	51905949	51905950	+	Intron	INS	-	TG	TG	rs149345524	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51905949_51905950insTG	uc001csq.1	-						EPS15_uc009vyz.1_Intron	NM_001981	NP_001972	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2						TATACATGTACtgtgtgtgtgt	0.262			T	MLL	ALL								11	5	---	---	---	---	
TTC22	55001	broad.mit.edu	37	1	55256531	55256533	+	Intron	DEL	CTT	-	-	rs71737449		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55256531_55256533delCTT	uc009vzt.1	-						TTC22_uc001cxz.3_Intron	NM_001114108	NP_001107580	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22 isoform 1								binding				0						cctcctcctcCttcttcttcttc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73032299	73032300	+	IGR	INS	-	G	G	rs142111736	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73032299_73032300insG								NEGR1 (283894 upstream) : None (None downstream)																							tgactctcagaccatcaatcac	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96834988	96834988	+	IGR	DEL	A	-	-	rs34820659		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96834988delA								None (None upstream) : PTBP2 (352187 downstream)																							actccatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	105509118	105509121	+	IGR	DEL	TCCT	-	-	rs71512598		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105509118_105509121delTCCT								None (None upstream) : None (None downstream)																							cttccttccatccttccttccttc	0.005													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121142799	121142800	+	IGR	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121142799_121142800delTG								FCGR1B (206855 upstream) : LOC647121 (118110 downstream)																							atgagatgaatgatgagatgaa	0.000													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142638168	142638168	+	Intron	DEL	C	-	-	rs137978360		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142638168delC	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		TCTGCACCCACACACACAGAC	0.348													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144009132	144009132	+	Intron	DEL	G	-	-	rs11364742		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144009132delG	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		tttttaatctgtttttttcag	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144015779	144015780	+	Intron	DEL	AC	-	-	rs57828590		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144015779_144015780delAC	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		ctccagtcctactataacaaga	0.094													5	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145054505	145054505	+	Intron	DEL	G	-	-	rs11296748		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145054505delG	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						actgaagtatgCTAGCAATAT	0.174													6	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145073411	145073412	+	Intron	INS	-	AA	AA	rs3978517		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145073411_145073412insAA	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						ctccatctctgaaaaaaaaaaa	0.114													5	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145268060	145268060	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145268060delC	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)		GTGGAATCCACCCACATTGAA	0.204													3	6	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145275507	145275508	+	Intron	INS	-	T	T	rs143422176	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									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													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	147394141	147394141	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147394141delA								GJA8 (12748 upstream) : GPR89B (6365 downstream)																							GAATTGCTTTAAAAAAAAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149059941	149059941	+	IGR	DEL	C	-	-	rs145909148	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149059941delC								LOC645166 (106887 upstream) : LOC388692 (219535 downstream)																							GTCAATGTTACCAGACTCCTC	0.502													12	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149272571	149272572	+	IGR	INS	-	CTGTC	CTGTC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149272571_149272572insCTGTC								LOC645166 (319517 upstream) : LOC388692 (6904 downstream)																							agttCTTGACTctgtcctgtcc	0.020													7	4	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153800932	153800939	+	Intron	DEL	ACACACAC	-	-	rs71677766		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153800932_153800939delACACACAC	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TCTcacacatacacacacacacacacac	0.236													5	3	---	---	---	---	
TDRD10	126668	broad.mit.edu	37	1	154492241	154492242	+	Intron	DEL	TG	-	-	rs72365002		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154492241_154492242delTG	uc009wow.2	+						TDRD10_uc001ffd.2_Intron|TDRD10_uc001ffe.2_5'Flank	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a								nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTGGTGCCTCTGTGGAGACACC	0.550													4	3	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154686602	154686603	+	Intron	INS	-	GT	GT	rs148139020		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154686602_154686603insGT	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			gtgtgtgtgggttgtgtgtgtg	0.000													4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154728252	154728253	+	Intron	DEL	GA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154728252_154728253delGA	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			ggtggaggaggagagagagagg	0.059													4	5	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154728319	154728325	+	Intron	DEL	AAGAAGG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154728319_154728325delAAGAAGG	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			aggagggggaaagaaggaagaaggaag	0.000													3	5	---	---	---	---	
PMF1	11243	broad.mit.edu	37	1	156193462	156193463	+	Intron	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156193462_156193463delCA	uc001fnq.2	+						PMF1_uc009wru.1_Intron|PMF1_uc001fnr.2_Intron|BGLAP_uc001fns.1_Intron	NM_007221	NP_009152	Q6P1K2	PMF1_HUMAN	polyamine-modulated factor 1						cell division|chromosome segregation|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytosol|MIS12/MIND type complex|transcription factor complex	leucine zipper domain binding|transcription coactivator activity				0	Hepatocellular(266;0.158)					tgtgcacgtgcacacacacaca	0.238													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158424890	158424890	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158424890delG								OR10K2 (34234 upstream) : OR10K1 (10462 downstream)																							AAAGACCCCTGGAAAAGCGTA	0.453													50	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158717184	158717184	+	IGR	DEL	A	-	-	rs11361819		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158717184delA								OR6K3 (29231 upstream) : OR6K6 (7422 downstream)																							AGACCTGAGGAAAAAAAAAAA	0.383													5	3	---	---	---	---	
ATP1A4	480	broad.mit.edu	37	1	160151346	160151346	+	Intron	DEL	A	-	-	rs113684338		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160151346delA	uc001fve.3	+						ATP1A4_uc001fvf.3_Intron|ATP1A4_uc001fvg.2_Intron|ATP1A4_uc001fvh.2_Intron	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1						ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			acttagtctcaaaaaaaaaaa	0.090													8	4	---	---	---	---	
ATP1B1	481	broad.mit.edu	37	1	169073348	169073348	+	5'Flank	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169073348delG	uc001gfs.1	+									P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					GTGATGAAGTGGTTAGATGAG	0.383													4	2	---	---	---	---	
NME7	29922	broad.mit.edu	37	1	169266214	169266215	+	Intron	INS	-	T	T	rs140621882	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169266214_169266215insT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_Intron	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					tatagtcattcttttttttttc	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172080947	172080948	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172080947_172080948insT	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						AGATGGACTCCTTTTTTTTTTT	0.327													5	3	---	---	---	---	
ABL2	27	broad.mit.edu	37	1	179187544	179187545	+	Intron	INS	-	T	T	rs147150015	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179187544_179187545insT	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	Cttttcttttctttttttgaga	0.158			T	ETV6	AML								4	4	---	---	---	---	
FAM163A	148753	broad.mit.edu	37	1	179773164	179773168	+	Intron	DEL	TCTTG	-	-	rs66979204		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179773164_179773168delTCTTG	uc009wxj.2	+						FAM163A_uc001gnj.2_Intron|FAM163A_uc009wxk.2_Intron	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753							integral to membrane				ovary(1)	1						CCAGAGCCACTCTTGTCTTGTCATG	0.580													3	3	---	---	---	---	
QSOX1	5768	broad.mit.edu	37	1	180158008	180158009	+	Intron	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180158008_180158009delCA	uc001gnz.2	+						QSOX1_uc001gny.2_Intron|QSOX1_uc001goa.2_Intron	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a						cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						TGcacacacgcacacacacaca	0.441													4	2	---	---	---	---	
ACBD6	84320	broad.mit.edu	37	1	180449414	180449415	+	Intron	INS	-	A	A	rs142206177	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180449414_180449415insA	uc001gog.2	-							NM_032360	NP_115736	Q9BR61	ACBD6_HUMAN	acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1						ggaggcattgcaacagcctagg	0.000													6	3	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180663910	180663911	+	Intron	DEL	CA	-	-	rs146171712		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180663910_180663911delCA	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						TTGTTGTGTGcacacacacaca	0.213													2	4	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181521023	181521024	+	Intron	INS	-	C	C	rs138031721	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181521023_181521024insC	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						catctttccttcccccctcctt	0.144													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181805510	181805511	+	IGR	INS	-	G	G	rs72503106		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181805510_181805511insG								CACNA1E (34797 upstream) : ZNF648 (218196 downstream)																							ggtgctggtatcatagctaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	183121353	183121354	+	IGR	INS	-	A	A	rs111811872		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183121353_183121354insA								LAMC1 (6627 upstream) : LAMC2 (33820 downstream)																							catctcaaaagaaaaaaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184067065	184067065	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184067065delA								TSEN15 (23724 upstream) : C1orf21 (289085 downstream)																							GCACagaaagaaaaaaagaag	0.338													4	2	---	---	---	---	
C1orf27	54953	broad.mit.edu	37	1	186382417	186382417	+	Intron	DEL	A	-	-	rs34199191		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186382417delA	uc001grw.2	+						C1orf27_uc010poq.1_Intron|C1orf27_uc010por.1_Intron	NM_017847	NP_060317	Q5SWX8	ODR4_HUMAN	odorant response abnormal 4 isoform 1							integral to membrane	oxidoreductase activity|zinc ion binding			ovary(1)	1						ccaaaatttgaaaaaaaaaat	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199441440	199441440	+	IGR	DEL	A	-	-	rs67505312		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199441440delA								MIR181A1 (613158 upstream) : NR5A2 (555330 downstream)																							TAGGGAAACCAAAAAAAAGGA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200833329	200833330	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200833329_200833330insA								CAMSAP1L1 (3500 upstream) : GPR25 (8836 downstream)																							TTGCTGTATGGAAAAAAAAAAA	0.252													9	4	---	---	---	---	
NAV1	89796	broad.mit.edu	37	1	201677385	201677386	+	Intron	INS	-	CT	CT	rs141310076	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201677385_201677386insCT	uc001gwu.2	+							NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						GTTGGGAGAGACTTGCATCTGT	0.525													4	3	---	---	---	---	
RPS6KC1	26750	broad.mit.edu	37	1	213257509	213257510	+	Intron	DEL	CT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213257509_213257510delCT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		cctctgtctcctctctctctcc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222464271	222464272	+	IGR	INS	-	A	A	rs150664151	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222464271_222464272insA								DUSP10 (548810 upstream) : HHIPL2 (231330 downstream)																							gaaagatgttgaaaaaAaaaat	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	225647175	225647182	+	IGR	DEL	GTGTGTGT	-	-	rs72232188		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225647175_225647182delGTGTGTGT								LBR (30656 upstream) : ENAH (27352 downstream)																							GAgtgagtgagtgtgtgtgtgtgtgtgt	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235059255	235059255	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235059255delT								IRF2BP2 (313984 upstream) : TOMM20 (213405 downstream)																							acttacctacttttttgcttc	0.000													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237323832	237323832	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237323832delT	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)			AATGTCTGGGTTTTTTTTGGT	0.348													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237401245	237401246	+	Intron	INS	-	TTTCCTTT	TTTCCTTT	rs144453604	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237401245_237401246insTTTCCTTT	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)			ctttcctttcccctttcctttc	0.000													3	5	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245343594	245343595	+	Intron	INS	-	AG	AG	rs139668358	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245343594_245343595insAG	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CTGCAGGTAGCagagagagaga	0.228													5	3	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246519436	246519437	+	Intron	INS	-	C	C	rs141022744	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246519436_246519437insC	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		tagcagtcactccccagtacca	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1601571	1601572	+	IGR	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1601571_1601572delAC								TPO (55073 upstream) : PXDN (34088 downstream)																							acacacgcaaacacacacacca	0.084													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9811654	9811654	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9811654delA								YWHAQ (40548 upstream) : TAF1B (171917 downstream)																							gacaggtctcaaaaaaaaaaa	0.090													4	3	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15574076	15574076	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15574076delA	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						aagaaaaaggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16270725	16270726	+	IGR	INS	-	AC	AC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16270725_16270726insAC								MYCN (183597 upstream) : FAM49A (463175 downstream)																							TTTatactcaaacacacacaca	0.208													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18038983	18038986	+	IGR	DEL	TTTC	-	-	rs71978119		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18038983_18038986delTTTC								MSGN1 (40617 upstream) : KCNS3 (20128 downstream)																							ccttccttcttttctttctttctc	0.000													2	4	---	---	---	---	
NCOA1	8648	broad.mit.edu	37	2	24906790	24906790	+	Intron	DEL	T	-	-	rs78050904		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24906790delT	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTTGTTACTTTTTTTCCCC	0.294			T	PAX3	alveolar rhadomyosarcoma								3	3	---	---	---	---	
ASXL2	55252	broad.mit.edu	37	2	25991449	25991449	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25991449delT	uc002rgs.2	-						ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCACACAACTTTTCCCATTT	0.184													4	2	---	---	---	---	
IFT172	26160	broad.mit.edu	37	2	27669365	27669366	+	Intron	INS	-	T	T	rs11430923		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27669365_27669366insT	uc002rku.2	-						IFT172_uc010ezb.2_Intron	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog						cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)					CTGGGTCTTAGttttttttttc	0.203													5	3	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29562109	29562109	+	Intron	DEL	A	-	-	rs138459851		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29562109delA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	actctatctcaaaaaaaaaaa	0.020			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
LCLAT1	253558	broad.mit.edu	37	2	30834455	30834455	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30834455delG	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2						TGGTGTGTATGGTAGGACCCT	0.478													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32792220	32792221	+	Intron	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32792220_32792221delAG	uc010ezu.2	+							NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					tatttttagtagagactgggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34763205	34763205	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34763205delT								MYADML (809921 upstream) : None (None downstream)																							tttgggtgccttttttttttt	0.015													3	3	---	---	---	---	
DYNC2LI1	51626	broad.mit.edu	37	2	44032038	44032038	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44032038delA	uc002rtk.2	+						DYNC2LI1_uc002rtj.2_Intron|DYNC2LI1_uc002rtl.2_Intron|DYNC2LI1_uc010ynz.1_Intron	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1							apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGTGGGGGTTAAAAAAAAAAA	0.363													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45374865	45374866	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45374865_45374866insA								SIX2 (138322 upstream) : SRBD1 (240954 downstream)																							caatagctgccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	45971134	45971134	+	Intron	DEL	T	-	-	rs66570850		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45971134delT	uc002rut.2	+						PRKCE_uc002ruu.2_Intron	NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			CCGTTGTGTGTTTTTTTTTTT	0.328													5	3	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47197649	47197649	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47197649delG	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TGCTGGACCCGGAGGTGTGGC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	50106653	50106656	+	IGR	DEL	AAAC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50106653_50106656delAAAC								FSHR (725023 upstream) : NRXN1 (38988 downstream)																							gtctcccacaaaacAAACAAACAA	0.088													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	52456993	52456994	+	IGR	DEL	AC	-	-	rs71822126		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52456993_52456994delAC								None (None upstream) : None (None downstream)																							Gcacacacgaacacacacacac	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57342646	57342649	+	IGR	DEL	TCTC	-	-	rs10567386		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57342646_57342649delTCTC								CCDC85A (729338 upstream) : VRK2 (792137 downstream)																							CCAGGCAATGtctctctctctctc	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59407911	59407912	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59407911_59407912insT								FANCL (939396 upstream) : None (None downstream)																							ATCAAAGAGTGTTTTTTTTTTC	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60218700	60218702	+	IGR	DEL	TTC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60218700_60218702delTTC								None (None upstream) : BCL11A (459601 downstream)																							ACATCCATGTTTCTTCTTCTTCT	0.266													4	2	---	---	---	---	
EHBP1	23301	broad.mit.edu	37	2	62966524	62966524	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62966524delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron|EHBP1_uc002sca.2_Intron	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TGATAGATTCTTTTTTTTTTT	0.348									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
EHBP1	23301	broad.mit.edu	37	2	63202058	63202058	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63202058delA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ttagtgacgtaaaaaaaaaat	0.100									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67923880	67923881	+	IGR	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67923880_67923881delAG								ETAA1 (286347 upstream) : C1D (345452 downstream)																							TCTTTATgaaagagagagagag	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70596757	70596758	+	IGR	INS	-	T	T	rs112111612		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70596757_70596758insT								FAM136A (67537 upstream) : TGFA (77661 downstream)																							GAACCACACTCttttttttttg	0.045													4	2	---	---	---	---	
SFXN5	94097	broad.mit.edu	37	2	73179097	73179098	+	Intron	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73179097_73179098delAC	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron|SFXN5_uc010fer.2_Intron|SFXN5_uc010feq.2_Intron|SFXN5_uc010fes.2_Intron	NM_144579	NP_653180	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1						TCCTGTTCCGACACACACACAT	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	77817012	77817013	+	IGR	DEL	AA	-	-	rs112087231		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77817012_77817013delAA								LRRTM4 (67510 upstream) : SNAR-H (365020 downstream)																							aaatcacaggaaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78272868	78272868	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78272868delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																		ctgatgtgataaaaaagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81708706	81708706	+	IGR	DEL	G	-	-	rs113256355		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81708706delG								CTNNA2 (832802 upstream) : None (None downstream)																							cccaagtggtggggggatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82877220	82877220	+	IGR	DEL	A	-	-	rs71787397		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82877220delA								None (None upstream) : None (None downstream)																							ACCCTACCACAAAAAAAAAAA	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83042811	83042814	+	IGR	DEL	GAAC	-	-	rs144406937		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83042811_83042814delGAAC								None (None upstream) : None (None downstream)																							TTGGTCTTAGGAACGAACCAAAAG	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83221199	83221200	+	IGR	INS	-	A	A	rs145815314	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83221199_83221200insA								None (None upstream) : None (None downstream)																							ACTAAATAAGGAAGACATAATA	0.287													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83755723	83755723	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83755723delA								None (None upstream) : FUNDC2P2 (762083 downstream)																							ATATGTGTGGAATTTGTGATC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84618407	84618408	+	IGR	INS	-	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84618407_84618408insC								FUNDC2P2 (99083 upstream) : SUCLG1 (32246 downstream)																							tcccaacatagcccccccataa	0.084													4	4	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87586644	87586645	+	Intron	DEL	TT	-	-	rs55885523		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87586644_87586645delTT	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						ataagatgacttgagatgagat	0.114													5	3	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87614184	87614185	+	Intron	INS	-	T	T	rs143929453		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87614184_87614185insT	uc002srs.3	+						uc002ssi.1_5'Flank			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						CTCtctctctcttttttttttt	0.188													3	3	---	---	---	---	
FABP1	2168	broad.mit.edu	37	2	88425487	88425487	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88425487delC	uc002sst.1	-						FABP1_uc002ssu.2_Intron	NM_001443	NP_001434	P07148	FABPL_HUMAN	fatty acid binding protein 1, liver						organ morphogenesis						0						GGCTGGAACACCCCCCAGACA	0.537													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89874095	89874104	+	IGR	DEL	AATGGAATGG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89874095_89874104delAATGGAATGG								FLJ40330 (767970 upstream) : None (None downstream)																							agtggaatgaaatggaatggaatggaatgg	0.052													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90469497	90469498	+	IGR	INS	-	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90469497_90469498insG								None (None upstream) : None (None downstream)																							ggttttaccacttggtcaggct	0.005													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91783492	91783495	+	IGR	DEL	AAAT	-	-	rs72069239		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91783492_91783495delAAAT								None (None upstream) : LOC654342 (21697 downstream)																							aataaaacacaaataaaGTAAGTA	0.044													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96610787	96610788	+	5'Flank	INS	-	A	A	rs148448972	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96610787_96610788insA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		actctgtctacaaaaaataaga	0.104													5	3	---	---	---	---	
VWA3B	200403	broad.mit.edu	37	2	98831386	98831386	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98831386delC	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron|VWA3B_uc002syp.1_Intron|VWA3B_uc002syq.1_Intron|VWA3B_uc002syr.1_Intron	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6						attgatactgccgaatagcag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102658816	102658816	+	IGR	DEL	A	-	-	rs66625952		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102658816delA								IL1R2 (13936 upstream) : IL1R1 (28020 downstream)																							agaaggaaggaaaaaaagaga	0.010													3	4	---	---	---	---	
IL1R1	3554	broad.mit.edu	37	2	102727562	102727563	+	Intron	DEL	AG	-	-	rs67388579		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102727562_102727563delAG	uc010fix.2	+							NM_000877	NP_000868	P14778	IL1R1_HUMAN	interleukin 1 receptor, type I precursor						innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity|platelet-derived growth factor receptor binding			skin(1)	1					Anakinra(DB00026)	AGCTGGAGACAGAGGCAGAGGC	0.515													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103827445	103827445	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103827445delT								TMEM182 (393309 upstream) : None (None downstream)																							cttcttcttcttttttttttt	0.383													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105629707	105629708	+	IGR	INS	-	TGTG	TGTG	rs139333211	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105629707_105629708insTGTG								POU3F3 (156237 upstream) : MRPS9 (24775 downstream)																							tttgtttcttttgtgtgtgtgt	0.000													6	3	---	---	---	---	
NCK2	8440	broad.mit.edu	37	2	106372802	106372802	+	Intron	DEL	C	-	-	rs72514153		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106372802delC	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						ATCAATCTTTCCCTTTCTTCA	0.368													2	4	---	---	---	---	
UXS1	80146	broad.mit.edu	37	2	106768908	106768908	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106768908delA	uc002tdm.2	-						UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						gaaagaaaagaaagaaaagaa	0.000													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109904486	109904487	+	Intron	DEL	GC	-	-	rs10551598		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109904486_109904487delGC	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						TTGGCTGACTGCCACCAGCAGG	0.460													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112456962	112456963	+	IGR	INS	-	AC	AC	rs144474494	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112456962_112456963insAC								LOC541471 (204270 upstream) : ANAPC1 (69678 downstream)																							CAAAACATGATacacacacaca	0.366													3	3	---	---	---	---	
MERTK	10461	broad.mit.edu	37	2	112781478	112781479	+	Intron	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112781478_112781479delAC	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						acacacacagacacacacacac	0.520													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113103992	113103992	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113103992delC								ZC3H6 (6352 upstream) : RGPD8 (21974 downstream)																							tcaccaccatcaccactgcca	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113235666	113235666	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113235666delG								RGPD8 (43604 upstream) : TTL (4077 downstream)																							GGATTATTTTGGGCTGTTCCA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114298849	114298850	+	Intron	INS	-	AC	AC	rs2024702		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114298849_114298850insAC	uc002tjx.3	-											Homo sapiens chromosome 2 mRNA sequence.																		AGGGTacacagacacacacaca	0.495													4	2	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116031664	116031665	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116031664_116031665delTG	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						CAGAATtgtttgtgtgtgtgtg	0.332													4	2	---	---	---	---	
PTPN18	26469	broad.mit.edu	37	2	131127130	131127131	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131127130_131127131delTG	uc002trc.2	+						PTPN18_uc002trd.2_Intron|PTPN18_uc002trb.2_Intron|PTPN18_uc002tre.2_5'Flank	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)					CAAAAGGGCTTGTGTTTTTATA	0.317													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134503402	134503402	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134503402delG								NCKAP5 (177371 upstream) : MGAT5 (508428 downstream)																							AAAGCACCTTGGAATTTCCAA	0.433													4	2	---	---	---	---	
ZRANB3	84083	broad.mit.edu	37	2	136046444	136046445	+	Intron	DEL	GT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136046444_136046445delGT	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		ttcatttatcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	153898929	153898929	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153898929delA								ARL6IP6 (281162 upstream) : RPRM (434923 downstream)																							aacgaaaaacaaaaaAaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170242715	170242715	+	IGR	DEL	A	-	-	rs78007740		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170242715delA								LRP2 (23593 upstream) : BBS5 (93291 downstream)																							accttgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
PLEKHA3	65977	broad.mit.edu	37	2	179352846	179352846	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179352846delA	uc002umn.2	+							NM_019091	NP_061964	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			cacaaaaaggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181526007	181526007	+	IGR	DEL	C	-	-	rs113667671		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181526007delC								CWC22 (654167 upstream) : UBE2E3 (319105 downstream)																							ttttttttttcccgcatgtga	0.070													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187386725	187386725	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187386725delC								ZC3H15 (12640 upstream) : ITGAV (68065 downstream)																							tcctgctcatcccctgggcaa	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	188731163	188731163	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188731163delT								TFPI (311944 upstream) : GULP1 (425441 downstream)																							ggagCTGGTGTTTTTTTGGTT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195038069	195038069	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195038069delA								None (None upstream) : None (None downstream)																							ATTTAGCAAGAAGACTGAGGA	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195452430	195452433	+	IGR	DEL	AAAG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195452430_195452433delAAAG								None (None upstream) : None (None downstream)																							TCCTCTGTGAAaagaaagaaagaa	0.152													4	2	---	---	---	---	
SF3B1	23451	broad.mit.edu	37	2	198294508	198294508	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198294508delA	uc002uue.2	-						SF3B1_uc010fsk.1_Intron|SF3B1_uc002uuf.2_Intron|SF3B1_uc002uug.2_Intron	NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)			actctgtctcaaaaaaaaaaa	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201622972	201622973	+	IGR	INS	-	A	A	rs148425887	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201622972_201622973insA								AOX1 (86757 upstream) : AOX2P (12422 downstream)																							atatcactcagaaaaatgcatt	0.119													1	6	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202693164	202693164	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202693164delA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	agagcatctgaaaaaaaaata	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204908916	204908916	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204908916delT								ICOS (82620 upstream) : PARD3B (501600 downstream)																							cggccCCAAATTTTTCTATCC	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	214089371	214089372	+	IGR	DEL	AC	-	-	rs62186590		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214089371_214089372delAC								IKZF2 (73038 upstream) : SPAG16 (59744 downstream)																							CTATTACAAAacacacacacac	0.337													4	4	---	---	---	---	
VWC2L	402117	broad.mit.edu	37	2	215340470	215340470	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215340470delA	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing							extracellular region					0						atgttggcTCAAAAAAAAAAA	0.129													3	3	---	---	---	---	
XRCC5	7520	broad.mit.edu	37	2	216985464	216985465	+	Intron	INS	-	TTGT	TTGT	rs143533309	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216985464_216985465insTTGT	uc002vfy.2	+						XRCC5_uc002vfz.2_Intron	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II						double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		tttcttggttgttgtttgtttt	0.005								Direct_reversal_of_damage|NHEJ					4	2	---	---	---	---	
DIRC3	729582	broad.mit.edu	37	2	218422608	218422608	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218422608delA	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0						gagagacctcaagtccaaaat	0.085													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218781314	218781314	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218781314delC	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron|TNS1_uc010fvk.1_Intron|TNS1_uc002vgv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CTCCATCCTGCCCCACCAGTG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220294782	220294783	+	IGR	INS	-	G	G	rs149129498	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220294782_220294783insG								DES (3323 upstream) : SPEG (4917 downstream)																							GACTCTGAACATCAAGAAGTAA	0.421													1	5	---	---	---	---	
ALPI	248	broad.mit.edu	37	2	233318520	233318521	+	5'Flank	INS	-	T	T	rs34466943		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233318520_233318521insT	uc002vst.3	+						ALPI_uc002vsu.3_5'Flank	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor						phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding			central_nervous_system(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GTACTTTCttcttttttttttt	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235613578	235613579	+	IGR	DEL	GA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235613578_235613579delGA								ARL4C (207885 upstream) : SH3BP4 (247049 downstream)																							GCTTCTTATTGAGAGTACATGT	0.406													2	4	---	---	---	---	
ASB18	401036	broad.mit.edu	37	2	237129513	237129513	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237129513delG	uc010znh.1	-							NM_212556	NP_997721	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box-containing 18						intracellular signal transduction					ovary(1)	1		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		CTCCTTTCGAGGTAAGGAGAA	0.403													4	2	---	---	---	---	
KIF1A	547	broad.mit.edu	37	2	241724234	241724234	+	Intron	DEL	G	-	-	rs113212728		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241724234delG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CCTCTGGGGCGGGGGGGGGGA	0.657													4	5	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2581753	2581754	+	Intron	INS	-	TG	TG	rs139806071	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2581753_2581754insTG	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TTCATCAgtgttgtgtgtgtgt	0.243													2	5	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4715262	4715273	+	Intron	DEL	TTTGTTTGTTTG	-	-	rs112871347		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4715262_4715273delTTTGTTTGTTTG	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		GTTTTTGGTTtttgtttgtttgtttgtttgtt	0.137													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	16584923	16584923	+	IGR	DEL	T	-	-	rs35555538		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16584923delT								RFTN1 (29701 upstream) : DAZL (43380 downstream)																							caatgtgttattttttttttt	0.035													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	38849741	38849742	+	IGR	DEL	TC	-	-	rs145676891		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38849741_38849742delTC								SCN10A (14240 upstream) : SCN11A (37518 downstream)																							catgcttttttctctctctctc	0.000													3	3	---	---	---	---	
CCDC13	152206	broad.mit.edu	37	3	42807704	42807704	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42807704delT	uc003cly.3	-						CCDC13_uc003clz.2_Intron|CCDC13_uc011azq.1_Intron	NM_144719	NP_653320	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13											ovary(1)	1						GGTGGTGGACTTTGAGATGCT	0.587													4	2	---	---	---	---	
SETD2	29072	broad.mit.edu	37	3	47145234	47145235	+	Intron	INS	-	CA	CA	rs140513890	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47145234_47145235insCA	uc003cqs.2	-						SETD2_uc003cqv.2_Intron	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		Gcacacgcacgcacacacacac	0.312			N|F|S|Mis		clear cell renal carcinoma								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	47409615	47409618	+	IGR	DEL	TCTC	-	-	rs4858824		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47409615_47409618delTCTC								KLHL18 (21310 upstream) : PTPN23 (12873 downstream)																							CAGAACACTTTCtctttctttctt	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	47591575	47591576	+	IGR	INS	-	TT	TT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47591575_47591576insTT								C3orf75 (36376 upstream) : CSPG5 (12153 downstream)																							tctccttcttcttcttcttctt	0.020													4	2	---	---	---	---	
ARIH2	10425	broad.mit.edu	37	3	49007326	49007326	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49007326delT	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_Intron|ARIH2_uc010hkl.2_Intron	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		CAGATATATGttttttttttt	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	50692829	50692830	+	IGR	DEL	CT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50692829_50692830delCT								MAPKAPK3 (6110 upstream) : DOCK3 (19842 downstream)																							CCCTTGAGGCCTCTCTCTCTCT	0.574													3	3	---	---	---	---	
CADPS	8618	broad.mit.edu	37	3	62741733	62741733	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62741733delT	uc003dll.2	-						CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		tttctttttcttttttttttt	0.000													4	2	---	---	---	---	
FAM19A1	407738	broad.mit.edu	37	3	68371904	68371904	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68371904delC	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		accagcctggccaacatggtg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72231720	72231721	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72231720_72231721insA								PROK2 (397363 upstream) : RYBP (192030 downstream)																							AGAATAGCTTTAAAAAAAAAAA	0.248													4	3	---	---	---	---	
ROBO2	6092	broad.mit.edu	37	3	77385666	77385667	+	Intron	DEL	TT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77385666_77385667delTT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ttcctctttctTTTTTTTTTTC	0.198													4	2	---	---	---	---	
CD96	10225	broad.mit.edu	37	3	111376261	111376262	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111376261_111376262insA	uc010hpy.1	+							NM_005816	NP_005807	P40200	TACT_HUMAN	CD96 antigen isoform 2 precursor						cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3						gactccatttcaaaaaaaaaaa	0.178									Opitz_Trigonocephaly_syndrome				3	3	---	---	---	---	
SLC9A10	285335	broad.mit.edu	37	3	111863538	111863539	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111863538_111863539delTG	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						tcctaaggtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112495916	112495917	+	IGR	INS	-	AG	AG	rs138852890	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112495916_112495917insAG								CCDC80 (135939 upstream) : CD200R1L (38639 downstream)																							CAGCTGGCTCAAGAGAGAGAGA	0.520													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115331018	115331018	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115331018delT								ZBTB20 (464891 upstream) : GAP43 (11133 downstream)																							gctagtgccctagacaacaaa	0.000													4	2	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115590463	115590466	+	Intron	DEL	TGTA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115590463_115590466delTGTA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		tgtgtgtgtgtgtAagagagacag	0.221													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116582869	116582869	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116582869delT								LOC285194 (146984 upstream) : None (None downstream)																							CCTGAAAAGGTTTTTTTTTTT	0.403													4	2	---	---	---	---	
FBXO40	51725	broad.mit.edu	37	3	121324703	121324703	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121324703delG	uc003eeg.2	+							NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40						muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)		gtccctgtgtgggggatatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122782383	122782384	+	IGR	DEL	TC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122782383_122782384delTC								SEMA5B (34931 upstream) : PDIA5 (3581 downstream)																							aggagtttgttctctctctctc	0.000													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124208304	124208304	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124208304delG	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						ACACCACCTTGGGAGACTTGA	0.473													4	2	---	---	---	---	
SLC12A8	84561	broad.mit.edu	37	3	124803094	124803095	+	Intron	INS	-	AG	AG	rs149355481	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124803094_124803095insAG	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc003eht.3_Intron|SLC12A8_uc003ehu.3_Intron|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0						ATAAAATAAAAAGAGACAGAGA	0.312													2	4	---	---	---	---	
KBTBD12	166348	broad.mit.edu	37	3	127687631	127687631	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127687631delA	uc010hsr.2	+						KBTBD12_uc003ejy.3_Intron|KBTBD12_uc010hsq.2_Intron|KBTBD12_uc003eka.3_Intron	NM_207335	NP_997218	Q3ZCT8	KBTBC_HUMAN	kelch domain containing 6											ovary(1)	1						aagttgaaggaaaaaaaaaag	0.000													4	2	---	---	---	---	
RHO	6010	broad.mit.edu	37	3	129252686	129252686	+	3'UTR	DEL	T	-	-	rs71811187		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129252686delT	uc003emt.2	+	5						NM_000539	NP_000530	P08100	OPSD_HUMAN	rhodopsin						protein-chromophore linkage|rhodopsin mediated signaling pathway	Golgi apparatus|integral to plasma membrane|photoreceptor inner segment membrane|photoreceptor outer segment membrane	G-protein coupled receptor activity|metal ion binding|photoreceptor activity|protein binding				0		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	GGCTCCttaattttttttttt	0.493													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129626087	129626088	+	RNA	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129626087_129626088delTG	uc003enb.1	+	3		c.1828_1829delTG								Homo sapiens cDNA FLJ45897 fis, clone OCBBF3025131.																		tctatagttctgtgtgtgtgtg	0.005													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131880834	131880834	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131880834delG	uc003eom.2	-							NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						tatggaaaatggactctctta	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137379274	137379274	+	IGR	DEL	A	-	-	rs66553049		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137379274delA								IL20RB (649354 upstream) : SOX14 (104305 downstream)																							aaagtctaataaaaaaaaaaa	0.139													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137420133	137420134	+	IGR	INS	-	GT	GT	rs72120885		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137420133_137420134insGT								IL20RB (690213 upstream) : SOX14 (63445 downstream)																							AGGGGGGGCACgtgtgtgtgtg	0.262													4	4	---	---	---	---	
MRPS22	56945	broad.mit.edu	37	3	139071669	139071669	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139071669delT	uc003etb.2	+						MRPS22_uc003etc.2_Intron|MRPS22_uc003etd.2_Intron|MRPS22_uc003ete.2_Intron	NM_020191	NP_064576	P82650	RT22_HUMAN	mitochondrial ribosomal protein S22							mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome			ovary(2)|skin(1)	3						AGAATCATTCTTATTGCTCTA	0.333													20	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139212618	139212620	+	IGR	DEL	CTC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139212618_139212620delCTC								RBP2 (17266 upstream) : RBP1 (23656 downstream)																							GGACTCTGTTCTCCCACCACTCT	0.433													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140884176	140884177	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140884176_140884177insT								SPSB4 (16724 upstream) : ACPL2 (66505 downstream)																							AAAAATCAGTCTTTTTTTTTCT	0.332													4	2	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141081497	141081498	+	Intron	INS	-	A	A	rs145584360	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141081497_141081498insA	uc003etw.2	+							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						GAACTGGACAGAGCGGAAGGAC	0.465													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141566606	141566606	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141566606delA								GRK7 (30716 upstream) : ATP1B3 (28864 downstream)																							ATCAGGGTTTAAAAAAAAAAA	0.363													4	2	---	---	---	---	
TFDP2	7029	broad.mit.edu	37	3	141697191	141697192	+	Intron	DEL	AC	-	-	rs147134052	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141697191_141697192delAC	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						cgcctaaaaaacaaaaaaaaaG	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145374460	145374460	+	IGR	DEL	T	-	-	rs151265228		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145374460delT								None (None upstream) : PLOD2 (412768 downstream)																							ttttttcttcttttttttcct	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	153108889	153108892	+	IGR	DEL	AGAT	-	-	rs57191684		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153108889_153108892delAGAT								RAP2B (222628 upstream) : C3orf79 (93392 downstream)																							atatggtaagagataggggtctag	0.000													3	3	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155359615	155359615	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155359615delA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTAAAACCTCAAAAAAAACCC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159881113	159881114	+	Intron	DEL	GA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159881113_159881114delGA	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		CTGTGTAGGTGAGAGAGAGAGA	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163139799	163139800	+	IGR	DEL	CA	-	-	rs62980260		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163139799_163139800delCA								None (None upstream) : MIR1263 (749459 downstream)																							tgtgtgtgtgcatgtgtgtgtg	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166452447	166452448	+	IGR	INS	-	A	A	rs147130621	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166452447_166452448insA								BCHE (897194 upstream) : ZBBX (505633 downstream)																							tgcctgaagggaaaaaaattcc	0.000													5	3	---	---	---	---	
ZBBX	79740	broad.mit.edu	37	3	167066050	167066057	+	Intron	DEL	GGAAGGAA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167066050_167066057delGGAAGGAA	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2						agggtggaagggaaggaaggaaggaagg	0.000													4	2	---	---	---	---	
PDCD10	11235	broad.mit.edu	37	3	167413770	167413770	+	Intron	DEL	A	-	-	rs11332538		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167413770delA	uc003fex.2	-						PDCD10_uc003fez.2_Intron|PDCD10_uc003fey.2_Intron	NM_007217	NP_009148	Q9BUL8	PDC10_HUMAN	programmed cell death 10						angiogenesis|apoptosis|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of MAP kinase activity	cytosol|Golgi membrane|plasma membrane	protein homodimerization activity|protein N-terminus binding			lung(1)|central_nervous_system(1)	2						ATGAAATCTTAAAAAAAAAAA	0.313									Familial_Cerebral_Cavernous_Angioma				4	2	---	---	---	---	
GOLIM4	27333	broad.mit.edu	37	3	167771619	167771619	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167771619delA	uc003ffe.2	-						GOLIM4_uc011bpe.1_Intron|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						CTTCTTCCATAATTTTACCTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167932482	167932482	+	IGR	DEL	T	-	-	rs111438851		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167932482delT								GOLIM4 (119065 upstream) : MIR551B (337160 downstream)																							ttttcttttgttttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168750644	168750645	+	IGR	DEL	TC	-	-	rs138868569		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168750644_168750645delTC								C3orf50 (202272 upstream) : MECOM (50642 downstream)																							CTATTCTACATCTCTCTCAAAT	0.396													4	2	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169846304	169846305	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169846304_169846305insT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AAACAATGGCATTTTTTTTTTT	0.307													3	3	---	---	---	---	
TNFSF10	8743	broad.mit.edu	37	3	172239871	172239872	+	Intron	INS	-	A	A	rs141884526	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172239871_172239872insA	uc003fid.2	-						TNFSF10_uc003fie.2_Intron|TNFSF10_uc010hwu.1_Intron	NM_003810	NP_003801	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily,						activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction	extracellular space|integral to plasma membrane|soluble fraction	cytokine activity|metal ion binding|tumor necrosis factor receptor binding			skin(4)|lung(1)	5	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			ttagaacaaatcctaatgcctg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176064201	176064202	+	IGR	INS	-	TG	TG	rs150808306	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176064201_176064202insTG								NAALADL2 (540775 upstream) : TBL1XR1 (674341 downstream)																							atgcatatgtatgtgtgtgtgt	0.045													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180135472	180135473	+	IGR	INS	-	TA	TA	rs149274216	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180135472_180135473insTA								PEX5L (380955 upstream) : TTC14 (184445 downstream)																							gtgtgtgtgtgtatatatatat	0.208													1	7	---	---	---	---	
KLHL6	89857	broad.mit.edu	37	3	183260453	183260453	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183260453delC	uc003flr.2	-						KLHL6_uc003fls.1_Intron|KLHL6_uc003flt.1_Intron	NM_130446	NP_569713	Q8WZ60	KLHL6_HUMAN	kelch-like 6											haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			cccagctccaccataacccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183808740	183808741	+	IGR	INS	-	T	T	rs58093899		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183808740_183808741insT								HTR3C (30281 upstream) : HTR3E (6111 downstream)																							ccaataatgtcttttttttttt	0.000													4	3	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184528527	184528527	+	5'Flank	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184528527delT	uc003fpb.1	+						VPS8_uc010hyd.1_5'Flank	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			gaaatgtatcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187272893	187272894	+	IGR	INS	-	TCCTT	TCCTT	rs139252944	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187272893_187272894insTCCTT								RTP4 (183526 upstream) : SST (113802 downstream)																							tttccatcctctctcagcccca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187593253	187593253	+	IGR	DEL	T	-	-	rs113864435		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187593253delT								BCL6 (129778 upstream) : LPP (278466 downstream)																							gactggctaattttttttttt	0.000													3	3	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188493722	188493722	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188493722delA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTTCCTTGGGAAAAGTGAGTG	0.299			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
TPRG1	285386	broad.mit.edu	37	3	188953006	188953007	+	Intron	INS	-	TTT	TTT	rs34934049		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188953006_188953007insTTT	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		atgaggtttgcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189166845	189166845	+	IGR	DEL	A	-	-	rs149085723		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189166845delA								TPRG1 (125575 upstream) : TP63 (182371 downstream)																							attttaacggaaaaaaaaaaa	0.085													4	2	---	---	---	---	
CLDN1	9076	broad.mit.edu	37	3	190040792	190040793	+	5'Flank	INS	-	AC	AC	rs147722582	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190040792_190040793insAC	uc003fsh.2	-							NM_021101	NP_066924	O95832	CLD1_HUMAN	claudin 1						calcium-independent cell-cell adhesion|interspecies interaction between organisms	integral to plasma membrane|tight junction	identical protein binding|structural molecule activity			lung(1)	1	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		CAACATGATTTacacacacaca	0.376											OREG0015986	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
TMEM207	131920	broad.mit.edu	37	3	190164296	190164297	+	Intron	INS	-	T	T	rs142554681	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190164296_190164297insT	uc003fsj.2	-							NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		TTGAGGGTTAATTTTTTTTTGT	0.317													3	3	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	191879294	191879295	+	Intron	INS	-	AC	AC	rs141765558	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191879294_191879295insAC	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)		AACGCCTATTTacacacacaca	0.153													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194546438	194546440	+	IGR	DEL	TGG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194546438_194546440delTGG								FAM43A (136674 upstream) : C3orf21 (242575 downstream)																							TACCCTGCCTTGGTGTCTCTGTG	0.596													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194604031	194604032	+	IGR	INS	-	C	C	rs143224022	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194604031_194604032insC								FAM43A (194267 upstream) : C3orf21 (184983 downstream)																							TTTTTTCTCCTTGCCAAAACCT	0.475													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194645745	194645746	+	IGR	INS	-	G	G	rs140858617	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194645745_194645746insG								FAM43A (235981 upstream) : C3orf21 (143269 downstream)																							tctttgtctctattcatctgcc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195439719	195439720	+	IGR	INS	-	CT	CT	rs63098860		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195439719_195439720insCT								MIR570 (13351 upstream) : MUC20 (8033 downstream)																							tcctgccctaactcctccctga	0.144													6	3	---	---	---	---	
TFRC	7037	broad.mit.edu	37	3	195792272	195792273	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195792272_195792273insA	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		GAAAAGAAAACAAAAAAAAAgc	0.322			T	BCL6	NHL								11	5	---	---	---	---	
DLG1	1739	broad.mit.edu	37	3	196776198	196776199	+	Intron	INS	-	A	A	rs139661147	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196776198_196776199insA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		aacaaaacaataaaaaacaaaa	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10077	10078	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10077_10078insT								None (None upstream) : ZNF595 (43149 downstream)																							aaccctaaccctaaccctaacc	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49345	49345	+	IGR	DEL	T	-	-	rs56012841		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49345delT								None (None upstream) : ZNF595 (3882 downstream)																							TAAATGCAGGTGATGTGGCCA	0.338													6	4	---	---	---	---	
ABCA11P	79963	broad.mit.edu	37	4	421775	421775	+	Intron	DEL	T	-	-	rs112212990		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:421775delT	uc003gae.2	-						ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc010ibd.1_Intron					RecName: Full=Putative ATP-binding cassette sub-family A member 11;												0						tgttgccACATTTTTTTTATA	0.075													8	5	---	---	---	---	
ABLIM2	84448	broad.mit.edu	37	4	7993011	7993011	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7993011delC	uc003gko.2	-						ABLIM2_uc003gkk.2_Intron|ABLIM2_uc003gkl.2_Intron|ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron	NM_001130084	NP_001123556	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2						axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3						GGATGCACAGCCCAGGCGTCA	0.498													4	2	---	---	---	---	
LCORL	254251	broad.mit.edu	37	4	17885296	17885297	+	Intron	INS	-	AC	AC	rs139656197	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17885296_17885297insAC	uc003gpq.2	-						LCORL_uc011bxk.1_Intron	NM_153686	NP_710153	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						cacacacgcaaacacacacaca	0.262													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19498731	19498732	+	IGR	DEL	CT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19498731_19498732delCT								None (None upstream) : SLIT2 (756503 downstream)																							cctcttcttgctctctctctct	0.000													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21424282	21424283	+	Intron	INS	-	TG	TG	rs140015102	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21424282_21424283insTG	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				Atgtgtgtgtttgtgtgtgtgt	0.327													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	30575103	30575104	+	IGR	INS	-	A	A	rs147136425	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30575103_30575104insA								None (None upstream) : PCDH7 (146933 downstream)																							AGAGTTTTAGGAAAAAAAATAT	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49216162	49216163	+	IGR	DEL	AC	-	-	rs112633743		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49216162_49216163delAC								CWH43 (152069 upstream) : None (None downstream)																							GTCCATCCAGACACCTGCTTTG	0.574													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49644568	49644569	+	IGR	INS	-	AA	AA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49644568_49644569insAA								CWH43 (580475 upstream) : None (None downstream)																							caatggaatggaaaaatccgag	0.000													3	5	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54479336	54479336	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54479336delA	uc003haa.2	+						LNX1_uc003hah.3_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GCACCAAGCCAAAAAAGGAAA	0.353			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	66084343	66084344	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66084343_66084344insA								TECRL (809165 upstream) : EPHA5 (100938 downstream)																							aagagtccgccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69148415	69148415	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69148415delT								TMPRSS11B (37003 upstream) : YTHDC1 (27691 downstream)																							TTTAGCAAGATTACTAATTGT	0.353													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79173072	79173073	+	Intron	INS	-	GA	GA	rs139128945	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79173072_79173073insGA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_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						CTGGAACAGTTgagagagagag	0.396													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80519946	80519947	+	IGR	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80519946_80519947delAC								GK2 (190574 upstream) : GDEP (228678 downstream)																							TTGGTGTGAAACACACACACAC	0.470													6	3	---	---	---	---	
GDEP	118425	broad.mit.edu	37	4	80769183	80769183	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80769183delT	uc003hlw.3	+							NR_026555				Homo sapiens GDEP mRNA, complete cds.												0						ccgATTCTAGTTTTTttggtg	0.010													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81307667	81307668	+	Intron	DEL	GG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81307667_81307668delGG	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						GGGCGGTGGTGGGGGGGGGGGG	0.678													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109101854	109101856	+	IGR	DEL	AAA	-	-	rs148060811		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109101854_109101856delAAA								LEF1 (12276 upstream) : LOC285456 (357490 downstream)																							aggaaaagagaaaaagaaaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	114765396	114765397	+	IGR	INS	-	GAG	GAG	rs147090705	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114765396_114765397insGAG								CAMK2D (82313 upstream) : ARSJ (56043 downstream)																							atagtgaagcagaggaggaggg	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126635554	126635555	+	IGR	DEL	TC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126635554_126635555delTC								MIR2054 (207092 upstream) : None (None downstream)																							TGACTTCAGAtctctctctctc	0.307													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128018840	128018841	+	IGR	DEL	GT	-	-	rs138254190		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128018840_128018841delGT								None (None upstream) : INTU (535279 downstream)																							ATGCGTGCACgtgtgtgtgtgt	0.282													4	4	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143474386	143474387	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143474386_143474387insA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					ttccaataaacaatattaacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	143833355	143833355	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143833355delA								INPP4B (65751 upstream) : USP38 (272715 downstream)																							TCCTGTGAATAAGAACACCGC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152709545	152709546	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152709545_152709546insA								PET112L (27399 upstream) : FBXW7 (532865 downstream)																							tttcttggttcaAAAAAAAAAC	0.168													4	2	---	---	---	---	
DCHS2	54798	broad.mit.edu	37	4	155190927	155190928	+	Intron	INS	-	A	A	rs142509761	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155190927_155190928insA	uc003inw.2	-							NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TAGGCTAGCTTAAAAAATTCTT	0.262													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174410661	174410662	+	IGR	INS	-	T	T	rs34038659		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174410661_174410662insT								SCRG1 (83133 upstream) : HAND2 (36990 downstream)																							TGCGTTTCTAATTTTTTTTTTT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185901002	185901003	+	IGR	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185901002_185901003delAG								ACSL1 (153787 upstream) : HELT (38992 downstream)																							ggagagagaaagagagagagag	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189886098	189886101	+	IGR	DEL	TTTG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189886098_189886101delTTTG								TRIML1 (817449 upstream) : FRG1 (975873 downstream)																							gatgggcttttttgtttgtttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190488619	190488619	+	IGR	DEL	T	-	-	rs71756780		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190488619delT								None (None upstream) : FRG1 (373355 downstream)																							TCTTTCCATCTTTTTTTTTTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190586436	190586437	+	IGR	INS	-	G	G	rs151044185		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190586436_190586437insG								None (None upstream) : FRG1 (275537 downstream)																							ccgctagggctccagcacattg	0.139													4	3	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190884023	190884023	+	Intron	DEL	A	-	-	rs113976741		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190884023delA	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATTTGGATTGAAAAAGCCCTT	0.254													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	754177	754177	+	IGR	DEL	A	-	-	rs111285360		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:754177delA								TPPP (60667 upstream) : ZDHHC11 (41543 downstream)																							CAGGGGAAACAACCTCTCGTT	0.577													3	3	---	---	---	---	
TRIP13	9319	broad.mit.edu	37	5	901716	901717	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:901716_901717insT	uc003jbr.2	+						TRIP13_uc010ite.1_Intron	NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13						double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CACTTGGGACAttttttgtttg	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1041455	1041456	+	IGR	INS	-	TGAA	TGAA	rs58433103		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1041455_1041456insTGAA								NKD2 (2530 upstream) : SLC12A7 (9035 downstream)																							caatgagtgagtgacagtgatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7931380	7931380	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7931380delT								MTRR (30147 upstream) : None (None downstream)																							CTCTGGTGCCTTTGATTTTAT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	11932515	11932516	+	IGR	DEL	TC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11932515_11932516delTC								CTNND2 (28405 upstream) : None (None downstream)																							tttctctgcttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17123650	17123651	+	IGR	INS	-	T	T	rs75248417		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17123650_17123651insT								MYO10 (187265 upstream) : LOC285696 (6486 downstream)																							ACATGAACTTCTTTTTTTTTTT	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23371970	23371971	+	IGR	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23371970_23371971delAC								CDH12 (518239 upstream) : PRDM9 (135753 downstream)																							GACTATacatacacacacacac	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29281516	29281516	+	IGR	DEL	A	-	-	rs11348406		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29281516delA								None (None upstream) : None (None downstream)																							ACGTTGTTTTAAAAAAAAATC	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32952003	32952004	+	Intron	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32952003_32952004delAG	uc011coa.1	+											Homo sapiens cDNA clone IMAGE:5166153.																		acacacacacagagtgggttaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38078700	38078701	+	IGR	INS	-	T	T	rs142603067	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38078700_38078701insT								GDNF (238918 upstream) : EGFLAM (179832 downstream)																							taatttttgtatttttttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	44725617	44725617	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44725617delC								FGF10 (336833 upstream) : MRPS30 (83410 downstream)																							GACAACTTTACCCAAGTGAAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	45896986	45896986	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45896986delG								HCN1 (200766 upstream) : None (None downstream)																							ctgagtagctgggactttaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50701335	50701335	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50701335delA								ISL1 (10778 upstream) : None (None downstream)																							GAAGAGTTTTAAAAAGCAGGA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51404176	51404177	+	IGR	INS	-	TT	TT	rs112255198		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51404176_51404177insTT								ISL1 (713619 upstream) : ITGA1 (679597 downstream)																							ttctttctttctttctttcttt	0.153													4	2	---	---	---	---	
SKIV2L2	23517	broad.mit.edu	37	5	54654664	54654664	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54654664delG	uc003jpy.3	+						SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TTGGGAAGATGGAAGGGTGTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56286870	56286870	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56286870delA								MIER3 (19369 upstream) : GPBP1 (182905 downstream)																							gtctaatgggaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	60523861	60523870	+	IGR	DEL	TGTGTGTGTG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60523861_60523870delTGTGTGTGTG								C5orf43 (65559 upstream) : ZSWIM6 (104230 downstream)																							ACGCAGGCGCtgtgtgtgtgtgtgtgtgtg	0.343													4	2	---	---	---	---	
CWC27	10283	broad.mit.edu	37	5	64213763	64213764	+	Intron	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64213763_64213764delAC	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						AGAGATacatacacacacacac	0.129													4	2	---	---	---	---	
OTP	23440	broad.mit.edu	37	5	76936042	76936053	+	5'Flank	DEL	TGTGTGTGTGTG	-	-	rs145863741		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76936042_76936053delTGTGTGTGTGTG	uc003kfg.2	-							NM_032109	NP_115485	Q5XKR4	OTP_HUMAN	orthopedia homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		CGAGAGGAATtgtgtgtgtgtgtgtgtgtgtg	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	78448240	78448241	+	IGR	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78448240_78448241delCA								BHMT (20128 upstream) : JMY (83713 downstream)																							ATACCCCATGcacacacacaca	0.129													4	2	---	---	---	---	
LOC441089	441089	broad.mit.edu	37	5	79650122	79650122	+	5'Flank	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79650122delG	uc010jaj.1	-							NR_003665				Homo sapiens CRSP8 pseudogene (LOC441089), non-coding RNA.												0						attggggggtgggggaaggaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	79659875	79659875	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79659875delA								LOC441089 (12090 upstream) : ZFYVE16 (43963 downstream)																							GTGTAAGGTTAAAAAAAAAAT	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90862725	90862725	+	IGR	DEL	G	-	-	rs60964362		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90862725delG								LOC100129716 (146194 upstream) : None (None downstream)																							aaactttagagcaacagcagt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	94691990	94691991	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94691990_94691991insT								MCTP1 (71711 upstream) : FAM81B (35057 downstream)																							tccacatcctcctgttgtttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95324074	95324075	+	IGR	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95324074_95324075delTG								ELL2 (26299 upstream) : MIR583 (90767 downstream)																							GCTGCCGgtatgtgtgtgtgtg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105138076	105138076	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105138076delA								RAB9BP1 (702278 upstream) : None (None downstream)																							aaacatgtataaagcggatga	0.000													4	2	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110622105	110622105	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110622105delA	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTAGAACACTAAATATGAAAT	0.303													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111513739	111513740	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111513739_111513740insA	uc003kpv.1	-						EPB41L4A_uc003kpp.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)		aggctagaattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117988849	117988854	+	IGR	DEL	TTGTTG	-	-	rs72076425		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117988849_117988854delTTGTTG								None (None upstream) : DTWD2 (183717 downstream)																							TGATATCTGCttgttgttgttgttgt	0.398													4	2	---	---	---	---	
C5orf56	441108	broad.mit.edu	37	5	131790323	131790324	+	Intron	INS	-	TTGG	TTGG	rs146108204	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131790323_131790324insTTGG	uc003kwy.1	+						C5orf56_uc003kwz.1_Intron|C5orf56_uc010jds.1_Intron|IRF1_uc003kxd.2_Intron	NM_001013717	NP_001013739	Q8N8D9	CE056_HUMAN	hypothetical protein LOC441108												0						gttaataccatttggttggttg	0.000													0	6	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153605355	153605355	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153605355delC	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			cctctgctttctttcctttgg	0.025													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166318116	166318116	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166318116delT								None (None upstream) : ODZ2 (393727 downstream)																							CTTCATTCCATTTTACCAGAT	0.124													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166718606	166718606	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166718606delG	uc010jjd.2	+							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)		AGGCTGGCCTGGCATGGGACA	0.428													4	2	---	---	---	---	
KCNIP1	30820	broad.mit.edu	37	5	170110728	170110729	+	Intron	INS	-	TT	TT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170110728_170110729insTT	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009	Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tatttttaaggttttttttttt	0.188													4	3	---	---	---	---	
BNIP1	662	broad.mit.edu	37	5	172587242	172587243	+	Intron	INS	-	T	T	rs10693152		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172587242_172587243insT	uc003mcj.3	+						BNIP1_uc003mci.3_Intron|BNIP1_uc003mck.3_Intron|BNIP1_uc003mcl.3_Intron	NM_001205	NP_001196	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 1						anti-apoptosis|apoptosis|endoplasmic reticulum membrane fusion|endoplasmic reticulum organization|induction of apoptosis|vesicle-mediated transport	integral to endoplasmic reticulum membrane|nuclear envelope|SNARE complex	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCCTAtttctcttttttttttt	0.248													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180380776	180380785	+	IGR	DEL	CACACACACA	-	-	rs112280894		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180380776_180380785delCACACACACA								BTNL8 (2872 upstream) : BTNL3 (35116 downstream)																							catgcatgtgcacacacacacacacacaca	0.000													3	3	---	---	---	---	
LOC285780	285780	broad.mit.edu	37	6	6494995	6494995	+	Intron	DEL	T	-	-	rs35601241		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6494995delT	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0						aactcctGGCTTTTGGTAGAG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14635340	14635341	+	IGR	DEL	TC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14635340_14635341delTC								CD83 (498194 upstream) : JARID2 (610393 downstream)																							TCCTTCTCCTTCTCTAGttctt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15986069	15986069	+	IGR	DEL	G	-	-	rs34042713		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15986069delG								DTNBP1 (322798 upstream) : MYLIP (143248 downstream)																							aggaacaaaagtgagacatct	0.025													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19281261	19281271	+	IGR	DEL	AAAAAAACAAC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19281261_19281271delAAAAAAACAAC								MIR548A1 (709150 upstream) : ID4 (556346 downstream)																							TGGAAAAAAAAAAAAAACAACAAAAAACAGT	0.384													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19420792	19420792	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19420792delG								MIR548A1 (848681 upstream) : ID4 (416825 downstream)																							tatattcctagggtttttttt	0.000													4	2	---	---	---	---	
SCGN	10590	broad.mit.edu	37	6	25676997	25677008	+	Intron	DEL	TTCCATCCCCTC	-	-	rs66797714		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25676997_25677008delTTCCATCCCCTC	uc003nfb.2	+						SCGN_uc010jpz.2_Intron	NM_006998	NP_008929	O76038	SEGN_HUMAN	secretagogin precursor							extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3						ctgtcttattttccatcccctcttccatcccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26670370	26670371	+	IGR	INS	-	ACAC	ACAC	rs141090413	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26670370_26670371insACAC								ZNF322A (10407 upstream) : GUSBL1 (168895 downstream)																							acacgtatacaacatacatccc	0.054													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29853802	29853803	+	Intron	INS	-	A	A	rs150144900	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29853802_29853803insA	uc011dmb.1	+						HLA-H_uc003nod.2_5'Flank|HLA-H_uc010jro.2_5'Flank	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						attccatccacattttgcccag	0.109													2	4	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29891293	29891293	+	Intron	DEL	C	-	-	rs68042301		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29891293delC	uc011dmb.1	+						HCG4P6_uc003nog.1_Intron|uc003noi.2_5'Flank	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						tcttgaacttctggagtcaac	0.010													1	6	---	---	---	---	
MICA	4276	broad.mit.edu	37	6	31372175	31372175	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31372175delC	uc003ntk.1	+						MICA_uc003rxz.1_Intron					RecName: Full=MHC class I polypeptide-related sequence A;          Short=MIC-A; Flags: Precursor;												0		Ovarian(999;0.0253)				TCTAAGGACACCAGATTCCCT	0.587													4	2	---	---	---	---	
MICA	4276	broad.mit.edu	37	6	31377749	31377752	+	Intron	DEL	CGTT	-	-	rs66509943		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31377749_31377752delCGTT	uc003ntk.1	+						MICA_uc003rxz.1_Intron					RecName: Full=MHC class I polypeptide-related sequence A;          Short=MIC-A; Flags: Precursor;												0		Ovarian(999;0.0253)				AAGCCCACACCGTTCGTTGCTCCC	0.559													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32358284	32358284	+	IGR	DEL	A	-	-	rs72002754		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32358284delA								C6orf10 (18628 upstream) : BTNL2 (4229 downstream)																							CATCATCCTCAATGCCACCAA	0.498													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33186424	33186424	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33186424delT								RING1 (5926 upstream) : VPS52 (31625 downstream)																							CATCCCAGGCTTCCTCCATCT	0.483													4	2	---	---	---	---	
PACSIN1	29993	broad.mit.edu	37	6	34500248	34500248	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34500248delG	uc003ojo.2	+	10	1482	c.1276delG	c.(1276-1278)GGGfs	p.G426fs	PACSIN1_uc003ojp.2_Frame_Shift_Del_p.G426fs	NM_020804	NP_065855	Q9BY11	PACN1_HUMAN	protein kinase C and casein kinase substrate in	426	SH3.				endocytosis		protein kinase activity				0						CTGGTGCCGTGGGCGGCTGGA	0.652													10	5	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38322694	38322695	+	Intron	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38322694_38322695delAG	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						acagagagaaagagagagagag	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40756891	40756894	+	IGR	DEL	ACAC	-	-	rs149712341		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40756891_40756894delACAC								LRFN2 (201765 upstream) : UNC5CL (237878 downstream)																							CTCTTTCTTTacacacacacacac	0.299													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44622775	44622778	+	IGR	DEL	GGAA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44622775_44622778delGGAA								CDC5L (207996 upstream) : SUPT3H (154276 downstream)																							agggagggatggaaggaaggaagg	0.064													5	3	---	---	---	---	
RUNX2	860	broad.mit.edu	37	6	45367926	45367927	+	Intron	INS	-	GGAA	GGAA	rs149457722		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45367926_45367927insGGAA	uc011dvx.1	+						RUNX2_uc011dvy.1_Intron	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						gagggaatgagggaaggaagga	0.144													5	3	---	---	---	---	
CD2AP	23607	broad.mit.edu	37	6	47534216	47534218	+	Intron	DEL	TTG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47534216_47534218delTTG	uc003oyw.2	+							NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein						cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TCTTGAGTTTTTGTTGTTGTTGT	0.202													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52021550	52021551	+	IGR	INS	-	AAAG	AAAG	rs150280071	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52021550_52021551insAAAG								MIR133B (7711 upstream) : IL17A (29634 downstream)																							acGTGTAGGGTAAAGAAAGAAA	0.386													4	2	---	---	---	---	
RAB23	51715	broad.mit.edu	37	6	57056642	57056643	+	Intron	DEL	TG	-	-	rs145337719	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57056642_57056643delTG	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	NM_183227	NP_899050	Q9ULC3	RAB23_HUMAN	Ras-related protein Rab-23						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ATTTCTGAGTTGTGTGTGTGTG	0.173													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57344143	57344144	+	Intron	INS	-	A	A	rs147853435	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57344143_57344144insA	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)		TGTAGACTACTAAAAAAAAGCA	0.302													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57364239	57364241	+	Intron	DEL	AGG	-	-	rs10535092		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57364239_57364241delAGG	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)		AACAGAAACAAGGAGGtcatttt	0.217													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57382191	57382191	+	Intron	DEL	G	-	-	rs62993861		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57382191delG	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)		AAGTTACAAAGGAAAATTAGT	0.294													6	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57402583	57402584	+	Intron	DEL	TT	-	-	rs72420484		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402583_57402584delTT	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)		GTTGTTGTTGtttttttttttt	0.040													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404370	57404371	+	Intron	INS	-	A	A	rs139203387		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404370_57404371insA	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)		aaagaaacacgaaaagcagctc	0.104													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415403	57415404	+	Intron	INS	-	A	A	rs151310189		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415403_57415404insA	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)		ACAAATGGACTAAAAATAATGT	0.302													5	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57471401	57471401	+	Intron	DEL	T	-	-	rs111855733		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57471401delT	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)		ggttgttaggtttttttattc	0.000													0	8	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57503445	57503445	+	Intron	DEL	C	-	-	rs11343070		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57503445delC	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)		aagagcttcacaaaatgagtt	0.080													3	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57504123	57504123	+	Intron	DEL	C	-	-	rs113225647		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57504123delC	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)		gtagataaatccacaaagact	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57515229	57515233	+	IGR	DEL	TTTGA	-	-	rs67538111		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515229_57515233delTTTGA								PRIM2 (1854 upstream) : GUSBL2 (730926 downstream)																							TCTTGACAATTTTGATTTGTTTTCT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57526906	57526906	+	IGR	DEL	G	-	-	rs5876678		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57526906delG								PRIM2 (13531 upstream) : GUSBL2 (719253 downstream)																							gaacttaataggggctcaata	0.124													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57527818	57527818	+	IGR	DEL	G	-	-	rs67858073		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57527818delG								PRIM2 (14443 upstream) : GUSBL2 (718341 downstream)																							AACCAGAACTGGGGGCTGACA	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57536210	57536210	+	IGR	DEL	C	-	-	rs112147444		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57536210delC								PRIM2 (22835 upstream) : GUSBL2 (709949 downstream)																							cttgagatcaccccccaaaca	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	69014018	69014018	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69014018delT								None (None upstream) : BAI3 (331614 downstream)																							aaaaaagaaataataaagatg	0.000													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69992929	69992930	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69992929_69992930insA	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron|BAI3_uc003pex.1_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				GGCAAAGGTGCAAAGGAAAAAA	0.416													4	2	---	---	---	---	
RIMS1	22999	broad.mit.edu	37	6	72702336	72702337	+	Intron	INS	-	TCTTCC	TCTTCC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72702336_72702337insTCTTCC	uc003pga.2	+							NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				cttcttcctcttcttcctcttc	0.000													9	4	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73641976	73641977	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73641976_73641977delTG	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		tatgtgtgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77340982	77340982	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77340982delG								IMPG1 (558647 upstream) : HTR1B (830966 downstream)																							gctgttagcagagataagaga	0.000													4	2	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80990744	80990745	+	Intron	INS	-	GT	GT	rs150406848	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80990744_80990745insGT	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		caggtgtatgcgtgtgtgtgtg	0.000													3	3	---	---	---	---	
IBTK	25998	broad.mit.edu	37	6	82886915	82886920	+	Intron	DEL	TTGTTG	-	-	rs138212074		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82886915_82886920delTTGTTG	uc003pjl.1	-						IBTK_uc011dyu.1_Intron|IBTK_uc011dyv.1_Intron|IBTK_uc011dyw.1_Intron|IBTK_uc010kbi.1_Intron	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase						negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TCTTTttgttttgttgttgttgttgt	0.150													4	2	---	---	---	---	
SESN1	27244	broad.mit.edu	37	6	109406719	109406720	+	Intron	DEL	CA	-	-	rs72355876		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109406719_109406720delCA	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)		gacactccgtcacacacacaca	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	109636760	109636760	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109636760delG								C6orf182 (151647 upstream) : CD164 (50958 downstream)																							TGAATGGGCTGGAGGGAGGGC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113109777	113109777	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113109777delT								RFPL4B (437279 upstream) : None (None downstream)																							AGTAAAGTGCTTTTCCTTTTC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	120852420	120852423	+	IGR	DEL	ACTT	-	-	rs72135358		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120852420_120852423delACTT								None (None upstream) : C6orf170 (548204 downstream)																							TCTTGGAGAAACTTAATTAAGTCT	0.240													4	2	---	---	---	---	
LAMA2	3908	broad.mit.edu	37	6	129799149	129799153	+	Intron	DEL	GTCTT	-	-	rs146322315		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129799149_129799153delGTCTT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		cctcaggctggtcttgtcttgaact	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145230981	145230981	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145230981delA								UTRN (56813 upstream) : EPM2A (715465 downstream)																							gtcttgggttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149240554	149240555	+	Intron	DEL	GT	-	-	rs142983347		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149240554_149240555delGT	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		TGTCAGAGCCgtgtgtgtgtgt	0.436													3	3	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	150919218	150919218	+	5'Flank	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150919218delA	uc003qny.1	+						PLEKHG1_uc011eel.1_5'Flank	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		cggtctctacaaaaaaaaaat	0.000													4	2	---	---	---	---	
ZBTB2	57621	broad.mit.edu	37	6	151688259	151688260	+	Intron	DEL	TT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151688259_151688260delTT	uc003qoh.2	-							NM_020861	NP_065912	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		AGTAAGTTAAtttttttttttt	0.158													4	2	---	---	---	---	
ESR1	2099	broad.mit.edu	37	6	152281427	152281427	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152281427delA	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Intron|ESR1_uc010kit.1_Intron|ESR1_uc011eey.1_Intron	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	agacagaaagaaagcaaacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170483924	170483925	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170483924_170483925insT								C6orf208 (280955 upstream) : LOC154449 (79497 downstream)																							CCTGTTTGGGGTTGTTCCTGCC	0.495													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1360376	1360377	+	IGR	DEL	GA	-	-	rs147432915		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1360376_1360377delGA								UNCX (83764 upstream) : MICALL2 (113619 downstream)																							GTGTCTGTGTGAGAGAGGCATG	0.356													4	5	---	---	---	---	
CARD11	84433	broad.mit.edu	37	7	3063217	3063218	+	Intron	INS	-	T	T	rs10543757		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3063217_3063218insT	uc003smv.2	-							NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		aacgtaatttcttttttttttt	0.000			Mis		DLBCL								7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3282119	3282122	+	IGR	DEL	TTCC	-	-	rs10452787	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3282119_3282122delTTCC								CARD11 (198540 upstream) : SDK1 (58958 downstream)																							TTCTTTttttttccttccttcctt	0.093													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	4123340	4123341	+	Intron	INS	-	GCTC	GCTC	rs66726277		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4123340_4123341insGCTC	uc003smx.2	+						SDK1_uc010kso.2_Intron	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ctcctttacttcctccctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	11265755	11265755	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11265755delG								PHF14 (56514 upstream) : THSD7A (148418 downstream)																							GAAGTAAATTGGAGCCATTCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25070382	25070383	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25070382_25070383insA								OSBPL3 (50622 upstream) : CYCS (87894 downstream)																							gagatatgtgtagaaagaatTT	0.094													4	2	---	---	---	---	
DPY19L2P1	554236	broad.mit.edu	37	7	35225155	35225156	+	Intron	INS	-	TC	TC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35225155_35225156insTC	uc003teq.1	-											RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						TATACTCCCTATCTCTCTCTCT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	40993905	40993905	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40993905delC								C7orf10 (93548 upstream) : INHBA (734698 downstream)																							tggaaaagcaccatattaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	44167245	44167245	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44167245delT								POLD2 (4098 upstream) : MYL7 (11220 downstream)																							tgccttgtgattttttttttg	0.000													4	2	---	---	---	---	
TNS3	64759	broad.mit.edu	37	7	47546545	47546545	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47546545delG	uc003tnv.2	-						TNS3_uc003tnw.2_Intron|TNS3_uc010kyo.1_Intron	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3							focal adhesion	protein binding			ovary(4)	4						CTTGCAGGCTGGGAAAAAAAA	0.423													6	3	---	---	---	---	
SUN3	256979	broad.mit.edu	37	7	48030023	48030023	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48030023delC	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1						cctgccacatcccccctctcc	0.000													4	2	---	---	---	---	
VSTM2A	222008	broad.mit.edu	37	7	54613373	54613373	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54613373delG	uc010kzf.2	+						VSTM2A_uc010kze.2_Intron|VSTM2A_uc003tqc.3_Intron	NM_182546	NP_872352	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2							extracellular region					0			STAD - Stomach adenocarcinoma(5;0.0525)			agagagggaagggggaaaaag	0.100													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56323777	56323777	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56323777delC								PSPH (139687 upstream) : DKFZp434L192 (240139 downstream)																							tgcacttaggcctctgtggtt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56557408	56557409	+	IGR	INS	-	G	G	rs146847538	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56557408_56557409insG								PSPH (373318 upstream) : DKFZp434L192 (6507 downstream)																							CCATGGATGATGGCCTGTGGCT	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57768830	57768831	+	IGR	INS	-	T	T	rs144648722		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768830_57768831insT								ZNF716 (235565 upstream) : None (None downstream)																							ATAATATCTTATTCTTTCTGAC	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57774612	57774613	+	IGR	INS	-	TCT	TCT	rs139419356	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57774612_57774613insTCT								ZNF716 (241347 upstream) : None (None downstream)																							catcatcctcatttttttcaat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57921311	57921312	+	IGR	INS	-	AA	AA	rs111543900		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57921311_57921312insAA								ZNF716 (388046 upstream) : None (None downstream)																							ATGCTGACAAGAAAAATTTAGG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57967730	57967730	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57967730delG								ZNF716 (434465 upstream) : None (None downstream)																							atattcccttgcagattctac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	70550476	70550476	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70550476delA								AUTS2 (292592 upstream) : WBSCR17 (47313 downstream)																							acttagacttaaaaaaaaaaa	0.085													2	4	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	71063804	71063805	+	Intron	INS	-	A	A	rs138957482	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71063804_71063805insA	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)				AGCAAATCGGGTAAATGATCAG	0.416													3	4	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90570944	90570944	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90570944delT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						ttttttttaattttttgtaga	0.000													1	5	---	---	---	---	
CCDC132	55610	broad.mit.edu	37	7	92949634	92949634	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92949634delC	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TGCCCCCCGTCTTTTTTTTTT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95960503	95960503	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95960503delG								SLC25A13 (9044 upstream) : SHFM1 (341734 downstream)																							ttcctcagcaggccaatccct	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108242311	108242312	+	IGR	INS	-	TT	TT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108242311_108242312insTT								DNAJB9 (27019 upstream) : C7orf66 (281728 downstream)																							CAGGCATTTAAttttttttttt	0.173													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118051026	118051027	+	IGR	DEL	GT	-	-	rs72425946		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118051026_118051027delGT								ANKRD7 (168244 upstream) : None (None downstream)																							tttcaagtcCgtgtgtgtgtgt	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121158546	121158547	+	IGR	INS	-	A	A	rs147072425		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121158546_121158547insA								FAM3C (122124 upstream) : PTPRZ1 (354612 downstream)																							GTTTAGCGGCTAAAAAAAAAAA	0.213													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121222046	121222047	+	IGR	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121222046_121222047delTG								FAM3C (185624 upstream) : PTPRZ1 (291112 downstream)																							tgtgtgacaatgtgtgtgtgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127121592	127121593	+	IGR	DEL	AC	-	-	rs72184704		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127121592_127121593delAC								ZNF800 (88825 upstream) : GCC1 (99090 downstream)																							aaccatatcaacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	132384473	132384474	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132384473_132384474insA	uc003vrd.1	+											Homo sapiens cDNA FLJ40288 fis, clone TESTI2028098.																		gactccgtctcaaaaaaaaaaa	0.233													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136900381	136900381	+	IGR	DEL	G	-	-	rs139809359		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136900381delG								CHRM2 (198610 upstream) : PTN (11711 downstream)																							GGAGTAGCCAGAGGTTGCCCA	0.478													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141466090	141466101	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs10634958		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141466090_141466101delTGTGTGTGTGTG								TAS2R3 (1093 upstream) : TAS2R4 (12188 downstream)																							aatagtaatttgtgtgtgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146643188	146643191	+	Intron	DEL	TTCC	-	-	rs71917990		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146643188_146643191delTTCC	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			cttccttcctttccttctttcctt	0.186										HNSCC(39;0.1)			6	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147255833	147255836	+	Intron	DEL	CTTT	-	-	rs57248998		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147255833_147255836delCTTT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			tccttccttcctttcttccttcct	0.039										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147650505	147650506	+	Intron	INS	-	T	T	rs148648109	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147650505_147650506insT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TCTAAGAAATACGATTCTCATT	0.213										HNSCC(39;0.1)			3	3	---	---	---	---	
ZNF786	136051	broad.mit.edu	37	7	148771739	148771740	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148771739_148771740insA	uc003wfh.2	-						ZNF786_uc011kuk.1_Intron|ZNF786_uc003wfi.2_Intron	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AACAACATGTCAAAAAAAAAAA	0.376													2	4	---	---	---	---	
WDR86	349136	broad.mit.edu	37	7	151094761	151094762	+	Intron	INS	-	GG	GG	rs117707482		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151094761_151094762insGG	uc003wkb.2	-						WDR86_uc003wka.2_Intron|WDR86_uc011kvk.1_Intron|WDR86_uc003wkc.2_Intron	NM_198285	NP_938026	Q86TI4	WDR86_HUMAN	WD repeat domain 86												0			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		cgggaggaagagcatagcggga	0.203													4	3	---	---	---	---	
WDR86	349136	broad.mit.edu	37	7	151094938	151094939	+	Intron	INS	-	AG	AG	rs71811097		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151094938_151094939insAG	uc003wkb.2	-						WDR86_uc003wka.2_Intron|WDR86_uc011kvk.1_Intron|WDR86_uc003wkc.2_Intron	NM_198285	NP_938026	Q86TI4	WDR86_HUMAN	WD repeat domain 86												0			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TAGCGGGAGGAAGGGTGTAGCG	0.411													4	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152106898	152106898	+	Intron	DEL	A	-	-	rs10707629		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152106898delA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GTTTTTTTTTAAATCATCATG	0.254			N		medulloblastoma								6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153211872	153211873	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153211872_153211873insT								ACTR3B (659409 upstream) : DPP6 (372546 downstream)																							agtcacttttcttttttttttg	0.000													3	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154463226	154463229	+	Intron	DEL	TGTC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154463226_154463229delTGTC	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)			CCTGCCTCATTGTCTGCACATGCA	0.475													4	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154570725	154570726	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154570725_154570726insA	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)			ccaccagcaccccaccatcacc	0.000													4	5	---	---	---	---	
CNPY1	285888	broad.mit.edu	37	7	155319294	155319294	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155319294delC	uc003wmc.1	-							NM_001103176	NP_001096646	Q3B7I2	CNPY1_HUMAN	canopy 1 homolog												0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		aataagaaatccaaatagcac	0.080													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157400224	157400224	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157400224delG	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)		AGCGCAGCCTGGAGCCCTCAG	0.612													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158320619	158320622	+	Intron	DEL	ACCT	-	-	rs3032743		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158320619_158320622delACCT	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)		AGCAGGGACCACCTACCTGTGTTG	0.569													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2208254	2208255	+	IGR	INS	-	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2208254_2208255insC								MYOM2 (114875 upstream) : CSMD1 (584621 downstream)																							CAGGGCCAGTGCCTTCTCTCCC	0.485													3	3	---	---	---	---	
MSRA	4482	broad.mit.edu	37	8	10275264	10275265	+	Intron	INS	-	TGTG	TGTG	rs144936992	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10275264_10275265insTGTG	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	AACCTGCATGTtgtgtgtgtgt	0.366											OREG0018542	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	4	---	---	---	---	
SOX7	83595	broad.mit.edu	37	8	10608184	10608185	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10608184_10608185insT	uc011kwz.1	-						uc003wtg.1_Intron	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN	SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)		tgcatggataattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	11735156	11735156	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11735156delA								CTSB (9510 upstream) : DEFB136 (96292 downstream)																							acaacgtctcaaaaaaaaaaa	0.199													4	3	---	---	---	---	
PDGFRL	5157	broad.mit.edu	37	8	17486889	17486890	+	Intron	INS	-	CAG	CAG	rs150833310	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17486889_17486890insCAG	uc003wxr.2	+							NM_006207	NP_006198	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like							extracellular region	platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity				0				Colorectal(111;0.0752)		ctgtgttggatcaggtcttcta	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20716187	20716187	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20716187delA								LZTS1 (603384 upstream) : GFRA2 (833343 downstream)																							ATAGTTGCTCAAAAAAAAAAA	0.373													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30778986	30778987	+	IGR	INS	-	A	A	rs146807720		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30778986_30778987insA								TEX15 (32764 upstream) : PURG (74334 downstream)																							TTGATTTCTACAAAAAAAAAAA	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	35781180	35781180	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35781180delG								UNC5D (129000 upstream) : KCNU1 (860662 downstream)																							gaaatgttctggaatttgata	0.000													4	2	---	---	---	---	
HGSNAT	138050	broad.mit.edu	37	8	43010604	43010604	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43010604delT	uc003xpx.3	+							NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			aaaatgagccttttttttgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	46845144	46845144	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46845144delT								None (None upstream) : BEYLA (907364 downstream)																							tgaaacactctttttttggaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58654538	58654538	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58654538delA								C8orf71 (457250 upstream) : FAM110B (252575 downstream)																							GGCGTGAAGTAAAAAGGGATG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58712997	58712997	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58712997delA								C8orf71 (515709 upstream) : FAM110B (194116 downstream)																							atgacaaaggaaaaaaggTCA	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65803666	65803666	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65803666delT								CYP7B1 (92318 upstream) : ARMC1 (711406 downstream)																							ACCAGACTGATTTTTTTTTTT	0.353													4	2	---	---	---	---	
DNAJC5B	85479	broad.mit.edu	37	8	67003001	67003001	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67003001delA	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			ACTGCCCAGGAAAAAGGCACC	0.408													4	2	---	---	---	---	
ADHFE1	137872	broad.mit.edu	37	8	67369551	67369552	+	Intron	INS	-	A	A	rs148427504		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67369551_67369552insA	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			ccatctctaccaaaaaaaaaaa	0.000													5	4	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68951551	68951551	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68951551delT	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						ttttctgctctttaaggtttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75431721	75431728	+	IGR	DEL	CACACACA	-	-	rs144326050		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75431721_75431728delCACACACA								GDAP1 (152388 upstream) : MIR2052 (186200 downstream)																							cacacaggcgcacacacacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80791170	80791171	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80791170_80791171insA								HEY1 (111072 upstream) : MRPS28 (39925 downstream)																							gaccttgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89556534	89556535	+	IGR	INS	-	ACAC	ACAC	rs71556467		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89556534_89556535insACAC								MMP16 (216817 upstream) : None (None downstream)																							TTCCAGATGAGacacacacaca	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92476252	92476253	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92476252_92476253insT								SLC26A7 (65872 upstream) : RUNX1T1 (494899 downstream)																							ATTCCTTTTTGTTTTTTTtcat	0.228													4	2	---	---	---	---	
RNF19A	25897	broad.mit.edu	37	8	101297005	101297005	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101297005delA	uc003yjj.1	-						RNF19A_uc003yjk.1_Intron	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19						microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			TATCACATATAAAAAAGGTTT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109587941	109587941	+	IGR	DEL	A	-	-	rs34837227		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109587941delA								TTC35 (88805 upstream) : TMEM74 (31139 downstream)																							CACTTTCTCTACTTCCCCACA	0.418													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119699469	119699469	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119699469delG								SAMD12 (65235 upstream) : TNFRSF11B (236328 downstream)																							cacactgtctggattactgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125408488	125408488	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125408488delG								TMEM65 (23548 upstream) : TRMT12 (54560 downstream)																							ctcaagaactgggtaggctta	0.000													1	5	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125633363	125633363	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125633363delC	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CCCCTTTCCTCCACCCAAACC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125859132	125859132	+	IGR	DEL	A	-	-	rs35983666		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125859132delA								MTSS1 (118402 upstream) : LOC157381 (92752 downstream)																							cagaacctgcaaataatgagg	0.164													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128028370	128028371	+	IGR	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128028370_128028371delCA								FAM84B (457904 upstream) : LOC727677 (273691 downstream)																							cacatgcatgcacacacacaca	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129996885	129996886	+	IGR	INS	-	CCA	CCA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129996885_129996886insCCA								MIR1208 (834451 upstream) : GSDMC (763557 downstream)																							ACCTTTCCCTCccaccaccacc	0.198													4	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139603731	139603731	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139603731delG	uc003yvd.2	-	64	5076	c.4629delC	c.(4627-4629)GCCfs	p.A1543fs	COL22A1_uc011ljo.1_Frame_Shift_Del_p.A823fs	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1543	Pro-rich.|Gly-rich.|Collagen-like 15.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGTCACCTTTGGCTCCTCGCT	0.612										HNSCC(7;0.00092)			7	11	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141468009	141468009	+	5'Flank	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141468009delA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						gggaggggacatggggaggga	0.164													5	3	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	141688098	141688100	+	Intron	DEL	AGG	-	-	rs148764887		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141688098_141688100delAGG	uc003yvu.2	-						PTK2_uc011ljp.1_Intron|PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			ccacaaagaaaggagatggctgg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142359627	142359628	+	IGR	INS	-	AC	AC	rs148211915	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142359627_142359628insAC								LOC731779 (4908 upstream) : GPR20 (6961 downstream)																							agtagactgagacacacacaca	0.000													4	2	---	---	---	---	
ZFP41	286128	broad.mit.edu	37	8	144347427	144347427	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144347427delA	uc003yxv.2	+						GLI4_uc003yxx.2_5'Flank	NM_173832		Q8N8Y5	ZFP41_HUMAN	zinc finger protein 41 homolog						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)			actccgtctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	762742	762742	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:762742delA								KANK1 (16638 upstream) : DMRT1 (78948 downstream)																							CTCCCTTGTGAGGTTCTGAGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2305423	2305425	+	IGR	DEL	CTC	-	-	rs148224313		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2305423_2305425delCTC								SMARCA2 (111802 upstream) : FLJ35024 (117277 downstream)																							GCACGACTGACTCCTCCTGCACT	0.488													2	5	---	---	---	---	
RCL1	10171	broad.mit.edu	37	9	4857932	4857933	+	Intron	DEL	TT	-	-	rs145751623		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4857932_4857933delTT	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron|RCL1_uc010mhl.1_Intron|RCL1_uc003ziv.1_5'Flank	NM_005772	NP_005763	Q9Y2P8	RCL1_HUMAN	RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)		gctctcccactttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	8313652	8313652	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8313652delC								C9orf123 (513853 upstream) : PTPRD (595 downstream)																							tagcactggtcccatgtgatg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11937152	11937153	+	IGR	INS	-	AG	AG			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11937152_11937153insAG								None (None upstream) : TYRP1 (756233 downstream)																							cgtctcaaaaaaaaaaaaaaaa	0.129													4	2	---	---	---	---	
BNC2	54796	broad.mit.edu	37	9	16475306	16475306	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16475306delA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc011lmv.1_Intron|BNC2_uc003zmo.1_Intron	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		CTCTTACCCTAAACATGGCTA	0.348													4	2	---	---	---	---	
KIAA1797	54914	broad.mit.edu	37	9	20942004	20942004	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20942004delA	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		AATCAGAGGGAAATCAGGAAT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25635746	25635747	+	IGR	INS	-	GT	GT	rs150310079	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25635746_25635747insGT								None (None upstream) : TUSC1 (40647 downstream)																							agagagagagagtgtgtgtgtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29098469	29098470	+	IGR	INS	-	CA	CA	rs150546262	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29098469_29098470insCA								MIR873 (209516 upstream) : None (None downstream)																							acacatatgcgcacacacacac	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33576441	33576441	+	5'Flank	DEL	C	-	-	rs79264286		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33576441delC	uc003ztd.1	-											DQ587539																		CCTGAGCCCACCCCCAAGGTG	0.532													2	5	---	---	---	---	
PRSS3	5646	broad.mit.edu	37	9	33793061	33793061	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33793061delT	uc003ztj.3	+						uc003ztk.1_Intron|PRSS3_uc003zti.3_Intron|PRSS3_uc003ztl.3_5'Flank	NM_007343	NP_031369	P35030	TRY3_HUMAN	mesotrypsin isoform 1 preproprotein						digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)			AGGTCATTCCTTTTTGAAGAA	0.423													4	2	---	---	---	---	
UBAP2	55833	broad.mit.edu	37	9	33940059	33940061	+	Intron	DEL	AAG	-	-	rs147216266		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33940059_33940061delAAG	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron|UBAP2_uc003zts.2_Intron	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ggagaggggAaagaagaagaaaa	0.133													4	5	---	---	---	---	
KIF24	347240	broad.mit.edu	37	9	34325418	34325418	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34325418delC	uc003zua.3	-						KIF24_uc010mkb.2_Intron	NM_194313	NP_919289	Q5T7B8	KIF24_HUMAN	kinesin family member 24						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)			gggccaggcacggtggctcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44109097	44109098	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44109097_44109098insA								FAM75A6 (478367 upstream) : FAM27C (881138 downstream)																							ATAAAGGTCTCAAAAATCCAGA	0.347													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66821222	66821223	+	IGR	DEL	CT	-	-	rs112498295		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66821222_66821223delCT								LOC442421 (318195 upstream) : AQP7P1 (433044 downstream)																							ttttgaaacactcttcttgtag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66839590	66839591	+	IGR	INS	-	A	A	rs143257044		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66839590_66839591insA								LOC442421 (336563 upstream) : AQP7P1 (414676 downstream)																							ttgttgctcacaaaaaAAAAaa	0.000													4	2	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67292297	67292298	+	5'Flank	INS	-	T	T	rs150097916		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67292297_67292298insT	uc004aen.1	-						AQP7P1_uc004aeo.1_5'Flank|AQP7P1_uc004aep.1_5'Flank					Homo sapiens cDNA FLJ46364 fis, clone TESTI4051015.												0						tttttttccccgagtttttaat	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68382518	68382519	+	IGR	INS	-	G	G	rs76005965		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68382518_68382519insG								FAM27B (588329 upstream) : MIR1299 (619720 downstream)																							gtttttgtttttttgtttttgt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68412348	68412348	+	RNA	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68412348delA	uc004aew.1	+	2		c.510delA			uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		GAGGGCAAAGAAACGTGGAAT	0.552													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68425242	68425242	+	IGR	DEL	A	-	-	rs66621105		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68425242delA								FAM27B (631053 upstream) : MIR1299 (576997 downstream)																							TTTTGTGGCTACTCAAATTTT	0.184													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69804754	69804754	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69804754delT								LOC100133920 (139805 upstream) : FOXD4L5 (370955 downstream)																							tcacataaccttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69840103	69840104	+	IGR	INS	-	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69840103_69840104insC								LOC100133920 (175154 upstream) : FOXD4L5 (335605 downstream)																							attttatttttttgagacagag	0.000													2	4	---	---	---	---	
CBWD3	445571	broad.mit.edu	37	9	70871932	70871939	+	Intron	DEL	GTTTTTTT	-	-	rs2482168		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70871932_70871939delGTTTTTTT	uc004agi.3	+						CBWD3_uc011lro.1_Intron|CBWD3_uc004agj.3_Intron|CBWD3_uc011lrp.1_Intron|CBWD3_uc004agl.3_Intron	NM_201453	NP_958861	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3								ATP binding				0				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		ATCTTTCTTGgtttttttttttgttttt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78141620	78141620	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78141620delC								OSTF1 (379507 upstream) : PCSK5 (363940 downstream)																							TCAGGCCCGGCCCCGAGACCC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82978757	82978758	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82978757_82978758insT								TLE4 (637100 upstream) : None (None downstream)																							ccactttttagttttttttttt	0.000													4	2	---	---	---	---	
KIF27	55582	broad.mit.edu	37	9	86457387	86457388	+	Intron	INS	-	T	T	rs113635305		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86457387_86457388insT	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						ttgtttgtttgttttttttgag	0.109													5	3	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87506149	87506149	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87506149delT	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						ATGGTCAAGCTTTTTTTTAAA	0.418										TSP Lung(25;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87788776	87788776	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87788776delC								NTRK2 (150271 upstream) : AGTPBP1 (372679 downstream)																							GTCCTGACATCCCCTCTGTTG	0.517													4	2	---	---	---	---	
ZCCHC6	79670	broad.mit.edu	37	9	88957837	88957837	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88957837delA	uc004aoq.2	-						ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron|ZCCHC6_uc004aov.2_Intron|ZCCHC6_uc004aow.2_Intron	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						GCAGAGTATTAAAAAAAAAAG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91485399	91485400	+	IGR	INS	-	T	T	rs143483261	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91485399_91485400insT								LOC286238 (218324 upstream) : C9orf47 (120378 downstream)																							CTGTTTTTTAGTTTTTTTAAGT	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92773151	92773152	+	IGR	INS	-	G	G	rs141787751	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92773151_92773152insG								LOC100129066 (438477 upstream) : DIRAS2 (598962 downstream)																							GCCAGGTGTGACAAGCACAAGG	0.574													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92902988	92902989	+	IGR	INS	-	A	A	rs140582491	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92902988_92902989insA								LOC100129066 (568314 upstream) : DIRAS2 (469125 downstream)																							TAGGACTCTCGGCTCCTGGTTT	0.480													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92909785	92909785	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92909785delC								LOC100129066 (575111 upstream) : DIRAS2 (462329 downstream)																							cacctgaaatccatagtttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104722782	104722782	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104722782delG								GRIN3A (221920 upstream) : None (None downstream)																							CCATTGCTCAGGGGCTGCCTT	0.403													4	2	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107631312	107631313	+	Intron	INS	-	A	A	rs140686337	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107631312_107631313insA	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)	gggaggctgggaaagaaggagg	0.213													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107782536	107782536	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107782536delA								ABCA1 (92100 upstream) : SLC44A1 (224393 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110152435	110152435	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110152435delC								RAD23B (57966 upstream) : KLF4 (94700 downstream)																							cattgcatctccctccactcc	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110712527	110712530	+	IGR	DEL	GTGT	-	-	rs5899768		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110712527_110712530delGTGT								KLF4 (460480 upstream) : ACTL7B (904341 downstream)																							CTAGTTTtgcgtgtgtgtgtgtgt	0.250													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	113873994	113873995	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113873994_113873995insT								LPAR1 (72468 upstream) : OR2K2 (215769 downstream)																							gctgaactagcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120536108	120536109	+	IGR	INS	-	TCTC	TCTC	rs139464083		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120536108_120536109insTCTC								TLR4 (56344 upstream) : None (None downstream)																							ctttctttctttctctctcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122298054	122298054	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122298054delG								DBC1 (166315 upstream) : MIR147 (709203 downstream)																							tcgtgggaatggttgggattc	0.000													4	2	---	---	---	---	
FAM129B	64855	broad.mit.edu	37	9	130293770	130293770	+	Intron	DEL	A	-	-	rs5900751		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130293770delA	uc004brh.2	-						FAM129B_uc004bri.2_Intron|FAM129B_uc004brj.3_Intron	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1								protein binding				0						ctcaaaaaagaaaaaaataat	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132172566	132172568	+	IGR	DEL	ACA	-	-	rs78168144		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132172566_132172568delACA								C9orf106 (87684 upstream) : C9orf50 (201938 downstream)																							catcaacatcacaaccaccacca	0.049													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132931541	132931542	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132931541_132931542insT								GPR107 (29093 upstream) : NCS1 (3315 downstream)																							cttttcttttccttccttcctt	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	134410518	134410519	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134410518_134410519insT								UCK1 (3856 upstream) : RAPGEF1 (41639 downstream)																							GGTGGTGTGGGttttttttttg	0.252													4	2	---	---	---	---	
MED27	9442	broad.mit.edu	37	9	134832213	134832213	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134832213delA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		attgatgattaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137393198	137393205	+	IGR	DEL	AAATGCTC	-	-	rs11278805		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137393198_137393205delAAATGCTC								RXRA (60767 upstream) : COL5A1 (140447 downstream)																							CTGTGCGCGGAAATGCTCAGCCTCGGGA	0.620													4	2	---	---	---	---	
GRIN1	2902	broad.mit.edu	37	9	140037874	140037875	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140037874_140037875delTG	uc004clk.2	+						GRIN1_uc004cli.1_Intron|GRIN1_uc004clj.1_Intron|GRIN1_uc004cll.2_Intron|GRIN1_uc004clm.2_Intron|GRIN1_uc004cln.2_Intron|GRIN1_uc004clo.2_Intron	NM_007327	NP_015566	Q05586	NMDZ1_HUMAN	NMDA receptor 1 isoform NR1-3 precursor						ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)	GTCTCATTCCtgtgccctcagg	0.312													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1275718	1275719	+	Intron	INS	-	TG	TG	rs139109316	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1275718_1275719insTG	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)		atatgtgcttctgtgtacatgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4734361	4734371	+	IGR	DEL	GGTAGGTGAAG	-	-	rs58423253		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4734361_4734371delGGTAGGTGAAG								LOC100216001 (14099 upstream) : AKR1E2 (134031 downstream)																							aaggaaggaaggtaggtgaagggaaggaagg	0.043													4	6	---	---	---	---	
GATA3	2625	broad.mit.edu	37	10	8109802	8109808	+	Intron	DEL	AAAACAA	-	-	rs66460154		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8109802_8109808delAAAACAA	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042	P23771	GATA3_HUMAN	GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22						aaaacataacaaaacaaaaaacaaaaa	0.145			F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						2	5	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14610334	14610336	+	Intron	DEL	GGG	-	-	rs10612412		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14610334_14610336delGGG	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						tgaagATACTGGGGGAGGAGGAG	0.300													4	2	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14786065	14786065	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14786065delC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						agaggtccttcccttgttagc	0.000													4	2	---	---	---	---	
PTPLA	9200	broad.mit.edu	37	10	17644072	17644072	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17644072delT	uc001ipg.2	-							NM_014241	NP_055056	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like, member A						fatty acid biosynthetic process|multicellular organismal development|signal transduction	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein tyrosine phosphatase activity			central_nervous_system(1)|skin(1)	2						ATGGGTTTAAttttttttttt	0.239													3	3	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24232764	24232764	+	Intron	DEL	T	-	-	rs12356758	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24232764delT	uc001irs.2	+							NM_001098500	NP_001091970	Q5T5P2	SKT_HUMAN	sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						caattcaatatggaaagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38939264	38939265	+	IGR	INS	-	AG	AG	rs142390219	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38939264_38939265insAG								LOC399744 (198184 upstream) : None (None downstream)																							CTTGGTTTAAAAAAAAAGAGCA	0.351													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42379610	42379614	+	IGR	DEL	TGTCA	-	-	rs139640914		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42379610_42379614delTGTCA								None (None upstream) : LOC441666 (447701 downstream)																							attccattcctgtcaattctactcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42415053	42415053	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42415053delT								None (None upstream) : LOC441666 (412262 downstream)																							aggaaatatcttcacataaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42640974	42640975	+	IGR	INS	-	GTCA	GTCA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42640974_42640975insGTCA								None (None upstream) : LOC441666 (186340 downstream)																							tcttcaaagctgacagggacat	0.000													7	4	---	---	---	---	
MARCH8	220972	broad.mit.edu	37	10	46058395	46058395	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46058395delT	uc001jcj.1	-						MARCH8_uc001jck.1_Intron	NM_001002265	NP_001002265	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						tatatgtgggttttttttttt	0.000													4	2	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65145854	65145855	+	Intron	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65145854_65145855delAC	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	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)					acatacacagacacacacacac	0.153													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67489984	67489985	+	IGR	DEL	AC	-	-	rs35096693		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67489984_67489985delAC								ANXA2P3 (903350 upstream) : CTNNA3 (189740 downstream)																							acacacacagacacacacacac	0.000													3	3	---	---	---	---	
TYSND1	219743	broad.mit.edu	37	10	71908546	71908547	+	5'Flank	INS	-	AAAC	AAAC	rs146500950	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71908546_71908547insAAAC	uc001jqr.2	-						TYSND1_uc001jqq.2_5'Flank|TYSND1_uc001jqs.2_5'Flank|TYSND1_uc001jqt.2_5'Flank	NM_173555	NP_775826	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1 isoform a						proteolysis	peroxisome	serine-type endopeptidase activity			large_intestine(1)	1						accAACTcaaaaaacaaacaaa	0.173													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72337060	72337067	+	IGR	DEL	TTTCATTG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72337060_72337067delTTTCATTG								KIAA1274 (8855 upstream) : PRF1 (20038 downstream)																							tccttccttctttcattgtttccttcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77373128	77373128	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77373128delG								MIR606 (60817 upstream) : C10orf11 (169391 downstream)																							GTGGAGACCAGGCAATGAGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	95026213	95026221	+	IGR	DEL	ATGTAACAC	-	-	rs113302070		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95026213_95026221delATGTAACAC								CYP26A1 (188572 upstream) : MYOF (39966 downstream)																							gtaccactaaatgtaacacatgtagcact	0.048													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103949066	103949066	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103949066delA								NOLC1 (25439 upstream) : ELOVL3 (37077 downstream)																							actctgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112356048	112356048	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112356048delC	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)		AAATTACTTTCAATTCTCATT	0.194													7	4	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114522108	114522109	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114522108_114522109insT	uc001kzz.2	+							NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		AGGCTGAGAACTTTTTTTTTTC	0.411													4	2	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114902837	114902837	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114902837delT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_Intron|TCF7L2_uc010qrw.1_Intron|TCF7L2_uc010qrx.1_Intron	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GTATTGTGCCTTTTGCCTCCC	0.453													4	2	---	---	---	---	
VWA2	340706	broad.mit.edu	37	10	116049752	116049753	+	Intron	DEL	AA	-	-	rs144902492		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116049752_116049753delAA	uc001lbl.1	+							NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		attctgcctcaaaaaaaaaaaa	0.218													3	3	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123792509	123792510	+	Intron	INS	-	ACT	ACT	rs142496257	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123792509_123792510insACT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				caacaacaacaacaacaaaaac	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132575082	132575083	+	IGR	DEL	CC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132575082_132575083delCC								GLRX3 (592298 upstream) : TCERG1L (315573 downstream)																							ATTTCTAATTCCACAGGAACCC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133577175	133577190	+	IGR	DEL	ATGGGAGGACGGGAGG	-	-	rs113113405		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133577175_133577190delATGGGAGGACGGGAGG								TCERG1L (467191 upstream) : PPP2R2D (170770 downstream)																							GGACAGGAGCATGGGAGGACGGGAGGATGGGAGCCT	0.569													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	7995225	7995226	+	IGR	INS	-	T	T	rs112804422		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7995225_7995226insT								NLRP10 (10166 upstream) : EIF3F (13219 downstream)																							aaactctacacttttttttttt	0.000													2	5	---	---	---	---	
ABCC8	6833	broad.mit.edu	37	11	17498869	17498870	+	5'Flank	INS	-	GTG	GTG	rs140985738	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17498869_17498870insGTG	uc001mnc.2	-						ABCC8_uc010rcy.1_5'Flank	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	AACGTTACCTTGTGGTGGTGGT	0.500													5	3	---	---	---	---	
PTPN5	84867	broad.mit.edu	37	11	18800906	18800906	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18800906delA	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						TTTTGCAAGGAAAAAAAAAAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	24207169	24207169	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24207169delA								None (None upstream) : LUZP2 (311387 downstream)																							gaaggaagggaagggaaggaa	0.000													8	5	---	---	---	---	
ABTB2	25841	broad.mit.edu	37	11	34231862	34231862	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34231862delT	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)				CCTGAAATCCTTTTTATCCCT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37287972	37287973	+	IGR	DEL	GT	-	-	rs5791164		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37287972_37287973delGT								C11orf74 (591582 upstream) : None (None downstream)																							TTCAGAAATGgtgtgtgtgtgt	0.262													3	3	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	41449709	41449709	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41449709delT	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)				gagtagctgattataaagtaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41651980	41651980	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41651980delA								LRRC4C (170657 upstream) : None (None downstream)																							cttttggtagaaagtcttttt	0.000													4	2	---	---	---	---	
DGKZ	8525	broad.mit.edu	37	11	46375635	46375635	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46375635delG	uc001nch.1	+						DGKZ_uc010rgq.1_Intron|DGKZ_uc001ncj.1_Intron|DGKZ_uc010rgr.1_Intron|DGKZ_uc001nck.1_Intron|DGKZ_uc001ncl.2_Intron|DGKZ_uc001ncm.2_Intron|DGKZ_uc009yky.1_Intron|DGKZ_uc010rgs.1_Intron|DGKZ_uc001nci.1_Intron	NM_201532	NP_963290	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GCATCCCCTTGGGGGAGACCT	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47223690	47223690	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47223690delA								PACSIN3 (15732 upstream) : DDB2 (12803 downstream)																							ctggaattacaggtgtgagcc	0.189													4	2	---	---	---	---	
OR4C45	403257	broad.mit.edu	37	11	48376212	48376212	+	5'Flank	DEL	T	-	-	rs33971529		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48376212delT	uc010rhw.1	-							NM_001005513	NP_001005513			olfactory receptor, family 4, subfamily C,												0						ATTCAAGTTCTTCTTTCAACT	0.368													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50737225	50737225	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50737225delA								LOC646813 (357422 upstream) : OR4A5 (674223 downstream)																							cttattttttatgtgaagata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	51578403	51578403	+	IGR	DEL	A	-	-	rs71308336		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51578403delA								OR4C46 (62194 upstream) : None (None downstream)																							ctgctttaccaaaataaaggt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57773252	57773252	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57773252delA								CTNND1 (186601 upstream) : OR9Q1 (18101 downstream)																							ACCATAATTTAATAGATTACA	0.279													4	2	---	---	---	---	
NRXN2	9379	broad.mit.edu	37	11	64456716	64456716	+	Intron	DEL	T	-	-	rs36122114		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64456716delT	uc001oar.2	-						NRXN2_uc001oas.2_Intron|NRXN2_uc001oaq.2_Intron	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor						cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10						TTCTCAATGAttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71997844	71997845	+	IGR	INS	-	GT	GT	rs141377628	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71997844_71997845insGT								PHOX2A (42624 upstream) : CLPB (5627 downstream)																							tttatcattccgtgtgtgtgtg	0.000													6	3	---	---	---	---	
XRRA1	143570	broad.mit.edu	37	11	74621291	74621293	+	Intron	DEL	ATT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74621291_74621293delATT	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron|XRRA1_uc001ovt.2_5'Flank	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1						gtaaaaggggattatgatgtggc	0.000													3	3	---	---	---	---	
GDPD4	220032	broad.mit.edu	37	11	77000863	77000864	+	5'Flank	INS	-	AGGG	AGGG	rs144198548	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77000863_77000864insAGGG	uc001oyf.2	-							NM_182833	NP_878253	Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding			skin(1)	1						ggagggaaggaagggagggagg	0.000													4	7	---	---	---	---	
NARS2	79731	broad.mit.edu	37	11	78278016	78278017	+	Intron	INS	-	TTTT	TTTT	rs146898776	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78278016_78278017insTTTT	uc001ozi.2	-						NARS2_uc010rsq.1_Intron	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial						asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	CTCATCCATTCTAAGTCTTGTA	0.322													3	3	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	79061474	79061474	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79061474delT	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						ctttcttggcttttttttttt	0.035													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79592863	79592863	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79592863delG								ODZ4 (441168 upstream) : None (None downstream)																							GACAGTGACTGGTAATTCATT	0.323													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84505970	84505970	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84505970delC	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				gccgtgggcaccatcgataga	0.000													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92286127	92286127	+	Intron	DEL	T	-	-	rs2846190		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92286127delT	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				caaaaaaaaataaaagaaaag	0.005										TCGA Ovarian(4;0.039)			5	3	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99929136	99929137	+	Intron	INS	-	A	A	rs147270924	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99929136_99929137insA	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)		ctgcatctgtcaaagttatcca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101532025	101532026	+	IGR	INS	-	A	A	rs150329071	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101532025_101532026insA								TRPC6 (77366 upstream) : ANGPTL5 (229380 downstream)																							acatgctgaggaaaaaaaagtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102114423	102114426	+	IGR	DEL	AAAG	-	-	rs111903349		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102114423_102114426delAAAG								YAP1 (10269 upstream) : BIRC3 (73768 downstream)																							agaaagagaaaaagaaagaaagaa	0.034													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	106981177	106981178	+	IGR	INS	-	AG	AG	rs144588624	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106981177_106981178insAG								GUCY1A2 (92006 upstream) : CWF19L2 (215896 downstream)																							gagatgtggacagagggaagat	0.000													3	3	---	---	---	---	
IL18	3606	broad.mit.edu	37	11	112024222	112024223	+	Intron	INS	-	T	T	rs78854082		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024222_112024223insT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553	Q14116	IL18_HUMAN	interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		CATGAGAACCATTTTTTTTTTT	0.356													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114818590	114818590	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114818590delA								FAM55B (240938 upstream) : CADM1 (221363 downstream)																							GGAGTAGCCTATGGGAGCCCC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116364305	116364305	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116364305delG								CADM1 (989064 upstream) : BUD13 (254583 downstream)																							GTTTGGCGGTGGGGGCAGGGG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	117298473	117298473	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117298473delA								CEP164 (14493 upstream) : DSCAML1 (16 downstream)																							GCCAGATGGGAAAAAAGCCAC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118166543	118166544	+	IGR	INS	-	A	A	rs145758383	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118166543_118166544insA								MPZL2 (31534 upstream) : CD3E (8751 downstream)																							actggcttacgaatgctcctgg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124030702	124030702	+	IGR	DEL	T	-	-	rs11312490		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124030702delT								VWA5A (13086 upstream) : OR8G2 (64696 downstream)																							gaaattgaccttttttttttt	0.000													3	3	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125179027	125179030	+	Intron	DEL	CTTT	-	-	rs112247938		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125179027_125179030delCTTT	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		ttacctcttcctttctttctttct	0.000													2	4	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126393493	126393497	+	Intron	DEL	CCTGC	-	-	rs61304161		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126393493_126393497delCCTGC	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		TGCCTCTCCTCCTGCCCACACTTCC	0.600													3	4	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133224114	133224115	+	Intron	INS	-	ACGTA	ACGTA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133224114_133224115insACGTA	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		tggtgatgatgctggtgctggt	0.153													4	3	---	---	---	---	
IQSEC3	440073	broad.mit.edu	37	12	235126	235127	+	Intron	INS	-	C	C	rs141671047	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:235126_235127insC	uc001qhu.1	+						IQSEC3_uc001qht.1_Intron	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AAGGGGCCCTGCTTTGGGGGCT	0.614													4	2	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	611724	611725	+	Intron	INS	-	AG	AG	rs141338451	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:611724_611725insAG	uc001qii.1	+							NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GAGAAACAGGCGGGTGAAAGAT	0.460													4	3	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2571544	2571544	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2571544delC	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	acctcctcggcccccgctgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5027460	5027460	+	IGR	DEL	T	-	-	rs3214309		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5027460delT								KCNA1 (40 upstream) : KCNA5 (125625 downstream)																							TTAACTGGTCTTTTGGGGGCC	0.388													4	2	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	13795124	13795131	+	Intron	DEL	AAACAAAC	-	-	rs141621215	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13795124_13795131delAAACAAAC	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	ctctgtctcaaaacaaacaaacaaacaa	0.096													4	2	---	---	---	---	
PDE3A	5139	broad.mit.edu	37	12	20794255	20794255	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20794255delG	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)	CATGGAAGTTGGAAGAGAAAC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30497331	30497331	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30497331delT								TMTC1 (559639 upstream) : IPO8 (284592 downstream)																							aatcacactgttaaactatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34299063	34299064	+	IGR	INS	-	AT	AT	rs151022106	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34299063_34299064insAT								ALG10 (117829 upstream) : None (None downstream)																							cacatgcacacgtttatttcag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42258910	42258910	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42258910delA								PDZRN4 (290526 upstream) : GXYLT1 (216740 downstream)																							aatttacaagaaaaaaaacaa	0.000													3	5	---	---	---	---	
PPHLN1	51535	broad.mit.edu	37	12	42664476	42664476	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42664476delA	uc001rmy.2	+							NM_201439	NP_958847	Q8NEY8	PPHLN_HUMAN	periphilin 1 isoform 3						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		tctcaaaaggaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46097441	46097442	+	IGR	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46097441_46097442delTG								ANO6 (263254 upstream) : LOC400027 (22368 downstream)																							gccctaagcttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
RHEBL1	121268	broad.mit.edu	37	12	49459415	49459415	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49459415delA	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						catctctattaaaaaaaaaaT	0.005													4	2	---	---	---	---	
RHEBL1	121268	broad.mit.edu	37	12	49463357	49463374	+	Intron	DEL	CCAATCCTCCACTCTTCC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49463357_49463374delCCAATCCTCCACTCTTCC	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						ACCAACTCTTCCAATCCTCCACTCTTCCATTCCTCCAC	0.569													6	3	---	---	---	---	
LMBR1L	55716	broad.mit.edu	37	12	49494862	49494863	+	Intron	INS	-	A	A	rs145985167	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49494862_49494863insA	uc001rth.3	-						LMBR1L_uc001rtg.3_Intron|LMBR1L_uc001rti.3_Intron	NM_018113	NP_060583	Q6UX01	LMBRL_HUMAN	lipocalin-interacting membrane receptor						endocytosis	integral to membrane|plasma membrane	receptor activity			pancreas(1)	1						GCCCTCCTTTCAAATTAAGTCT	0.317													8	8	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49901106	49901106	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49901106delG	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						TATTTACACTGGCGGAAAGGT	0.458													4	2	---	---	---	---	
ATF1	466	broad.mit.edu	37	12	51203157	51203157	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51203157delA	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162	P18846	ATF1_HUMAN	activating transcription factor 1						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|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				EWSR1/ATF1(323)|FUS/ATF1(4)	soft_tissue(321)|ovary(2)|NS(2)|bone(2)|skin(2)	329						atcttgtctcaaaaaaaaaaa	0.095			T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								9	4	---	---	---	---	
PCBP2	5094	broad.mit.edu	37	12	53865708	53865709	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53865708_53865709insT	uc001sdl.3	+						PCBP2_uc001sdc.3_Intron|PCBP2_uc001sdb.3_Intron|PCBP2_uc001sde.3_Intron|PCBP2_uc001sdi.3_Intron|PCBP2_uc001sdd.3_Intron|PCBP2_uc001sdf.3_Intron|PCBP2_uc009zna.2_Intron|PCBP2_uc010soi.1_Intron|PCBP2_uc001sdj.3_Intron|PCBP2_uc010soj.1_Intron|PCBP2_uc001sdk.3_Intron	NM_001128911	NP_001122383	Q15366	PCBP2_HUMAN	poly(rC) binding protein 2 isoform d						innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0						TGGCCAAAAGGTTTTTTTTTTT	0.411													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65342355	65342364	+	Intron	DEL	CACACACACA	-	-	rs72348675		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65342355_65342364delCACACACACA	uc001ssj.1	+											Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																		CTGCTTATGCcacacacacacacacacaca	0.362													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67345679	67345679	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67345679delT								GRIP1 (147785 upstream) : CAND1 (317382 downstream)																							aggaagagggttttaaattgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	72653629	72653630	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72653629_72653630insA								TPH2 (227408 upstream) : LOC283392 (2698 downstream)																							AACACCCTTTCAATGGAAAGAA	0.480													4	2	---	---	---	---	
PTPRQ	374462	broad.mit.edu	37	12	81063246	81063246	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81063246delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						TTGAAAGGGTAAAAAAAAAAG	0.328													4	2	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83298443	83298443	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83298443delT	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						GCAAGCCACATTATATCTGAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107539824	107539825	+	IGR	INS	-	T	T	rs139546706	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107539824_107539825insT								CRY1 (52226 upstream) : BTBD11 (172372 downstream)																							TTCTCCAGGTATTTTTTCCATA	0.267													4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109652910	109652910	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109652910delA	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	caaaaaaaagaaaaaaaaaaa	0.149													2	4	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109868410	109868410	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109868410delA	uc010sxn.1	+							NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H							myosin complex	motor activity				0						CGATACCCTTAAAGAACATGC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112954842	112954843	+	IGR	DEL	CA	-	-	rs71445576		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112954842_112954843delCA								PTPN11 (7126 upstream) : RPH3A (58058 downstream)																							gactacatttcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	120396904	120396905	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120396904_120396905insT								CIT (81812 upstream) : CCDC64 (30743 downstream)																							gtgactcaatcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	120398272	120398272	+	IGR	DEL	T	-	-	rs34378325		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120398272delT								CIT (83180 upstream) : CCDC64 (29376 downstream)																							gcacccggccttttttttttt	0.000													4	2	---	---	---	---	
ATP6V0A2	23545	broad.mit.edu	37	12	124208917	124208917	+	Intron	DEL	A	-	-	rs11326601		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124208917delA	uc001ufr.2	+						ATP6V0A2_uc001ufq.1_Intron	NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		ctaacaatacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125164923	125164927	+	IGR	DEL	TGTTT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125164923_125164927delTGTTT								NCOR2 (112913 upstream) : SCARB1 (97248 downstream)																							tttgtttgtctgttttgttttgttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127097325	127097325	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127097325delT								LOC100128554 (139995 upstream) : None (None downstream)																							cactttgtgatggctcccctg	0.000													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129872257	129872259	+	Intron	DEL	ATA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129872257_129872259delATA	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)		AGCACTGATGATAATATTAACAC	0.291													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131742762	131742763	+	IGR	INS	-	G	G	rs145841355	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131742762_131742763insG								LOC116437 (45287 upstream) : SFRS8 (452872 downstream)																							gcagaaatccagggaagaacag	0.069													3	3	---	---	---	---	
EP400NL	347918	broad.mit.edu	37	12	132600261	132600261	+	5'Flank	DEL	A	-	-	rs67591694		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132600261delA	uc001ujx.1	+											Homo sapiens cDNA FLJ33915 fis, clone CTONG2016658.												0						ggatgtggccaatgtggtgtc	0.224													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	133040917	133040918	+	IGR	INS	-	CAC	CAC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133040917_133040918insCAC								GALNT9 (135012 upstream) : FBRSL1 (26239 downstream)																							atcaccatcatcatcatcacca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	133344751	133344751	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133344751delT								ANKLE2 (6300 upstream) : GOLGA3 (744 downstream)																							TGGTTAACtcttttttttttt	0.229													4	2	---	---	---	---	
PAN3	255967	broad.mit.edu	37	13	28777267	28777267	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28777267delT	uc001urz.2	+						PAN3_uc010tdo.1_Intron|PAN3_uc001ury.2_Intron|PAN3_uc001urx.2_Intron	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		gcctggctaattttttttttt	0.000													4	2	---	---	---	---	
KL	9365	broad.mit.edu	37	13	33593937	33593938	+	Intron	INS	-	AG	AG	rs141796177	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33593937_33593938insAG	uc001uus.2	+						KL_uc001uur.1_Intron	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor						aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		ggaggagggacagagagagaga	0.238													3	3	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41142509	41142509	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41142509delC	uc001uxl.3	-						FOXO1_uc010acc.1_Intron	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase 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 factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		GGCCTTTATTCCCTCCCTCCT	0.413													4	2	---	---	---	---	
ENOX1	55068	broad.mit.edu	37	13	43945045	43945045	+	Intron	DEL	C	-	-	rs112274784		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43945045delC	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		CCTGTCCCCACCCCCTCCTGC	0.567													4	3	---	---	---	---	
KLF12	11278	broad.mit.edu	37	13	74415079	74415079	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74415079delA	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		ctctttttgcaaaggtcttcc	0.000													4	2	---	---	---	---	
KLF12	11278	broad.mit.edu	37	13	74624110	74624112	+	Intron	DEL	TTG	-	-	rs10532541		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74624110_74624112delTTG	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		gatggtggttttgttgttgttgt	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74960933	74960933	+	IGR	DEL	G	-	-	rs142834850		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74960933delG								KLF12 (252539 upstream) : LOC647288 (850957 downstream)																							tccattgtttgttgactttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79033186	79033186	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79033186delA	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		TTTCCCGTGTACTCTCCATCT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83523658	83523661	+	IGR	DEL	AGAT	-	-	rs150353657		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83523658_83523661delAGAT								None (None upstream) : SLITRK1 (927683 downstream)																							TAGTGCACACAGATAGAAATATGG	0.230													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87763492	87763493	+	IGR	INS	-	A	A	rs138294327	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87763492_87763493insA								None (None upstream) : SLITRK5 (561377 downstream)																							TGTTATCTCCTAAAAAAAAATC	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89711360	89711360	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89711360delT								None (None upstream) : None (None downstream)																							ggttattctcttttacttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95068687	95068688	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95068687_95068688insA								GPC6 (8420 upstream) : DCT (23155 downstream)																							AAAAACAAAACAAAAAAAAACA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95202846	95202849	+	IGR	DEL	TGGA	-	-	rs33918047		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95202846_95202849delTGGA								DCT (70910 upstream) : TGDS (23460 downstream)																							gatggatggttggatggatggatg	0.225													4	2	---	---	---	---	
STK24	8428	broad.mit.edu	37	13	99145743	99145744	+	Intron	INS	-	T	T	rs148540482	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99145743_99145744insT	uc001vnm.1	-						STK24_uc001vnn.1_Intron|STK24_uc010tim.1_Intron	NM_003576	NP_003567	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform a						cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CAAGAGAGAGATTTTTTCTTTC	0.257													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	101693282	101693284	+	IGR	DEL	CTT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101693282_101693284delCTT								TMTC4 (366179 upstream) : NALCN (12846 downstream)																							tcctcctccccttcttcttcttc	0.000													4	2	---	---	---	---	
ITGBL1	9358	broad.mit.edu	37	13	102215745	102215746	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102215745_102215746insT	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					aaattgatttatttttaagcag	0.000													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107936671	107936671	+	Intron	DEL	T	-	-	rs113471337		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107936671delT	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						acaaagtatatgagtaagcag	0.000													0	6	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110941384	110941385	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110941384_110941385insA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			gaccccatctcaaaaaaaaaaG	0.248													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112182068	112182070	+	IGR	DEL	CCT	-	-	rs3077332		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112182068_112182070delCCT								C13orf16 (185475 upstream) : SOX1 (539843 downstream)																							cccccctccccctcctcctccct	0.399													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114026168	114026169	+	IGR	INS	-	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114026168_114026169insG								GRTP1 (7705 upstream) : ADPRHL1 (50091 downstream)																							cctcctcctgagaccccctccc	0.050													4	2	---	---	---	---	
LOC100130386	100130386	broad.mit.edu	37	13	114454130	114454131	+	5'Flank	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114454130_114454131delTG	uc010tkg.1	-							NR_028064				Homo sapiens cDNA FLJ32873 fis, clone TESTI2003998, weakly similar to T-CELL RECEPTOR BETA CHAIN ANA 11.												0						tgcgtgcatctgtgcgtgtgtg	0.010													4	5	---	---	---	---	
UPF3A	65110	broad.mit.edu	37	13	115049824	115049824	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115049824delA	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_5'Flank|UPF3A_uc001vuu.2_5'Flank	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		gcgacggagcaaaaAAATAtg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19011478	19011478	+	IGR	DEL	A	-	-	rs77033728		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19011478delA								None (None upstream) : OR11H12 (366116 downstream)																							ttccaacaagaccctcaaagc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19366318	19366318	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19366318delC								None (None upstream) : OR11H12 (11276 downstream)																							CAGTCAGCAGCCCACTGGGGT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19455991	19455991	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19455991delA								OR11H12 (77419 upstream) : POTEG (97374 downstream)																							actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19699094	19699095	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19699094_19699095insA								POTEG (114152 upstream) : P704P (284859 downstream)																							gactctgtctcaaaaaaaaaaa	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20368017	20368018	+	IGR	DEL	CT	-	-	rs57651176		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20368017_20368018delCT								OR4K2 (22646 upstream) : OR4K5 (20748 downstream)																							gcccccccccctcagaaagtca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22012147	22012148	+	IGR	INS	-	A	A	rs146740048	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22012147_22012148insA								SALL2 (6810 upstream) : OR10G3 (25787 downstream)																							TTGGCCATTAGAAAAAAAAATC	0.426													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22050108	22050108	+	IGR	DEL	A	-	-	rs111999969		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22050108delA								OR10G3 (11233 upstream) : OR10G2 (51959 downstream)																							atcgtttgttaaaaaaaaaaa	0.070													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22355895	22355898	+	Intron	DEL	GTGT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22355895_22355898delGTGT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_5'Flank|uc001wby.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		TCAAGTGCTCgtgtgtgtgtgtgt	0.260													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22478279	22478279	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22478279delG	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		gaaggaggaaggggaCAGGAG	0.269													6	4	---	---	---	---	
PRKD1	5587	broad.mit.edu	37	14	30051234	30051234	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30051234delT	uc001wqh.2	-							NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		ttttaggctattttttttttc	0.000													4	2	---	---	---	---	
G2E3	55632	broad.mit.edu	37	14	31039312	31039312	+	Intron	DEL	T	-	-	rs55882754		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31039312delT	uc001wqk.2	+						G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Intron	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase						apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						caggtttgggtttttttcctg	0.090													4	2	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35037351	35037351	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35037351delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		GTTACTCCAAttttttttttt	0.234													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35363586	35363586	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35363586delT								BAZ1A (18733 upstream) : C14orf19 (45542 downstream)																							TTTGATAttcttttttttttt	0.189													4	2	---	---	---	---	
KIAA0391	9692	broad.mit.edu	37	14	35630284	35630285	+	Intron	DEL	CG	-	-	rs3985307		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35630284_35630285delCG	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487	O15091	MRRP3_HUMAN	mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		ATGTGAAGACCGGAGCCCATTT	0.401													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39964867	39964867	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39964867delG								FBXO33 (63163 upstream) : None (None downstream)																							agcatgtcttggggaggcctc	0.005													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46755925	46755925	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46755925delG								None (None upstream) : RPL10L (364297 downstream)																							cattgcaggcggattatctga	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50340734	50340734	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50340734delT								SDCCAG1 (21195 upstream) : ARF6 (19002 downstream)																							gagcattcagttttttaccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54068996	54068996	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54068996delT								DDHD1 (448950 upstream) : BMP4 (347461 downstream)																							CTCTGACATCTCCAGGATCTT	0.443													4	2	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62458048	62458049	+	Intron	INS	-	TG	TG	rs148245040	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62458048_62458049insTG	uc010tsd.1	+									Q17RD7	SYT16_HUMAN	SubName: Full=cDNA FLJ60997, highly similar to Homo sapiens synaptotagmin XVI (SYT16), mRNA;											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		TGTTTTTCATTtgtgtgtgtgt	0.287													3	3	---	---	---	---	
FUT8	2530	broad.mit.edu	37	14	66113327	66113328	+	Intron	INS	-	A	A	rs142680606	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66113327_66113328insA	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GTAAGTCAGCCATACCCTAGGT	0.441													1	5	---	---	---	---	
FUT8	2530	broad.mit.edu	37	14	66135889	66135890	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66135889_66135890insA	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron|FUT8_uc001xis.2_5'Flank	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		gatgaaagattaaaaaaaaaaa	0.183													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66223558	66223559	+	IGR	INS	-	T	T	rs146130585	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66223558_66223559insT								FUT8 (13597 upstream) : C14orf53 (729550 downstream)																							AACAATTGGCCTTTTTTTTTCA	0.381													4	2	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68944322	68944322	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68944322delT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						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)		TTCATAACAATTTTTTTTTTT	0.403			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					10	6	---	---	---	---	
AHSA1	10598	broad.mit.edu	37	14	77932170	77932171	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77932170_77932171insT	uc001xtw.2	+						AHSA1_uc010tvk.1_Intron	NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase						protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		CCTCTAttctcttttttttttt	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84673394	84673395	+	IGR	INS	-	TT	TT	rs34356712		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84673394_84673395insTT								None (None upstream) : None (None downstream)																							TTACTTTTGGGTTTTTTTTTTT	0.371													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89934800	89934801	+	Intron	INS	-	ACAC	ACAC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89934800_89934801insACAC	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.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						tgtgtctcaaaacacacacaca	0.000													4	2	---	---	---	---	
ITPK1	3705	broad.mit.edu	37	14	93410125	93410126	+	Intron	INS	-	AA	AA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93410125_93410126insAA	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CAGCACTGTGCAAAAGCCATCT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95307928	95307928	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95307928delT								GSC (71429 upstream) : DICER1 (244637 downstream)																							agtgctgggattacaggcgtg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97602878	97602879	+	IGR	INS	-	ACT	ACT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97602878_97602879insACT								VRK1 (254928 upstream) : C14orf64 (789068 downstream)																							tcaccatcatcatcaccaccac	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102074445	102074446	+	IGR	INS	-	CTC	CTC	rs139732110	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102074445_102074446insCTC								DIO3 (44656 upstream) : C14orf72 (122328 downstream)																							ctactccacctctcctcctcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20107795	20107799	+	IGR	DEL	ATGAA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20107795_20107799delATGAA								None (None upstream) : GOLGA6L6 (629295 downstream)																							tgatgaaatgatgaaatgaaatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20124382	20124382	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20124382delT								None (None upstream) : GOLGA6L6 (612712 downstream)																							AATATTTTAATAAATTGGATC	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20556972	20556973	+	IGR	INS	-	C	C	rs55977129		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20556972_20556973insC								None (None upstream) : GOLGA6L6 (180121 downstream)																							AGAGAGCATGGGGGGGGCGGTC	0.658													4	2	---	---	---	---	
BCL8	606	broad.mit.edu	37	15	20871163	20871164	+	RNA	INS	-	AA	AA	rs142973274		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20871163_20871164insAA	uc010tzd.1	-	4		c.1923_1924insTT								Homo sapiens mRNA; cDNA DKFZp686P1536 (from clone DKFZp686P1536).												0						CTTATAGAGCCAGAGGCAAGTG	0.550													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21926911	21926912	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21926911_21926912insT								NF1P1 (792286 upstream) : LOC646214 (5602 downstream)																							AGCATGCACCATGTGTCATGCC	0.282													4	3	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	27164500	27164501	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27164500_27164501insT	uc001zbb.2	-						GABRA5_uc001zbd.1_Intron	NM_021912	NP_068712	P28472	GBRB3_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			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	gtgcttcattattttttttgta	0.000													4	2	---	---	---	---	
CHRFAM7A	89832	broad.mit.edu	37	15	30665727	30665728	+	Intron	DEL	GT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30665727_30665728delGT	uc001zdt.1	-						CHRFAM7A_uc001zdu.1_Intron|CHRFAM7A_uc010azn.2_Intron|CHRFAM7A_uc001zdv.2_5'Flank	NM_139320	NP_647536	Q494W8	CRFM7_HUMAN	CHRNA7-FAM7A fusion isoform 1							integral to membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity			skin(1)	1		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		AATCTAAAAGgtgtgtgtgtgt	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	33555810	33555810	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33555810delC								FMN1 (195725 upstream) : RYR3 (47367 downstream)																							tcctagttttcctttcacctt	0.000													4	2	---	---	---	---	
SPATA5L1	79029	broad.mit.edu	37	15	45711665	45711665	+	Intron	DEL	A	-	-	rs111803369		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45711665delA	uc001zve.2	+						SPATA5L1_uc001zvf.2_Intron	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1							cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		gtctcttaggaaaaaaaaaaa	0.090													4	2	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54485096	54485097	+	Intron	DEL	CA	-	-	rs36106076		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54485096_54485097delCA	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)		TTCTCTGTGCcacacacacaca	0.228													4	2	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	67847462	67847462	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67847462delA	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc010ujw.1_Intron	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						TTTTCTTATTAAAAGGACCTC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70250029	70250030	+	IGR	INS	-	CA	CA	rs137931157	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70250029_70250030insCA								C15orf50 (114724 upstream) : TLE3 (90513 downstream)																							TGCTTTCTCTTcacacacacac	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	75255747	75255747	+	IGR	DEL	T	-	-	rs35269287		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75255747delT								RPP25 (5972 upstream) : SCAMP5 (32154 downstream)																							TCATTATCaattacagctgac	0.194													3	3	---	---	---	---	
SGK269	79834	broad.mit.edu	37	15	77468353	77468353	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77468353delC	uc002bcm.2	-						SGK269_uc002bcn.2_Intron	NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member						cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		ggacaaaaaaccaaacactgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78998528	78998529	+	IGR	INS	-	TG	TG	rs141172659	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78998528_78998529insTG								CHRNB4 (45654 upstream) : ADAMTS7 (53017 downstream)																							atatgtatgtttgtgtgtgtgt	0.069													6	3	---	---	---	---	
ALPK3	57538	broad.mit.edu	37	15	85377188	85377189	+	Intron	INS	-	TG	TG	rs111934164		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85377188_85377189insTG	uc002ble.2	+							NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3						heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGATTCtgtgttgtgtgtgtgt	0.401													4	4	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92551720	92551720	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92551720delA	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			TCAATGAGCTAAAAAAATAAA	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94550614	94550615	+	IGR	INS	-	TTT	TTT	rs11324022		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94550614_94550615insTTT								RGMA (918181 upstream) : MCTP2 (224186 downstream)																							GGTTTTTTGGGttttttttttt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95848090	95848090	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95848090delA	uc002btm.2	-											Homo sapiens hypothetical gene supported by BC040875, mRNA (cDNA clone IMAGE:5721930).																		CTTTGCCATTAAAGTGGTCCC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97937440	97937440	+	IGR	DEL	C	-	-	rs12440829	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97937440delC								SPATA8 (608596 upstream) : LOC91948 (348406 downstream)																							TTTTttttttcaattttttta	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101708253	101708254	+	IGR	INS	-	AGG	AGG	rs141264617	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101708253_101708254insAGG								LRRK1 (97938 upstream) : CHSY1 (7678 downstream)																							GCTTCCTCTTCAGGAGGAGGAG	0.614													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3481896	3481897	+	IGR	DEL	CA	-	-	rs140801375		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3481896_3481897delCA								ZNF174 (22534 upstream) : ZNF597 (4214 downstream)																							CACCGTTCACCACAGTCCACTT	0.599													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5470393	5470396	+	Intron	DEL	ACAC	-	-	rs111916064		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5470393_5470396delACAC	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																		ACCCCcatatacacacacacacac	0.186													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8984047	8984047	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8984047delT								CARHSP1 (21184 upstream) : USP7 (1904 downstream)																							GGGGCCTCCCTTTGGAACCTG	0.567													4	2	---	---	---	---	
C16orf75	116028	broad.mit.edu	37	16	11415874	11415875	+	Intron	INS	-	CATG	CATG	rs59043083		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11415874_11415875insCATG	uc002daq.1	+									Q96E14	RMI2_HUMAN	Homo sapiens cDNA FLJ41770 fis, clone IMR322007225.						DNA replication	nucleus	DNA binding				0						gcatacacatacatacacatgc	0.035			T	CIITA	PMBL|Hodgkin Lymphona|								4	2	---	---	---	---	
C16orf62	57020	broad.mit.edu	37	16	19658481	19658481	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19658481delT	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						CCCAAGTCGCTCTCCTTTGCC	0.358													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22134675	22134675	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22134675delA	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		CAATGCCTTTAAAAAAAAAAA	0.478													4	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	23945166	23945169	+	Intron	DEL	CATC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23945166_23945169delCATC	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	attttctattcatccatccatcca	0.000													3	3	---	---	---	---	
IL4R	3566	broad.mit.edu	37	16	27345210	27345210	+	Intron	DEL	T	-	-	rs150876630		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27345210delT	uc002don.2	+						IL4R_uc002dom.2_Intron|IL4R_uc002dop.3_Intron|IL4R_uc010bxy.2_Intron|IL4R_uc002doo.2_Intron	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a						immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2						CAGGAATCTCttttttttttt	0.045													5	3	---	---	---	---	
CD19	930	broad.mit.edu	37	16	28944602	28944602	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28944602delC	uc002drs.2	+	4	669	c.607delC	c.(607-609)CCCfs	p.P203fs	uc010vct.1_Intron|CD19_uc010byo.1_Frame_Shift_Del_p.P203fs	NM_001770	NP_001761	P15391	CD19_HUMAN	CD19 antigen precursor	203	Extracellular (Potential).|Ig-like C2-type 2.				cellular defense response	external side of plasma membrane|integral to plasma membrane	protein binding|receptor signaling protein activity			ovary(2)|central_nervous_system(1)	3						CTGTGGGGTACCCCCTGACTC	0.617													23	14	---	---	---	---	
MVP	9961	broad.mit.edu	37	16	29840879	29840885	+	Intron	DEL	GTCCAAA	-	-	rs36225031		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29840879_29840885delGTCCAAA	uc002dui.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc010bzh.1_Intron|MVP_uc010vdz.1_Intron|MVP_uc002duj.2_Intron|MVP_uc010vea.1_5'Flank	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein						mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						AAAGGGACATGTCCAAAGTCCAAAGTG	0.469													4	4	---	---	---	---	
ZNF771	51333	broad.mit.edu	37	16	30422032	30422032	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30422032delC	uc002dyd.2	+						ZNF771_uc002dyc.2_Intron|ZNF771_uc010ver.1_Intron|ZNF771_uc010bzx.2_Intron	NM_001142305	NP_001135777	Q7L3S4	ZN771_HUMAN	zinc finger protein 771						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.193)			TTCTGTGGCACCATAAGAAGC	0.119													4	2	---	---	---	---	
ITGAD	3681	broad.mit.edu	37	16	31420221	31420221	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31420221delA	uc002ebv.1	+						ITGAD_uc010vfl.1_3'UTR|ITGAD_uc010cap.1_Intron|ITGAD_uc002ebw.1_3'UTR	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor						cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						cgggcttgccagagcccaggg	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33040268	33040268	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33040268delG								SLC6A10P (143805 upstream) : MIR1826 (925240 downstream)																							GCAGTAAAAAGCCGCGGCGCC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33537920	33537921	+	IGR	DEL	AG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33537920_33537921delAG								SLC6A10P (641457 upstream) : MIR1826 (427587 downstream)																							GTGTAAAAAAAGTCAAAGTACA	0.332													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33831935	33831936	+	IGR	INS	-	T	T	rs147532074		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33831935_33831936insT								SLC6A10P (935472 upstream) : MIR1826 (133572 downstream)																							tcaaaaaaaaaaatgtatttta	0.099													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34179236	34179236	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34179236delC								MIR1826 (213644 upstream) : UBE2MP1 (224566 downstream)																							GATTCTAAGGCAATCCTTAAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46673955	46673956	+	IGR	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46673955_46673956delAC								SHCBP1 (18644 upstream) : VPS35 (19635 downstream)																							gtacacacagacacacacacac	0.079													7	4	---	---	---	---	
ITFG1	81533	broad.mit.edu	37	16	47320552	47320552	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47320552delA	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)				accctgcctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54725114	54725114	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54725114delA								IRX3 (404736 upstream) : IRX5 (239997 downstream)																							ataagaacttaaaaaaaaact	0.100													4	2	---	---	---	---	
MT1X	4501	broad.mit.edu	37	16	56716070	56716071	+	5'Flank	INS	-	G	G	rs140699532	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56716070_56716071insG	uc002ejy.2	+						MT1X_uc002ejz.2_5'Flank	NM_005952	NP_005943	P80297	MT1X_HUMAN	metallothionein 1X						response to metal ion		metal ion binding				0						CACAGTGGAGCGGGGGCTGGGG	0.619													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61644688	61644689	+	IGR	INS	-	A	A	rs145719481	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61644688_61644689insA								None (None upstream) : CDH8 (42546 downstream)																							ccatctcaaagaaaaaaaaaag	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64744872	64744872	+	IGR	DEL	G	-	-	rs34285799		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64744872delG								None (None upstream) : CDH11 (235813 downstream)																							TGAATTTAGTGGCATAAGAAG	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66396476	66396483	+	IGR	DEL	CATTCATT	-	-	rs71376796		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66396476_66396483delCATTCATT								LOC283867 (786273 upstream) : CDH5 (4042 downstream)																							actattcacgcattcattcattcattca	0.399													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66448646	66448646	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66448646delT								CDH5 (9958 upstream) : BEAN (12594 downstream)																							ggttttcttatttctagcctc	0.000													4	2	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71130381	71130382	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71130381_71130382delTG	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron|HYDIN_uc002ezw.3_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				ctctgtcttttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72673533	72673533	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72673533delA								PMFBP1 (467184 upstream) : ZFHX3 (143255 downstream)																							catctctgccaaaaaaaaaaa	0.000													4	3	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	79186571	79186571	+	Intron	DEL	A	-	-	rs5818205		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79186571delA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		catctcaaagaaaaaaaaaaa	0.234													4	2	---	---	---	---	
KIAA1609	57707	broad.mit.edu	37	16	84535750	84535751	+	Intron	INS	-	A	A	rs77402126		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84535750_84535751insA	uc002fib.2	-						KIAA1609_uc010vod.1_Intron|KIAA1609_uc002fic.2_Intron	NM_020947	NP_065998	Q6P9B6	K1609_HUMAN	hypothetical protein LOC57707								protein binding			ovary(2)	2						aactcggtctcaaaaaaaaaaa	0.134													3	3	---	---	---	---	
COTL1	23406	broad.mit.edu	37	16	84612282	84612283	+	Intron	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84612282_84612283delCA	uc002fid.2	-						COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_Intron|COTL1_uc002fif.1_5'Flank	NM_021149	NP_066972	Q14019	COTL1_HUMAN	coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1						cacaagtgtgcacacacacaca	0.000													4	2	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	744651	744651	+	Intron	DEL	T	-	-	rs66855800		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:744651delT	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	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)		AGGTCCCCCCTGACCACGGCG	0.692													5	3	---	---	---	---	
PITPNA	5306	broad.mit.edu	37	17	1464428	1464429	+	Intron	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1464428_1464429delCA	uc002fst.3	-						PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron|PITPNA_uc010vqn.1_5'Flank	NM_006224	NP_006215	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha						axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)		cacgcacacgcacacacacaca	0.421													3	4	---	---	---	---	
SMG6	23293	broad.mit.edu	37	17	2202012	2202012	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2202012delA	uc002fub.1	-							NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						actccgtcttaaaaaaaaaaa	0.169													2	4	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9968070	9968073	+	Intron	DEL	TGTT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9968070_9968073delTGTT	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						ctgctgacactgtttgtttaagcc	0.000			T	MLL	AML*								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15088995	15088995	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15088995delC								HS3ST3B1 (839503 upstream) : PMP22 (44102 downstream)																							AGGAAACTTTCCCCTACCCCT	0.294													4	2	---	---	---	---	
SLC5A10	125206	broad.mit.edu	37	17	18856048	18856048	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18856048delG	uc002guu.1	+						SLC5A10_uc002gur.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron|uc002gus.1_Intron	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose						sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1						ggagggccctgggaactgggg	0.269													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21233549	21233550	+	IGR	INS	-	ATCAGA	ATCAGA	rs71291786		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21233549_21233550insATCAGA								MAP2K3 (15000 upstream) : KCNJ12 (46149 downstream)																							gaggcaactagatcagaatcct	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21244088	21244089	+	IGR	INS	-	A	A	rs139026617		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21244088_21244089insA								MAP2K3 (25539 upstream) : KCNJ12 (35610 downstream)																							ACAGACAAAAGGGTTggccggg	0.094													5	5	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21313451	21313451	+	Intron	DEL	C	-	-	rs147481555		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21313451delC	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)	CTGGCAGTGTCCCCCAGGAGT	0.657										Prostate(3;0.18)			11	6	---	---	---	---	
RHBDL3	162494	broad.mit.edu	37	17	30620814	30620815	+	Intron	DEL	AC	-	-	rs150022121		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30620814_30620815delAC	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)				CGGCCATTTGACACAAAATAAG	0.342													6	3	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31733044	31733045	+	Intron	INS	-	G	G	rs145616314	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31733044_31733045insG	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)	gctctttccatgaaaaaaaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33238629	33238630	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33238629_33238630insA								TMEM132E (272293 upstream) : CCT6B (16310 downstream)																							gtctctgaaagaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34981871	34981873	+	IGR	DEL	CTC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34981871_34981873delCTC								MRM1 (16465 upstream) : LHX1 (312626 downstream)																							tcttcctcttctcctcctcctcc	0.010													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43661575	43661576	+	IGR	INS	-	TA	TA	rs149312176	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43661575_43661576insTA								LRRC37A4 (66059 upstream) : LOC644172 (15915 downstream)																							TTCCAGAAAACTACCAAAACAA	0.376													4	2	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43908477	43908477	+	Intron	DEL	T	-	-	rs56396707		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43908477delT	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		tccctgcctgtgctctgCCTG	0.199													5	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44213548	44213550	+	Intron	DEL	AAT	-	-	rs67496658		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44213548_44213550delAAT	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				TATTTGGGAAAATAATAATCCAT	0.360													4	2	---	---	---	---	
TBX21	30009	broad.mit.edu	37	17	45815971	45815971	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45815971delT	uc002ilv.1	+							NM_013351	NP_037483	Q9UL17	TBX21_HUMAN	T-box 21						lymphocyte migration|multicellular organismal development|positive regulation of transcription, DNA-dependent|response to virus	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0						tattatcacattttttttttt	0.000													4	2	---	---	---	---	
MYCBPAP	84073	broad.mit.edu	37	17	48585504	48585504	+	5'Flank	DEL	C	-	-	rs112843017		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48585504delC	uc010wmr.1	+						MYCBPAP_uc002iqx.2_5'Flank|MYCBPAP_uc002iqz.2_5'Flank	NM_032133	NP_115509	Q8TBZ2	MYBPP_HUMAN	Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			AAGGCCCGATCCCCCCCCAGA	0.667													3	3	---	---	---	---	
NME1-NME2	654364	broad.mit.edu	37	17	49239773	49239773	+	Intron	DEL	A	-	-	rs71355726		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49239773delA	uc002itk.2	+						NME1-NME2_uc002itj.2_Intron	NM_002512	NP_002503	P22392	NDKB_HUMAN	nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			ctgtctcactaaaaaaaaaaa	0.015													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50816115	50816115	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50816115delT								CA10 (578738 upstream) : None (None downstream)																							CTTTTATCCCTTTTTACTCAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54856450	54856452	+	IGR	DEL	GAT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54856450_54856452delGAT								NOG (183499 upstream) : C17orf67 (12823 downstream)																							tgtaaaatgggatgatgatgatg	0.010													4	2	---	---	---	---	
BRIP1	83990	broad.mit.edu	37	17	59942494	59942494	+	5'Flank	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59942494delA	uc002izk.1	-							NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.164			F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
EFCAB3	146779	broad.mit.edu	37	17	60454404	60454405	+	Intron	DEL	AG	-	-	rs111680352		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60454404_60454405delAG	uc010wpc.1	+							NM_001144933	NP_001138405	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3 isoform a								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			GCCAAGCAATAGAGAGAGAGAG	0.431													4	2	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60817411	60817414	+	Intron	DEL	GTGT	-	-	rs72191101		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60817411_60817414delGTGT	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						CTTCTCTGCAgtgtgtgtgtgtgt	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66965746	66965747	+	IGR	INS	-	TT	TT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66965746_66965747insTT								ABCA8 (14213 upstream) : ABCA9 (5027 downstream)																							cagagtcttgctttgttgccca	0.040													4	2	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73659596	73659596	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73659596delA	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jpb.1_Intron|RECQL5_uc002joz.3_Intron|RECQL5_uc002jpa.3_Intron	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			cgtcagcactaaaattttttg	0.015								Other_identified_genes_with_known_or_suspected_DNA_repair_function					4	2	---	---	---	---	
FOXJ1	2302	broad.mit.edu	37	17	74136908	74136909	+	5'Flank	INS	-	C	C			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74136908_74136909insC	uc002jqw.2	-						FOXJ1_uc002jqx.2_Intron|uc002jqy.1_Intron	NM_001454	NP_001445	Q92949	FOXJ1_HUMAN	forkhead box J1						actin cytoskeleton organization|activation of Rho GTPase activity|central tolerance induction|cilium assembly|epithelial cell differentiation|establishment of apical/basal cell polarity|heart looping|humoral immune response|left/right pattern formation|leukocyte migration|lung development|negative regulation of B cell activation|negative regulation of germinal center formation|negative regulation of humoral immune response mediated by circulating immunoglobulin|negative regulation of interleukin-6 biosynthetic process|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell differentiation in thymus|negative regulation of T cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of central B cell tolerance induction|spermatogenesis	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			pancreas(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)			GGAAATCAGGACCCCCTTCCTC	0.559													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76532852	76532853	+	IGR	INS	-	A	A	rs147988376	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76532852_76532853insA								DNAH17 (63996 upstream) : CYTH1 (137278 downstream)																							GATGATGAGGGAATGAAACCCA	0.485													3	3	---	---	---	---	
BAIAP2	10458	broad.mit.edu	37	17	79068204	79068204	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79068204delT	uc002jzg.2	+						BAIAP2_uc002jyz.3_Intron|BAIAP2_uc002jza.2_Intron|BAIAP2_uc002jzc.2_Intron|BAIAP2_uc002jzb.2_Intron|BAIAP2_uc002jzd.2_Intron|BAIAP2_uc002jzf.2_Intron|BAIAP2_uc002jze.2_Intron|BAIAP2_uc010wuh.1_Intron|BAIAP2_uc002jzh.2_Intron	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2						axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			gctctgggcctttttcccagg	0.423													4	2	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80152185	80152186	+	Intron	INS	-	T	T	rs140430398		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80152185_80152186insT	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GACTCAATGACttttttttttt	0.193													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	80613179	80613179	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80613179delG								WDR45L (6768 upstream) : RAB40B (1765 downstream)																							ggggacttctggtggtGTTTC	0.264													4	2	---	---	---	---	
B3GNTL1	146712	broad.mit.edu	37	17	80984843	80984843	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80984843delG	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron	NM_001009905	NP_001009905	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			GAGCGGGGCAGGGAGCCTGCA	0.647													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10288	10289	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10288_10289insA								None (None upstream) : USP14 (148194 downstream)																							accctaaccctaccctaaccct	0.000													4	2	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3134953	3134954	+	Intron	INS	-	TT	TT			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3134953_3134954insTT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TTATTTTACGAttttttttttt	0.168													3	3	---	---	---	---	
NAPG	8774	broad.mit.edu	37	18	10530665	10530665	+	Intron	DEL	T	-	-	rs71360247		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10530665delT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron	NM_003826	NP_003817	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0						TGGTTTCTCCTTTTTTTTTTT	0.398													4	2	---	---	---	---	
FAM38B	63895	broad.mit.edu	37	18	10887063	10887064	+	Intron	INS	-	T	T	rs61402527		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10887063_10887064insT	uc002kow.1	-									Q9H5I5	PIEZ2_HUMAN	RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1						aggtgacacacttttttttttt	0.000													3	3	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13497350	13497351	+	Intron	INS	-	T	T	rs141325343	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13497350_13497351insT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		taatttgtttgttttttttgta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14144044	14144044	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14144044delT								ZNF519 (11615 upstream) : LOC284233 (193378 downstream)																							CAATGTGCTCTGGTCTCACAT	0.587													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15223166	15223166	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15223166delC								ANKRD30B (370429 upstream) : LOC644669 (90389 downstream)																							aaccttggtgctacttacctt	0.174													4	2	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21479634	21479634	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21479634delA	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCATGCAAAGAAAAAAAAAAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23987193	23987193	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23987193delA								TAF4B (15546 upstream) : KCTD1 (47684 downstream)																							AGTTTGAGGGAAAAAAAAAAA	0.453													4	2	---	---	---	---	
ACAA2	10449	broad.mit.edu	37	18	47328930	47328931	+	Intron	INS	-	A	A	rs74176744		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47328930_47328931insA	uc002ldw.3	-						ACAA2_uc002ldx.3_Intron	NM_006111	NP_006102	P42765	THIM_HUMAN	acetyl-coenzyme A acyltransferase 2						anti-apoptosis|cholesterol biosynthetic process		acetyl-CoA C-acyltransferase activity|protein binding			ovary(1)	1						gactccatctcaaaaaaaaaaa	0.104													6	4	---	---	---	---	
CCDC68	80323	broad.mit.edu	37	18	52627542	52627543	+	5'Flank	INS	-	T	T	rs141642553	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52627542_52627543insT	uc002lfs.2	-						CCDC68_uc002lft.2_5'Flank	NM_001143829	NP_001137301	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68											skin(1)	1				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		attgtctactgtttttttctca	0.000													2	4	---	---	---	---	
CDH20	28316	broad.mit.edu	37	18	59074237	59074237	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59074237delC	uc002lif.2	+							NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				catccttttaccatgtggtac	0.000													4	2	---	---	---	---	
PIGN	23556	broad.mit.edu	37	18	59829578	59829578	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59829578delA	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)				GATCGAGGAGAAAAAAAAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	66826843	66826844	+	IGR	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66826843_66826844insA								CCDC102B (104417 upstream) : DOK6 (241447 downstream)																							cacaagcaaagaaaaaaaaaaa	0.312													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	77393602	77393604	+	IGR	DEL	ATA	-	-	rs137906533		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77393602_77393604delATA								NFATC1 (104280 upstream) : CTDP1 (46197 downstream)																							ggtggtggtgataatggtggtgg	0.000													4	2	---	---	---	---	
ZFR2	23217	broad.mit.edu	37	19	3871116	3871117	+	5'Flank	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3871116_3871117insT	uc002lyw.2	-						ZFR2_uc010xhx.1_5'Flank|ZFR2_uc002lyx.3_5'Flank|ZFR2_uc010xhy.1_5'Flank	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		ttttttgcttgttttttttttg	0.267													4	2	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	8982615	8982616	+	Intron	INS	-	TA	TA			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8982615_8982616insTA	uc002mkp.2	-						MUC16_uc010dwi.2_Intron|MUC16_uc010dwj.2_Intron|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						cttcctcctcctcttcctcctc	0.000													6	3	---	---	---	---	
SLC44A2	57153	broad.mit.edu	37	19	10718903	10718903	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10718903delA	uc002mpe.3	+							NM_001145056	NP_001138528	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 2						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	cgtctcaaagaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	10807905	10807905	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10807905delT								ILF3 (4812 upstream) : QTRT1 (4207 downstream)																							tttctttttcttttttttttt	0.209													4	2	---	---	---	---	
ELAVL3	1995	broad.mit.edu	37	19	11565283	11565284	+	3'UTR	DEL	TT	-	-	rs144868210	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11565283_11565284delTT	uc002mry.1	-	7					ELAVL3_uc002mrx.1_3'UTR	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3						tctctctctctttctctctctc	0.569													7	4	---	---	---	---	
ZNF833	401898	broad.mit.edu	37	19	11779100	11779100	+	Intron	DEL	A	-	-	rs34958870		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11779100delA	uc002msl.3	+											Homo sapiens cDNA FLJ44800 fis, clone BRACE3041162, moderately similar to Homo sapiens zinc finger protein 14 (KOX 6) (ZNF14).												0						actccacctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FBXW9	84261	broad.mit.edu	37	19	12799467	12799467	+	Intron	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12799467delC	uc010xmp.1	-						uc002mul.1_5'Flank			Q5XUX1	FBXW9_HUMAN	Homo sapiens cDNA FLJ41042 fis, clone NT2RI2005166, highly similar to F-box/WD repeat protein 9.								protein binding			ovary(1)	1						GGTACCCTTTCCCACCGTGCA	0.572													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13134928	13134928	+	5'Flank	DEL	A	-	-	rs113861190		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13134928delA	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_5'Flank|NFIX_uc002mwg.1_5'Flank			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)			gcaaacaaccaaaaaaaaaaa	0.323													4	2	---	---	---	---	
ZSWIM4	65249	broad.mit.edu	37	19	13929682	13929683	+	Intron	INS	-	T	T	rs35655398		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13929682_13929683insT	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)			CCTGCCTCCtcttttttttttt	0.059													2	4	---	---	---	---	
RFX1	5989	broad.mit.edu	37	19	14088529	14088529	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14088529delT	uc002mxv.2	-						RFX1_uc010dzi.2_Intron	NM_002918	NP_002909	P22670	RFX1_HUMAN	regulatory factor X1						immune response	nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			lung(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			gtgcctggccTTTTTTTTTTT	0.234													3	3	---	---	---	---	
RASAL3	64926	broad.mit.edu	37	19	15564239	15564239	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15564239delG	uc002nbe.2	-	15	2435	c.2349delC	c.(2347-2349)TCCfs	p.S783fs	RASAL3_uc002nbd.2_Frame_Shift_Del_p.S123fs|RASAL3_uc010eaa.1_Frame_Shift_Del_p.S271fs	NM_022904	NP_075055	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	783					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity				0						ACTGGCTCTTGGAGATGAGAG	0.711													4	2	---	---	---	---	
RASAL3	64926	broad.mit.edu	37	19	15575174	15575174	+	5'UTR	DEL	G	-	-	rs76267899		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15575174delG	uc002nbe.2	-	2						NM_022904	NP_075055	Q86YV0	RASL3_HUMAN	RAS protein activator like 3						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity				0						GTCCATGGTTGGGGGGGGGGG	0.542													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15923186	15923188	+	IGR	DEL	AGG	-	-	rs72338635		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15923186_15923188delAGG								OR10H1 (4250 upstream) : UCA1 (16569 downstream)																							GAGAGAGAAAAGGAGGAGGAGGA	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16271271	16271271	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16271271delG								HSH2D (1896 upstream) : CIB3 (909 downstream)																							tgctgaggctggtctcaaatt	0.030													4	2	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17124695	17124698	+	Intron	DEL	TTCC	-	-	rs77591148		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17124695_17124698delTTCC	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						CACTACACAAttccttccttcctt	0.074													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20764949	20764949	+	IGR	DEL	A	-	-	rs34931847		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20764949delA								ZNF737 (16323 upstream) : ZNF626 (37796 downstream)																							attgccttgtatactacatca	0.000													3	4	---	---	---	---	
ZNF492	57615	broad.mit.edu	37	19	22829886	22829886	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22829886delT	uc002nqw.3	+							NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				agagacgaagtttctccatgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24538348	24538348	+	IGR	DEL	G	-	-	rs61326588		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24538348delG								LOC100101266 (192099 upstream) : None (None downstream)																							tgaaaatgctgtttttttggt	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27743254	27743254	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27743254delT								None (None upstream) : LOC148189 (538148 downstream)																							cattgagcagttttgaaacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27760316	27760317	+	IGR	INS	-	G	G	rs139162881		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27760316_27760317insG								None (None upstream) : LOC148189 (521085 downstream)																							aaaaaactagacagaagcattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27882741	27882741	+	IGR	DEL	A	-	-	rs113167415		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27882741delA								None (None upstream) : LOC148189 (398661 downstream)																							cctgtggtggaaaaggaaata	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28635419	28635420	+	IGR	DEL	GA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28635419_28635420delGA								LOC148189 (350571 upstream) : LOC148145 (820620 downstream)																							ACACATACACgagagagagaga	0.193													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29501160	29501161	+	Intron	INS	-	CACT	CACT	rs72045999		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29501160_29501161insCACT	uc002nsc.1	+											Homo sapiens cDNA FLJ30538 fis, clone BRAWH2001238.																		actcacacacacctaacacaca	0.059													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31460425	31460428	+	IGR	DEL	ACAC	-	-	rs71333495		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31460425_31460428delACAC								ZNF536 (411460 upstream) : DKFZp566F0947 (180355 downstream)																							acacacacagacacacacacacac	0.000													2	5	---	---	---	---	
PEPD	5184	broad.mit.edu	37	19	33913329	33913330	+	Intron	INS	-	CTAT	CTAT	rs149802080	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33913329_33913330insCTAT	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)					gatctacctacctatcatctac	0.025													4	2	---	---	---	---	
ATP4A	495	broad.mit.edu	37	19	36043793	36043793	+	Intron	DEL	C	-	-	rs66822505		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36043793delC	uc002oal.1	-						ATP4A_uc010eee.1_Intron	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A						ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)	AAGGCCCTTGCCCCCCCGAAC	0.373													11	7	---	---	---	---	
UPK1A	11045	broad.mit.edu	37	19	36157321	36157322	+	5'Flank	DEL	AC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36157321_36157322delAC	uc002oaw.2	+						UPK1A_uc010eeh.2_5'Flank	NM_007000	NP_008931	O00322	UPK1A_HUMAN	uroplakin 1A						epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTGCCCCAAAacacacacacac	0.564													4	2	---	---	---	---	
CYP2F1	1572	broad.mit.edu	37	19	41870951	41870951	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41870951delT	uc010xvw.1	+						TMEM91_uc002oqi.2_Intron|B9D2_uc002oqj.2_5'Flank|TMEM91_uc010ehq.2_Intron			P24903	CP2F1_HUMAN	SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						tggctaattcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47009198	47009199	+	IGR	INS	-	T	T	rs34860256		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47009198_47009199insT								PNMAL2 (10029 upstream) : CALM3 (95313 downstream)																							CAACTGTTGACttttttttttt	0.069													2	6	---	---	---	---	
GRLF1	2909	broad.mit.edu	37	19	47507176	47507177	+	3'UTR	DEL	CA	-	-	rs35048370		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47507176_47507177delCA	uc010ekv.2	+	6						NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		TCTGGacacgcacacacacaca	0.495													5	3	---	---	---	---	
CARD8	22900	broad.mit.edu	37	19	48713355	48713356	+	3'UTR	INS	-	AAAGAA	AAAGAA	rs148551120	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48713355_48713356insAAAGAA	uc002pie.3	-	10					CARD8_uc002pii.3_3'UTR|CARD8_uc002pid.1_Intron|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_3'UTR|CARD8_uc010xzj.1_3'UTR|CARD8_uc010xzk.1_3'UTR|CARD8_uc002pif.3_3'UTR|CARD8_uc002pig.3_3'UTR|CARD8_uc002pih.3_3'UTR|CARD8_uc010xzl.1_3'UTR|CARD8_uc010xzm.1_3'UTR	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		aaactaaagataaataccttga	0.000													4	2	---	---	---	---	
LRRC4B	94030	broad.mit.edu	37	19	51069099	51069102	+	Intron	DEL	TCTT	-	-	rs141559792		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51069099_51069102delTCTT	uc002pss.2	-							NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor							cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)|skin(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GCTCCCCGACTCTTTCTTTCGGAA	0.539													5	4	---	---	---	---	
KLK12	43849	broad.mit.edu	37	19	51538606	51538606	+	5'Flank	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51538606delA	uc002pvg.1	-						KLK12_uc010ycp.1_5'Flank|KLK12_uc010ycq.1_5'Flank|KLK12_uc010ycr.1_5'Flank|KLK12_uc010ycs.1_5'Flank|KLK12_uc002pvh.1_5'Flank|KLK12_uc002pvi.1_5'Flank|KLK12_uc002pvj.1_5'Flank	NM_145894	NP_665901	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 2						proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		CATGCAGTGCaggggaggggc	0.373													4	2	---	---	---	---	
TTYH1	57348	broad.mit.edu	37	19	54925442	54925443	+	5'Flank	INS	-	CAT	CAT	rs146951043		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54925442_54925443insCAT	uc002qfq.2	+						TTYH1_uc010yey.1_5'Flank|TTYH1_uc002qfr.2_5'Flank|TTYH1_uc002qft.2_5'Flank	NM_020659	NP_065710	Q9H313	TTYH1_HUMAN	tweety 1 isoform 1						cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		catgtcttcaccatcatcatca	0.000													4	2	---	---	---	---	
LAIR2	3904	broad.mit.edu	37	19	55014674	55014675	+	Intron	INS	-	CAA	CAA	rs145014373	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55014674_55014675insCAA	uc002qgc.2	+						LAIR2_uc002qga.1_Intron|LAIR2_uc002qgb.1_Intron|LAIR2_uc002qgd.2_Intron|LAIR2_uc010erl.2_Intron	NM_002288	NP_002279	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like							extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		aactccgtctccaacaacacca	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56075514	56075515	+	IGR	INS	-	C	C	rs143539582	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56075514_56075515insC								SBK2 (27853 upstream) : ZNF579 (13377 downstream)																							ctccctctctgcccctctgtct	0.252													4	2	---	---	---	---	
NLRP5	126206	broad.mit.edu	37	19	56539152	56539152	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56539152delG	uc002qmj.2	+	7	1553	c.1553delG	c.(1552-1554)CGCfs	p.R518fs	NLRP5_uc002qmi.2_Frame_Shift_Del_p.R499fs	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	518	NACHT.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GTGGTCCGGCGCTGTCTCAAT	0.592													30	13	---	---	---	---	
ZSCAN5A	79149	broad.mit.edu	37	19	56813917	56813920	+	Intron	DEL	CCTC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56813917_56813920delCCTC	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						cctccccgttcctccctccctccc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	600990	600990	+	IGR	DEL	G	-	-	rs63283561		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:600990delG								TCF15 (10080 upstream) : SRXN1 (26280 downstream)																							CTGGGGCAAAGTGGGGGCCAG	0.532													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	937267	937267	+	IGR	DEL	T	-	-	rs6118354	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:937267delT								ANGPT4 (40307 upstream) : RSPO4 (1831 downstream)																							TTGACTGCCGTCATCCGGTGG	0.612											OREG0025712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
C20orf46	55321	broad.mit.edu	37	20	1165266	1165267	+	5'Flank	DEL	AC	-	-	rs72407722		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1165266_1165267delAC	uc010gaa.1	-						C20orf46_uc002weq.1_5'Flank	NM_018354	NP_060824	Q9NUR3	CT046_HUMAN	hypothetical protein LOC55321							integral to membrane	protein binding			ovary(1)	1						acacgcgcgtacacacacacac	0.465													4	2	---	---	---	---	
TGM3	7053	broad.mit.edu	37	20	2287118	2287119	+	Intron	INS	-	T	T	rs33929365		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2287118_2287119insT	uc002wfx.3	+							NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor						cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)	Cttttcctttcttttttttttt	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5337306	5337309	+	IGR	DEL	TGTC	-	-	rs34333551		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5337306_5337309delTGTC								PROKR2 (39928 upstream) : LOC149837 (141909 downstream)																							agttggtaagtgtctggtaattta	0.118													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7549433	7549434	+	IGR	DEL	GT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7549433_7549434delGT								BMP2 (788523 upstream) : HAO1 (314197 downstream)																							CCAGgtgtgcgtgtgtgtgtgt	0.307													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8590029	8590029	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8590029delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						GCTCCAGCACTTGGATGAGGC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19757495	19757495	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19757495delT								SLC24A3 (53955 upstream) : RIN2 (112715 downstream)																							catgtattgattatgtcttag	0.000													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20276779	20276784	+	Intron	DEL	CTCCCT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20276779_20276784delCTCCCT	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		tccttccttcctccctccctccctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22201842	22201843	+	IGR	INS	-	A	A	rs11477593		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22201842_22201843insA								PAX1 (505222 upstream) : LOC284788 (179128 downstream)																							GTGCTCACGTGAAAAAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25878212	25878213	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25878212_25878213insT								FAM182B (29426 upstream) : LOC100134868 (112222 downstream)																							GGTAAAAAAAAAAAATAGGACT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26080322	26080334	+	IGR	DEL	CCACAGGCTCTTT	-	-	rs111960742		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26080322_26080334delCCACAGGCTCTTT								FAM182A (12770 upstream) : C20orf191 (3719 downstream)																							ACAGTCCTTCCCACAGGCTCTTTTTCTTACATT	0.451													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26107562	26107567	+	IGR	DEL	ATCAGA	-	-	rs111523622		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26107562_26107567delATCAGA								C20orf191 (12885 upstream) : MIR663 (81255 downstream)																							acaaaaggccatcagaatcacatttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26117644	26117645	+	IGR	INS	-	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26117644_26117645insG								C20orf191 (22967 upstream) : MIR663 (71177 downstream)																							caaggaggaacgggggaaagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29458820	29458820	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29458820delA								None (None upstream) : FRG1B (153059 downstream)																							tgccacttttaaaaccatcag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29465614	29465614	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29465614delT								None (None upstream) : FRG1B (146265 downstream)																							agattccaaattttttttccc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29587776	29587776	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29587776delG								None (None upstream) : FRG1B (24103 downstream)																							aatgatttttgtatgtcaatt	0.000													4	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29651067	29651070	+	Intron	DEL	ATTT	-	-	rs113518453		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29651067_29651070delATTT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						tgctgaattcatttaccagtccta	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31342225	31342225	+	IGR	DEL	T	-	-	rs113487486		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31342225delT								COMMD7 (10411 upstream) : DNMT3B (7966 downstream)																							gtcctgctGAttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36740455	36740457	+	IGR	DEL	TTT	-	-	rs149380856	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36740455_36740457delTTT								RPRD1B (19691 upstream) : TGM2 (16409 downstream)																							tccttccttctttccttctttcc	0.099													6	3	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45905654	45905655	+	Intron	INS	-	A	A			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45905654_45905655insA	uc002xta.1	-						ZMYND8_uc010ghq.1_5'Flank|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			CTTATTCtattaaaaaaaaaaa	0.297													4	2	---	---	---	---	
NFATC2	4773	broad.mit.edu	37	20	50143711	50143711	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50143711delA	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)					aagtgttgtgattacagacga	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52496428	52496429	+	IGR	DEL	GA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52496428_52496429delGA								SUMO1P1 (4180 upstream) : BCAS1 (63650 downstream)																							GGGGGGTGGGGagagagagaga	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55324935	55324936	+	IGR	DEL	CT	-	-	rs11467830		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55324935_55324936delCT								TFAP2C (110599 upstream) : BMP7 (418873 downstream)																							tgctctgtgGctctctctctct	0.144													4	3	---	---	---	---	
PMEPA1	56937	broad.mit.edu	37	20	56242302	56242302	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56242302delG	uc002xyq.2	-						PMEPA1_uc002xyr.2_Intron|PMEPA1_uc002xys.2_Intron|PMEPA1_uc002xyt.2_Intron	NM_020182	NP_064567	Q969W9	PMEPA_HUMAN	transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1						ctcTGTTCTTGGGGGCAGAGC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61680570	61680571	+	Intron	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61680570_61680571insT	uc002yec.1	+											Homo sapiens cDNA FLJ46471 fis, clone THYMU3023394.																		cctcttcctcccctcctcctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9669199	9669200	+	IGR	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9669199_9669200delCA								None (None upstream) : None (None downstream)																							ctttttgactcacagggtattt	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10513830	10513833	+	Intron	DEL	ATAC	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10513830_10513833delATAC	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		AACATATCAAATACATATTTTTCC	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10603457	10603457	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10603457delA								None (None upstream) : TPTE (303286 downstream)																							ggcataaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10609042	10609043	+	IGR	INS	-	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10609042_10609043insG								None (None upstream) : TPTE (297700 downstream)																							AGTATCCACTTGGGGCCTCATA	0.594													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10763132	10763133	+	IGR	INS	-	A	A	rs77491741		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10763132_10763133insA								None (None upstream) : TPTE (143610 downstream)																							gctccatcaagaaaagatcaac	0.000													5	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11048049	11048049	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11048049delA	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)		ctgtgtcactaaacaacttag	0.055													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088325	11088325	+	Intron	DEL	T	-	-	rs141258995		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088325delT	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)		TTATTGGTAATTTTTCAAAAA	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11116167	11116168	+	IGR	INS	-	AG	AG	rs138129426		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11116167_11116168insAG								BAGE (17230 upstream) : None (None downstream)																							cagtgatagaaagggagacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11120163	11120164	+	IGR	DEL	TT	-	-	rs112214687		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11120163_11120164delTT								BAGE (21226 upstream) : None (None downstream)																							ctttggaaactttgaactcttc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20229947	20229948	+	IGR	INS	-	T	T	rs140136910	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20229947_20229948insT								TMPRSS15 (453977 upstream) : None (None downstream)																							taagatctgcataaaaaaacaa	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	27617627	27617628	+	IGR	DEL	CT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27617627_27617628delCT								APP (74181 upstream) : CYYR1 (220901 downstream)																							cctccccttgctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40910280	40910280	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40910280delG								SH3BGR (22854 upstream) : B3GALT5 (18089 downstream)																							ggggaagaatgaaaggaagtg	0.000													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41412510	41412510	+	Intron	DEL	A	-	-	rs143706329		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41412510delA	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)				GGAGAAAAATAAAAGCAAGAA	0.488													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42278191	42278192	+	IGR	INS	-	TCC	TCC	rs144795481	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42278191_42278192insTCC								DSCAM (59152 upstream) : C21orf130 (235235 downstream)																							ACCCTGGCTAATCCTGATGTAA	0.411													4	4	---	---	---	---	
UMODL1	89766	broad.mit.edu	37	21	43542773	43542774	+	Intron	DEL	GT	-	-	rs111885176		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43542773_43542774delGT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.1_Intron	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						atatgtgtgcgtgtgtgtgtgt	0.223													3	3	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47819269	47819270	+	Intron	INS	-	CC	CC	rs10645543		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47819269_47819270insCC	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					GGTCTAGGTCTCTGTTCAGCCT	0.589													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17792885	17792885	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17792885delT								CECR1 (90147 upstream) : CECR2 (47954 downstream)																							ACCAAAAGTGTTTGACCAAGA	0.408													4	2	---	---	---	---	
TOP3B	8940	broad.mit.edu	37	22	22327230	22327231	+	Intron	INS	-	CAGAGG	CAGAGG	rs144883685	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22327230_22327231insCAGAGG	uc002zvs.2	-						TOP3B_uc010gtl.2_Intron|TOP3B_uc002zvt.3_Intron	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta						DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		atcctgatgatcagaggcagag	0.163													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22879185	22879186	+	Intron	INS	-	TT	TT	rs144156757	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22879185_22879186insTT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						ATTTTACTGACATTTTAATTTG	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	26915447	26915447	+	IGR	DEL	A	-	-	rs147972713		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26915447delA								TFIP11 (7010 upstream) : TPST2 (6269 downstream)																							CTTTGAGGACAGGGGTAAGAG	0.438													3	3	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29518220	29518221	+	Intron	INS	-	G	G			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29518220_29518221insG	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						accagttgtcagggaaatacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32656495	32656496	+	IGR	INS	-	A	A	rs112479269		TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32656495_32656496insA								SLC5A4 (5177 upstream) : RFPL3 (94376 downstream)																							ATTTTGGTGACAaaaaaaaaaa	0.416													4	3	---	---	---	---	
IL2RB	3560	broad.mit.edu	37	22	37526912	37526912	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37526912delT	uc003aqv.1	-							NM_000878	NP_000869	P14784	IL2RB_HUMAN	interleukin 2 receptor beta precursor						interspecies interaction between organisms|positive regulation of survival gene product expression|protein complex assembly	external side of plasma membrane|integral to plasma membrane	interleukin-2 receptor activity				0					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	ACATTAAGAGTACTGCAACTA	0.100													4	2	---	---	---	---	
SEPT3	55964	broad.mit.edu	37	22	42390888	42390889	+	Intron	DEL	TG	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42390888_42390889delTG	uc003bbr.3	+						WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_3'UTR|SEPT3_uc010gyr.2_Intron|SEPT3_uc011apj.1_3'UTR|SEPT3_uc010gys.2_Intron	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A						cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0						GCATCTtgtctgtgtgtgtgtg	0.411													7	4	---	---	---	---	
NFAM1	150372	broad.mit.edu	37	22	42798644	42798645	+	Intron	INS	-	GAGGAT	GAGGAT	rs147662601	by1000genomes	TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42798644_42798645insGAGGAT	uc003bcn.3	-							NM_145912	NP_666017	Q8NET5	NFAM1_HUMAN	NFAT activation molecule 1 precursor						B cell differentiation|inflammatory response|intracellular signal transduction|positive regulation of B cell receptor signaling pathway|positive regulation of cytokine production|positive regulation of sequence-specific DNA binding transcription factor activity	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity				0						caatgccatgagaggatgagga	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47667677	47667677	+	IGR	DEL	C	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47667677delC								TBC1D22A (97955 upstream) : None (None downstream)																							agctgggactccaggcatgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49243977	49243978	+	IGR	DEL	CA	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49243977_49243978delCA								FAM19A5 (96235 upstream) : C22orf34 (564198 downstream)																							atgcgagttccacacacacaca	0.000													4	2	---	---	---	---	
SFRS17A	8227	broad.mit.edu	37	X	1714127	1714154	+	Intron	DEL	TCTGCACCGGACATGAGTGGTGAGCGGT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1714127_1714154delTCTGCACCGGACATGAGTGGTGAGCGGT	uc004cqa.2	+						SFRS17A_uc010ncx.1_Intron|SFRS17A_uc004cqb.2_Intron|ASMT_uc004cqd.2_5'Flank	NM_005088	NP_005079	Q02040	AK17A_HUMAN	DNA segment on chromosome X and Y (unique) 155						B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding				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)				ACTGTCTGGGTCTGCACCGGACATGAGTGGTGAGCGGTGAGCGGTGAG	0.623													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	2030347	2030350	+	IGR	DEL	TCAT	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2030347_2030350delTCAT								ASMT (268374 upstream) : DHRSX (107207 downstream)																							tgtctctctctcattctcttctct	0.000													4	3	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2287530	2287530	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2287530delT	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TTAGTTtttgtttttttttgt	0.214													2	5	---	---	---	---	
XG	7499	broad.mit.edu	37	X	2675265	2675265	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2675265delT	uc011mhg.1	+						XG_uc010ndb.2_Intron|XG_uc004cqp.2_Intron	NM_175569	NP_780778	P55808	XG_HUMAN	XG glycoprotein isoform 1 precursor							integral to membrane|plasma membrane				ovary(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				tgtgctgctctttggttcctc	0.000													4	2	---	---	---	---	
SMS	6611	broad.mit.edu	37	X	22003150	22003150	+	Intron	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22003150delG	uc004dag.2	+						SMS_uc010nfs.2_Intron|SMS_uc010nft.2_Intron	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	TCTTACACTCGTGGCTCTTTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61746118	61746118	+	IGR	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61746118delA								None (None upstream) : SPIN4 (820990 downstream)																							agagtgtttcaaaactgctct	0.000													4	2	---	---	---	---	
RAB41	347517	broad.mit.edu	37	X	69502909	69502909	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69502909delA	uc004dyc.2	+						RAB41_uc010nkv.2_Intron	NM_001032726	NP_001027898	Q5JT25	RAB41_HUMAN	RAB41, member RAS oncogene family						protein transport|small GTPase mediated signal transduction		GTP binding			ovary(2)|breast(2)	4						GCTGTGCTGTAGGGTCTTCCT	0.433													4	2	---	---	---	---	
NHSL2	340527	broad.mit.edu	37	X	71291576	71291576	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71291576delT	uc011mqa.1	+							NM_001013627	NP_001013649	Q5HYW2	NHSL2_HUMAN	NHS-like 2												0	Renal(35;0.156)					cttttctctcttccattttcg	0.159													4	2	---	---	---	---	
APOOL	139322	broad.mit.edu	37	X	84309335	84309335	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84309335delT	uc004eem.2	+						APOOL_uc010nmp.2_Intron	NM_198450	NP_940852	Q6UXV4	APOOL_HUMAN	apolipoprotein O-like precursor							extracellular region					0						CTTCCCCCCCTTTTTTTTTGC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	92643878	92643879	+	IGR	INS	-	T	T			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92643878_92643879insT								PCDH11X (765652 upstream) : NAP1L3 (282050 downstream)																							CCAtttttttcttttttttttt	0.312													3	3	---	---	---	---	
COL4A6	1288	broad.mit.edu	37	X	107512391	107512391	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107512391delA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.2_Intron	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						TGCTGCAGACAAAAAAAAAAT	0.438									Alport_syndrome_with_Diffuse_Leiomyomatosis				4	2	---	---	---	---	
ALG13	79868	broad.mit.edu	37	X	111000722	111000722	+	Intron	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111000722delT	uc011msy.1	+						ALG13_uc011msx.1_Intron|ALG13_uc011msz.1_Intron|ALG13_uc011mta.1_Intron|ALG13_uc011mtb.1_Intron			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);						dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1						CCAATTCTTATTTTTTTTTTT	0.338													3	3	---	---	---	---	
KLHL13	90293	broad.mit.edu	37	X	117079088	117079088	+	Intron	DEL	A	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117079088delA	uc004eql.2	-						KLHL13_uc004eqk.2_Intron|KLHL13_uc011mtn.1_Intron|KLHL13_uc011mto.1_Intron|KLHL13_uc011mtp.1_Intron|KLHL13_uc004eqm.2_Intron|KLHL13_uc011mtq.1_Intron	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13						cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)|skin(1)	2						GCATACTGGCAAAATGTCCTT	0.338													4	2	---	---	---	---	
MMGT1	93380	broad.mit.edu	37	X	135053241	135053241	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135053241delT	uc004ezi.1	-	2	408	c.108delA	c.(106-108)AAAfs	p.K36fs	MMGT1_uc011mvw.1_Frame_Shift_Del_p.K101fs	NM_173470	NP_775741	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1 precursor	36	Lumenal (Potential).					early endosome membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	magnesium ion transmembrane transporter activity				0						ATTCATCTTCTTTTTCTGTTA	0.284													32	38	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13419496	13419496	+	IGR	DEL	T	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13419496delT								None (None upstream) : None (None downstream)																							TATACTCCACTGAAATGTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13640949	13640949	+	IGR	DEL	G	-	-			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13640949delG								None (None upstream) : None (None downstream)																							gaaggagagagaagaagagaa	0.090													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59033127	59033128	+	IGR	INS	-	CTTTC	CTTTC			TCGA-66-2791-01	TCGA-66-2791-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59033127_59033128insCTTTC								None (None upstream) : None (None downstream)																							tttctttctttttattgtattt	0.000													4	2	---	---	---	---	
