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
MST1P2	11209	broad.mit.edu	37	1	16974182	16974182	+	RNA	SNP	C	A	A	rs144074313	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974182C>A	uc009vow.2	+	5		c.992C>A			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GAGCATATCCCGTGGAGTACC	0.672													6	35	---	---	---	---	PASS
USP33	23032	broad.mit.edu	37	1	78189117	78189117	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78189117A>G	uc001dht.2	-	13	1728	c.1381T>C	c.(1381-1383)TCT>CCT	p.S461P	USP33_uc001dhs.2_Missense_Mutation_p.S182P|USP33_uc001dhu.2_Missense_Mutation_p.S430P|USP33_uc001dhv.2_Missense_Mutation_p.S266P|USP33_uc001dhw.2_Missense_Mutation_p.S461P	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1	461					axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						CTCTTTGGAGATGCAGACTGA	0.333													8	624	---	---	---	---	PASS
FAM73A	374986	broad.mit.edu	37	1	78249000	78249000	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78249000T>C	uc001dhx.2	+	2	191	c.159T>C	c.(157-159)TTT>TTC	p.F53F	FAM73A_uc010ork.1_Silent_p.F53F|FAM73A_uc010orl.1_Intron	NM_198549	NP_940951	Q8NAN2	FA73A_HUMAN	hypothetical protein LOC374986	53						integral to membrane				ovary(1)	1				Colorectal(170;0.226)		TAAGAGTGTTTGATCTTCCTC	0.353													156	339	---	---	---	---	PASS
FRRS1	391059	broad.mit.edu	37	1	100212941	100212941	+	Missense_Mutation	SNP	C	T	T	rs141729391		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100212941C>T	uc001dsh.1	-	4	844	c.242G>A	c.(241-243)CGT>CAT	p.R81H		NM_001013660	NP_001013682	Q6ZNA5	FRRS1_HUMAN	stromal cell derived factor receptor 2 homolog	81	Reelin.				electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		CTCAGCATTACGCGCTTCTAG	0.388													4	245	---	---	---	---	PASS
HIAT1	64645	broad.mit.edu	37	1	100503796	100503796	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100503796A>T	uc001dst.2	+	1	8	c.8A>T	c.(7-9)CAG>CTG	p.Q3L		NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	3	Extracellular (Potential).				transmembrane transport	integral to membrane|plasma membrane	transporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		AAAATGACCCAGGGGAAGAAG	0.632													11	34	---	---	---	---	PASS
GPSM2	29899	broad.mit.edu	37	1	109466798	109466798	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109466798G>A	uc010ovc.1	+	14	2273	c.1777G>A	c.(1777-1779)GCT>ACT	p.A593T	AKNAD1_uc010ovb.1_Intron|GPSM2_uc010ovd.1_Missense_Mutation_p.A593T|GPSM2_uc010ove.1_Missense_Mutation_p.A593T	NM_013296	NP_037428	P81274	GPSM2_HUMAN	LGN protein	593					G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CAACAAAGAGGCTGATGAAGA	0.408													66	142	---	---	---	---	PASS
MAGI3	260425	broad.mit.edu	37	1	114193677	114193677	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114193677A>T	uc001edk.2	+	14	2470	c.2289A>T	c.(2287-2289)AAA>AAT	p.K763N	MAGI3_uc001edh.3_Missense_Mutation_p.K788N|MAGI3_uc001edi.3_Missense_Mutation_p.K763N|MAGI3_uc010owm.1_Missense_Mutation_p.K788N|MAGI3_uc001edj.2_Missense_Mutation_p.K484N	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	788	Interaction with BAI1.|PDZ 4.				apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGCTGAGAAAGATGGTCGGC	0.428													111	236	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118483544	118483544	+	Missense_Mutation	SNP	C	T	T	rs142439174	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118483544C>T	uc010oxe.1	+	7	836	c.770C>T	c.(769-771)ACG>ATG	p.T257M	WDR3_uc001ehi.2_Intron|WDR3_uc001ehh.2_Missense_Mutation_p.T86M	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	257						nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GCCTTTGAGACGGATGAAGCC	0.393													85	154	---	---	---	---	PASS
RPTN	126638	broad.mit.edu	37	1	152127611	152127611	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152127611C>T	uc001ezs.1	-	3	2029	c.1964G>A	c.(1963-1965)AGC>AAC	p.S655N		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	655	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						GTGATGTTGGCTATCCTCTTC	0.517													241	511	---	---	---	---	PASS
FDPS	2224	broad.mit.edu	37	1	155279736	155279736	+	Silent	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155279736A>G	uc001fkc.2	+	2	375	c.156A>G	c.(154-156)CAA>CAG	p.Q52Q	RAG1AP1_uc010pey.1_Intron|FDPS_uc001fkd.2_Intron|FDPS_uc001fke.2_Silent_p.Q52Q|FDPS_uc001fkf.2_Intron	NM_002004	NP_001995	P14324	FPPS_HUMAN	farnesyl diphosphate synthase isoform a	52					cholesterol biosynthetic process|interspecies interaction between organisms|isoprenoid biosynthetic process	cytosol|nucleus	dimethylallyltranstransferase activity|geranyltranstransferase activity|metal ion binding				0	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	GCTGGTGCCAAGCGTGGACAG	0.637													12	28	---	---	---	---	PASS
RNASEL	6041	broad.mit.edu	37	1	182551376	182551376	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182551376G>A	uc001gpj.1	-	3	1751	c.1584C>T	c.(1582-1584)GTC>GTT	p.V528V	RNASEL_uc009wxz.1_Silent_p.V528V|RNASEL_uc001gpk.2_Silent_p.V528V|RNASEL_uc009wya.1_Missense_Mutation_p.P500S	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	528	Protein kinase.				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						CCACATAGAGGACCAGCCGTC	0.363									Hereditary_Prostate_Cancer				50	93	---	---	---	---	PASS
NFASC	23114	broad.mit.edu	37	1	204955082	204955082	+	Intron	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204955082G>A	uc001hbj.2	+						NFASC_uc010pra.1_Silent_p.V873V|NFASC_uc001hbi.2_Silent_p.V873V|NFASC_uc010prb.1_Silent_p.V888V|NFASC_uc010prc.1_Silent_p.V444V|NFASC_uc001hbk.1_Silent_p.V683V|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_5'Flank|NFASC_uc001hbn.1_5'Flank	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ACCTGTGGGTGTCTCAGAAGA	0.602													17	37	---	---	---	---	PASS
C1orf55	163859	broad.mit.edu	37	1	226180697	226180697	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226180697C>A	uc001hpu.3	-	3	298	c.245G>T	c.(244-246)GGA>GTA	p.G82V	C1orf55_uc001hpv.2_Missense_Mutation_p.G82V	NM_152608	NP_689821	Q6IQ49	CA055_HUMAN	hypothetical protein LOC163859	82										lung(1)	1	Breast(184;0.197)					GAGCATAGATCCAAAACCTGA	0.413													54	94	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228403481	228403481	+	Silent	SNP	G	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228403481G>C	uc009xez.1	+	6	2090	c.2046G>C	c.(2044-2046)CTG>CTC	p.L682L	OBSCN_uc001hsn.2_Silent_p.L682L|uc001hsm.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	682	Ig-like 6.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				GGGCGCAGCTGAAGTTCGTGG	0.652													7	11	---	---	---	---	PASS
PLD5	200150	broad.mit.edu	37	1	242253179	242253179	+	Missense_Mutation	SNP	C	T	T	rs150166315	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253179C>T	uc001hzn.1	-	10	1715	c.1588G>A	c.(1588-1590)GGA>AGA	p.G530R	PLD5_uc001hzl.3_Missense_Mutation_p.G468R|PLD5_uc001hzm.3_Missense_Mutation_p.G320R|PLD5_uc001hzo.1_Missense_Mutation_p.G438R			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;	530						integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GGATCCTTTCCGCCTGTGTCG	0.443													10	527	---	---	---	---	PASS
CNST	163882	broad.mit.edu	37	1	246797267	246797267	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246797267C>A	uc001ibp.2	+	5	1036	c.658C>A	c.(658-660)CAT>AAT	p.H220N	CNST_uc001ibo.3_Missense_Mutation_p.H220N	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	220					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						ACGATTGTATCATGAGCAATT	0.353													95	228	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9468004	9468004	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9468004T>C	uc002qzh.2	+	7	990	c.650T>C	c.(649-651)CTT>CCT	p.L217P	ASAP2_uc002qzi.2_Missense_Mutation_p.L217P	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	217					regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						GTAGATTTACTTCAGAATCTG	0.348													9	637	---	---	---	---	PASS
TSGA10	80705	broad.mit.edu	37	2	99695231	99695231	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99695231A>G	uc002szg.3	-	10	1401	c.773T>C	c.(772-774)ATT>ACT	p.I258T	TSGA10_uc002szh.3_Missense_Mutation_p.I258T|TSGA10_uc002szi.3_Missense_Mutation_p.I258T|TSGA10_uc010fin.1_Missense_Mutation_p.I258T|TSGA10_uc010yvn.1_Missense_Mutation_p.I258T	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	258					spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2						TCCACCAAGAATGCTGATTTC	0.338													7	602	---	---	---	---	PASS
TNFAIP6	7130	broad.mit.edu	37	2	152220485	152220485	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152220485A>C	uc002txk.2	+	2	199	c.123A>C	c.(121-123)GAA>GAC	p.E41D		NM_007115	NP_009046	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	41	Link.				cell adhesion|cell-cell signaling|inflammatory response|signal transduction		hyaluronic acid binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)		ACCACAGAGAAGCACGGTCTG	0.502													36	88	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170026249	170026249	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170026249G>A	uc002ues.2	-	60	11673	c.11460C>T	c.(11458-11460)TCC>TCT	p.S3820S		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3820	Extracellular (Potential).|LDL-receptor class A 33.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	AACAGTCAGCGGATCCATCGC	0.423													77	164	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179393748	179393748	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179393748T>C	uc010zfg.1	-	309	99250	c.99026A>G	c.(99025-99027)AAG>AGG	p.K33009R	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K26704R|TTN_uc010zfi.1_Missense_Mutation_p.K26637R|TTN_uc010zfj.1_Missense_Mutation_p.K26512R|TTN_uc002umq.2_Missense_Mutation_p.K26R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33936							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)			TGCTGATTTCTTGACTTCTTC	0.403													7	524	---	---	---	---	PASS
PARD3B	117583	broad.mit.edu	37	2	206050508	206050508	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206050508G>A	uc002var.1	+	14	2152	c.1945G>A	c.(1945-1947)GGA>AGA	p.G649R	PARD3B_uc010fub.1_Missense_Mutation_p.G649R|PARD3B_uc002vao.1_Missense_Mutation_p.G649R|PARD3B_uc002vap.1_Missense_Mutation_p.G587R|PARD3B_uc002vaq.1_Missense_Mutation_p.G649R	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	649					cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GCCCAATGACGGATGGGCCGA	0.448													5	428	---	---	---	---	PASS
SLC19A3	80704	broad.mit.edu	37	2	228552128	228552128	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228552128C>T	uc002vpi.2	-	6	1565	c.1476G>A	c.(1474-1476)ATG>ATA	p.M492I	SLC19A3_uc002vpj.2_RNA|SLC19A3_uc010zlv.1_Missense_Mutation_p.M488I	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	492	Cytoplasmic (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	GTTTTGTTGACATGATGATAT	0.413													5	348	---	---	---	---	PASS
UGT1A7	54577	broad.mit.edu	37	2	234590879	234590879	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234590879C>T	uc002vut.2	+	1	296	c.296C>T	c.(295-297)ACG>ATG	p.T99M	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Missense_Mutation_p.T99M	NM_019077	NP_061950	Q9HAW7	UD17_HUMAN	UDP glycosyltransferase 1 family, polypeptide A7	99					drug metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	drug binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|retinoic acid binding			ovary(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GCTCGCTGGACGGCACCATTG	0.418													5	234	---	---	---	---	PASS
UGT1A4	54657	broad.mit.edu	37	2	234628268	234628268	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234628268C>A	uc002vux.2	+	1	831	c.802C>A	c.(802-804)CCG>ACG	p.P268T	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Missense_Mutation_p.P268T	NM_007120	NP_009051	P22310	UD14_HUMAN	UDP glycosyltransferase 1 family, polypeptide A4	268					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Imipramine(DB00458)|Lamotrigine(DB00555)|Paricalcitol(DB00910)|Trifluoperazine(DB00831)	CTACCCCAGGCCGATCATGCC	0.522													77	139	---	---	---	---	PASS
NSUN3	63899	broad.mit.edu	37	3	93813022	93813022	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93813022A>G	uc003drl.1	+	4	621	c.505A>G	c.(505-507)AGG>GGG	p.R169G		NM_022072	NP_071355	Q9H649	NSUN3_HUMAN	NOL1/NOP2/Sun domain family, member 3	169							methyltransferase activity			skin(1)	1						TCTGAGATTGAGGTGGCTAAG	0.353													6	338	---	---	---	---	PASS
OR5K4	403278	broad.mit.edu	37	3	98073661	98073661	+	3'UTR	SNP	T	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98073661T>A	uc011bgv.1	+	1						NM_001005517	NP_001005517	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						tttaatttattaaaatGCTTT	0.219													3	32	---	---	---	---	PASS
BOC	91653	broad.mit.edu	37	3	112998705	112998705	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112998705C>A	uc003dzx.2	+	13	2676	c.2055C>A	c.(2053-2055)AAC>AAA	p.N685K	BOC_uc003dzy.2_Missense_Mutation_p.N685K|BOC_uc003dzz.2_Missense_Mutation_p.N686K|BOC_uc003eab.2_Missense_Mutation_p.N386K|BOC_uc003eac.2_5'UTR	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	685	Fibronectin type-III 2.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			GGGCTCTGAACATGCTGGGGG	0.602													22	21	---	---	---	---	PASS
MUC13	56667	broad.mit.edu	37	3	124635228	124635228	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124635228C>T	uc003ehq.1	-	6	921	c.897G>A	c.(895-897)AAG>AAA	p.K299K		NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane	299	SEA.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane					0						CAGTCACAGTCTTCTCATTGT	0.333													152	377	---	---	---	---	PASS
SLC7A14	57709	broad.mit.edu	37	3	170204133	170204133	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170204133A>G	uc003fgz.2	-	5	1100	c.784T>C	c.(784-786)TTC>CTC	p.F262L	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	262	Helical; (Potential).					integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			AAAGCGTAGAAGCATGTTGCT	0.507													7	326	---	---	---	---	PASS
KIAA1239	57495	broad.mit.edu	37	4	37432275	37432275	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37432275G>A	uc011bxz.1	+	4	439	c.439G>A	c.(439-441)GCC>ACC	p.A147T		NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495	147											0						TTTGGATGCCGCCATAGAGGC	0.463													5	395	---	---	---	---	PASS
LIN54	132660	broad.mit.edu	37	4	83905762	83905762	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83905762T>C	uc003hnx.3	-	2	614	c.236A>G	c.(235-237)AAT>AGT	p.N79S	LIN54_uc003hnz.3_Intron|LIN54_uc003hny.3_Intron|LIN54_uc010ijt.2_Missense_Mutation_p.N79S|LIN54_uc010iju.2_5'UTR|LIN54_uc010ijv.2_Intron	NM_194282	NP_919258	Q6MZP7	LIN54_HUMAN	lin-54 homolog isoform a	79					cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)				AATTGTGGTATTCACTGCAAC	0.428													8	828	---	---	---	---	PASS
PAPSS1	9061	broad.mit.edu	37	4	108574727	108574727	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108574727C>T	uc003hyk.2	-	9	1241	c.1157G>A	c.(1156-1158)CGA>CAA	p.R386Q	PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase	386	Adenylyl-sulfate kinase.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CCAATAAACTCGATCCAAGAC	0.348													124	289	---	---	---	---	PASS
GLRA3	8001	broad.mit.edu	37	4	175649781	175649781	+	Silent	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175649781A>G	uc003ity.1	-	4	839	c.336T>C	c.(334-336)CCT>CCC	p.P112P	GLRA3_uc003itz.1_Silent_p.P112P	NM_006529	NP_006520	O75311	GLRA3_HUMAN	glycine receptor, alpha 3 isoform a	112	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(3)	3		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)	AAGAGTCGTCAGGATATTCAC	0.398													93	201	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629900	9629900	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629900C>G	uc003jem.1	-	1	564	c.245G>C	c.(244-246)TGT>TCT	p.C82S		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	82	Helical; Name=3; (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						GAGAATTGCACAATTCGCAGA	0.403													6	130	---	---	---	---	PASS
EDIL3	10085	broad.mit.edu	37	5	83356119	83356119	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83356119C>T	uc003kio.1	-	9	1556	c.1137G>A	c.(1135-1137)CAG>CAA	p.Q379Q	EDIL3_uc003kip.1_Silent_p.Q369Q|EDIL3_uc011ctt.1_Silent_p.Q156Q	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	379	F5/8 type C 2.				cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		AAAACTTTACCTGTAACCATT	0.453													4	291	---	---	---	---	PASS
AFF4	27125	broad.mit.edu	37	5	132223802	132223802	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132223802T>C	uc003kyd.2	-	15	3191	c.2783A>G	c.(2782-2784)AAT>AGT	p.N928S	AFF4_uc011cxk.1_Missense_Mutation_p.N606S	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	928					transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGCATCTGCATTGTGCTTTAG	0.274													7	722	---	---	---	---	PASS
SLC35A4	113829	broad.mit.edu	37	5	139946853	139946853	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139946853T>C	uc003lgg.1	+	3	827	c.99T>C	c.(97-99)CAT>CAC	p.H33H	APBB3_uc003lgc.1_5'Flank|APBB3_uc003lgd.1_5'Flank|APBB3_uc003lge.1_5'Flank|APBB3_uc003lgf.1_5'Flank|APBB3_uc010jfp.1_5'Flank|APBB3_uc011czi.1_5'Flank|APBB3_uc010jfr.1_5'Flank|SLC35A4_uc003lgh.1_Silent_p.H33H	NM_080670	NP_542401	Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	33	Leu-rich.|Helical; (Potential).					Golgi membrane|integral to membrane	sugar:hydrogen symporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGTGCCCATGCCCCATTGC	0.632													10	37	---	---	---	---	PASS
TCP11	6954	broad.mit.edu	37	6	35086231	35086231	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35086231G>A	uc003okd.2	-	10	1547	c.1366C>T	c.(1366-1368)CAG>TAG	p.Q456*	TCP11_uc003ojz.1_Nonsense_Mutation_p.Q381*|TCP11_uc003oka.2_Nonsense_Mutation_p.Q381*|TCP11_uc003okb.2_Nonsense_Mutation_p.Q380*|TCP11_uc003okc.2_Nonsense_Mutation_p.Q380*|TCP11_uc011dsu.1_Nonsense_Mutation_p.Q438*|TCP11_uc011dsv.1_Nonsense_Mutation_p.Q405*|TCP11_uc011dsw.1_Nonsense_Mutation_p.Q410*	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	443					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						AGAGACCGCTGCACACCAAGA	0.458													59	133	---	---	---	---	PASS
CLIC5	53405	broad.mit.edu	37	6	45882036	45882036	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45882036G>A	uc003oxv.3	-	5	1100	c.994C>T	c.(994-996)CGC>TGC	p.R332C	CLIC5_uc003oxu.3_Missense_Mutation_p.R173C|CLIC5_uc003oxw.2_RNA|CLIC5_uc003oxx.2_Missense_Mutation_p.R173C	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a	332	GST C-terminal.				female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2						AGGAACTTGCGCCGGGACCCC	0.557													4	272	---	---	---	---	PASS
FAM135A	57579	broad.mit.edu	37	6	71186909	71186909	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71186909A>G	uc003pfj.2	+	6	549	c.416A>G	c.(415-417)AAG>AGG	p.K139R	FAM135A_uc003pfi.2_Missense_Mutation_p.K139R|FAM135A_uc003pfh.2_Missense_Mutation_p.K96R|FAM135A_uc003pfk.2_Missense_Mutation_p.K139R|FAM135A_uc003pfl.2_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c	139										central_nervous_system(1)	1						CGAACATTGAAGCTGCACTTT	0.388													7	585	---	---	---	---	PASS
HTR1E	3354	broad.mit.edu	37	6	87725912	87725912	+	Missense_Mutation	SNP	G	A	A	rs61735411		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725912G>A	uc003pli.2	+	2	1563	c.860G>A	c.(859-861)CGG>CAG	p.R287Q		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	287	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)	ACCAGGGAACGGAAGGCAGCA	0.502													66	134	---	---	---	---	PASS
RNGTT	8732	broad.mit.edu	37	6	89322311	89322311	+	3'UTR	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89322311A>T	uc003pmr.2	-	16					RNGTT_uc003pms.2_3'UTR|RNGTT_uc011dzu.1_3'UTR	NM_003800	NP_003791	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		TTCTTTTTTTAAAAAAAATTC	0.348													9	73	---	---	---	---	PASS
FBXO30	84085	broad.mit.edu	37	6	146126842	146126842	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146126842T>C	uc003qla.2	-	2	899	c.700A>G	c.(700-702)AAA>GAA	p.K234E	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	234							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		TCTTGGTCTTTCAAGTTTTGA	0.393													140	250	---	---	---	---	PASS
IGF2R	3482	broad.mit.edu	37	6	160501218	160501218	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160501218A>G	uc003qta.2	+	39	5892	c.5744A>G	c.(5743-5745)GAG>GGG	p.E1915G		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	1915	13.|Lumenal (Potential).|Fibronectin type-II.				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		AAGAGCTACGAGGAGTGCATC	0.537													5	177	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4218194	4218194	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4218194G>A	uc003smx.2	+	35	5213	c.5074G>A	c.(5074-5076)GTG>ATG	p.V1692M	SDK1_uc010kso.2_Missense_Mutation_p.V948M|SDK1_uc003smy.2_Missense_Mutation_p.V179M	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1692	Fibronectin type-III 10.				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)		CAGCGCGCCCGTGGAGGTCTT	0.592													19	28	---	---	---	---	PASS
RBAK	57786	broad.mit.edu	37	7	5105059	5105059	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5105059A>G	uc010kss.1	+	6	2296	c.1972A>G	c.(1972-1974)AAA>GAA	p.K658E	LOC389458_uc003snr.2_Intron|RBAK_uc003sns.1_Missense_Mutation_p.K658E	NM_021163	NP_066986	Q9NYW8	RBAK_HUMAN	RB-associated KRAB repressor	658	C2H2-type 15.|Interaction with AR.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(3)|kidney(1)|skin(1)	5		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGAATGTGGGAAAGTCTTTTC	0.408													67	137	---	---	---	---	PASS
CCDC126	90693	broad.mit.edu	37	7	23650959	23650959	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23650959A>C	uc003swl.2	+	3	482	c.25A>C	c.(25-27)AAT>CAT	p.N9H	CCDC126_uc003swm.2_Missense_Mutation_p.N9H|CCDC126_uc003swn.2_Missense_Mutation_p.N9H	NM_138771	NP_620126	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126 precursor	9						extracellular region				ovary(1)|skin(1)	2						CTCAAGAAAAAATATGTCCCA	0.338													137	315	---	---	---	---	PASS
GARS	2617	broad.mit.edu	37	7	30638464	30638464	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30638464A>G	uc003tbm.2	+	2	632	c.275A>G	c.(274-276)GAC>GGC	p.D92G		NM_002047	NP_002038	P41250	SYG_HUMAN	glycyl-tRNA synthetase	92	WHEP-TRS.				cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)	GTAGACGTAGACAAAGCAGTG	0.428													6	333	---	---	---	---	PASS
POM121C	100101267	broad.mit.edu	37	7	75048070	75048070	+	3'UTR	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75048070G>T	uc003udk.3	-	15						NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						CAGGGACAGGGGACAAAGGCT	0.602													26	82	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91668055	91668055	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91668055C>T	uc003ulg.2	+	17	4886	c.4661C>T	c.(4660-4662)TCC>TTC	p.S1554F	AKAP9_uc003ule.2_Missense_Mutation_p.S1566F|AKAP9_uc003ulf.2_Missense_Mutation_p.S1554F|AKAP9_uc003uli.2_Missense_Mutation_p.S1179F	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1566					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAAATGTTCTCCAAAGATAAA	0.284			T	BRAF	papillary thyroid								4	179	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91709305	91709305	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91709305A>T	uc003ulg.2	+	31	8083	c.7858A>T	c.(7858-7860)ACT>TCT	p.T2620S	AKAP9_uc003ulf.2_Missense_Mutation_p.T2612S|AKAP9_uc003uli.2_Missense_Mutation_p.T2243S|AKAP9_uc003ulj.2_Missense_Mutation_p.T390S	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2632	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAAATGCATACTAGTTTGAT	0.323			T	BRAF	papillary thyroid								80	357	---	---	---	---	PASS
AZGP1	563	broad.mit.edu	37	7	99573623	99573623	+	Silent	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99573623G>T	uc003ush.2	-	1	65	c.21C>A	c.(19-21)GTC>GTA	p.V7V		NM_001185	NP_001176	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc	7					antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GAGACAGCAGGACAGGCACCA	0.587													45	176	---	---	---	---	PASS
STAG3	10734	broad.mit.edu	37	7	99799821	99799821	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99799821T>C	uc003utx.1	+	24	2576	c.2421T>C	c.(2419-2421)CTT>CTC	p.L807L	STAG3_uc011kjk.1_Silent_p.L749L|GATS_uc003uty.3_RNA|GATS_uc003utz.3_RNA|GATS_uc003uua.3_3'UTR|GATS_uc010lgt.2_RNA|STAG3_uc003uub.1_Silent_p.L31L	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3	807					chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTGATCTACTTCTCATCTTTA	0.433													8	497	---	---	---	---	PASS
TSGA13	114960	broad.mit.edu	37	7	130364122	130364122	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130364122T>C	uc003vqi.2	-	5	715	c.258A>G	c.(256-258)AAA>AAG	p.K86K	TSGA13_uc003vqj.2_Silent_p.K86K	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13	86										ovary(2)	2	Melanoma(18;0.0435)					ACTGTGTTACTTTTAACATGA	0.448													8	836	---	---	---	---	PASS
CALD1	800	broad.mit.edu	37	7	134632494	134632494	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134632494G>A	uc003vrz.2	+	8	2227	c.1768G>A	c.(1768-1770)GAA>AAA	p.E590K	CALD1_uc003vry.2_Missense_Mutation_p.E335K|CALD1_uc003vsa.2_Missense_Mutation_p.E361K|CALD1_uc003vsb.2_Missense_Mutation_p.E335K|CALD1_uc010lmm.2_Missense_Mutation_p.E361K|CALD1_uc011kpt.1_Missense_Mutation_p.E109K|CALD1_uc003vsc.2_Missense_Mutation_p.E355K|CALD1_uc003vsd.2_Missense_Mutation_p.E329K|CALD1_uc011kpu.1_Missense_Mutation_p.E340K|CALD1_uc011kpv.1_Missense_Mutation_p.E199K|CALD1_uc003vse.2_Missense_Mutation_p.E454K	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	590	Tropomyosin-binding (Potential).				cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0						gaagcaggaggaagCCGATCG	0.279													7	96	---	---	---	---	PASS
CTAGE6	340307	broad.mit.edu	37	7	143453714	143453714	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143453714G>C	uc003wdk.3	-	1	1130	c.1038C>G	c.(1036-1038)GAC>GAG	p.D346E	uc011ktn.1_Intron|uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_178561	NP_848656	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	346	Potential.					integral to membrane					0	Melanoma(164;0.0903)					CCTTTGTTTTGTCCACTTCAG	0.318													68	441	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151877902	151877902	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151877902T>C	uc003wla.2	-	36	7262	c.7043A>G	c.(7042-7044)CAG>CGG	p.Q2348R	MLL3_uc003wkz.2_Missense_Mutation_p.Q1409R|MLL3_uc003wky.2_5'Flank	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	2348					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)		ACCAGAGAACTGCTGGCCTTG	0.488			N		medulloblastoma								72	199	---	---	---	---	PASS
NOM1	64434	broad.mit.edu	37	7	156759742	156759742	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156759742G>A	uc003wmy.2	+	9	2269	c.2254G>A	c.(2254-2256)GCC>ACC	p.A752T		NM_138400	NP_612409	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	752	MI.				RNA metabolic process	nucleolus	protein binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TCATCTGGTGGCCCACTTGTT	0.388													150	547	---	---	---	---	PASS
MTMR7	9108	broad.mit.edu	37	8	17157530	17157530	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17157530G>A	uc003wxm.2	-	14	2063	c.1824C>T	c.(1822-1824)GAC>GAT	p.D608D	MTMR7_uc011kya.1_Silent_p.D242D|MTMR7_uc011kyb.1_Silent_p.D199D	NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	608							protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)		TTTTCAGATTGTCTTGGGTTA	0.498													95	213	---	---	---	---	PASS
DOCK5	80005	broad.mit.edu	37	8	25199969	25199969	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25199969C>T	uc003xeg.2	+	25	2700	c.2563C>T	c.(2563-2565)CAG>TAG	p.Q855*	DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Nonsense_Mutation_p.Q569*|DOCK5_uc003xei.2_Nonsense_Mutation_p.Q425*|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	855						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GCTGGTTCGGCAGAAACTTAA	0.408													5	235	---	---	---	---	PASS
IDO2	169355	broad.mit.edu	37	8	39847333	39847333	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39847333A>G	uc010lwy.1	+	8	924	c.682A>G	c.(682-684)ACC>GCC	p.T228A	IDO2_uc003xno.1_RNA|IDO2_uc010lwz.1_5'UTR|IDO2_uc003xnp.1_5'UTR	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1	215					tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2						TCAGGACATCACCAAAACCTT	0.577											OREG0018729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	215	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100779048	100779048	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100779048T>C	uc003yiv.2	+	40	7283	c.7172T>C	c.(7171-7173)GTT>GCT	p.V2391A	VPS13B_uc003yiw.2_Missense_Mutation_p.V2366A	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	2391					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AAGGTTTTTGTTGCATTTAGA	0.328													7	330	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125103699	125103699	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125103699C>T	uc003yqw.2	+	34	4633	c.4427C>T	c.(4426-4428)CCC>CTC	p.P1476L	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1476	Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ACGTCCAAACCCACCGAAATC	0.458													7	281	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33395238	33395238	+	Intron	SNP	C	T	T	rs140061469	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33395238C>T	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_5'Flank|AQP7_uc010mjt.2_5'UTR|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_5'UTR|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		AGACTCAAGTCTGCCTGCTGC	0.582													3	45	---	---	---	---	PASS
ZCCHC6	79670	broad.mit.edu	37	9	88967659	88967659	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88967659T>C	uc004aoq.2	-	2	671	c.456A>G	c.(454-456)AGA>AGG	p.R152R	ZCCHC6_uc011ltf.1_RNA|ZCCHC6_uc004aor.2_RNA|ZCCHC6_uc004aos.2_RNA|ZCCHC6_uc004aot.2_Silent_p.R152R|ZCCHC6_uc004aou.2_Silent_p.R152R|ZCCHC6_uc004aov.2_Silent_p.R152R|ZCCHC6_uc004aow.2_Silent_p.R152R|ZCCHC6_uc010mqf.1_Silent_p.R152R	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	152					RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						GAAACAGTCGTCTTACAGTTC	0.418													7	540	---	---	---	---	PASS
MAPKAP1	79109	broad.mit.edu	37	9	128322013	128322013	+	Silent	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128322013A>G	uc004bpv.2	-	6	1080	c.747T>C	c.(745-747)GAT>GAC	p.D249D	MAPKAP1_uc011lzt.1_Silent_p.D52D|MAPKAP1_uc010mwz.2_RNA|MAPKAP1_uc011lzu.1_Silent_p.D52D|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Silent_p.D57D|MAPKAP1_uc004bpx.2_Silent_p.D57D|MAPKAP1_uc004bpy.2_Silent_p.D249D|MAPKAP1_uc004bpz.2_Silent_p.D249D|MAPKAP1_uc010mxa.2_RNA|MAPKAP1_uc010mxb.1_Silent_p.D52D|MAPKAP1_uc004bqa.2_Silent_p.D249D|MAPKAP1_uc010mxc.1_Silent_p.D121D	NM_001006617	NP_001006618	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated	249					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4						GCTCATTGGAATCCAGCGGGG	0.483													5	165	---	---	---	---	PASS
PRTFDC1	56952	broad.mit.edu	37	10	25147333	25147333	+	Silent	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25147333A>G	uc001ise.1	-	5	440	c.411T>C	c.(409-411)GTT>GTC	p.V137V	PRTFDC1_uc010qdd.1_Silent_p.V137V|PRTFDC1_uc001isf.1_Intron|PRTFDC1_uc009xkm.1_RNA	NM_020200	NP_064585	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	137					adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1						CAACAATGAGAACATTCTGAA	0.328													6	356	---	---	---	---	PASS
BMS1	9790	broad.mit.edu	37	10	43315719	43315719	+	Silent	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43315719A>G	uc001jaj.2	+	16	2974	c.2616A>G	c.(2614-2616)GAA>GAG	p.E872E		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	872					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3						AAGATGATGAAGCCAGAGTTC	0.403													6	348	---	---	---	---	PASS
C10orf25	220979	broad.mit.edu	37	10	45495991	45495991	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45495991A>G	uc001jbv.1	-	1	346	c.317T>C	c.(316-318)CTC>CCC	p.L106P	C10orf25_uc010qff.1_RNA|ZNF22_uc001jbw.2_5'Flank	NM_001039380	NP_001034469	Q5T742	CJ025_HUMAN	hypothetical protein LOC220979 precursor	106						extracellular region					0						cggtgaacggagcacatttct	0.065													6	353	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55779999	55779999	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55779999A>T	uc001jju.1	-	20	3099	c.2704T>A	c.(2704-2706)TAT>AAT	p.Y902N	PCDH15_uc010qhq.1_Missense_Mutation_p.Y907N|PCDH15_uc010qhr.1_Missense_Mutation_p.Y902N|PCDH15_uc010qhs.1_Missense_Mutation_p.Y914N|PCDH15_uc010qht.1_Missense_Mutation_p.Y909N|PCDH15_uc010qhu.1_Missense_Mutation_p.Y902N|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.Y902N|PCDH15_uc010qhw.1_Missense_Mutation_p.Y865N|PCDH15_uc010qhx.1_Missense_Mutation_p.Y831N|PCDH15_uc010qhy.1_Missense_Mutation_p.Y907N|PCDH15_uc010qhz.1_Missense_Mutation_p.Y902N|PCDH15_uc010qia.1_Missense_Mutation_p.Y880N|PCDH15_uc010qib.1_Missense_Mutation_p.Y880N|PCDH15_uc001jjw.2_Missense_Mutation_p.Y902N	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	902	Extracellular (Potential).|Cadherin 8.				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ATTGTTCCATAAATATCAAAG	0.418										HNSCC(58;0.16)			152	254	---	---	---	---	PASS
SLC18A2	6571	broad.mit.edu	37	10	119029622	119029622	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119029622C>T	uc001ldd.1	+	14	1258	c.1227C>T	c.(1225-1227)CTC>CTT	p.L409L	SLC18A2_uc009xyy.1_Silent_p.L206L	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	409	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)	TGGGCTACCTCGTAGACCTGC	0.483													5	482	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1266194	1266194	+	Intron	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1266194C>A	uc009ycr.1	+						MUC5B_uc001ltb.2_Missense_Mutation_p.T2698N	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		accacggccactacgatcacg	0.209													6	164	---	---	---	---	PASS
TPH1	7166	broad.mit.edu	37	11	18045491	18045491	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18045491C>A	uc001mnp.2	-	8	996	c.970G>T	c.(970-972)GAT>TAT	p.D324Y	TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	324					aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	AGCTGTCCATCTTGTTTACAT	0.343													119	311	---	---	---	---	PASS
FBXO3	26273	broad.mit.edu	37	11	33790514	33790514	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33790514C>A	uc001muz.2	-	3	269	c.241G>T	c.(241-243)GAT>TAT	p.D81Y	FBXO3_uc001muy.2_5'UTR|FBXO3_uc009ykb.2_RNA|FBXO3_uc001mva.1_Missense_Mutation_p.D81Y|FBXO3_uc001mvb.1_Missense_Mutation_p.D76Y|FBXO3_uc010rek.1_RNA	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1	81					proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		GAGTAAGTATCTATGAAGAGA	0.338													176	431	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68183829	68183829	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68183829C>A	uc001ont.2	+	13	2936	c.2861C>A	c.(2860-2862)TCT>TAT	p.S954Y	LRP5_uc009ysg.2_Missense_Mutation_p.S364Y	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	954	Beta-propeller 4.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						AGCCAGAAATCTGCCATCAGT	0.587													16	35	---	---	---	---	PASS
CLPB	81570	broad.mit.edu	37	11	72012879	72012879	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72012879C>T	uc001osj.2	-	12	1437	c.1387G>A	c.(1387-1389)GTG>ATG	p.V463M	CLPB_uc010rqx.1_Missense_Mutation_p.V418M|CLPB_uc010rqy.1_Missense_Mutation_p.V404M|CLPB_uc001osk.2_Missense_Mutation_p.V433M|CLPB_uc009ytg.2_RNA|CLPB_uc010rqz.1_Missense_Mutation_p.V262M|CLPB_uc001osi.2_Missense_Mutation_p.V71M	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	463					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1						ATGGTGAGCACATCTGGATGG	0.557													5	83	---	---	---	---	PASS
MOGAT2	80168	broad.mit.edu	37	11	75438650	75438650	+	Silent	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75438650G>T	uc010rru.1	+	3	441	c.441G>T	c.(439-441)CGG>CGT	p.R147R	MOGAT2_uc001oww.1_Silent_p.R147R|MOGAT2_uc010rrv.1_Silent_p.R65R	NM_025098	NP_079374	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	147					glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)					TGTGGTTCCGGGCCCCCTTCT	0.532													45	90	---	---	---	---	PASS
DPAGT1	1798	broad.mit.edu	37	11	118968667	118968667	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118968667C>T	uc001pvi.2	-	6	1235	c.815G>A	c.(814-816)AGC>AAC	p.S272N	H2AFX_uc001pvg.2_5'Flank|H2AFX_uc001pvh.1_5'Flank|DPAGT1_uc001pvj.2_Missense_Mutation_p.S165N|DPAGT1_uc009zaq.2_Intron|DPAGT1_uc001pvk.2_Missense_Mutation_p.S100N|DPAGT1_uc010ryz.1_Missense_Mutation_p.S272N|DPAGT1_uc001pvm.1_3'UTR|DPAGT1_uc010rza.1_Missense_Mutation_p.S165N	NM_001382	NP_001373	Q9H3H5	GPT_HUMAN	UDP-N-acetylglucosamine-dolichyl-phosphate	272	Lumenal (Potential).				dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|ovary(1)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CATGGTCTTGCTGAAGTGTCC	0.547													95	171	---	---	---	---	PASS
USP2	9099	broad.mit.edu	37	11	119243611	119243611	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119243611A>G	uc001pwm.3	-	2	875	c.580T>C	c.(580-582)TAC>CAC	p.Y194H	USP2_uc001pwn.3_Intron	NM_004205	NP_004196	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2 isoform a	194	Necessary for interaction with MDM4.				cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity			ovary(2)|urinary_tract(1)|skin(1)	4		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		TCGACCAGGTATTCAGGGCAG	0.637													16	30	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	463393	463393	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:463393A>G	uc001qif.1	-	8	1241	c.878T>C	c.(877-879)CTC>CCC	p.L293P	KDM5A_uc001qie.1_Missense_Mutation_p.L293P|KDM5A_uc010sdn.1_Missense_Mutation_p.L252P|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	293	PHD-type 1.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ACAAACATAGAGATCAACCTG	0.269			T 	NUP98	AML								7	263	---	---	---	---	PASS
CSDA	8531	broad.mit.edu	37	12	10871731	10871731	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10871731G>A	uc001qyt.2	-	2	517	c.274C>T	c.(274-276)CTT>TTT	p.L92F	CSDA_uc001qyu.2_Missense_Mutation_p.L92F	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a	92					negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					ACAGTGCCAAGGACTTTGGTG	0.333													7	404	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13717070	13717070	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717070C>A	uc001rbt.2	-	13	3281	c.3102G>T	c.(3100-3102)CAG>CAT	p.Q1034H		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	1034	Cytoplasmic (Potential).				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)	GGTCACTGAGCTGGCTGTGCT	0.587													4	114	---	---	---	---	PASS
KIF21A	55605	broad.mit.edu	37	12	39735383	39735383	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39735383C>T	uc001rly.2	-	14	1991	c.1845G>A	c.(1843-1845)GAG>GAA	p.E615E	KIF21A_uc001rlw.2_5'Flank|KIF21A_uc001rlx.2_Silent_p.E602E|KIF21A_uc001rlz.2_Silent_p.E602E|KIF21A_uc010skl.1_Silent_p.E602E	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	615					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				cctcctcctcctcttcttcat	0.303													5	474	---	---	---	---	PASS
SENP1	29843	broad.mit.edu	37	12	48439012	48439012	+	3'UTR	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48439012G>A	uc001rqx.2	-	18					SENP1_uc001rqw.2_3'UTR|SENP1_uc001rqy.2_3'UTR|SENP1_uc001rqz.2_3'UTR|SENP1_uc009zkx.2_3'UTR	NM_014554	NP_055369	Q9P0U3	SENP1_HUMAN	sentrin/SUMO-specific protease 1						activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity			pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TACAACAGCAGAGGGCTGGGA	0.498													30	59	---	---	---	---	PASS
ADCY6	112	broad.mit.edu	37	12	49171407	49171407	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49171407T>C	uc001rsh.3	-	3	1787	c.1127A>G	c.(1126-1128)GAC>GGC	p.D376G	ADCY6_uc001rsj.3_Missense_Mutation_p.D376G|ADCY6_uc001rsi.3_Missense_Mutation_p.D376G|ADCY6_uc010slw.1_5'Flank	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a	376	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding				0						CCTGACATTGTCATGCTTCTG	0.493													7	532	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57548478	57548478	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57548478C>T	uc001snd.2	+	8	1687	c.1221C>T	c.(1219-1221)GGC>GGT	p.G407G	LRP1_uc001snc.1_Silent_p.G407G	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	407	Extracellular (Potential).|LDL-receptor class B 3.				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)	TCATCCAGGGCATCCTGGTGA	0.577													25	42	---	---	---	---	PASS
ALX1	8092	broad.mit.edu	37	12	85677542	85677542	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85677542C>T	uc001tae.3	+	2	423	c.419C>T	c.(418-420)ACC>ATC	p.T140I		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	140	Homeobox.				brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)		ACCACCTTCACCAGTTTGCAG	0.483													4	178	---	---	---	---	PASS
CCDC53	51019	broad.mit.edu	37	12	102437970	102437970	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102437970T>C	uc010svw.1	-	4	396	c.237A>G	c.(235-237)CTA>CTG	p.L79L	CCDC53_uc010svx.1_RNA|CCDC53_uc010svy.1_RNA|CCDC53_uc010svz.1_Silent_p.L79L	NM_016053	NP_057137	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	79						WASH complex	protein binding				0						TGACATCATCTAGGCCTGGGA	0.368													5	399	---	---	---	---	PASS
ALDH1L2	160428	broad.mit.edu	37	12	105433584	105433584	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105433584C>T	uc001tlc.2	-	17	2079	c.1952G>A	c.(1951-1953)GGT>GAT	p.G651D	ALDH1L2_uc009zuo.2_Missense_Mutation_p.G106D|ALDH1L2_uc009zup.2_RNA	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	651	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1						TGCTATGCCACCTGTAGAATT	0.303													5	299	---	---	---	---	PASS
TMEM132B	114795	broad.mit.edu	37	12	125834194	125834194	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125834194T>C	uc001uhe.1	+	2	257	c.249T>C	c.(247-249)ATT>ATC	p.I83I		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	83	Extracellular (Potential).					integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CACCCCCTATTATCAATGCCA	0.498													70	153	---	---	---	---	PASS
NAA16	79612	broad.mit.edu	37	13	41932483	41932483	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41932483G>C	uc001uyf.2	+	11	1455	c.1131G>C	c.(1129-1131)CAG>CAC	p.Q377H	NAA16_uc010tfg.1_RNA|NAA16_uc001uye.3_Missense_Mutation_p.Q377H|NAA16_uc001uyd.3_3'UTR	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform	377	TPR 5.				N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1						TCTGGGTTCAGTATTTCCTGG	0.348													127	305	---	---	---	---	PASS
LOC220429	220429	broad.mit.edu	37	13	50466749	50466749	+	Missense_Mutation	SNP	C	G	G	rs57976037	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50466749C>G	uc001vdk.2	+	1	2205	c.2023C>G	c.(2023-2025)CCT>GCT	p.P675A		NR_003268				Homo sapiens CTAGE family, member 5 pseudogene, mRNA (cDNA clone IMAGE:5270026).												0						TTTAAATGTGCCTGATTCATC	0.428													11	39	---	---	---	---	PASS
DOCK9	23348	broad.mit.edu	37	13	99459928	99459928	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99459928T>C	uc001vnt.2	-	50	5601	c.5546A>G	c.(5545-5547)CAG>CGG	p.Q1849R	DOCK9_uc001vnw.2_Missense_Mutation_p.Q1848R|DOCK9_uc001vnq.2_Missense_Mutation_p.Q396R|DOCK9_uc001vnr.2_Missense_Mutation_p.Q478R|DOCK9_uc010tin.1_Missense_Mutation_p.Q467R|DOCK9_uc001vns.2_Missense_Mutation_p.Q384R|DOCK9_uc010tio.1_Missense_Mutation_p.Q504R|DOCK9_uc010tip.1_Missense_Mutation_p.Q545R	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1849	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)					GCCAGAATCCTGTATCATTTT	0.318													8	667	---	---	---	---	PASS
RASA3	22821	broad.mit.edu	37	13	114782719	114782719	+	Silent	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114782719G>T	uc001vui.2	-	12	1331	c.1200C>A	c.(1198-1200)ATC>ATA	p.I400I	RASA3_uc010tkk.1_Silent_p.I368I|RASA3_uc001vuj.2_Silent_p.I17I|RASA3_uc010tkl.1_RNA	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	400	Ras-GAP.				intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TCACCTCCTCGATGGCGGGCT	0.617											OREG0022538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	21	---	---	---	---	PASS
METT11D1	64745	broad.mit.edu	37	14	21461323	21461323	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21461323T>G	uc001vyn.2	+	6	772	c.575T>G	c.(574-576)TTT>TGT	p.F192C	METT11D1_uc001vym.2_Missense_Mutation_p.F192C|METT11D1_uc001vyo.2_Missense_Mutation_p.F192C|METT11D1_uc001vyp.2_Missense_Mutation_p.F34C|METT11D1_uc001vyq.2_Missense_Mutation_p.F34C	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform	192					translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TTGATGGACTTTGGCTCAGGT	0.418													126	346	---	---	---	---	PASS
TBPL2	387332	broad.mit.edu	37	14	55881091	55881091	+	3'UTR	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55881091A>G	uc001xby.2	-	7					FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbx.1_5'Flank	NM_199047	NP_950248	Q6SJ96	TBPL2_HUMAN	TATA box binding protein like 2						multicellular organismal development|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding				0						ATGCTGAATGATATGCTCAGG	0.358													6	477	---	---	---	---	PASS
MAX	4149	broad.mit.edu	37	14	65569042	65569042	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65569042C>A	uc001xif.1	-	1	186	c.16G>T	c.(16-18)GAC>TAC	p.D6Y	MAX_uc001xic.1_Missense_Mutation_p.D6Y|MAX_uc001xie.1_Missense_Mutation_p.D6Y|MAX_uc010aql.1_Missense_Mutation_p.D6Y|MAX_uc001xig.1_Missense_Mutation_p.D6Y|MAX_uc001xih.1_RNA|MAX_uc001xii.1_Missense_Mutation_p.D6Y|MAX_uc001xij.1_Missense_Mutation_p.D6Y|MAX_uc001xik.2_Missense_Mutation_p.D6Y	NM_002382	NP_002373	P61244	MAX_HUMAN	MAX protein isoform a	6					transcription from RNA polymerase II promoter	cytoplasm|MLL1 complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(1)	1				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		ACCTCGATGTCATCGTTATCG	0.557													12	33	---	---	---	---	PASS
TDP1	55775	broad.mit.edu	37	14	90437547	90437547	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90437547G>A	uc001xxy.2	+	6	987	c.688G>A	c.(688-690)GAT>AAT	p.D230N	TDP1_uc010atm.2_RNA|TDP1_uc001xxz.2_Missense_Mutation_p.D230N|TDP1_uc010atn.2_Missense_Mutation_p.D230N|TDP1_uc001xya.2_Silent_p.V2V|TDP1_uc001xyb.2_RNA|TDP1_uc010ato.2_Missense_Mutation_p.D230N	NM_018319	NP_060789	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	230					cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TGTGCATGGTGATAAGCGAGA	0.403								Repair_of_DNA-protein_crosslinks					30	69	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94112974	94112974	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94112974T>C	uc001ybv.1	+	34	5800	c.5717T>C	c.(5716-5718)TTT>TCT	p.F1906S	KIAA1409_uc001ybs.1_Missense_Mutation_p.F1884S	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	2061						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		AGTACTACCTTTTCTAATCAA	0.403													6	437	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28508219	28508219	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28508219T>C	uc001zbj.2	-	15	2073	c.1967A>G	c.(1966-1968)GAC>GGC	p.D656G	HERC2_uc001zbl.1_Missense_Mutation_p.D351G	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	656	RCC1 3.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CACATCCAAGTCTTGAAGCTT	0.468													7	512	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33842489	33842489	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33842489C>G	uc001zhi.2	+	10	1014	c.944C>G	c.(943-945)TCC>TGC	p.S315C	RYR3_uc010bar.2_Missense_Mutation_p.S315C	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	315	Cytoplasmic (By similarity).|MIR 4.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GACACCAAGTCCACAGCTTTC	0.498													49	108	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52720650	52720650	+	Silent	SNP	C	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52720650C>G	uc002aby.2	-	3	499	c.255G>C	c.(253-255)GTG>GTC	p.V85V	MYO5A_uc002abx.3_Silent_p.V85V|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	85	Myosin head-like.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GATTATGGAGCACAGCAGGCT	0.428													26	304	---	---	---	---	PASS
CILP	8483	broad.mit.edu	37	15	65502087	65502087	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65502087C>T	uc002aon.2	-	2	188	c.7G>A	c.(7-9)GGG>AGG	p.G3R		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	3					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7						GCCTTGGTCCCCACCATCTTT	0.552													4	121	---	---	---	---	PASS
BLM	641	broad.mit.edu	37	15	91310216	91310216	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91310216A>G	uc002bpr.2	+	10	2367	c.2270A>G	c.(2269-2271)GAC>GGC	p.D757G	BLM_uc010uqh.1_Missense_Mutation_p.D757G|BLM_uc010uqi.1_Missense_Mutation_p.D382G|BLM_uc010bnx.2_Missense_Mutation_p.D757G|BLM_uc002bps.1_Missense_Mutation_p.D319G	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	757	Helicase ATP-binding.				double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TCAAAAAAAGACCCAATCATA	0.269			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				6	368	---	---	---	---	PASS
ABAT	18	broad.mit.edu	37	16	8844355	8844355	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8844355G>A	uc002czc.3	+	5	441	c.275G>A	c.(274-276)CGA>CAA	p.R92Q	ABAT_uc002czd.3_Missense_Mutation_p.R92Q|ABAT_uc010buh.2_Missense_Mutation_p.R34Q|ABAT_uc010bui.2_Missense_Mutation_p.R92Q	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor	92					behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	GACGGCAACCGAATGCTGGAT	0.463													97	286	---	---	---	---	PASS
ACSM2B	348158	broad.mit.edu	37	16	20548590	20548590	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20548590C>T	uc002dhj.3	-	15	1934	c.1724G>A	c.(1723-1725)CGT>CAT	p.R575H	ACSM2B_uc002dhk.3_Missense_Mutation_p.R575H	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	575					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5						TCACTGCGCACGGGCTTTTCC	0.468													113	321	---	---	---	---	PASS
TNRC6A	27327	broad.mit.edu	37	16	24828245	24828245	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24828245G>T	uc002dmm.2	+	20	5054	c.4940G>T	c.(4939-4941)CGG>CTG	p.R1647L	TNRC6A_uc010bxs.2_Missense_Mutation_p.R1394L|TNRC6A_uc002dmn.2_Missense_Mutation_p.R1345L|TNRC6A_uc002dmo.2_Missense_Mutation_p.R1286L	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1647					negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)		AATACTGTGCGGGAAGTTGAC	0.423													4	224	---	---	---	---	PASS
LOC440354	440354	broad.mit.edu	37	16	29516882	29516882	+	Intron	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29516882T>C	uc002dsp.3	-						uc002dtf.2_Intron|uc010vdr.1_Missense_Mutation_p.Q11R					Homo sapiens IMAA mRNA for hLAT1-3TM, complete cds.												0						GGACAGGAACTGTGGGGTCAG	0.483													6	209	---	---	---	---	PASS
SNX20	124460	broad.mit.edu	37	16	50709790	50709790	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50709790C>T	uc002egk.2	-	3	346	c.173G>A	c.(172-174)CGG>CAG	p.R58Q	SNX20_uc010vgp.1_Missense_Mutation_p.R58Q|SNX20_uc002egi.3_Missense_Mutation_p.R58Q	NM_182854	NP_878274	Q7Z614	SNX20_HUMAN	sorting nexin 20 isoform 1	58					cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1						CTGAAGCTCCCGCGTGGTCAT	0.552													14	114	---	---	---	---	PASS
PDPR	55066	broad.mit.edu	37	16	70182440	70182440	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70182440T>C	uc002eyf.1	+	17	2993	c.2036T>C	c.(2035-2037)CTC>CCC	p.L679P	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.L579P|PDPR_uc002eyg.1_Missense_Mutation_p.L407P|PDPR_uc002eyh.2_Missense_Mutation_p.L24P|PDPR_uc010vls.1_Missense_Mutation_p.L24P	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	679					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		GGATTCATGCTCTACATCCCC	0.418													10	189	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70889122	70889122	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70889122A>T	uc002ezr.2	-	73	12477	c.12349T>A	c.(12349-12351)TTT>ATT	p.F4117I	HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4118										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				TGGAAGGAAAAATCGAACCCC	0.537													44	107	---	---	---	---	PASS
LOC283922	283922	broad.mit.edu	37	16	74366481	74366481	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74366481A>G	uc002fcr.2	-	14	2233	c.887T>C	c.(886-888)CTC>CCC	p.L296P	LOC283922_uc010vms.1_RNA					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						GGGGATGTAGAGCATGAATCC	0.512													12	99	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74442859	74442859	+	3'UTR	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74442859G>A	uc002fct.2	-	13					CLEC18B_uc002fcu.2_3'UTR	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						CAGGTAAGCAGAGCCGGTGCT	0.607													10	172	---	---	---	---	PASS
SMG6	23293	broad.mit.edu	37	17	2201226	2201226	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2201226T>C	uc002fub.1	-	3	2026	c.1971A>G	c.(1969-1971)CAA>CAG	p.Q657Q		NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	657					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						CCTTGACAAGTTGCCTGAACT	0.408													6	345	---	---	---	---	PASS
TXNDC17	84817	broad.mit.edu	37	17	6546299	6546299	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6546299T>C	uc002gdf.3	+	4	513	c.332T>C	c.(331-333)CTT>CCT	p.L111P	KIAA0753_uc002gde.3_5'Flank|KIAA0753_uc010vte.1_5'Flank	NM_032731	NP_116120	Q9BRA2	TXD17_HUMAN	thioredoxin-like 5	111	Thioredoxin.				tumor necrosis factor-mediated signaling pathway	cytosol	electron carrier activity|peroxidase activity|protein binding|protein-disulfide reductase activity			ovary(1)	1						TCTGAGTGTCTTCAGGCCAAC	0.368													7	573	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8053793	8053793	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8053793C>T	uc002gkd.2	-	2	470	c.232G>A	c.(232-234)GGC>AGC	p.G78S	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Missense_Mutation_p.G62S|PER1_uc010vus.1_Missense_Mutation_p.G78S	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	78	Ser-rich.				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						GAGTCCTTGCCGTTGCCTGAG	0.562			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					4	112	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10399440	10399440	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10399440G>A	uc002gmo.2	-	35	5090	c.4996C>T	c.(4996-4998)CGG>TGG	p.R1666W	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1666	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						TCCTGGCTCCGGAGAGCATCA	0.577													9	114	---	---	---	---	PASS
SLC47A2	146802	broad.mit.edu	37	17	19610039	19610039	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19610039A>G	uc002gwe.3	-	9	1046	c.871T>C	c.(871-873)TTC>CTC	p.F291L	SLC47A2_uc002gwg.3_Missense_Mutation_p.F255L|SLC47A2_uc002gwf.3_Missense_Mutation_p.F255L|SLC47A2_uc002gwh.3_RNA|SLC47A2_uc002gwi.2_RNA|SLC47A2_uc010cqs.1_RNA|SLC47A2_uc010cqt.1_RNA	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1	291	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)					AGGGAGAAGAAGGGGCCCCAG	0.617													16	46	---	---	---	---	PASS
ARHGAP23	57636	broad.mit.edu	37	17	36636039	36636039	+	Silent	SNP	C	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36636039C>T	uc010wdp.1	+	14	2924	c.2262C>T	c.(2260-2262)CGC>CGT	p.R754R	ARHGAP23_uc002hqc.2_Silent_p.R642R	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	848					signal transduction	intracellular	GTPase activator activity			lung(1)	1						AAGGCTCTCGCGGCCTGGGGG	0.622													3	26	---	---	---	---	PASS
KRT13	3860	broad.mit.edu	37	17	39659227	39659227	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39659227T>C	uc002hwu.1	-	4	922	c.859A>G	c.(859-861)AGG>GGG	p.R287G	KRT13_uc002hwv.1_Missense_Mutation_p.R287G|KRT13_uc002hww.2_Missense_Mutation_p.R180G|KRT13_uc010wfr.1_Missense_Mutation_p.R180G|KRT13_uc010cxo.2_Missense_Mutation_p.R287G|KRT13_uc002hwx.1_Missense_Mutation_p.R275G	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a	287	Rod.|Coil 2.				epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)				CGGCGGTTCCTCTCTGCCATG	0.647													27	66	---	---	---	---	PASS
NPEPPS	9520	broad.mit.edu	37	17	45699310	45699310	+	3'UTR	SNP	G	C	C	rs149267740	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45699310G>C	uc002ilr.3	+	23					NPEPPS_uc010wkt.1_3'UTR|NPEPPS_uc010wku.1_3'UTR|NPEPPS_uc010wkv.1_3'UTR	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						GCCATTGGCGGTTCTGCTGCT	0.542													17	26	---	---	---	---	PASS
PDK2	5164	broad.mit.edu	37	17	48183306	48183306	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48183306G>T	uc002iqc.2	+	4	494	c.390G>T	c.(388-390)ATG>ATT	p.M130I	PDK2_uc002iqb.2_Missense_Mutation_p.M66I	NM_002611	NP_002602	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase 2 precursor	130					glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|nucleus	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			central_nervous_system(3)	3						TGCCCACCATGGCACAAGGCG	0.602									Autosomal_Dominant_Polycystic_Kidney_Disease				20	33	---	---	---	---	PASS
SPAG9	9043	broad.mit.edu	37	17	49197990	49197990	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49197990G>C	uc002itc.2	-	1	237	c.28C>G	c.(28-30)CAG>GAG	p.Q10E	SPAG9_uc002itb.2_Missense_Mutation_p.Q10E|SPAG9_uc002itd.2_Missense_Mutation_p.Q10E	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1	10					positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GGCTCCTCCTGATACACCACA	0.602													4	2	---	---	---	---	PASS
CDK3	1018	broad.mit.edu	37	17	73999331	73999331	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73999331T>A	uc010dgt.2	+	7	720	c.644T>A	c.(643-645)ATC>AAC	p.I215N	CDK3_uc002jqg.3_Missense_Mutation_p.I243N	NM_001258	NP_001249	Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	215	Protein kinase.				cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1						CTCTTTCGTATCTTTCGTATG	0.547													33	86	---	---	---	---	PASS
CDK3	1018	broad.mit.edu	37	17	73999332	73999332	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73999332C>G	uc010dgt.2	+	7	721	c.645C>G	c.(643-645)ATC>ATG	p.I215M	CDK3_uc002jqg.3_Missense_Mutation_p.I243M	NM_001258	NP_001249	Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	215	Protein kinase.				cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1						TCTTTCGTATCTTTCGTATGC	0.552													33	84	---	---	---	---	PASS
BAHCC1	57597	broad.mit.edu	37	17	79426336	79426336	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79426336G>A	uc002kaf.2	+	20	5778	c.5778G>A	c.(5776-5778)GAG>GAA	p.E1926E	BAHCC1_uc002kae.2_Silent_p.E1156E	NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1	1926							DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)			ACTCACTGGAGCAGCTGCTGC	0.572													7	15	---	---	---	---	PASS
ESCO1	114799	broad.mit.edu	37	18	19154217	19154217	+	Silent	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19154217T>C	uc002kth.1	-	4	1522	c.588A>G	c.(586-588)GAA>GAG	p.E196E	ESCO1_uc002kti.1_RNA	NM_052911	NP_443143	Q5FWF5	ESCO1_HUMAN	establishment of cohesion 1 homolog 1	196					cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0						AATTTATTACTTCATTAATTA	0.353													6	313	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	50683750	50683750	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50683750C>A	uc002lfe.1	+	8	1873	c.1286C>A	c.(1285-1287)CCT>CAT	p.P429H	DCC_uc010xdr.1_Missense_Mutation_p.P277H|DCC_uc010dpf.1_Missense_Mutation_p.P84H	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	429	Extracellular (Potential).|Fibronectin type-III 1.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGTGTCCTCCCTTCGGCTCCC	0.542													93	193	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2206769	2206769	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2206769T>C	uc002lvb.3	+	10	865	c.829T>C	c.(829-831)TTC>CTC	p.F277L		NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase	277						nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTCTGAACTTCAGAATAAA	0.428													6	437	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8162185	8162185	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8162185G>A	uc002mjf.2	-	41	5296	c.5275C>T	c.(5275-5277)CTG>TTG	p.L1759L		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1759	EGF-like 26; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						TCACAAGCCAGCAGGATGCTG	0.512													14	22	---	---	---	---	PASS
ZNF93	81931	broad.mit.edu	37	19	20044770	20044770	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20044770A>G	uc002non.2	+	4	1117	c.1006A>G	c.(1006-1008)ACT>GCT	p.T336A		NM_031218	NP_112495	P35789	ZNF93_HUMAN	zinc finger protein 93	336						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1						GAGAATTCATACTGGAGAGAA	0.373													4	158	---	---	---	---	PASS
C19orf12	83636	broad.mit.edu	37	19	30193856	30193856	+	Silent	SNP	G	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30193856G>T	uc002nsk.2	-	3	620	c.189C>A	c.(187-189)GCC>GCA	p.A63A	C19orf12_uc002nsj.2_Silent_p.A74A|C19orf12_uc002nsl.2_3'UTR|C19orf12_uc002nsm.2_RNA	NM_031448	NP_113636	Q9NSK7	CS012_HUMAN	hypothetical protein LOC83636 isoform 2	63						integral to membrane					0	Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			TTGTCATCCAGGCACCTAACA	0.522													31	59	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	39077188	39077188	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39077188A>G	uc002oit.2	+	105	15123	c.14993A>G	c.(14992-14994)AAC>AGC	p.N4998S	RYR1_uc002oiu.2_Missense_Mutation_p.N4993S	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4998					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	TATTTGATAAACAAGGATGAG	0.433													7	485	---	---	---	---	PASS
ATRN	8455	broad.mit.edu	37	20	3624805	3624805	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3624805T>C	uc002wim.2	+	28	4145	c.4055T>C	c.(4054-4056)GTT>GCT	p.V1352A		NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1	1352	Cytoplasmic (Potential).				inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						TGCCAGACTGTTCCCAAACCC	0.348													6	292	---	---	---	---	PASS
SLC23A2	9962	broad.mit.edu	37	20	4839999	4839999	+	Silent	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4839999G>A	uc002wlg.1	-	16	2031	c.1656C>T	c.(1654-1656)GTC>GTT	p.V552V	SLC23A2_uc010zqr.1_Silent_p.V437V|SLC23A2_uc002wlh.1_Silent_p.V552V	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase	552	Helical; (Potential).				L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2						TTGTGAGAAGGACGTTCAACA	0.453													60	152	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29628269	29628269	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628269T>A	uc010ztl.1	+	3	213	c.181T>A	c.(181-183)TGC>AGC	p.C61S	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.C13S					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CTTTATTAGATGCAATGAAGC	0.363													13	526	---	---	---	---	PASS
URB1	9875	broad.mit.edu	37	21	33744827	33744827	+	Silent	SNP	A	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33744827A>T	uc002ypn.2	-	8	1083	c.990T>A	c.(988-990)GGT>GGA	p.G330G		NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog	330						nucleolus	protein binding				0						TGCCAAAGGTACCCAAAGATG	0.443													64	132	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	20724443	20724443	+	5'UTR	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20724443G>A	uc011ahp.1	-	2					uc011ahq.1_Silent_p.N75N					SubName: Full=cDNA FLJ59031, highly similar to Ubl carboxyl-terminal hydrolase 18 (EC 3.1.2.-);																		CCTTAATCAGGTTCCAGAGTT	0.463													71	148	---	---	---	---	PASS
SEPT3	55964	broad.mit.edu	37	22	42388679	42388679	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42388679G>A	uc003bbr.3	+	8	915	c.777G>A	c.(775-777)ATG>ATA	p.M259I	WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_Missense_Mutation_p.M259I|SEPT3_uc010gyr.2_Missense_Mutation_p.M195I|SEPT3_uc011apj.1_Missense_Mutation_p.M195I|SEPT3_uc010gys.2_Missense_Mutation_p.M39I	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A	259					cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0						AGGAGAGCATGCCTTTTGCTG	0.532													6	325	---	---	---	---	PASS
GAB3	139716	broad.mit.edu	37	X	153906394	153906394	+	3'UTR	SNP	G	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153906394G>A	uc004fmj.1	-	10					GAB3_uc004fmk.1_3'UTR|GAB3_uc010nve.1_3'UTR|GAB3_uc004fml.1_3'UTR	NM_080612	NP_542179	Q8WWW8	GAB3_HUMAN	Gab3 protein isoform 2											ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					aaaaaaaaaagaaaaaaCTCA	0.413													11	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	155252868	155252868	+	Silent	SNP	T	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155252868T>A	uc004fnw.1	+	6	1571	c.912T>A	c.(910-912)CCT>CCA	p.P304P	uc004fnx.3_Silent_p.P90P	NM_182905	NP_878908			WAS protein family homolog 1																		TAGCCGAGCCTCTCAAGGCAG	0.632													4	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3396	3396	+	RNA	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3396T>C	uc004cos.3	+	2		c.1689T>C			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		ATTCTAGGCTATATACAACTA	0.453													89	14	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14987	14987	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14987T>C	uc004coy.2	+	1	227	c.152T>C	c.(151-153)CTA>CCA	p.L51P	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GAATCATCCGCTACCTTCACG	0.478													87	17	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	10352	10353	+	5'Flank	INS	-	A	A	rs145072688		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10352_10353insA	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		accctaaccctaccctaaccct	0.000													5	4	---	---	---	---	
MEGF6	1953	broad.mit.edu	37	1	3451888	3451888	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3451888delC	uc001akl.2	-							NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor							extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GTCTTTTCTGCCCCAAAACCC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5076798	5076799	+	IGR	INS	-	GTTT	GTTT	rs138398355	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5076798_5076799insGTTT								AJAP1 (232948 upstream) : NPHP4 (846071 downstream)																							TGTTTCTTAACgtttgtttgtt	0.243													4	2	---	---	---	---	
APITD1	378708	broad.mit.edu	37	1	10504976	10504976	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10504976delC	uc001arf.2	+						APITD1_uc001arg.2_Intron	NM_198544	NP_940946	Q8N2Z9	CENPS_HUMAN	apoptosis-inducing, TAF9-like domain 1 isoform						DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		TAAGCTATGGCCGGAGTAGGG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	10967197	10967198	+	IGR	INS	-	AT	AT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10967197_10967198insAT								CASZ1 (110490 upstream) : C1orf127 (39335 downstream)																							AGCACACACACACAGAACCGCA	0.545													4	2	---	---	---	---	
PRDM2	7799	broad.mit.edu	37	1	14069454	14069456	+	Intron	DEL	AAG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14069454_14069456delAAG	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger							Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AATTGTTGAAAAGAAGAAGAAAG	0.350													5	4	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15044890	15044891	+	Intron	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15044890_15044891insC	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						AGACCAGATTTCCCCCAACCTG	0.475													4	2	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16967662	16967663	+	Intron	INS	-	A	A	rs145771302		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16967662_16967663insA	uc001azg.1	-						CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0						gactctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17040226	17040226	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17040226delG	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						GTGTGATGCAGGGCCCAGCCA	0.413													4	2	---	---	---	---	
PADI1	29943	broad.mit.edu	37	1	17546510	17546510	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17546510delC	uc001bah.1	+							NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	ggatgatagtccaggagactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17610880	17610880	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17610880delG								PADI3 (155 upstream) : PADI4 (23810 downstream)																							GCCTTGTCTTGGCCAGAGGAT	0.478													4	2	---	---	---	---	
MUL1	79594	broad.mit.edu	37	1	20826783	20826784	+	3'UTR	DEL	CT	-	-	rs71743511		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20826783_20826784delCT	uc001bdi.3	-	4						NM_024544	NP_078820	Q969V5	MUL1_HUMAN	mitochondrial ubiquitin ligase activator of NFKB						activation of caspase activity|activation of JUN kinase activity|induction of apoptosis|mitochondrial fission|mitochondrion localization|negative regulation of cell growth|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to mitochondrial outer membrane|nucleus|peroxisome	identical protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CTTTCCTCCCCTCTGAGTCCTC	0.535													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	23605419	23605419	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23605419delT								HTR1D (84197 upstream) : HNRNPR (30858 downstream)																							TTCCTACTCCTTTTATTTCAG	0.378													4	2	---	---	---	---	
E2F2	1870	broad.mit.edu	37	1	23856216	23856217	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23856216_23856217delCA	uc001bhe.1	-							NM_004091	NP_004082	Q14209	E2F2_HUMAN	E2F transcription factor 2						G1 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|skin(2)	4		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		gtggcagagtcacaccagaaac	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31869274	31869275	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31869274_31869275delTC								FABP3 (23351 upstream) : SERINC2 (13773 downstream)																							GGGGCTGACATCTCTCTCTCTC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38811699	38811699	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38811699delC								POU3F1 (299249 upstream) : RRAGC (493316 downstream)																							TCGAACTAGACGGTCTGCTGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48446692	48446692	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48446692delT								FOXD2 (540330 upstream) : SKINTL (120695 downstream)																							ttttcttttctttttttttga	0.214													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51165916	51165917	+	Intron	INS	-	CA	CA	rs146704469	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51165916_51165917insCA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		AAAAGGGGGCTGTGTGTAATGG	0.431											OREG0002742	type=REGULATORY REGION|Gene=FAF1(intragenic)|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	2	4	---	---	---	---	
OSBPL9	114883	broad.mit.edu	37	1	52162842	52162842	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52162842delA	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron	NM_024586	NP_078862	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1						tcaaaaaaagaaaaaaaaaag	0.134													4	2	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55534414	55534415	+	3'UTR	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55534414_55534415delGT	uc001cyg.3	-	65						NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						TTGTATGTTCGTGTAACAAAAA	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59120074	59120074	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59120074delC								TACSTD2 (76908 upstream) : MYSM1 (5516 downstream)																							GGAGCATCCTCCCACAAATGC	0.408													4	2	---	---	---	---	
MYSM1	114803	broad.mit.edu	37	1	59134892	59134892	+	Intron	DEL	A	-	-	rs68056344		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59134892delA	uc009wab.1	-						MYSM1_uc009waa.1_5'Flank|MYSM1_uc001czc.2_Intron	NM_001085487	NP_001078956	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1						histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(1)	1	all_cancers(7;9.36e-06)					TAACAAGAACAAAAAAAAAAC	0.174													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59219583	59219583	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59219583delA								MYSM1 (53836 upstream) : JUN (26881 downstream)																							AAATGAGTCCAAAAAAATGAT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62068198	62068199	+	IGR	INS	-	GG	GG	rs150822408	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62068198_62068199insGG								NFIA (139739 upstream) : TM2D1 (78520 downstream)																							aaacaggcggtggggggcggtg	0.020													4	2	---	---	---	---	
IL23R	149233	broad.mit.edu	37	1	67672362	67672362	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67672362delT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_5'Flank|IL23R_uc001ddt.2_5'Flank	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0						TAGAGTTCAGTTTTTTTTTTT	0.323													4	2	---	---	---	---	
IL23R	149233	broad.mit.edu	37	1	67696230	67696232	+	Intron	DEL	TTA	-	-	rs71803252		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67696230_67696232delTTA	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_Intron|IL23R_uc001ddt.2_Intron	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0						TTTCCTCCTCTTATTCTTTCTTT	0.379													2	4	---	---	---	---	
LRRIQ3	127255	broad.mit.edu	37	1	74502309	74502309	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74502309delG	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											ovary(2)	2						TGTTATTGCTGGTATTATTAT	0.249													4	2	---	---	---	---	
TYW3	127253	broad.mit.edu	37	1	75206678	75206678	+	Intron	DEL	A	-	-	rs35496866		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75206678delA	uc001dgn.2	+						TYW3_uc010oqw.1_Intron|TYW3_uc010oqx.1_Intron|TYW3_uc010oqy.1_Intron	NM_138467	NP_612476	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog isoform						tRNA processing		methyltransferase activity			ovary(2)	2						cctgctggataggggtgaaga	0.000													3	3	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	75911892	75911892	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75911892delT	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						aaactttccatttttttatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	77316157	77316158	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77316157_77316158insA								ST6GALNAC3 (219488 upstream) : ST6GALNAC5 (17028 downstream)																							TGGATAAAATGAAAAAAAAACA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79524343	79524344	+	IGR	INS	-	ACAC	ACAC	rs137861467	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79524343_79524344insACAC								ELTD1 (51848 upstream) : None (None downstream)																							acaacacacatacacacacaca	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79715390	79715390	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79715390delC								ELTD1 (242895 upstream) : None (None downstream)																							taatgtgaagcaaaaaaaaaa	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80779946	80779946	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80779946delT								None (None upstream) : LPHN2 (991899 downstream)																							ttacttgaacttcagattaca	0.179													4	2	---	---	---	---	
CLCA2	9635	broad.mit.edu	37	1	86913878	86913878	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86913878delG	uc001dlr.3	+							NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor						cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAGTGACAGCGAACCCACTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88611229	88611229	+	IGR	DEL	T	-	-	rs71811787		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88611229delT								LMO4 (796626 upstream) : PKN2 (538693 downstream)																							CTCCTAAATGTTTTTTTTTTT	0.393													3	3	---	---	---	---	
ABCD3	5825	broad.mit.edu	37	1	94982960	94982960	+	3'UTR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94982960delT	uc001dqn.3	+	23					ABCD3_uc010oto.1_3'UTR|ABCD3_uc010otp.1_3'UTR|ABCD3_uc009wdr.2_3'UTR|ABCD3_uc001dqo.3_3'UTR	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TAAATTGGGCTTCAATCACTG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95995056	95995056	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95995056delC								RWDD3 (282283 upstream) : None (None downstream)																							TGGGGCCTTTCCCCCAATACT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96034860	96034860	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96034860delG								RWDD3 (322087 upstream) : None (None downstream)																							CACTCCAGATGGGGCACATAT	0.443													4	2	---	---	---	---	
AGL	178	broad.mit.edu	37	1	100367227	100367228	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100367227_100367228insT	uc001dsi.1	+						AGL_uc001dsj.1_Intron|AGL_uc001dsk.1_Intron|AGL_uc001dsl.1_Intron|AGL_uc001dsm.1_Intron|AGL_uc001dsn.1_Intron	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATTTTTGAGTGTTTTTTTTTCC	0.376													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101849955	101849956	+	IGR	INS	-	TTA	TTA	rs147058373	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101849955_101849956insTTA								S1PR1 (142879 upstream) : OLFM3 (418171 downstream)																							TCCACTGGGATATAGCCCAGTG	0.436													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101908906	101908906	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101908906delA								S1PR1 (201830 upstream) : OLFM3 (359221 downstream)																							tgaaaaaattaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102678241	102678241	+	IGR	DEL	T	-	-	rs5776621		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102678241delT								OLFM3 (215451 upstream) : COL11A1 (663783 downstream)																							TTTACTTTTCTTTTTTTTCAC	0.313													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	106320468	106320468	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106320468delC								None (None upstream) : None (None downstream)																							CACTGCATCACCACATCCATC	0.328													4	2	---	---	---	---	
FAM102B	284611	broad.mit.edu	37	1	109127876	109127876	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109127876delT	uc010ouy.1	+							NM_001010883	NP_001010883	Q5T8I3	F102B_HUMAN	hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		TCAAGAGCTATTTTTGCTAAG	0.343													4	2	---	---	---	---	
FAM102B	284611	broad.mit.edu	37	1	109167054	109167055	+	Intron	INS	-	AA	AA	rs34112326		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109167054_109167055insAA	uc010ouy.1	+							NM_001010883	NP_001010883	Q5T8I3	F102B_HUMAN	hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		CTTGTTATGTTAAAAAAAAAAA	0.356													7	5	---	---	---	---	
SORT1	6272	broad.mit.edu	37	1	109881505	109881505	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109881505delT	uc001dxm.1	-						SORT1_uc010ovi.1_Intron	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein						endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		actctgatacttttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110313805	110313805	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110313805delA								EPS8L3 (7241 upstream) : CSF1 (139428 downstream)																							GCCTTAGATGAAAAAGACAAG	0.373													4	2	---	---	---	---	
DENND2C	163259	broad.mit.edu	37	1	115127989	115127989	+	3'UTR	DEL	A	-	-	rs5777195		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115127989delA	uc001efd.1	-	21					DENND2C_uc001eez.2_Intron|DENND2C_uc001efc.1_3'UTR	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGCTGCTATAAAAAAAAAAT	0.408													7	5	---	---	---	---	
PHGDH	26227	broad.mit.edu	37	1	120267598	120267598	+	Intron	DEL	C	-	-	rs3838425		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120267598delC	uc001ehz.2	+						PHGDH_uc009whl.2_Intron|PHGDH_uc009whm.2_Intron|PHGDH_uc001eia.2_Intron|PHGDH_uc009whn.2_Intron|PHGDH_uc001eib.2_Intron	NM_006623	NP_006614	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase						brain development|L-serine biosynthetic process		electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity			ovary(1)	1	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)	NADH(DB00157)	AGTGTGGGTGCCTATATGTAG	0.552													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142600321	142600321	+	IGR	DEL	T	-	-	rs71210537		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142600321delT								None (None upstream) : None (None downstream)																							CAAttctttattttttttttc	0.035													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142794623	142794624	+	Intron	INS	-	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142794623_142794624insG	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		ctctcccacccccggatattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142963340	142963340	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142963340delT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		GATTTGCCAATTTCAGCACAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143412865	143412865	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143412865delA								None (None upstream) : LOC100286793 (234774 downstream)																							aggctgacagaaggatggaca	0.000													5	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144943601	144943602	+	Intron	INS	-	AATATA	AATATA	rs138603977	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144943601_144943602insAATATA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		acctagaacttTATATAGGAGC	0.158			T	PDGFRB	MPD								5	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145012913	145012914	+	Intron	INS	-	T	T	rs67707497		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145012913_145012914insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_5'Flank	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATCAAAGAGCCTTTTTTCTCTA	0.317			T	PDGFRB	MPD								2	5	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145018102	145018103	+	Intron	INS	-	AGAA	AGAA	rs4068417		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145018102_145018103insAGAA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_RNA	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAACGAGAGAGAGAAAGAGAGA	0.366			T	PDGFRB	MPD								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146592040	146592041	+	IGR	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146592040_146592041delAG								LOC728989 (77441 upstream) : PRKAB2 (34646 downstream)																							CCACTGCGATAGAGAGAGAGAG	0.371													4	3	---	---	---	---	
GJA5	2702	broad.mit.edu	37	1	147228835	147228836	+	3'UTR	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147228835_147228836delCA	uc001eps.1	-	2					GJA5_uc001ept.1_3'UTR	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40						angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			CATCAGCACCCACACACACACA	0.460													4	2	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149982897	149982897	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149982897delA	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			ATTCTTGAACAGGAGTTGGAG	0.587													4	2	---	---	---	---	
PRPF3	9129	broad.mit.edu	37	1	150325178	150325178	+	Intron	DEL	T	-	-	rs78725366		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150325178delT	uc001eum.3	+						PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		GAGGTCACAATTTTTTTTTAA	0.189													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	151705598	151705598	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151705598delT								C1orf230 (3516 upstream) : MRPL9 (26527 downstream)																							tgtGTTTTTGTTTTTTTTTGT	0.060													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153362052	153362052	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153362052delT								S100A12 (13977 upstream) : S100A8 (457 downstream)																							ctctccccccttccctctctt	0.244													4	2	---	---	---	---	
UBAP2L	9898	broad.mit.edu	37	1	154227047	154227049	+	Intron	DEL	TTG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154227047_154227049delTTG	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc010pen.1_Intron|UBAP2L_uc001feq.2_5'Flank|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGTTTTAGGTTTGGGGTGTCTTC	0.419													5	4	---	---	---	---	
TDRD10	126668	broad.mit.edu	37	1	154513926	154513928	+	Intron	DEL	GGT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154513926_154513928delGGT	uc009wow.2	+						TDRD10_uc001ffd.2_Intron|TDRD10_uc001ffe.2_Intron	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)			AAGGTGCGTGGGTGGTGGTGGTA	0.547													4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154838246	154838246	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154838246delA	uc001ffp.2	-						KCNN3_uc009wox.1_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)			AACCCCACGGAAAAAAAAGCA	0.498													4	2	---	---	---	---	
KIAA0907	22889	broad.mit.edu	37	1	155886695	155886695	+	Intron	DEL	T	-	-	rs113079820		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155886695delT	uc001fmi.1	-						KIAA0907_uc001fmj.1_Intron|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_Intron	NM_014949	NP_055764	Q7Z7F0	K0907_HUMAN	hypothetical protein LOC22889												0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			AAAGTAGGGATTTTTTTTTTT	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157618455	157618455	+	IGR	DEL	T	-	-	rs66529407		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157618455delT								FCRL4 (50585 upstream) : FCRL3 (27823 downstream)																							ttttgatgtgttttttttttc	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157626251	157626251	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157626251delT								FCRL4 (58381 upstream) : FCRL3 (20027 downstream)																							tgcatgcaaattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158544201	158544201	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158544201delT								OR6P1 (10807 upstream) : OR10X1 (4517 downstream)																							ttttttcatgttttttttttc	0.000													3	3	---	---	---	---	
IFI16	3428	broad.mit.edu	37	1	159002146	159002147	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159002146_159002147insA	uc001ftg.2	+						IFI16_uc010pis.1_Intron|IFI16_uc001fth.2_5'Flank|IFI16_uc010pit.1_5'Flank	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					cacattttagcaaaaaaaatat	0.109													4	2	---	---	---	---	
RXRG	6258	broad.mit.edu	37	1	165372746	165372747	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165372746_165372747delAA	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)	GGCACCATCTAAAAAAGTAGAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173370884	173370885	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173370884_173370885delAC	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																		cacatacacaacacacacacac	0.094													4	2	---	---	---	---	
SLC9A11	284525	broad.mit.edu	37	1	173529870	173529870	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173529870delC	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						TTGCACAGAACCCCGCAGCTA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177651629	177651629	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177651629delT								FAM5B (400072 upstream) : SEC16B (245860 downstream)																							tgccttttaattgtctgagtt	0.075													4	2	---	---	---	---	
RASAL2	9462	broad.mit.edu	37	1	178136869	178136869	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178136869delT	uc001glq.2	+						RASAL2_uc009wxb.2_Intron	NM_170692	NP_733793	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 2						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						tctttcttcctttttttttaa	0.005													4	2	---	---	---	---	
STX6	10228	broad.mit.edu	37	1	180985486	180985486	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180985486delT	uc010pnq.1	-						STX6_uc001goo.2_Intron|STX6_uc010pnr.1_Intron	NM_005819	NP_005810	O43752	STX6_HUMAN	syntaxin 6						Golgi vesicle transport|intracellular protein transport|vesicle fusion	clathrin-coated vesicle|early endosome|integral to membrane|perinuclear region of cytoplasm|plasma membrane|trans-Golgi network membrane	SNAP receptor activity			ovary(1)	1						TGGGTCTTTCTTTTTTTTTCA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182254273	182254273	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182254273delA								ZNF648 (223426 upstream) : GLUL (97396 downstream)																							gtctacagggaaaaaaaaaag	0.189													4	2	---	---	---	---	
LAMC1	3915	broad.mit.edu	37	1	182993568	182993568	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182993568delT	uc001gpy.3	+						LAMC1_uc001gpx.2_Intron	NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GATTTCCCCCTTTTTTTTCTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	183134600	183134600	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183134600delT								LAMC1 (19874 upstream) : LAMC2 (20574 downstream)																							GGGAATTGGCTTTAGACTATT	0.279													4	2	---	---	---	---	
RGL1	23179	broad.mit.edu	37	1	183843645	183843645	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183843645delT	uc001gqo.2	+						RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron|RGL1_uc010poi.1_Intron	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation						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						GCCGTGGAGGTTTTTTTTTTT	0.458													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	190741668	190741668	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190741668delT								FAM5C (294909 upstream) : None (None downstream)																							TTTGTTTTTATTTTTTTCTAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191873250	191873250	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191873250delC								None (None upstream) : RGS18 (254342 downstream)																							CTCTTTCTCTCCTGCCCTACA	0.338													4	2	---	---	---	---	
KCNT2	343450	broad.mit.edu	37	1	196308651	196308654	+	Intron	DEL	AGAG	-	-	rs71923003		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196308651_196308654delAGAG	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc001gth.1_Intron	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						ACACACACACagagagagagagag	0.230													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196817895	196817895	+	IGR	DEL	A	-	-	rs59176524		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196817895delA								CFHR1 (16579 upstream) : CFHR4 (39317 downstream)																							tagtttatttagagacacaat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199035648	199035648	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199035648delT								MIR181A1 (207366 upstream) : NR5A2 (961122 downstream)																							ACAGAAAGTCTTCCCCTGAAC	0.383													4	2	---	---	---	---	
TRAF3IP3	80342	broad.mit.edu	37	1	209931939	209931939	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209931939delG	uc001hho.2	+						TRAF3IP3_uc001hhl.2_Intron|TRAF3IP3_uc001hhm.1_Intron|TRAF3IP3_uc001hhn.2_Intron|TRAF3IP3_uc009xcr.2_5'UTR	NM_025228	NP_079504	Q9Y228	T3JAM_HUMAN	TRAF3-interacting JNK-activating modulator							integral to membrane	protein binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.045)		TAAACCCCAAGGGGTTAGAGC	0.527													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210804875	210804875	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210804875delT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TTGCATTAGATTGCTCCCACG	0.433													4	2	---	---	---	---	
PROX1	5629	broad.mit.edu	37	1	214208978	214208978	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214208978delC	uc001hkh.2	+							NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1						aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		GCCATTGTCTCCTTGTATCAG	0.423													98	50	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215946855	215946856	+	Intron	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215946855_215946856delTC	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		tctctctctgtctctctctctc	0.000										HNSCC(13;0.011)			4	2	---	---	---	---	
GPATCH2	55105	broad.mit.edu	37	1	217716288	217716288	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217716288delA	uc001hlf.1	-							NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GCAGCTCACTAAAGAGAGTAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219410328	219410329	+	IGR	INS	-	T	T	rs151202848	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219410328_219410329insT								LYPLAL1 (24122 upstream) : SLC30A10 (448440 downstream)																							TTCAGTTGTTGTTTTTTTTGTT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221399149	221399149	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221399149delC								HLX (340751 upstream) : LOC400804 (104121 downstream)																							TCCTCACCTACCCCAAATCAT	0.274													4	2	---	---	---	---	
EPHX1	2052	broad.mit.edu	37	1	225996190	225996190	+	5'Flank	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225996190delG	uc001hpk.2	+							NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1						aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)					tctaggaaaagggtagtaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229036249	229036249	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229036249delG								RHOU (153840 upstream) : RAB4A (370630 downstream)																							GCATGGCCATGGGAGAGAGCC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229303549	229303549	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229303549delC								RHOU (421140 upstream) : RAB4A (103330 downstream)																							acttgtgactcccccaaagct	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229345343	229345343	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229345343delT								RHOU (462934 upstream) : RAB4A (61536 downstream)																							aaggggtgggtgggtaggata	0.080													4	2	---	---	---	---	
NUP133	55746	broad.mit.edu	37	1	229626149	229626150	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229626149_229626150delAA	uc001htn.2	-							NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				attcagtagtaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229727736	229727736	+	IGR	DEL	A	-	-	rs139285852		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229727736delA								ABCB10 (33294 upstream) : TAF5L (1132 downstream)																							TCTCTGCGCTAACCCACAAAC	0.423													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233192657	233192658	+	Intron	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233192657_233192658delTT	uc001hvl.2	-						PCNXL2_uc001hvk.1_Intron|PCNXL2_uc001hvm.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				TTCCAAAGAATTTTTTTTTCCT	0.342													4	2	---	---	---	---	
ARID4B	51742	broad.mit.edu	37	1	235394234	235394234	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235394234delA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron|ARID4B_uc001hwt.3_Intron	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			ctctgtctccaaaaaaaaaaa	0.104													11	6	---	---	---	---	
B3GALNT2	148789	broad.mit.edu	37	1	235615089	235615089	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235615089delG	uc001hxc.2	-							NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			CACCTTCGATGGCCAAAGTGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238487778	238487778	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238487778delT								LOC100130331 (396161 upstream) : LOC339535 (155908 downstream)																							AAGCTAATTCTTTTTTAGGTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238855092	238855092	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238855092delA								LOC339535 (205775 upstream) : CHRM3 (694773 downstream)																							TGACTTGAACAAAATGTGTAT	0.418													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241415350	241415350	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241415350delT	uc001hyv.2	-						RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			tttctttttcttttttttttt	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	549126	549126	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:549126delA								FAM150B (260818 upstream) : TMEM18 (118849 downstream)																							gtcaattcttaaaaaAAAAAC	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6777765	6777765	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6777765delC								LOC400940 (649401 upstream) : CMPK2 (202738 downstream)																							TTGCAGTTAACCCCCTGAGTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7881116	7881117	+	IGR	INS	-	TG	TG	rs141973117	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7881116_7881117insTG								RNF144A (696809 upstream) : LOC339788 (181441 downstream)																							gtgtgtgtgtttgtgtgtgtgt	0.000													3	4	---	---	---	---	
GRHL1	29841	broad.mit.edu	37	2	10139017	10139018	+	Intron	INS	-	AT	AT	rs146407055	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10139017_10139018insAT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		catatatatacatatatatata	0.149													33	17	---	---	---	---	
PQLC3	130814	broad.mit.edu	37	2	11318225	11318235	+	3'UTR	DEL	CCATTTTGAGG	-	-	rs3832137		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11318225_11318235delCCATTTTGAGG	uc002rbc.2	+	7					PQLC3_uc010yjk.1_3'UTR	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor							integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		TCCAAGAAGCCCATTTTGAGGCCATTTTGAG	0.412													4	2	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11758049	11758049	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11758049delC	uc002rbk.1	+						GREB1_uc002rbp.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							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)		CTCCCAGATGCCCCCGATGGA	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19332849	19332849	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19332849delA								NT5C1B (562011 upstream) : OSR1 (218398 downstream)																							TTATGTTTTCAAGTACTAGCC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19438716	19438716	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19438716delA								NT5C1B (667878 upstream) : OSR1 (112531 downstream)																							GATCCAAGCCAAAAAAATAAC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19569129	19569130	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19569129_19569130insA								OSR1 (10757 upstream) : TTC32 (527388 downstream)																							TTGATTCAGCCAAAAAATAACT	0.406											OREG0014468	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20296558	20296558	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20296558delA								LAPTM4A (44769 upstream) : SDC1 (104000 downstream)																							TTTGTGCTCTAAAACATTCTC	0.264													4	2	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	20891304	20891304	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20891304delG	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTGTGTCATGGGGGTGATAA	0.328													4	2	---	---	---	---	
EPT1	85465	broad.mit.edu	37	2	26578253	26578254	+	Intron	INS	-	A	A	rs146815203	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26578253_26578254insA	uc010ykz.1	+						EPT1_uc010eyl.1_Intron	NM_033505	NP_277040	Q9C0D9	EPT1_HUMAN	selenoprotein I						phospholipid biosynthetic process	integral to membrane	ethanolaminephosphotransferase activity|metal ion binding				0						TGTAATAGCACAGAGACAATAA	0.371													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30887379	30887379	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30887379delC								LCLAT1 (20289 upstream) : CAPN13 (58261 downstream)																							GTCAGAAGGGCCCTGCTAAGG	0.547													4	2	---	---	---	---	
SRD5A2	6716	broad.mit.edu	37	2	31757851	31757851	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31757851delC	uc002rnw.1	-							NM_000348	NP_000339	P31213	S5A2_HUMAN	3-oxo-5 alpha-steroid 4-dehydrogenase 2						androgen biosynthetic process|cell differentiation|cell-cell signaling|male gonad development	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|sterol 5-alpha reductase activity				0	Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)	GAAAGGGTATCTGGGgcaggg	0.189													4	2	---	---	---	---	
DPY30	84661	broad.mit.edu	37	2	32262935	32262935	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32262935delA	uc002roa.1	-						MEMO1_uc010ymv.1_Intron|DPY30_uc002rob.1_Intron	NM_032574	NP_115963	Q9C005	DPY30_HUMAN	dpy-30-like protein						endosome transport|histone H3-K4 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Set1C/COMPASS complex|trans-Golgi network	protein homodimerization activity				0	Acute lymphoblastic leukemia(172;0.155)					ATGCTTTATTAAAAAAAACAA	0.139													4	2	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32337907	32337907	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32337907delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GGCTTTTGTCTTTTTTTTTGG	0.284													4	2	---	---	---	---	
SLC30A6	55676	broad.mit.edu	37	2	32397457	32397457	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32397457delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ctttttgttcttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34562259	34562259	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34562259delG								MYADML (608975 upstream) : None (None downstream)																							gtcatacactggaataatatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34816499	34816499	+	IGR	DEL	G	-	-	rs71411410		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34816499delG								MYADML (863215 upstream) : None (None downstream)																							cttcccaattgggatgcttct	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35348215	35348215	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35348215delT								None (None upstream) : None (None downstream)																							ACTTAGGCCCTTTTTAAGAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37994529	37994530	+	IGR	DEL	CT	-	-	rs142632267		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37994529_37994530delCT								CDC42EP3 (95203 upstream) : FAM82A1 (157932 downstream)																							TCAGAGAAAACTCTCTGATACA	0.421													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38685688	38685690	+	IGR	DEL	TTC	-	-	rs114637499	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38685688_38685690delTTC								ATL2 (81256 upstream) : HNRPLL (104638 downstream)																							CTGTTGCTGTTTCTTCTTCTTCT	0.330													4	2	---	---	---	---	
ARHGEF33	100271715	broad.mit.edu	37	2	39148939	39148939	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39148939delT	uc010ynq.1	+							NM_001145451	NP_001138923			DH and coiled-coil domain-containing protein												0						TCAACTCTGCTTCTCTTGCCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	50118779	50118779	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50118779delT								FSHR (737149 upstream) : NRXN1 (26865 downstream)																							ctaagtatacttttttttgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57319956	57319956	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57319956delC								CCDC85A (706648 upstream) : VRK2 (814830 downstream)																							atgtattctgccatgactgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62531825	62531825	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62531825delA								B3GNT2 (79961 upstream) : TMEM17 (195531 downstream)																							CCAAGATTTTAAAAAATGGAC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62830117	62830119	+	IGR	DEL	TCC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62830117_62830119delTCC								TMEM17 (67337 upstream) : EHBP1 (70894 downstream)																							TGACATAGTGtcctcctcctcct	0.177													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65019637	65019637	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65019637delT								SERTAD2 (138591 upstream) : SLC1A4 (195942 downstream)																							TGGCTTATGCTTTTTTTTTTC	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65777260	65777261	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65777260_65777261insA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		AGCGGGAGGTTAAAAAATGACT	0.460													4	2	---	---	---	---	
PLEK	5341	broad.mit.edu	37	2	68615867	68615867	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68615867delA	uc002sen.3	+						PLEK_uc010fde.2_Intron	NM_002664	NP_002655	P08567	PLEK_HUMAN	pleckstrin						actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		ATATCATAGGAAAAAAAAAGG	0.363													4	2	---	---	---	---	
GFPT1	2673	broad.mit.edu	37	2	69575715	69575716	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69575715_69575716insT	uc002sfh.2	-							NM_002056	NP_002047	Q06210	GFPT1_HUMAN	glucosamine-fructose-6-phosphate						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			skin(1)	1						AAGCATGGTTGTTTCctcctca	0.203													4	3	---	---	---	---	
TIA1	7072	broad.mit.edu	37	2	70453139	70453141	+	Intron	DEL	AAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70453139_70453141delAAC	uc002sgj.3	-						TIA1_uc002sgk.3_Intron|TIA1_uc002sgl.3_Intron|TIA1_uc002sgm.3_Intron	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0						TATCTCCTTTAACAACAACAAAA	0.310													4	2	---	---	---	---	
VAX2	25806	broad.mit.edu	37	2	71157377	71157378	+	Intron	INS	-	A	A	rs144792191	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71157377_71157378insA	uc002shh.2	+							NM_012476	NP_036608	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2						ectoderm development|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ttcaaaacaccaactcacatct	0.178													2	4	---	---	---	---	
TET3	200424	broad.mit.edu	37	2	74292747	74292748	+	Intron	INS	-	TCCT	TCCT	rs150547831	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74292747_74292748insTCCT	uc002skb.3	+						TET3_uc010fez.1_Intron	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						ccgtccgtccgtccttccttcc	0.050													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80856616	80856616	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80856616delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_Intron|CTNNA2_uc010ysj.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						ttttattcctaaatctttcgg	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82575391	82575391	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82575391delT								None (None upstream) : None (None downstream)																							CATTTAGCTATTTTTTTATGA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	86228872	86228873	+	IGR	DEL	AC	-	-	rs71712370		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86228872_86228873delAC								ST3GAL5 (112715 upstream) : LOC90784 (18466 downstream)																							ATCTTTGGCTacacacacacac	0.347													2	5	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87607170	87607173	+	Intron	DEL	AGAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87607170_87607173delAGAC	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						ACAGAGAGAGAGACAGAAAAGTGA	0.500													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89872664	89872668	+	IGR	DEL	ATTCC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89872664_89872668delATTCC								FLJ40330 (766539 upstream) : None (None downstream)																							attccgttctattccattccattcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90371692	90371693	+	Intron	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90371692_90371693delGA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		gatttcgttcgagtccatttga	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91751423	91751423	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91751423delA								None (None upstream) : LOC654342 (53769 downstream)																							ACGCTTCCCCATGGTGAGAAA	0.393													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92076875	92076875	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076875delT								GGT8P (106722 upstream) : FKSG73 (52284 downstream)																							ttttaaattgtttatagagat	0.000													4	2	---	---	---	---	
TMEM131	23505	broad.mit.edu	37	2	98458074	98458095	+	Intron	DEL	CAGACTGCTGTATTCCAAAATT	-	-	rs150737514	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98458074_98458095delCAGACTGCTGTATTCCAAAATT	uc002syh.3	-						TMEM131_uc010yvg.1_Intron	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6						ATTCAAAATCCAGACTGCTGTATTCCAAAATTCAGACTGCTG	0.338													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	99025579	99025580	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99025579_99025580delTG								CNGA3 (10522 upstream) : INPP4A (35741 downstream)																							ctaacatgcctgtgtgtgtgtg	0.000													4	3	---	---	---	---	
C2orf55	343990	broad.mit.edu	37	2	99453161	99453161	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99453161delC	uc002szf.1	-							NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990												0						GTTAGAGTTTCCCTGGGGCTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101237612	101237613	+	IGR	DEL	CA	-	-	rs137869997		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101237612_101237613delCA								PDCL3 (44411 upstream) : NPAS2 (199000 downstream)																							GTGTTCATGTcacacacacaca	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101257141	101257141	+	IGR	DEL	T	-	-	rs71718599		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101257141delT								PDCL3 (63940 upstream) : NPAS2 (179472 downstream)																							ATGTTTTTTCTTTTTTTTTTT	0.383													4	2	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101524484	101524485	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101524484_101524485delGT	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4						GTGTTGTAGGGTGTGTGTGTGT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102515376	102515377	+	IGR	INS	-	AGTT	AGTT	rs140237191	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102515376_102515377insAGTT								MAP4K4 (4225 upstream) : IL1R2 (92929 downstream)																							CTCATTGGCTCAGCGCACTCTC	0.510													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107342203	107342203	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107342203delT								RGPD3 (257402 upstream) : ST6GAL2 (75855 downstream)																							taccatgagctttttttgtac	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114320684	114320684	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114320684delT	uc002tjy.1	+											DQ598479																		ACTGGATTGATTTTTTTTTTT	0.403													5	3	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116551914	116551914	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116551914delC	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						AGAAAGACTGCCCTGGAAGAA	0.448													4	2	---	---	---	---	
PTPN4	5775	broad.mit.edu	37	2	120515849	120515849	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120515849delT	uc002tmf.1	+							NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)	TCTCTCTCTCTTTTTTTTAAG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127070300	127070300	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127070300delG								None (None upstream) : GYPC (343384 downstream)																							TTGCTCGACAGGATagcagca	0.274													4	2	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128386121	128386125	+	Intron	DEL	GGGTG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128386121_128386125delGGGTG	uc002top.2	+						MYO7B_uc002tor.1_Intron	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GTGCCAGACTgggtggggtggggtg	0.527													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132779428	132779429	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132779428_132779429insA								C2orf27B (220194 upstream) : NCRNA00164 (125735 downstream)																							AAGTATCTTTTAAAAACACTTC	0.406													4	2	---	---	---	---	
RAB3GAP1	22930	broad.mit.edu	37	2	135852333	135852333	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135852333delT	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365	Q15042	RB3GP_HUMAN	RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)		agtttgtttgtttttttagct	0.114													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138048212	138048212	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138048212delA	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATTTCAAGGGAAGTCTCCCTG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139359548	139359548	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139359548delT								SPOPL (28745 upstream) : NXPH2 (67181 downstream)																							tcaggaagacttttttggcag	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	148405881	148405882	+	IGR	INS	-	G	G	rs141732942	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148405881_148405882insG								None (None upstream) : ACVR2A (196204 downstream)																							ttttaaacacatgagagccaaa	0.059													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157477851	157477851	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157477851delT								GPD2 (7604 upstream) : GALNT5 (636489 downstream)																							taatggagtgttttttttcaa	0.095													4	2	---	---	---	---	
PLA2R1	22925	broad.mit.edu	37	2	160804401	160804404	+	Intron	DEL	AGAG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160804401_160804404delAGAG	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3						TATGACTCCCAGAGAGAGTGGCAG	0.451													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164884503	164884503	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164884503delG								FIGN (291990 upstream) : GRB14 (464830 downstream)																							gcaagaatgtggagaaaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164980591	164980591	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164980591delG								FIGN (388078 upstream) : GRB14 (368742 downstream)																							GGAAAGGGCTGGGTCTTTCTG	0.373													4	2	---	---	---	---	
SSB	6741	broad.mit.edu	37	2	170653497	170653497	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170653497delA	uc002ufk.2	+						SSB_uc002ufl.2_5'Flank	NM_003142	NP_003133	P05455	LA_HUMAN	autoantigen La						histone mRNA metabolic process|tRNA modification	nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding|tRNA binding			skin(3)|pancreas(1)	4						gagactgtctaaaaaaaaaga	0.070													4	2	---	---	---	---	
DYNC1I2	1781	broad.mit.edu	37	2	172596133	172596133	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172596133delT	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron|DYNC1I2_uc002uhg.1_Intron|DYNC1I2_uc010zdu.1_Intron	NM_001378	NP_001369	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)			cagtgttcaattttttttttc	0.000													4	2	---	---	---	---	
CHN1	1123	broad.mit.edu	37	2	175698327	175698327	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175698327delT	uc002uji.2	-						CHN1_uc010zeq.1_Intron|CHN1_uc002ujj.2_Intron|CHN1_uc002ujg.2_Intron	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)			aatctctgccttttaatggtg	0.000			T	TAF15	extraskeletal myxoid chondrosarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177063989	177063989	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177063989delA								HOXD1 (8354 upstream) : MTX2 (70134 downstream)																							ATATAGGGGGAAAAAAACTAC	0.199													4	2	---	---	---	---	
ZNF385B	151126	broad.mit.edu	37	2	180413135	180413136	+	Intron	INS	-	GTTT	GTTT	rs139887932	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180413135_180413136insGTTT	uc002unn.3	-						ZNF385B_uc002unj.2_Intron|ZNF385B_uc002unk.2_Intron|ZNF385B_uc002unl.2_Intron|ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733	Q569K4	Z385B_HUMAN	zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TGGCATGTAAGgtttgtttgtt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187160263	187160263	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187160263delA								None (None upstream) : ZC3H15 (190622 downstream)																							AGACCAAAAGAAAAAAAAACA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	189093508	189093508	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189093508delA								TFPI (674289 upstream) : GULP1 (63096 downstream)																							TATTGAggccaggcactgtgg	0.100													4	2	---	---	---	---	
STAT4	6775	broad.mit.edu	37	2	191912329	191912329	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191912329delA	uc002usm.1	-						STAT4_uc002usn.1_Intron|STAT4_uc010zgk.1_Intron|STAT4_uc002uso.2_Intron	NM_003151	NP_003142	Q14765	STAT4_HUMAN	signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			gtaagagtagaaaaaagttta	0.090													4	2	---	---	---	---	
ORC2L	4999	broad.mit.edu	37	2	201778390	201778402	+	Intron	DEL	ACTTGGCAGATAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201778390_201778402delACTTGGCAGATAC	uc002uwr.2	-						ORC2L_uc010zhj.1_3'UTR	NM_006190	NP_006181	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0						AAAAATATGTACTTGGCAGATACACATCCATAG	0.357													9	12	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202676386	202676387	+	Intron	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202676386_202676387delAG	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)	gaggaaatgaagagagagagaa	0.074													4	2	---	---	---	---	
ZDBF2	57683	broad.mit.edu	37	2	207154203	207154205	+	Intron	DEL	CTT	-	-	rs71410881		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207154203_207154205delCTT	uc002vbp.2	+							NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2								nucleic acid binding|zinc ion binding			ovary(3)	3						agtggcttcacttcttcttggtt	0.000													4	3	---	---	---	---	
FN1	2335	broad.mit.edu	37	2	216287903	216287904	+	Intron	INS	-	CA	CA	rs139663301	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216287903_216287904insCA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vfl.2_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TGATGTAACATcacacacacac	0.193													5	8	---	---	---	---	
TMEM198	130612	broad.mit.edu	37	2	220412692	220412692	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220412692delC	uc002vme.2	+	4	1216	c.631delC	c.(631-633)CCCfs	p.P211fs	TMEM198_uc002vmf.2_Frame_Shift_Del_p.P211fs	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	211	Leu-rich.					integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGCTCCTGTGCCCCCACTCTG	0.677													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221496027	221496027	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221496027delA								SLC4A3 (989326 upstream) : EPHA4 (786722 downstream)																							ATATGGAGAGAAAGGGGGAGC	0.204													4	2	---	---	---	---	
RHBDD1	84236	broad.mit.edu	37	2	227808847	227808847	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227808847delA	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		TGGCAGATTCAATCTAAACCA	0.423													4	2	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230690490	230690490	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230690490delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		tagcagggagaaaaaaataag	0.000													4	2	---	---	---	---	
SP100	6672	broad.mit.edu	37	2	231344189	231344189	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231344189delT	uc002vqt.2	+						SP100_uc002vqs.2_Intron|SP100_uc002vqu.1_Intron	NM_003113	NP_003104	P23497	SP100_HUMAN	nuclear antigen Sp100 isoform 2						DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CACGCTTCCCTTTTTATTGTT	0.378													4	2	---	---	---	---	
GIGYF2	26058	broad.mit.edu	37	2	233697115	233697116	+	Intron	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233697115_233697116delAG	uc002vti.3	+						GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|GIGYF2_uc002vtq.3_Intron	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b						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)		ACAAGGGGCAAGAGCCAGGGAT	0.495													4	2	---	---	---	---	
ATG16L1	55054	broad.mit.edu	37	2	234170955	234170956	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234170955_234170956insT	uc002vty.2	+						ATG16L1_uc002vtx.1_Intron|ATG16L1_uc002vua.2_Intron|ATG16L1_uc002vub.2_Intron|ATG16L1_uc002vtz.2_Intron|ATG16L1_uc002vud.3_Intron	NM_030803	NP_110430	Q676U5	A16L1_HUMAN	APG16 autophagy 16-like isoform 1						autophagic vacuole assembly|protein homooligomerization|protein transport	autophagic vacuole|pre-autophagosomal structure membrane	protein binding				0		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		gctggctggtcttcctgtttcg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238368747	238368747	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238368747delG								COL6A3 (45897 upstream) : MLPH (26306 downstream)																							TGaagagtgtggacatcggtg	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240833718	240833719	+	IGR	INS	-	TCA	TCA			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240833718_240833719insTCA								HDAC4 (510372 upstream) : NDUFA10 (66439 downstream)																							cctcagctccatcccagcctca	0.000													4	2	---	---	---	---	
KIF1A	547	broad.mit.edu	37	2	241706136	241706139	+	Intron	DEL	CAAA	-	-	rs148936546	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241706136_241706139delCAAA	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)		tctctctctccaaatctctctctc	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	670963	670963	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:670963delA	uc003boy.1	+											Homo sapiens cDNA FLJ44328 fis, clone TRACH3002871.																		aacagatcttaaggttctgga	0.000													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10121606	10121606	+	Intron	DEL	T	-	-	rs79933580		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10121606delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		cttcgtcttcttttttttttt	0.119			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	28721536	28721536	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28721536delT								ZCWPW2 (154906 upstream) : RBMS3 (601407 downstream)																							atctttgtggttacctgggga	0.114													4	2	---	---	---	---	
STT3B	201595	broad.mit.edu	37	3	31669195	31669196	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31669195_31669196insT	uc011axe.1	+							NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0						AGTAAACATTATTTTTTTGTAT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35356127	35356128	+	IGR	DEL	AG	-	-	rs113054869		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35356127_35356128delAG								None (None upstream) : ARPP21 (324953 downstream)																							CAGCAAAAAAAGAGTTTTAAAG	0.317													2	4	---	---	---	---	
ARPP21	10777	broad.mit.edu	37	3	35722290	35722290	+	Intron	DEL	T	-	-	rs36013801		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35722290delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cfz.2_Intron|ARPP21_uc003cgc.2_Intron|ARPP21_uc003cgd.2_Intron|ARPP21_uc011axx.1_Intron|ARPP21_uc003cge.2_5'Flank	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						ctctttcttcttTTTTTTTCT	0.189													3	3	---	---	---	---	
ZNF197	10168	broad.mit.edu	37	3	44678983	44678983	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44678983delT	uc003cnm.2	+						ZNF197_uc003cnn.2_Intron|ZNF197_uc003cno.2_Intron|ZNF197_uc003cnp.2_Intron	NM_006991	NP_008922	O14709	ZN197_HUMAN	zinc finger protein 197 isoform 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|skin(1)	4				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		tgaattccagttttttttttc	0.000													4	2	---	---	---	---	
SETD2	29072	broad.mit.edu	37	3	47129985	47129986	+	Intron	INS	-	TTA	TTA	rs141138642	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47129985_47129986insTTA	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)		gtagcaagaacttatatgagtc	0.109			N|F|S|Mis		clear cell renal carcinoma								4	3	---	---	---	---	
CYB561D2	11068	broad.mit.edu	37	3	50390492	50390493	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50390492_50390493insT	uc003dak.2	+						NPRL2_uc003dai.1_5'Flank|NPRL2_uc003daj.1_5'Flank|CYB561D2_uc003dal.2_Intron|CYB561D2_uc003dam.2_Intron	NM_007022	NP_008953	O14569	C56D2_HUMAN	cytochrome b-561 domain containing 2						electron transport chain|transport	integral to membrane	metal ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CAGGGCACATATATCATCCCAG	0.480											OREG0031799	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	5	3	---	---	---	---	
ABHD14B	84836	broad.mit.edu	37	3	52003724	52003725	+	Intron	INS	-	GA	GA			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52003724_52003725insGA	uc003dcm.2	-						PCBP4_uc003dch.1_5'Flank|PCBP4_uc003dci.1_5'Flank|PCBP4_uc003dcj.1_5'Flank|PCBP4_uc003dck.1_5'Flank|ABHD14B_uc010hly.2_Intron|ABHD14B_uc011bdy.1_Intron|ABHD14B_uc003dcn.2_Intron|ABHD14B_uc011bdz.1_3'UTR	NM_032750	NP_116139	Q96IU4	ABHEB_HUMAN	abhydrolase domain containing 14B							cytoplasm|nucleus	hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000548)|KIRC - Kidney renal clear cell carcinoma(197;0.00072)		CCCATATGAGGGAGAGAGACAA	0.589													4	9	---	---	---	---	
NT5DC2	64943	broad.mit.edu	37	3	52559178	52559181	+	Intron	DEL	GGGT	-	-	rs61419666		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52559178_52559181delGGGT	uc003deo.2	-						NT5DC2_uc003dem.2_Intron|NT5DC2_uc003den.2_Intron|NT5DC2_uc010hmi.2_Intron|NT5DC2_uc010hmj.2_Intron	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2								hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		GGGGGGGGGGGGGTTTCCTGGCCC	0.701													6	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52582090	52582090	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52582090delC	uc003des.2	-	30	5071	c.5059delG	c.(5059-5061)GAAfs	p.E1687fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.E1580fs|PBRM1_uc003der.2_Frame_Shift_Del_p.E1600fs|PBRM1_uc003det.2_Frame_Shift_Del_p.E1595fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.E1650fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.E1632fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.E1607fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.E1580fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1687					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TAAACATTTTCTAGGTTGTAT	0.463			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								132	118	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	57719707	57719707	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57719707delA								FAM116A (40891 upstream) : SLMAP (23467 downstream)																							ttcattctttaaacacactgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	59165949	59165950	+	IGR	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59165949_59165950delGT								C3orf67 (130191 upstream) : FHIT (569088 downstream)																							ccacctggaagtgacatacatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	67956776	67956776	+	Intron	DEL	A	-	-	rs35138335		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67956776delA	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																		CATAAAAAGGAAAAAAAAAAA	0.398													3	4	---	---	---	---	
MITF	4286	broad.mit.edu	37	3	69928025	69928026	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69928025_69928026insA	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron|MITF_uc003dob.2_Intron|MITF_uc003dod.2_5'Flank|MITF_uc003doc.1_Intron	NM_198159	NP_937802	O75030	MITF_HUMAN	microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GCataaaatgtaaaaaaaaaaa	0.337			A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70352558	70352558	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70352558delA								MITF (335072 upstream) : FOXP1 (652179 downstream)																							GAATAGGAGGAAAAAAAATTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73737025	73737026	+	IGR	INS	-	TTC	TTC	rs140132641	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73737025_73737026insTTC								PDZRN3 (62953 upstream) : CNTN3 (574696 downstream)																							CCCAGACCTTATTCTTTTCACT	0.441													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80003942	80003942	+	IGR	DEL	G	-	-	rs77429452		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80003942delG								ROBO1 (186883 upstream) : None (None downstream)																							CGTCCTGAAAGATAAGCCCAA	0.403													2	4	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	86021165	86021165	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86021165delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AAAGAGTTCCTTTTTATGAAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94963267	94963267	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94963267delG								LOC255025 (68188 upstream) : None (None downstream)																							CGTATCACCTGATTATTTTAT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122063256	122063256	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122063256delA								CSTA (2443 upstream) : CCDC58 (15181 downstream)																							accctgtctcaaaaaaaaaga	0.000													8	5	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	123770661	123770661	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123770661delG	uc003ehd.2	+									O60229	KALRN_HUMAN	Homo sapiens cDNA FLJ41073 fis, clone 3NB692008178.						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						CAAGCCGGGTGGGGCAAGCAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127548509	127548509	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127548509delT								MGLL (6458 upstream) : KBTBD12 (85809 downstream)																							ttcattttggttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128580215	128580216	+	3'UTR	DEL	CA	-	-	rs68112373		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128580215_128580216delCA	uc011bkr.1	-	2										SubName: Full=cDNA FLJ53777, moderately similar to Intraflagellar transport 122 homolog;																		CACATGTGCTCACACACACACA	0.554													6	3	---	---	---	---	
NEK11	79858	broad.mit.edu	37	3	130871047	130871047	+	Intron	DEL	T	-	-	rs150507740	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130871047delT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_Intron	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						ACTTTTTTGGTTTTTTTTTTG	0.323													11	5	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134916924	134916924	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134916924delG	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						CAAAAGCACAGGATAGGAGTT	0.259													4	6	---	---	---	---	
NCK1	4690	broad.mit.edu	37	3	136652994	136652995	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136652994_136652995insT	uc003erh.2	+						NCK1_uc011bme.1_Intron	NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1						axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1						ttatgaatttatttttttacac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140458245	140458245	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140458245delC								TRIM42 (38254 upstream) : SLC25A36 (202417 downstream)																							GAGACTGGTTCAAGGAAGGGC	0.493													4	2	---	---	---	---	
PCOLCE2	26577	broad.mit.edu	37	3	142551596	142551596	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142551596delA	uc003evd.2	-							NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						aacagaatTCAATGGCATTGA	0.234													3	3	---	---	---	---	
CPA3	1359	broad.mit.edu	37	3	148613949	148613950	+	Intron	INS	-	G	G	rs140478704	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148613949_148613950insG	uc003ewm.2	+							NM_001870	NP_001861	P15088	CBPA3_HUMAN	carboxypeptidase A3 precursor						proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGTTTTTCCCTGGTGGTTTTCA	0.416													2	4	---	---	---	---	
LEKR1	389170	broad.mit.edu	37	3	156661220	156661220	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156661220delC	uc003fba.1	+							NM_001004316	NP_001004316	Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			tgaattatttctatctgttct	0.144													4	2	---	---	---	---	
NMD3	51068	broad.mit.edu	37	3	160964722	160964722	+	Intron	DEL	T	-	-	rs113830976		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160964722delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			GAATGAGGTGTTTTTTTTTTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164120367	164120368	+	IGR	INS	-	TG	TG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164120367_164120368insTG								MIR720 (61129 upstream) : SI (576319 downstream)																							ACGTGTGTGTCTGTGTGTGTTG	0.238													4	2	---	---	---	---	
SI	6476	broad.mit.edu	37	3	164727551	164727551	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164727551delT	uc003fei.2	-							NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CAAAGGGCCATAGTATAAAGC	0.423										HNSCC(35;0.089)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168194553	168194553	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168194553delT								GOLIM4 (381136 upstream) : MIR551B (75089 downstream)																							TTCTAAGTGCTTTTTTTTCTT	0.438													4	2	---	---	---	---	
LOC100128164	100128164	broad.mit.edu	37	3	169682002	169682002	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169682002delA	uc011bpp.1	-						LOC100128164_uc003fgf.2_Intron|SEC62_uc003fgg.2_5'Flank|SEC62_uc003fgh.2_5'Flank	NR_027622				Homo sapiens cDNA FLJ41016 fis, clone UTERU2018784.												0						GGAGTCATGGAAGGAAGAAGG	0.229													4	2	---	---	---	---	
RPL22L1	200916	broad.mit.edu	37	3	170583143	170583143	+	3'UTR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170583143delA	uc003fhc.3	-	4					RPL22L1_uc003fhb.3_RNA	NM_001099645	NP_001093115	Q6P5R6	RL22L_HUMAN	ribosomal protein L22-like 1						translation	ribosome	structural constituent of ribosome				0	all_cancers(22;1.96e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.137)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)			TCAGCAGTACAAAAAGGCACA	0.433													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179489738	179489738	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179489738delC	uc003fkh.2	+							NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			ctcctctgtgccaggcacttc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181890962	181890962	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181890962delT								SOX2OT (431959 upstream) : ATP11B (620329 downstream)																							TCAGTGGTTCTTTGGGGATAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184242935	184242935	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184242935delC								CHRD (135316 upstream) : EPHB3 (36652 downstream)																							accagttccgcccccctcccc	0.000													4	2	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185365571	185365571	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185365571delC	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GGGCCTGCTTCCCAACAGGAC	0.627													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187963975	187963976	+	Intron	INS	-	T	T	rs11294253		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187963975_187963976insT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.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)		ctgtctaCAACTTTTTTTTTTT	0.183			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189352140	189352140	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189352140delA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|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|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TACAGAATAGAAAAAAAAATG	0.259									Hay-Wells_syndrome	HNSCC(45;0.13)			4	2	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189497956	189497959	+	Intron	DEL	AAAG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189497956_189497959delAAAG	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|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|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TGTGGGTGTTAAAGAATGTGTTTG	0.392									Hay-Wells_syndrome	HNSCC(45;0.13)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189877001	189877001	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189877001delT								LEPREL1 (36775 upstream) : CLDN1 (146502 downstream)																							GAGAATATGATAACTACATTA	0.373													4	2	---	---	---	---	
IL1RAP	3556	broad.mit.edu	37	3	190240449	190240450	+	Intron	INS	-	GG	GG	rs149024580		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190240449_190240450insGG	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		AGCTGGTCTAAGAATGTGCCAC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195362799	195362803	+	IGR	DEL	TCTTG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195362799_195362803delTCTTG								APOD (51723 upstream) : SDHAP2 (22107 downstream)																							TCTGAGGGAATCTTGTCTTGTCTGT	0.478													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195428679	195428682	+	Intron	DEL	AAAT	-	-	rs112452749		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195428679_195428682delAAAT	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		TTCATTAATCAAATAATTCATGTA	0.368													2	4	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195490839	195490841	+	Intron	DEL	TCC	-	-	rs63306962		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195490839_195490841delTCC	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTACTCCTTATCCAGATGCCACC	0.626													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196168488	196168489	+	IGR	INS	-	CA	CA	rs140411399	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196168488_196168489insCA								UBXN7 (9143 upstream) : RNF168 (30140 downstream)																							tgggttatctcgttaggggcaa	0.000													5	4	---	---	---	---	
C3orf43	255798	broad.mit.edu	37	3	196237688	196237688	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196237688delT	uc003fws.2	-						C3orf43_uc003fwr.2_Intron	NM_001077657	NP_001071125	Q147U7	CC043_HUMAN	hypothetical protein LOC255798							integral to membrane				ovary(1)	1	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;2.13e-23)|all cancers(36;2e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00298)		agactatttcttagatacctt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197072014	197072015	+	IGR	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197072014_197072015delCA								DLG1 (45871 upstream) : BDH1 (164640 downstream)																							accacacacgcacacacacagc	0.158													4	2	---	---	---	---	
ZNF141	7700	broad.mit.edu	37	4	368452	368453	+	Intron	INS	-	AA	AA	rs144341413	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:368452_368453insAA	uc003gab.2	+							NM_003441	NP_003432	Q15928	ZN141_HUMAN	zinc finger protein 141						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0						ATGAATATAAGAATTCATCCTA	0.327													2	4	---	---	---	---	
PCGF3	10336	broad.mit.edu	37	4	761103	761103	+	3'UTR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:761103delT	uc003gbe.2	+	11					PCGF3_uc003gbd.1_RNA|PCGF3_uc010ibh.2_3'UTR|PCGF3_uc003gbh.2_3'UTR	NM_006315	NP_006306	Q3KNV8	PCGF3_HUMAN	ring finger protein 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0						CACACACACATTTTTTTTTTT	0.443													5	3	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5321298	5321299	+	Intron	INS	-	C	C	rs145903712	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5321298_5321299insC	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						tccagcacgcacccaggcatac	0.064													4	4	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7852747	7852748	+	Intron	INS	-	GG	GG	rs147061084	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7852747_7852748insGG	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						cccattgtaatttctgctgttc	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10121656	10121657	+	IGR	INS	-	TGC	TGC	rs149811386	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10121656_10121657insTGC								WDR1 (3083 upstream) : ZNF518B (319848 downstream)																							TATACTTGAGTTGCTTTCAGCT	0.485													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10140825	10140826	+	IGR	DEL	TC	-	-	rs36040473		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10140825_10140826delTC								WDR1 (22252 upstream) : ZNF518B (300679 downstream)																							CTACTCAGTGTCTCTCATTACT	0.475													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10293288	10293288	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10293288delA								WDR1 (174715 upstream) : ZNF518B (148217 downstream)																							CTGGACTATTAATGCTGTTTT	0.368													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21782103	21782103	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21782103delG	uc003gqi.1	-							NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				tttttggagagggtgaaactg	0.000													4	2	---	---	---	---	
SEPSECS	51091	broad.mit.edu	37	4	25148753	25148754	+	Intron	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25148753_25148754delTC	uc003grg.2	-						SEPSECS_uc003gri.2_Intron|SEPSECS_uc003grh.2_Intron	NM_153825	NP_722547	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine)						selenocysteine incorporation	cytoplasm|nucleus	pyridoxal phosphate binding|transferase activity, transferring selenium-containing groups|tRNA binding				0		Breast(46;0.173)			Pyridoxal Phosphate(DB00114)	ctgactggaatctctctctcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25903124	25903124	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25903124delC								SEL1L3 (38514 upstream) : C4orf52 (12690 downstream)																							AAAACCCTGACCATGAATGAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29381260	29381261	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29381260_29381261insC								None (None upstream) : None (None downstream)																							cggaatggaatcccccccagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32591893	32591893	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32591893delA								None (None upstream) : None (None downstream)																							agctctccagaaaaaaagaag	0.035													4	2	---	---	---	---	
FAM114A1	92689	broad.mit.edu	37	4	38880181	38880182	+	Intron	INS	-	TGTGT	TGTGT	rs142950595	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38880181_38880182insTGTGT	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron	NM_138389	NP_612398	Q8IWE2	NXP20_HUMAN	hypothetical protein LOC92689							cytoplasm				ovary(1)	1						GTCATCAGAAATGTGTAGTGAG	0.307													10	6	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40426607	40426607	+	3'UTR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40426607delA	uc003gvc.2	-	7					RBM47_uc003gvd.2_3'UTR|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_3'UTR	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						AAACTTCTACAGGTCTCTCCT	0.383													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54382671	54382671	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54382671delA	uc003haa.2	+						LNX1_uc003haf.3_Intron|LNX1_uc003hag.3_Intron|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)	tgcttggggtaattggagaag	0.184			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
CEP135	9662	broad.mit.edu	37	4	56884135	56884135	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56884135delT	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)					GAGTAGTTACttttttttttg	0.159													11	6	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62473905	62473905	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62473905delC	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						CTACCAGCTTCCCACATTTGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69242368	69242368	+	IGR	DEL	A	-	-	rs34520796		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69242368delA								YTHDC1 (26544 upstream) : UGT2B15 (269948 downstream)																							CTTTGACTTGAAAAAAAAAAA	0.239													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70025548	70025548	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70025548delT								UGT2B7 (46844 upstream) : UGT2B11 (40505 downstream)																							tcttctactatttatggacct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70247290	70247291	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70247290_70247291delTC								UGT2B28 (86523 upstream) : UGT2B4 (98593 downstream)																							ttgatccatgtctctctctcac	0.005													4	2	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70392345	70392345	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70392345delA	uc011cap.1	-							NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						AAAAAAATGCAAAAAAATAGT	0.289													4	2	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73232491	73232492	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73232491_73232492insT	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						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)			GTGTCCCAAGCTTTTTTTTTTT	0.312													4	2	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77425317	77425317	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77425317delT	uc011cbx.1	+							NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			CTCAAAAAAAttttttttttt	0.184													5	3	---	---	---	---	
SEPT11	55752	broad.mit.edu	37	4	77931151	77931151	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77931151delT	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						GTAAAGTTCCTTTTTTTTTCC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82755493	82755493	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82755493delA								RASGEF1B (362432 upstream) : HNRNPD (518974 downstream)																							cgtctcaaagaaaaaaaaaaG	0.045													3	4	---	---	---	---	
C4orf11	439934	broad.mit.edu	37	4	83542135	83542137	+	Intron	DEL	CAC	-	-	rs66550714		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83542135_83542137delCAC	uc010ijs.1	-						C4orf11_uc011cck.1_Intron	NR_024088				Homo sapiens hypothetical C4orf11 protein mRNA, complete cds, alternatively spliced.												0						TCTGTGGAATCACCACCACCTCG	0.498													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84424225	84424225	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84424225delT								FAM175A (17935 upstream) : AGPAT9 (33036 downstream)																							tttctttttcttttttttttt	0.154													2	4	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91815744	91815744	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91815744delT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						ctgcctccccttttttgtctt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	93068163	93068163	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93068163delA								FAM190A (544794 upstream) : GRID2 (157387 downstream)																							tagattaacgaaaaaaaaaga	0.000													4	2	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94412248	94412249	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94412248_94412249insA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	TGAAAAGGAAGAAAAAAAAGAG	0.337													4	2	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	108091500	108091500	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108091500delT	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		CCAACAAAGCTTTTGGTCTAC	0.363													4	2	---	---	---	---	
HADH	3033	broad.mit.edu	37	4	108945274	108945274	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108945274delT	uc003hyq.2	+						HADH_uc010ilx.2_Intron|HADH_uc010ily.2_Intron|HADH_uc003hyr.2_Intron	NM_005327	NP_005318	Q16836	HCDH_HUMAN	L-3-hydroxyacyl-Coenzyme A dehydrogenase						fatty acid beta-oxidation	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|NAD+ binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)	NADH(DB00157)	GACCTCCATCTTTTTTTtccc	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111369849	111369849	+	IGR	DEL	T	-	-	rs35701308		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111369849delT								ELOVL6 (250029 upstream) : ENPEP (27380 downstream)																							GAATTCTGGAttttttttttt	0.169													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	127797484	127797484	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127797484delT								None (None upstream) : INTU (756636 downstream)																							gaatagaaaataattttacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128263260	128263260	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128263260delA								None (None upstream) : INTU (290860 downstream)																							aagaaaaaagaaaaaagccca	0.000													4	2	---	---	---	---	
ELF2	1998	broad.mit.edu	37	4	140057574	140057574	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140057574delA	uc003ihp.1	-						ELF2_uc003ihq.2_Intron	NM_201999	NP_973728	Q15723	ELF2_HUMAN	E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)					ACCAAGGAGCAAAAAAAAAAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145841737	145841737	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145841737delT								HHIP (181856 upstream) : ANAPC10 (74577 downstream)																							AGAATTCCAATTTTTTTTTCT	0.234													4	2	---	---	---	---	
OTUD4	54726	broad.mit.edu	37	4	146072229	146072229	+	Intron	DEL	A	-	-	rs137967791	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146072229delA	uc003ika.3	-						OTUD4_uc003ijz.3_Intron	NM_001102653	NP_001096123	Q01804	OTUD4_HUMAN	OTU domain containing 4 protein isoform 3								protein binding			ovary(2)|breast(1)	3	all_hematologic(180;0.151)					TAATTCTAATAAAAAAAAATG	0.204													9	4	---	---	---	---	
ZNF827	152485	broad.mit.edu	37	4	146860684	146860684	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146860684delT	uc003ikn.2	-						ZNF827_uc003ikm.2_5'Flank|ZNF827_uc010iox.2_5'Flank	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					GAAAATAAGATTAGGTCACCC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	147937837	147937837	+	IGR	DEL	A	-	-	rs35008941		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147937837delA								TTC29 (70803 upstream) : MIR548G (327944 downstream)																							GTGTATTAAGAAAAAAAAATA	0.383													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148936196	148936196	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148936196delT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron|ARHGAP10_uc003ilh.2_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TGTTCCCTTATTCCCTCTCTT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153847956	153847956	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153847956delA								ARFIP1 (14895 upstream) : FHDC1 (16179 downstream)																							acccaatgggaaaaaaaaaac	0.000													4	2	---	---	---	---	
GUCY1A3	2982	broad.mit.edu	37	4	156624604	156624604	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156624604delG	uc003iov.2	+						GUCY1A3_uc003iou.2_Intron|GUCY1A3_uc010iqc.2_Intron|GUCY1A3_uc003iow.2_Intron|GUCY1A3_uc010iqd.2_Intron|GUCY1A3_uc003iox.2_Intron|GUCY1A3_uc003ioz.2_Intron|GUCY1A3_uc003ioy.2_Intron|GUCY1A3_uc010iqe.2_Intron|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Intron	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A						blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GAGAGTCACTGGGGCAGCTGG	0.438													4	2	---	---	---	---	
ACCN5	51802	broad.mit.edu	37	4	156758052	156758052	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156758052delT	uc003ipe.1	-							NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,							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)		AAGAGAAATATTTCATCATGG	0.328													172	102	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	176232815	176232815	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176232815delT								ADAM29 (333485 upstream) : GPM6A (321274 downstream)																							GCACACtttcttttttttctt	0.244													4	2	---	---	---	---	
SPCS3	60559	broad.mit.edu	37	4	177250202	177250202	+	3'UTR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177250202delT	uc003iur.3	+	5						NM_021928	NP_068747	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to membrane|microsome|signal peptidase complex	peptidase activity			ovary(1)	1		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		AGCTTTGTACTTTTTTTTTTA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179196473	179196473	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179196473delG								LOC285501 (284570 upstream) : None (None downstream)																							aaaggaacctgggatgacttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181373300	181373302	+	IGR	DEL	AAG	-	-	rs67110987		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181373300_181373302delAAG								None (None upstream) : None (None downstream)																							aaaaaaaacaaagaaccataagt	0.128													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190201055	190201055	+	IGR	DEL	C	-	-	rs10706116		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190201055delC								None (None upstream) : FRG1 (660919 downstream)																							ctactggacaccttcttcaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190201058	190201059	+	IGR	DEL	TC	-	-	rs10535852		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190201058_190201059delTC								None (None upstream) : FRG1 (660915 downstream)																							ctggacaccttcttcacaagcc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190544300	190544301	+	IGR	INS	-	CCCT	CCCT	rs33912339		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190544300_190544301insCCCT								None (None upstream) : FRG1 (317673 downstream)																							ccccctccctctccccctccat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190597276	190597277	+	IGR	INS	-	A	A	rs149616832		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190597276_190597277insA								None (None upstream) : FRG1 (264697 downstream)																							TGATTTTTAAGAAAAAAATCTA	0.342													8	6	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190878301	190878315	+	Intron	DEL	CTCATCTACTTAGAA	-	-	rs149605091	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190878301_190878315delCTCATCTACTTAGAA	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)		GCAATCCTACCTCATCTACTTAGAATTTAGTCCTA	0.172													10	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4068477	4068477	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4068477delG								IRX1 (466961 upstream) : LOC340094 (965995 downstream)																							GGCGTACAGTGGGGTGAAGTG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4131804	4131804	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4131804delA								IRX1 (530288 upstream) : LOC340094 (902668 downstream)																							TTTCCTTTGTAAAATGGAGGT	0.284													4	2	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5180369	5180370	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5180369_5180370insA	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron|ADAMTS16_uc003jdj.1_Intron	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						CAAAATCACTGAAAAAAAAATC	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8953447	8953448	+	IGR	INS	-	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8953447_8953448insG								None (None upstream) : SEMA5A (81690 downstream)																							GCAATGAATGTGGGGGGAAAAA	0.376													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11718734	11718734	+	Intron	DEL	A	-	-	rs78002240		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11718734delA	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						CTTTTTTTACAAAAAAAAAAA	0.343													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13718728	13718731	+	Intron	DEL	ATTA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13718728_13718731delATTA	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CATTTTTGATATTAATTATGTCTA	0.377									Kartagener_syndrome				2	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23244280	23244280	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23244280delT								CDH12 (390549 upstream) : PRDM9 (263444 downstream)																							GTAAAAGTGGTtttttttttg	0.224													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24927924	24927925	+	IGR	INS	-	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24927924_24927925insG								CDH10 (283013 upstream) : None (None downstream)																							AGTCAAGGATAGGGGGAGTGAT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25809341	25809341	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25809341delT								None (None upstream) : None (None downstream)																							tttcctaaacttttccttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30475745	30475745	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30475745delT								None (None upstream) : CDH6 (718051 downstream)																							TCTCTCCTGGTTATTTACTTG	0.413													4	2	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31312823	31312823	+	Intron	DEL	A	-	-	rs66484477		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31312823delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						acaaacaaacaaaaaaaccct	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32671216	32671217	+	IGR	INS	-	T	T	rs146862360	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32671216_32671217insT								SUB1 (67031 upstream) : NPR3 (39543 downstream)																							aagggaaaatattttgttgaac	0.040													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33789282	33789283	+	Intron	DEL	TC	-	-	rs33943765		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33789282_33789283delTC	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						GACAGAAAGGTCTCTCACACAC	0.525										HNSCC(64;0.19)			3	3	---	---	---	---	
SPEF2	79925	broad.mit.edu	37	5	35708795	35708797	+	Intron	DEL	CAC	-	-	rs113363488	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35708795_35708797delCAC	uc003jjo.2	+						SPEF2_uc003jjq.3_Intron|SPEF2_uc003jjp.1_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ctacctccatcaccatcaccacc	0.113													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36082450	36082450	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36082450delC								UGT3A2 (15466 upstream) : LMBRD2 (20964 downstream)																							gtctgagagaccccagaatct	0.000													4	2	---	---	---	---	
SLC1A3	6507	broad.mit.edu	37	5	36652428	36652429	+	Intron	DEL	AC	-	-	rs35501123		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36652428_36652429delAC	uc003jkj.3	+						SLC1A3_uc011cox.1_Intron|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity						D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)	acacacacatacacacacacac	0.391													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38139211	38139211	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38139211delT								GDNF (299429 upstream) : EGFLAM (119322 downstream)																							AAAGATAAACTTTTTTTTTTG	0.338													3	4	---	---	---	---	
SEPP1	6414	broad.mit.edu	37	5	42827783	42827784	+	5'Flank	INS	-	T	T	rs143941294	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42827783_42827784insT	uc003jna.2	-									P49908	SEPP1_HUMAN	Homo sapiens cDNA FLJ37321 fis, clone BRAMY2018122.						response to oxidative stress	extracellular region	selenium binding				0						aaaagcttccctggggaggtaa	0.099													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43523413	43523413	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43523413delG								C5orf34 (8226 upstream) : PAIP1 (2959 downstream)																							agcagagataggactgtggtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50576086	50576086	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50576086delA								PARP8 (437917 upstream) : ISL1 (102872 downstream)																							CCCAGCTTACAAGCAGCACTA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50625824	50625824	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50625824delA								PARP8 (487655 upstream) : ISL1 (53134 downstream)																							AAGTTTTTTTAAAAAAACATG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51823099	51823099	+	IGR	DEL	T	-	-	rs113775240		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51823099delT								None (None upstream) : ITGA1 (260675 downstream)																							gttttttggctttttaataat	0.000													3	3	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52161834	52161835	+	Intron	INS	-	TTTTTTC	TTTTTTC	rs143046695	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52161834_52161835insTTTTTTC	uc003jou.2	+						ITGA1_uc003jov.2_Intron	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTATTTTCTATttttttctttt	0.114													8	5	---	---	---	---	
ITGA2	3673	broad.mit.edu	37	5	52379871	52379872	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52379871_52379872delAA	uc003joy.2	+						ITGA2_uc011cqa.1_Intron|ITGA2_uc011cqb.1_Intron|ITGA2_uc011cqc.1_Intron|ITGA2_uc011cqd.1_Intron|ITGA2_uc011cqe.1_Intron	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor						axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				AAGTTTGAAGAAAAAGCCAAAA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55129448	55129448	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55129448delT								DDX4 (16475 upstream) : IL31RA (17886 downstream)																							GGGAAAGGAATTAGATGATTC	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62542077	62542077	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62542077delT								ISCA1P1 (468907 upstream) : HTR1A (714202 downstream)																							GAAAGTTTTGTTTTTGGACTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62544752	62544755	+	IGR	DEL	TCTG	-	-	rs72142413		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62544752_62544755delTCTG								ISCA1P1 (471582 upstream) : HTR1A (711524 downstream)																							CTCCTTAAGctctgtctgaaggcc	0.225													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63758848	63758848	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63758848delA								RNF180 (90154 upstream) : RGS7BP (43604 downstream)																							tccaaataataaaggctatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71176501	71176501	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71176501delC								CARTPT (159629 upstream) : MAP1B (226617 downstream)																							GCAGCCTCTTCGGCTCAGCTC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72037766	72037766	+	IGR	DEL	T	-	-	rs72238186		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72037766delT								ZNF366 (234517 upstream) : TNPO1 (74652 downstream)																							caagacttcctttttgagcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72387506	72387506	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72387506delA								FCHO2 (1158 upstream) : TMEM171 (28882 downstream)																							aaccaactgcaaaaaaagatg	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73863774	73863774	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73863774delT								RGNEF (626361 upstream) : ENC1 (59461 downstream)																							CTTTTGATGCttttttttttc	0.194													3	4	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75829004	75829004	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75829004delA	uc003kek.2	+							NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ttttttttttaactcactttg	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	76916952	76916952	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76916952delA								WDR41 (128620 upstream) : OTP (7586 downstream)																							CCAGGTCAAGAAAAAAAAAAA	0.323													3	4	---	---	---	---	
HOMER1	9456	broad.mit.edu	37	5	78721074	78721074	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78721074delA	uc003kfy.2	-						HOMER1_uc010jab.2_Intron|HOMER1_uc010jac.2_Intron|HOMER1_uc010jad.2_Intron	NM_004272	NP_004263	Q86YM7	HOME1_HUMAN	homer 1						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		CCGGAGTAGGAAAAAAAAAAA	0.378													3	4	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	79970119	79970119	+	Intron	DEL	T	-	-	rs66514560		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79970119delT	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AATGGACTCATTTTATACACA	0.358								MMR					4	2	---	---	---	---	
ATG10	83734	broad.mit.edu	37	5	81281368	81281368	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81281368delT	uc003khs.2	+						ATG10_uc003khq.2_Intron|ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron|ATG10_uc003kht.1_5'Flank	NM_001131028	NP_001124500	Q9H0Y0	ATG10_HUMAN	APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		aacccaactctcttcccaaac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82024223	82024224	+	IGR	INS	-	A	A	rs77317361		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82024223_82024224insA								ATP6AP1L (410077 upstream) : TMEM167A (324443 downstream)																							CCCAGTTATGGAAAAAAAAAAA	0.421													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82150995	82150996	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82150995_82150996insA								ATP6AP1L (536849 upstream) : TMEM167A (197671 downstream)																							TGCTGACTAAGCCCTAGGAGGT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84618912	84618912	+	IGR	DEL	A	-	-	rs5869266		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84618912delA								EDIL3 (938301 upstream) : NBPF22P (959350 downstream)																							taagtttggcaaaagccatta	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87041398	87041398	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87041398delA								CCNH (332562 upstream) : TMEM161B (449626 downstream)																							TTCCTGCTTTAAAAAAGAGAT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87733222	87733222	+	IGR	DEL	T	-	-	rs74956633		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87733222delT								TMEM161B (168557 upstream) : LOC645323 (103375 downstream)																							ATGTCACGGATTTTTTTTTTT	0.373													1	6	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90037194	90037195	+	Intron	INS	-	TCAT	TCAT	rs148604675	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90037194_90037195insTCAT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGAGTGACTTATCATTCAACAA	0.272													1	5	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90278563	90278564	+	Intron	INS	-	T	T	rs72545412	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90278563_90278564insT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ttggctcagccgggccaggctt	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91690928	91690928	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91690928delA	uc003kkb.1	+											Homo sapiens cDNA FLJ31923 fis, clone NT2RP7005323.																		CTGATGATGCAAAAACATTGA	0.383													4	2	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93347031	93347032	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93347031_93347032insT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						aatggctttaattttttccaaa	0.000													4	2	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93420478	93420478	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93420478delT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						aaaacagggatttttttaaca	0.000													4	2	---	---	---	---	
C5orf36	285600	broad.mit.edu	37	5	93528321	93528321	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93528321delT	uc011cuk.1	-						C5orf36_uc003kkn.2_Intron	NM_001145678	NP_001139150	Q8IV33	K0825_HUMAN	hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)		TTAATGAGACTTTTTTTTTAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95500882	95500883	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95500882_95500883insT								MIR583 (85966 upstream) : PCSK1 (225236 downstream)																							ATTCCTTAGTCTTTTTTTTTCC	0.500													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96588564	96588564	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96588564delT								RIOK2 (69559 upstream) : None (None downstream)																							TTTAATCTGATTTTTTTTTTC	0.199													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96775522	96775523	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96775522_96775523delTG								RIOK2 (256517 upstream) : None (None downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.292													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97074730	97074730	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97074730delT								RIOK2 (555725 upstream) : None (None downstream)																							CTCTAAAAGCTTTTTTTTTTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	100416868	100416868	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100416868delA								ST8SIA4 (177881 upstream) : None (None downstream)																							TTGGGAAAGGAAAGGGTGAGT	0.373													4	2	---	---	---	---	
NUDT12	83594	broad.mit.edu	37	5	102901446	102901446	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102901446delA	uc003koi.2	-						NUDT12_uc011cvb.1_5'Flank|NUDT12_uc010jbq.1_5'Flank	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN	nudix-type motif 12							nucleus|peroxisome	metal ion binding|NAD+ diphosphatase activity				0		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		cccttgcaccaaagagttagc	0.000													4	2	---	---	---	---	
EFNA5	1946	broad.mit.edu	37	5	106893967	106893967	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106893967delT	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		GATTATACTGTTTTTTTTTTG	0.154													3	3	---	---	---	---	
FBXL17	64839	broad.mit.edu	37	5	107474147	107474147	+	Intron	DEL	G	-	-	rs12523367	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107474147delG	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		GATATCATACGTTTTTTTCTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109010502	109010502	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109010502delG								PJA2 (264827 upstream) : MAN2A1 (14654 downstream)																							CATGATGCTTGGAATTCTAAT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109383745	109383746	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109383745_109383746delTC								MAN2A1 (180316 upstream) : TMEM232 (241188 downstream)																							TTAGCAGTATTCAGAAAAAATA	0.376													4	2	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109987386	109987386	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109987386delG	uc011cvh.1	-						TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						cagagaacaagggggtgagag	0.000													4	2	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111155918	111155918	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111155918delA	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947	Q16612	NP311_HUMAN	neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		aatagatcacaaaaaaaaagt	0.040													4	3	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111557926	111557926	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111557926delG	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)		AATCACACATGGGGAAAAAAC	0.294													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111724766	111724766	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111724766delA	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TTGGACGTGGAAAAAAAAAAT	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	113164882	113164883	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113164882_113164883insT								YTHDC2 (233903 upstream) : KCNN2 (533133 downstream)																							accagcatctgttttttttttt	0.000													4	2	---	---	---	---	
PGGT1B	5229	broad.mit.edu	37	5	114590299	114590299	+	Intron	DEL	T	-	-	rs71971881		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114590299delT	uc003kqw.3	-						PGGT1B_uc003kqx.3_Intron|PGGT1B_uc010jch.2_Intron	NM_005023	NP_005014	P53609	PGTB1_HUMAN	geranylgeranyltransferase type 1 beta						protein geranylgeranylation	CAAX-protein geranylgeranyltransferase complex	CAAX-protein geranylgeranyltransferase activity				0		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)	Pravastatin(DB00175)	ATTTCTTCTCTTTTTTTTTTT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115365062	115365066	+	IGR	DEL	CTTCC	-	-	rs140886447		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115365062_115365066delCTTCC								AQPEP (1764 upstream) : COMMD10 (55661 downstream)																							GACTCTTCCTCTTCCCTTCCCTTCA	0.424													4	2	---	---	---	---	
SEMA6A	57556	broad.mit.edu	37	5	115887784	115887787	+	Intron	DEL	CAGT	-	-	rs2067140		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115887784_115887787delCAGT	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		TCCCTGACACCAGTCAAAGAATCA	0.407													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120927207	120927207	+	IGR	DEL	G	-	-	rs6872388	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120927207delG								PRR16 (904245 upstream) : FTMT (260443 downstream)																							taagggaaaagaaaaacaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	121861725	121861725	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121861725delA								SNCAIP (61931 upstream) : SNX2 (249025 downstream)																							ACTGAGCCTGAAAAAAAAGGT	0.403													4	2	---	---	---	---	
PRDM6	93166	broad.mit.edu	37	5	122480321	122480322	+	Intron	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122480321_122480322delGA	uc003kti.2	+						PRDM6_uc003ktj.2_Intron	NM_001136239	NP_001129711	Q9NQX0	PRDM6_HUMAN	PR domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding				0						CCAACACTTGGAGAGAGAGAGG	0.480													4	2	---	---	---	---	
MEGF10	84466	broad.mit.edu	37	5	126689439	126689440	+	Intron	DEL	CT	-	-	rs150375027		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126689439_126689440delCT	uc003kuh.3	+						MEGF10_uc010jdc.1_Intron|MEGF10_uc010jdd.1_Intron|MEGF10_uc003kui.3_Intron	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGTCTGCTAACTCTGTTTTTGT	0.441													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127636000	127636000	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127636000delG	uc003kuu.2	-							NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CTTTTGATGTGGTTACAGTGT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129116190	129116190	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129116190delA								ADAMTS19 (41814 upstream) : CHSY3 (124333 downstream)																							cagaaaagacaaaaaaaaaaa	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	130227947	130227948	+	IGR	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130227947_130227948delCA								CHSY3 (705621 upstream) : HINT1 (266927 downstream)																							gagcttgcagcaaggatgtaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	130408202	130408202	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130408202delT								CHSY3 (885876 upstream) : HINT1 (86673 downstream)																							tatcactatattagaatattc	0.000													4	2	---	---	---	---	
PDLIM4	8572	broad.mit.edu	37	5	131594384	131594384	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131594384delT	uc003kwn.2	+						uc003kwm.3_Intron|PDLIM4_uc003kwp.2_Intron|PDLIM4_uc003kwo.2_Intron	NM_003687	NP_003678	P50479	PDLI4_HUMAN	PDZ and LIM domain 4 isoform 1								protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GACCCTGCCCTTGGGGGTCCC	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133099323	133099324	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133099323_133099324insC								FSTL4 (151100 upstream) : C5orf15 (191875 downstream)																							GGCCTTTGTTTCCCCAAGTACC	0.317													4	2	---	---	---	---	
SKP1	6500	broad.mit.edu	37	5	133503220	133503220	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133503220delT	uc003kzc.3	-						SKP1_uc003kzd.3_Intron|SKP1_uc010jdv.2_Intron	NM_170679	NP_733779	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1 isoform b						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|G1/S transition of mitotic cell cycle|histone H2A monoubiquitination|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			tagagaggggttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134361650	134361650	+	IGR	DEL	T	-	-	rs112686623		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134361650delT								CATSPER3 (14265 upstream) : PITX1 (1775 downstream)																							GAATTCTGCCTTTTTTTTTTT	0.413													11	6	---	---	---	---	
H2AFY	9555	broad.mit.edu	37	5	134680064	134680064	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134680064delT	uc003lam.1	-						uc003laj.1_RNA|H2AFY_uc003lal.1_Intron|H2AFY_uc003lao.1_Intron|H2AFY_uc003lan.1_Intron|H2AFY_uc003lap.1_Intron|H2AFY_uc003laq.1_Intron|H2AFY_uc003lar.1_Intron|H2AFY_uc011cxz.1_Intron|H2AFY_uc003las.1_Intron|H2AFY_uc003lat.1_Intron	NM_138610	NP_613258	O75367	H2AY_HUMAN	H2A histone family, member Y isoform 3						chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTTCTGAAACTTTTTTTTTTT	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135409863	135409864	+	IGR	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135409863_135409864delGA								TGFBI (10357 upstream) : MIR886 (6313 downstream)																							GGGCTGGCTGGAGAGAGAGAGA	0.401													4	2	---	---	---	---	
PCDHB14	56122	broad.mit.edu	37	5	140605198	140605198	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140605198delG	uc003ljb.2	+	1	2121	c.2121delG	c.(2119-2121)CTGfs	p.L707fs	PCDHB14_uc011dal.1_Frame_Shift_Del_p.L554fs	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	707	Helical; (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGTGCTCCTGTTCGTGGCGG	0.701													4	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	140643832	140643833	+	IGR	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140643832_140643833delAC								PCDHB15 (16033 upstream) : SLC25A2 (38364 downstream)																							gcagcatattacacacacacac	0.000													4	3	---	---	---	---	
ARAP3	64411	broad.mit.edu	37	5	141051926	141051926	+	Intron	DEL	T	-	-	rs3214933		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141051926delT	uc003llm.2	-						ARAP3_uc011dbe.1_Intron|ARAP3_uc003lln.2_Intron|ARAP3_uc003llo.1_Intron	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH						cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7						CCCATCCCCCTGGCTCTTCCT	0.637													5	10	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142186292	142186293	+	Intron	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142186292_142186293delTT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCCACTACTTAGACATCTAA	0.406													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142326009	142326009	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142326009delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTAGCTTCAATTTTTTTTTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143257002	143257002	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143257002delT								HMHB1 (56720 upstream) : YIPF5 (280729 downstream)																							ATACCAACTGTTTTCAACTAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145733039	145733039	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145733039delA								POU4F3 (12956 upstream) : TCERG1 (93834 downstream)																							ccaaagaaagaaaaaaaaaag	0.134													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145757740	145757741	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145757740_145757741insT								POU4F3 (37657 upstream) : TCERG1 (69132 downstream)																							GTGTGTATGTATTTTTTTTGTC	0.302													4	2	---	---	---	---	
PPP2R2B	5521	broad.mit.edu	37	5	146403399	146403400	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146403399_146403400delAA	uc011dbv.1	-						PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron	NM_181675	NP_858061	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gcccagacagaaaaaaaaaaag	0.000													4	2	---	---	---	---	
JAKMIP2	9832	broad.mit.edu	37	5	147140172	147140172	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147140172delA	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			atgacaatggaagcccaacta	0.000													4	2	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147493803	147493804	+	Intron	INS	-	A	A	rs142874955		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147493803_147493804insA	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATAACTGCCAGAAAAAAAATTC	0.337													24	12	---	---	---	---	
SPINK14	408187	broad.mit.edu	37	5	147548894	147548894	+	5'Flank	DEL	T	-	-	rs10711219		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147548894delT	uc003loz.1	+							NM_001001325	NP_001001325	Q6IE38	ISK14_HUMAN	Kazal type serine protease inhibitor 5-like 2							extracellular region	serine-type endopeptidase inhibitor activity				0						TAGCCCCATCTTTTTTTTTGC	0.373													2	4	---	---	---	---	
HTR4	3360	broad.mit.edu	37	5	148012575	148012575	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148012575delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron|SH3TC2_uc003lpp.1_Intron|HTR4_uc003lpq.1_Intron	NM_000870	NP_000861	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)	TCAACCCTTCAAAAAAAAATG	0.443													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148210598	148210598	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148210598delT	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCATCGTGAGTTTTTTTTTTG	0.443													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149720068	149720068	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149720068delT								ARSI (37543 upstream) : TCOF1 (17134 downstream)																							gtcattaaccttgcaaagcct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151547069	151547069	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151547069delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																		agaaggagagttatagatcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151959807	151959807	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151959807delT								NMUR2 (174967 upstream) : GRIA1 (909368 downstream)																							gtttttatggttttatgtttt	0.000													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155252238	155252238	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155252238delA	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AATAAGGAGGAAAAAAAGAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157844563	157844563	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157844563delG								CLINT1 (558395 upstream) : EBF1 (278361 downstream)																							gatctgctttggccaacaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161387150	161387150	+	IGR	DEL	A	-	-	rs67723732		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161387150delA								GABRA1 (60187 upstream) : GABRG2 (107498 downstream)																							TTAGAGAAAGAATATCTGGCT	0.303													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162657261	162657261	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162657261delT								None (None upstream) : CCNG1 (207316 downstream)																							ctaccacagcttttttatact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163397626	163397626	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163397626delT								MAT2B (451293 upstream) : None (None downstream)																							cagaccgttcttTTTTTTATG	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164991969	164991970	+	IGR	INS	-	T	T	rs148445653	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164991969_164991970insT								None (None upstream) : None (None downstream)																							AAAGGTTCATGTTTTTTTTTGT	0.312													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166074853	166074853	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166074853delC								None (None upstream) : ODZ2 (636990 downstream)																							CACAGGTGCTCCAATGAATTT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166314301	166314302	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166314301_166314302delTG								None (None upstream) : ODZ2 (397541 downstream)																							ACTAAAAGGAtgtgtgtgtgtg	0.272													3	3	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167610950	167610950	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167610950delC	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron|uc003lzs.1_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TGTGGATCCTCCCAGCACTCC	0.308													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168187561	168187561	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168187561delC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGAGTCCCACCCACCAGCCC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170195017	170195017	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170195017delG								KCNIP1 (31383 upstream) : GABRP (15706 downstream)																							TCAGGATTCAGGGGTAGTAAC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171038478	171038478	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171038478delC								FGF18 (154316 upstream) : FBXW11 (250078 downstream)																							ggaaacgtggcaggacaccaa	0.000													20	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172732117	172732117	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172732117delG								NKX2-5 (69855 upstream) : STC2 (9609 downstream)																							ccaccttactggggggcatcg	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174376657	174376657	+	IGR	DEL	T	-	-	rs112011335		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174376657delT								MSX2 (218756 upstream) : DRD1 (491019 downstream)																							ACTTAGCAGATTTTTTTTTTT	0.363													9	5	---	---	---	---	
SFXN1	94081	broad.mit.edu	37	5	174938744	174938745	+	Intron	DEL	TG	-	-	rs3834721		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174938744_174938745delTG	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TGCCTGACTCTGTGTACGAAGT	0.490													10	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	176231431	176231432	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176231431_176231432delTG								TSPAN17 (145373 upstream) : UNC5A (6128 downstream)																							GCTGGCTTGCTGTGTGTGTGTG	0.515													4	3	---	---	---	---	
FAM153C	653316	broad.mit.edu	37	5	177475447	177475448	+	Intron	INS	-	ACAG	ACAG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177475447_177475448insACAG	uc011dge.1	+							NM_001079527	NP_001072995			hypothetical protein LOC653316												0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCATGACACTCACACTCTCTGT	0.564													3	3	---	---	---	---	
ZNF354B	117608	broad.mit.edu	37	5	178293700	178293702	+	Intron	DEL	CTT	-	-	rs139238783		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178293700_178293702delCTT	uc003mjl.2	+						ZNF354B_uc003mjm.2_Intron	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTACCTCATCCTTCTTCATCGAC	0.419													5	4	---	---	---	---	
CANX	821	broad.mit.edu	37	5	179142826	179142826	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179142826delT	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc010jlb.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTTTTTTTTGTTTTTTTTTTT	0.308													4	4	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1678761	1678761	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1678761delC	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		gtgacaacttccttgctcctt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5075803	5075803	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5075803delA	uc003mwn.1	+											Homo sapiens cDNA FLJ37615 fis, clone BRCOC2011996.																		AGCAATCTGGAAAAGGAAGGA	0.443													4	2	---	---	---	---	
F13A1	2162	broad.mit.edu	37	6	6264612	6264612	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6264612delA	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTTTTGTAATAAAAAGAAAGT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	6339124	6339125	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6339124_6339125delAA								F13A1 (18200 upstream) : LOC285780 (7574 downstream)																							ATTGATAAGGAAAAAAAAACAG	0.292													4	2	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7220655	7220655	+	Intron	DEL	T	-	-	rs111756816		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7220655delT	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCACTGATGATTTTTTTTTTC	0.323													4	2	---	---	---	---	
CAGE1	285782	broad.mit.edu	37	6	7334024	7334025	+	Intron	INS	-	G	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7334024_7334025insG	uc003mxi.2	-						CAGE1_uc003mxh.2_Intron|CAGE1_uc003mxj.2_Intron|CAGE1_uc003mxk.1_Intron	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1												0	Ovarian(93;0.0418)					gcctcagccccccagtagctgg	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8123123	8123123	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8123123delG								EEF1E1 (20295 upstream) : SLC35B3 (288610 downstream)																							CTTATTAGATGGGGTCCAGTG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8872546	8872546	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8872546delT								HULC (218469 upstream) : None (None downstream)																							TTGTTTCCAGTTTTAGAAGTT	0.323													4	2	---	---	---	---	
DTNBP1	84062	broad.mit.edu	37	6	15525109	15525110	+	Intron	INS	-	T	T	rs141761036	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15525109_15525110insT	uc003nbm.2	-						DTNBP1_uc003nbl.2_Intron|DTNBP1_uc003nbn.2_Intron|DTNBP1_uc003nbo.2_Intron|DTNBP1_uc003nbp.2_Intron|DTNBP1_uc010jph.2_Intron	NM_032122	NP_115498	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1 isoform a						actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			ACCTTTTACACTTCCTTAATCT	0.426									Hermansky-Pudlak_syndrome				4	4	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17488790	17488790	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17488790delA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TCTTGGTTTTAAAAAAAAACA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18320416	18320416	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18320416delT								DEK (55617 upstream) : RNF144B (67178 downstream)																							catttttttcttttttttttc	0.000													3	3	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	21122251	21122251	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21122251delA	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ATTTCATTTTAAAAATAACTA	0.368													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21837344	21837344	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21837344delT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						acctagagaatttttttttcc	0.124													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	22063744	22063744	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22063744delG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						TTCTTTCAGTGGTGTTTTGCA	0.303													4	2	---	---	---	---	
KIAA0319	9856	broad.mit.edu	37	6	24547583	24547584	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24547583_24547584insA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron|KIAA0319_uc010jpt.1_Intron	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						TAGAGAGAAGCACAGAAGCATC	0.550													169	100	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25498704	25498704	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25498704delT	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						TGTTGCCTCCTAATCATTGGG	0.338													4	2	---	---	---	---	
KIFC1	3833	broad.mit.edu	37	6	33367780	33367780	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33367780delT	uc003oef.3	+						KIFC1_uc011drf.1_Intron|uc011drg.1_RNA	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1						blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						TTTTTTTAACTTTTTTTTTTC	0.254													11	5	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34040216	34040217	+	Intron	DEL	CT	-	-	rs114000580	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34040216_34040217delCT	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	cacacacacactcaccacacgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34130340	34130341	+	IGR	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34130340_34130341delAG								GRM4 (16471 upstream) : HMGA1 (74236 downstream)																							GAACTTGTCCAGAGAGAGAAAC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34546777	34546779	+	IGR	DEL	CTT	-	-	rs71725653		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34546777_34546779delCTT								SPDEF (22686 upstream) : C6orf106 (8287 downstream)																							caaacatcaccttctcagtgagg	0.005													4	6	---	---	---	---	
UHRF1BP1	54887	broad.mit.edu	37	6	34834867	34834870	+	Intron	DEL	AGTC	-	-	rs149761751		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34834867_34834870delAGTC	uc003oju.3	+						UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron|UHRF1BP1_uc010jvo.2_Intron	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1											ovary(3)	3						atatctagttagtcctcaaatttc	0.113													8	12	---	---	---	---	
ANKS1A	23294	broad.mit.edu	37	6	34945425	34945425	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34945425delT	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron|ANKS1A_uc010jvr.1_Intron	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4						aaaccttccatttttttttgg	0.060													4	2	---	---	---	---	
RNF8	9025	broad.mit.edu	37	6	37338390	37338391	+	Intron	DEL	GC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37338390_37338391delGC	uc003onq.3	+						RNF8_uc003onr.3_Intron|RNF8_uc011dtx.1_Intron	NM_003958	NP_003949	O76064	RNF8_HUMAN	ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1						TTTATCAGCTGCATCTCCCTCT	0.411													4	2	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39768709	39768709	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39768709delC	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					tgtactccatcccagagtctg	0.000													4	2	---	---	---	---	
NFKBIE	4794	broad.mit.edu	37	6	44231958	44231958	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44231958delA	uc003oxe.1	-							NM_004556	NP_004547	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene						cytoplasmic sequestering of transcription factor		protein binding			breast(2)	2	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTGGGGGGCTAAATCCTCAAC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44661450	44661453	+	IGR	DEL	CTCT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44661450_44661453delCTCT								CDC5L (246671 upstream) : SUPT3H (115601 downstream)																							gcccctagccctctctctctcctt	0.157													4	2	---	---	---	---	
CYP39A1	51302	broad.mit.edu	37	6	46585486	46585486	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46585486delG	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						gcataaaatagggcaaacaat	0.000													4	2	---	---	---	---	
MEP1A	4224	broad.mit.edu	37	6	46793414	46793415	+	Intron	INS	-	T	T	rs144936463	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46793414_46793415insT	uc010jzh.1	+						MEP1A_uc011dwg.1_Intron|MEP1A_uc011dwh.1_Intron|MEP1A_uc011dwi.1_Intron	NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A alpha precursor						digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3			Lung(136;0.192)			gtctatggctgtttttgcgctt	0.158													6	6	---	---	---	---	
GSTA4	2941	broad.mit.edu	37	6	52847151	52847151	+	Intron	DEL	A	-	-	rs67398044		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52847151delA	uc003pbc.2	-						GSTA4_uc003pbd.2_Intron|GSTA4_uc003pbe.2_Intron|GSTA4_uc003pbf.2_Intron	NM_001512	NP_001503	O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4						glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity|protein homodimerization activity				0	Lung NSC(77;0.103)				Glutathione(DB00143)	atcccaccttaaaaaaaaaaa	0.139													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54845926	54845927	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54845926_54845927delTG								FAM83B (39109 upstream) : HCRTR2 (163575 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.153													5	3	---	---	---	---	
GFRAL	389400	broad.mit.edu	37	6	55192680	55192681	+	Intron	DEL	AT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55192680_55192681delAT	uc003pcm.1	+							NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor							integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GAATTCACACATGTGTTAGAAC	0.262													5	4	---	---	---	---	
GFRAL	389400	broad.mit.edu	37	6	55250053	55250053	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55250053delC	uc003pcm.1	+							NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor							integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CACTTTATCTCCACATTGTAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	55882120	55882120	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55882120delA								BMP5 (141745 upstream) : COL21A1 (39269 downstream)																							TCTTTCGTCTAAAGCAAGTTT	0.303													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	56218280	56218280	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56218280delC	uc003pcu.1	-							NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			atgacccagtcccagacattc	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57284785	57284786	+	Intron	INS	-	T	T	rs11442279		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57284785_57284786insT	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)		CTTCATCGAGCTTTTGTGTTTG	0.366													5	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57339798	57339798	+	Intron	DEL	C	-	-	rs72200125		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57339798delC	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)		CTCTGGGCATCCGATTTTATT	0.463													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57339801	57339802	+	Intron	DEL	AT	-	-	rs10560301		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57339801_57339802delAT	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)		TGGGCATCCGATTTTATTTGCA	0.455													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57474000	57474001	+	Intron	DEL	TC	-	-	rs113450576		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57474000_57474001delTC	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)		tttttttttttcccctgaactc	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538773	57538773	+	IGR	DEL	G	-	-	rs10707154		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538773delG								PRIM2 (25398 upstream) : GUSBL2 (707386 downstream)																							GATTCTCTAAGATTAATTAGC	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57559924	57559927	+	IGR	DEL	GGGC	-	-	rs78389325		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57559924_57559927delGGGC								PRIM2 (46549 upstream) : GUSBL2 (686232 downstream)																							tggttaccaggggctggggtggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57559933	57559934	+	IGR	INS	-	TACCA	TACCA	rs75585139		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57559933_57559934insTACCA								PRIM2 (46558 upstream) : GUSBL2 (686225 downstream)																							ggggctggggtggaggaagtta	0.000													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	64574392	64574393	+	Intron	INS	-	TT	TT	rs146770807	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64574392_64574393insTT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						TTTTCTCCCTCTTTTCTGTTTC	0.292													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	66980642	66980642	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66980642delC								MCART3P (481267 upstream) : None (None downstream)																							caacaacaaacaaacaaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67484471	67484471	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67484471delG								MCART3P (985096 upstream) : None (None downstream)																							gagaagtcatggggagagagg	0.154													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69950744	69950744	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69950744delT	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)				CTACTTGTCCTTCAACCTCCA	0.398													4	2	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71236469	71236470	+	Intron	INS	-	AC	AC	rs111717563		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71236469_71236470insAC	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						cacacacacatacacacacaca	0.213													7	4	---	---	---	---	
RIMS1	22999	broad.mit.edu	37	6	73036731	73036731	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73036731delA	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_Intron	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)				aaaggcaaagaaacatattct	0.000													4	2	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73351034	73351035	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73351034_73351035delCA	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)		TCATCAGCATCACACACACACA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	76788799	76788800	+	IGR	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76788799_76788800delTT								IMPG1 (6464 upstream) : None (None downstream)																							aggacttcaattttttttttga	0.000													4	2	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80878277	80878278	+	Intron	INS	-	GAAC	GAAC			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80878277_80878278insGAAC	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)		ggagggaggaaggaaggaaggg	0.198													6	5	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80878281	80878282	+	Intron	INS	-	GGAGATT	GGAGATT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80878281_80878282insGGAGATT	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)		ggaggaaggaaggaagggaaag	0.208													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82680608	82680608	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82680608delC								FAM46A (218180 upstream) : IBTK (199348 downstream)																							aacaaaaaggcccccacaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83388494	83388495	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83388494_83388495delAA								TPBG (311880 upstream) : UBE2CBP (213691 downstream)																							CCAATAGCCTAAAATAGGTTCA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	84983444	84983444	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84983444delT								KIAA1009 (46109 upstream) : TBX18 (413637 downstream)																							ttgcggtgagttgaaccatca	0.219													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85585719	85585720	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85585719_85585720insT								TBX18 (111820 upstream) : NT5E (573582 downstream)																							tttcctacctatttttttttct	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	88641928	88641929	+	IGR	INS	-	A	A	rs143950978	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88641928_88641929insA								AKIRIN2 (229943 upstream) : SPACA1 (115578 downstream)																							GCTCCCTTCTGAAAAAATTGTA	0.342													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	89850873	89850873	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89850873delC								SFRS13B (23073 upstream) : PM20D2 (4896 downstream)																							CATCAATTTGCCCCTCACTCT	0.468													4	2	---	---	---	---	
POU3F2	5454	broad.mit.edu	37	6	99284220	99284220	+	3'UTR	DEL	C	-	-	rs71545770		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99284220delC	uc003ppe.2	+	1						NM_005604	NP_005595	P20265	PO3F2_HUMAN	POU domain, class 3, transcription factor 2						positive regulation of cell proliferation		identical protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		CTTAAAAAGACAAAAAAAATA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99604497	99604499	+	IGR	DEL	TTG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99604497_99604499delTTG								FBXL4 (208648 upstream) : C6orf168 (116295 downstream)																							TTTGGTATTTttgttgttgttgt	0.310													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100290675	100290675	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100290675delA								PRDM13 (227221 upstream) : MCHR2 (77111 downstream)																							ggggtcctctaagcttgagtt	0.000													4	2	---	---	---	---	
ASCC3	10973	broad.mit.edu	37	6	101205118	101205119	+	Intron	INS	-	T	T	rs140978278	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101205118_101205119insT	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		agatacagatatacacacacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	101404051	101404054	+	IGR	DEL	TGTG	-	-	rs72039637		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101404051_101404054delTGTG								ASCC3 (74827 upstream) : GRIK2 (442851 downstream)																							GTCCTTGCTCtgtgtgtgtgtgtg	0.289													4	3	---	---	---	---	
PRDM1	639	broad.mit.edu	37	6	106533071	106533072	+	5'Flank	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106533071_106533072delGT	uc003prd.2	+							NM_001198	NP_001189	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain isoform						negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(54)|ovary(1)|skin(1)	56	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		gtgtatgtgggtgtgtgtgtgg	0.272			D|N|Mis|F|S		DLBCL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	110290136	110290136	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110290136delA								FIG4 (143502 upstream) : GPR6 (9373 downstream)																							AGGAAAAATGAAAAAAAAAAT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	111931495	111931495	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111931495delA								TRAF3IP2 (4021 upstream) : FYN (50992 downstream)																							TTAAGAAGGGAAAAAAAGGTG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112276199	112276199	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112276199delT								FYN (81572 upstream) : WISP3 (99079 downstream)																							tgattcctggtttttttttta	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	118646497	118646497	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118646497delC								SLC35F1 (7660 upstream) : C6orf204 (139742 downstream)																							AATGTGACCTCCCCCAGCCCC	0.328													4	2	---	---	---	---	
FAM184A	79632	broad.mit.edu	37	6	119472426	119472427	+	5'Flank	INS	-	A	A	rs35513453		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119472426_119472427insA	uc003pyk.3	-						FAM184A_uc003pyl.3_5'Flank	NM_001100411	NP_001093881	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 2											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						CCTTGGTGGCTGCTTTTTTTTT	0.436													3	3	---	---	---	---	
PKIB	5570	broad.mit.edu	37	6	122986307	122986307	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122986307delA	uc003pyz.2	+						PKIB_uc003pza.2_Intron|PKIB_uc003pzb.2_Intron|PKIB_uc003pzc.2_Intron	NM_181794	NP_861459	Q9C010	IPKB_HUMAN	cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)		CAGCAATGACAAAAAAAATAA	0.313													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124817029	124817029	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124817029delT	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		AGCAGTGGCCTTTTGAGATGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	126042810	126042810	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126042810delT	uc003qac.2	-											Homo sapiens cDNA clone IMAGE:5268006.																		GATGGGGGGATTTTTTTTTAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	127109861	127109862	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127109861_127109862delAA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																		TCTCAGTGCTAAAAAAAATGTT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	132385748	132385748	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132385748delA								CTGF (113230 upstream) : MOXD1 (231447 downstream)																							ACATTTCAATAAGGGAGAGCG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134877358	134877358	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134877358delC	uc003qev.1	-											AJ606331																		CCATTAGAGTCCGGGACTGAG	0.448													4	2	---	---	---	---	
C6orf217	100131814	broad.mit.edu	37	6	136015605	136015605	+	Intron	DEL	T	-	-	rs144698166		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136015605delT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0						aatggaaagattttttttttt	0.045													6	3	---	---	---	---	
RAB32	10981	broad.mit.edu	37	6	146868483	146868483	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146868483delT	uc003qln.1	+							NM_006834	NP_006825	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	mitochondrion	GTP binding				0		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		TCTAGTATACTTTAGCCTTCA	0.313													4	2	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150117924	150117924	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150117924delT	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		GATAATCAGGTTttttttgtt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156233424	156233425	+	IGR	INS	-	AG	AG	rs141642009	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156233424_156233425insAG								NOX3 (456387 upstream) : MIR1202 (34506 downstream)																							aaacaacataaagagagagaga	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160258045	160258045	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160258045delC								PNLDC1 (16310 upstream) : MAS1 (69929 downstream)																							tcagctggctcccccattcct	0.124													4	2	---	---	---	---	
SLC22A1	6580	broad.mit.edu	37	6	160546077	160546077	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160546077delT	uc003qtc.2	+						SLC22A1_uc003qtd.2_Intron	NM_003057	NP_003048	O15245	S22A1_HUMAN	solute carrier family 22 member 1 isoform a							basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		CTCCATGTTCTTTTGGGGTCG	0.517													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	161973616	161973616	+	Intron	DEL	C	-	-	rs7765268	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161973616delC	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TGaaaaaaaacaaaaacaaaa	0.264													5	3	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162189495	162189495	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162189495delA	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CCCTATTAGTAAAAATAAAGA	0.214													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162775077	162775077	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162775077delT	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		ACCAAACTAGTTTCCTTTATC	0.308													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	163139984	163139985	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163139984_163139985delAC	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		acacacacatacacacacacac	0.332													4	2	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163257755	163257756	+	Intron	DEL	AA	-	-	rs62740860		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163257755_163257756delAA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		CATTTGATTTAAAAGAGTGTTT	0.213													4	2	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163595798	163595800	+	Intron	DEL	CAT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163595798_163595800delCAT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron|uc011egg.1_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		gcaccgtctccATCATCATCATC	0.148													4	2	---	---	---	---	
PDE10A	10846	broad.mit.edu	37	6	165773289	165773289	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165773289delT	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	gtcacatatctttttttttct	0.005													4	2	---	---	---	---	
PDE10A	10846	broad.mit.edu	37	6	165818572	165818573	+	Intron	INS	-	T	T	rs144856358	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165818572_165818573insT	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	CTGGGAACAAATTAAAAAAAAA	0.396													3	4	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2157427	2157427	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2157427delA	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		gaactaacacaGGGGTAAGAG	0.299													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3787331	3787332	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3787331_3787332delGT	uc003smx.2	+							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)		TTAGCCTGGGgtgtgtgtgtgt	0.411													4	2	---	---	---	---	
TNRC18	84629	broad.mit.edu	37	7	5352305	5352305	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5352305delG	uc003soi.3	-	27	8566	c.8217delC	c.(8215-8217)CCCfs	p.P2739fs		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2739							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCTGAGCCTTGGGCTGCAGAG	0.736													4	2	---	---	---	---	
EIF2AK1	27102	broad.mit.edu	37	7	6066057	6066058	+	Intron	INS	-	C	C	rs150669417	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6066057_6066058insC	uc003spp.2	-						EIF2AK1_uc003spq.2_Intron|EIF2AK1_uc011jwm.1_Intron	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha						negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GCCCCAGGAAGTTTCCTACCGG	0.619													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	11255241	11255241	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11255241delG								PHF14 (46000 upstream) : THSD7A (158932 downstream)																							GTACGGGGCTGGTAGCAATGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13246616	13246616	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13246616delT								ARL4A (516060 upstream) : ETV1 (684242 downstream)																							ttttctttgcttttttttttg	0.000													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15331700	15331700	+	Intron	DEL	T	-	-	rs67847253		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15331700delT	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						GAGTCAAAGATTTTTTTACAA	0.343													2	4	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15336679	15336680	+	Intron	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15336679_15336680delTC	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						tctctctctgtctctctctctc	0.317													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15454144	15454145	+	Intron	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15454144_15454145delGA	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						GAAAGGTGGGGAGAGAGAGAGA	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	15803075	15803075	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15803075delG								MEOX2 (76767 upstream) : ISPD (324077 downstream)																							aaataaatgtggggggcaaag	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	16097261	16097262	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16097261_16097262insA								MEOX2 (370953 upstream) : ISPD (29890 downstream)																							aatttaaatggaaaaaaaaatg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17762852	17762859	+	IGR	DEL	TGCCAGTG	-	-	rs61498993		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17762852_17762859delTGCCAGTG								AHR (377077 upstream) : SNX13 (67527 downstream)																							CGTTTTGTTTTGCCAGTGCTGCCATCCA	0.399													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20495783	20495783	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20495783delT								ITGB8 (40405 upstream) : ABCB5 (159462 downstream)																							tgACAACCTATTTTTTGCttt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25729106	25729106	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25729106delT								NPVF (461001 upstream) : MIR148A (260433 downstream)																							TTGTTTTGTCTTTTTTTTTGT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26047267	26047267	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26047267delA								MIR148A (57661 upstream) : NFE2L3 (144580 downstream)																							ACTGCACCTGAAAAAACAAGA	0.388													4	2	---	---	---	---	
CBX3	11335	broad.mit.edu	37	7	26252044	26252045	+	3'UTR	DEL	CC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26252044_26252045delCC	uc003sxt.2	+	6					CBX3_uc003sxu.2_3'UTR|CBX3_uc003sxv.2_3'UTR	NM_007276	NP_009207	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome, centromeric region|nuclear centromeric heterochromatin|nuclear euchromatin|nuclear inner membrane|spindle	enzyme binding|protein domain specific binding			ovary(1)	1						GTAGTTGCTTCCTTTATCAGAA	0.347													3	4	---	---	---	---	
SKAP2	8935	broad.mit.edu	37	7	26756156	26756156	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26756156delA	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1						ctagacttttaaaaatgtcta	0.000													4	2	---	---	---	---	
CCDC129	223075	broad.mit.edu	37	7	31603611	31603611	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31603611delT	uc003tcj.1	+						CCDC129_uc011kad.1_Intron|CCDC129_uc003tci.1_Intron|CCDC129_uc011kae.1_Intron|CCDC129_uc003tck.1_Intron	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129												0						cagaaagctgtagaatgctat	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	33716528	33716528	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33716528delT								BBS9 (70848 upstream) : BMPER (228584 downstream)																							AGACATGAGATTTTTTTTCTC	0.328													4	2	---	---	---	---	
EPDR1	54749	broad.mit.edu	37	7	37972368	37972368	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37972368delG	uc003tfp.2	+						EPDR1_uc003tfq.2_Intron|EPDR1_uc010kxh.2_Intron	NM_017549	NP_060019	Q9UM22	EPDR1_HUMAN	ependymin related protein 1 precursor						cell-matrix adhesion	extracellular region	calcium ion binding			upper_aerodigestive_tract(1)	1						TTCTTTTTGTGGTGGTGAAAC	0.393													4	2	---	---	---	---	
VPS41	27072	broad.mit.edu	37	7	38940632	38940632	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38940632delT	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1						Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						GTTTTCAAACTTTTTTTTTAG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39905812	39905812	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39905812delT								LOC349114 (71591 upstream) : CDK13 (84147 downstream)																							AATAGGCTACTTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46175760	46175761	+	IGR	INS	-	T	T	rs35203805		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46175760_46175761insT								IGFBP3 (214889 upstream) : None (None downstream)																							acattcagaccTAAGAGTTCTA	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46258763	46258764	+	IGR	INS	-	A	A	rs143138942		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46258763_46258764insA								IGFBP3 (297892 upstream) : None (None downstream)																							ACATTGCACTTAAAAAAAAACA	0.411													2	4	---	---	---	---	
IKZF1	10320	broad.mit.edu	37	7	50464386	50464386	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50464386delT	uc003tow.3	+						IKZF1_uc003tox.3_Intron|IKZF1_uc003toy.3_Intron|IKZF1_uc011kck.1_Intron|IKZF1_uc003toz.3_Intron|IKZF1_uc010kyx.2_Intron|IKZF1_uc003tpa.3_Intron	NM_006060	NP_006051	Q13422	IKZF1_HUMAN	zinc finger protein, subfamily 1A, 1 (Ikaros)						cell cycle|chromatin modification|mesoderm development	cytoplasm|nucleus	zinc ion binding			haematopoietic_and_lymphoid_tissue(147)|lung(1)	148	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				tcccactatatttTTTTTTCC	0.050			D		ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57768830	57768831	+	IGR	INS	-	T	T	rs144648722		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768830_57768831insT								ZNF716 (235565 upstream) : None (None downstream)																							ATAATATCTTATTCTTTCTGAC	0.238													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61078944	61078944	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61078944delA								None (None upstream) : None (None downstream)																							ttttctaaataaaaaataaaa	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63656589	63656589	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63656589delC								ZNF727 (117664 upstream) : ZNF735 (10992 downstream)																							cctcatgaaaccccaggaatt	0.000													4	2	---	---	---	---	
ZNF680	340252	broad.mit.edu	37	7	63983013	63983013	+	Intron	DEL	A	-	-	rs34852861		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63983013delA	uc003tta.2	-						ZNF680_uc010kzr.2_Intron	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1						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)				cctaaaagttaaaaaaaaaaa	0.080													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65829736	65829736	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65829736delC								TPST1 (4299 upstream) : NCRNA00174 (11296 downstream)																							acctccgactcccaggttcta	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67587829	67587830	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67587829_67587830insC								STAG3L4 (801317 upstream) : None (None downstream)																							ggccttgttttccccatttcct	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67908105	67908106	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67908105_67908106insT								None (None upstream) : None (None downstream)																							CTTTGTGTTCATTTTTTGCCTG	0.436													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70858540	70858541	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70858540_70858541insT	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)				CAGTGCCCCCCTTTTTTTTTTA	0.366													4	2	---	---	---	---	
TBL2	26608	broad.mit.edu	37	7	72989141	72989142	+	Intron	INS	-	A	A	rs150029834	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72989141_72989142insA	uc003tyh.2	-						TBL2_uc011kex.1_Intron|TBL2_uc010lbg.2_Intron|TBL2_uc003tyi.2_Intron|TBL2_uc011key.1_Intron|TBL2_uc010lbh.2_Intron	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2												0		Lung NSC(55;0.0659)|all_lung(88;0.152)				gaccctgtctcaaaaaaaaaca	0.054													4	2	---	---	---	---	
SRRM3	222183	broad.mit.edu	37	7	75890436	75890461	+	Intron	DEL	GGGGACATTGTTGTCCCCACAATTGT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75890436_75890461delGGGGACATTGTTGTCCCCACAATTGT	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0						CAATGCCAGGGGGGACATTGTTGTCCCCACAATTGTGGGGACAACA	0.575													14	7	---	---	---	---	
YWHAG	7532	broad.mit.edu	37	7	75990797	75990797	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75990797delT	uc011kgj.1	-							NM_012479	NP_036611	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan						G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2						tttctttttcttttttttttt	0.164													8	6	---	---	---	---	
CD36	948	broad.mit.edu	37	7	80124204	80124204	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80124204delG	uc003uhc.2	+						GNAT3_uc011kgu.1_Intron	NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1						tccctctcatgctctcacttt	0.000													3	10	---	---	---	---	
CACNA2D1	781	broad.mit.edu	37	7	81646926	81646927	+	Intron	INS	-	T	T	rs144383536	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81646926_81646927insT	uc003uhr.1	-						uc003uhs.1_Intron	NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	TTCTTCAGATGTTTTTTTTTTA	0.307													4	3	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82457498	82457499	+	Intron	INS	-	T	T	rs146095985	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82457498_82457499insT	uc003uhx.2	-						PCLO_uc003uhv.2_Intron|PCLO_uc003uht.1_Intron|PCLO_uc003uhu.1_Intron	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TGCCCTTATGATTTTTTTTTAA	0.287													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84854647	84854648	+	IGR	DEL	CT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84854647_84854648delCT								SEMA3D (38476 upstream) : None (None downstream)																							cttctccttcctctctctctct	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84895512	84895512	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84895512delT								SEMA3D (79341 upstream) : None (None downstream)																							ATTATCTTGGTAAGAGGCCAT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	87945281	87945284	+	IGR	DEL	ACTC	-	-	rs111272262		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87945281_87945284delACTC								STEAP4 (9072 upstream) : ZNF804B (443469 downstream)																							tagttcctTTactcactcactcac	0.113													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	91527106	91527106	+	IGR	DEL	T	-	-	rs79044779		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91527106delT								MTERF (17090 upstream) : AKAP9 (43083 downstream)																							AAGAAAAGAATTCTCAACCAT	0.249													2	4	---	---	---	---	
PPP1R9A	55607	broad.mit.edu	37	7	94734290	94734291	+	Intron	INS	-	C	C	rs147344017	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94734290_94734291insC	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			AGCACACTTTGCTAGCCATCAT	0.450										HNSCC(28;0.073)			2	4	---	---	---	---	
DYNC1I1	1780	broad.mit.edu	37	7	95440006	95440007	+	Intron	INS	-	G	G	rs149930159	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95440006_95440007insG	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			ATGGGAGGAAAGTTGTAGAATT	0.361													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96678179	96678179	+	IGR	DEL	T	-	-	rs72275199		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96678179delT								DLX5 (24036 upstream) : ACN9 (67726 downstream)																							ctttacagacttttttttttt	0.090													6	3	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98562769	98562770	+	Intron	INS	-	CA	CA			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98562769_98562770insCA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTGTGCATGTGCACACACACAC	0.257													3	3	---	---	---	---	
ZKSCAN5	23660	broad.mit.edu	37	7	99115612	99115613	+	Intron	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99115612_99115613delAG	uc003uqv.2	+						ZKSCAN5_uc010lfx.2_Intron|ZKSCAN5_uc003uqw.2_Intron|ZKSCAN5_uc003uqx.2_Intron|ZKSCAN5_uc003uqy.2_Intron	NM_145102	NP_659570	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			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)					TGAGATGGGCAGAGAGAGAGAG	0.252													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101860106	101860107	+	Intron	DEL	CA	-	-	rs72011907		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101860106_101860107delCA	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						actctcccaccacacacacaca	0.030													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	103639505	103639505	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103639505delA								RELN (9542 upstream) : ORC5L (127285 downstream)																							gttcccttctaaacaggaaat	0.000													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110391469	110391469	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110391469delT	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		TTTCTAAGCCTTTTACAAACA	0.318													4	2	---	---	---	---	
TMEM168	64418	broad.mit.edu	37	7	112415656	112415656	+	Intron	DEL	A	-	-	rs10256800	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112415656delA	uc003vgn.2	-						TMEM168_uc010lju.2_Intron|TMEM168_uc011kmr.1_Intron	NM_022484	NP_071929	Q9H0V1	TM168_HUMAN	transmembrane protein 168							integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2						TCCAGACGAGAAAAAAAAAAA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112960329	112960329	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112960329delC								LOC401397 (201692 upstream) : PPP1R3A (556553 downstream)																							TTTGTTCTTTCCATTGTggtc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114435363	114435363	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114435363delC								FOXP2 (104271 upstream) : MDFIC (126846 downstream)																							AAAGAGGAAGCCCAGGGGAGA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117651449	117651450	+	IGR	INS	-	T	T	rs112823711		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117651449_117651450insT								CTTNBP2 (137888 upstream) : NAA38 (172636 downstream)																							TTGTCAGTTCATTTTTTTTTAC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118360241	118360241	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118360241delA								ANKRD7 (477459 upstream) : None (None downstream)																							TGTCTGTGACAAAAATAATTT	0.294													4	2	---	---	---	---	
ING3	54556	broad.mit.edu	37	7	120596744	120596744	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120596744delA	uc003vjn.2	+						ING3_uc003vjl.2_3'UTR|ING3_uc003vjm.1_3'UTR|ING3_uc003vjo.2_Intron|ING3_uc003vjp.2_Intron|ING3_uc011kns.1_Intron	NM_019071	NP_061944	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3 isoform 1						histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding			ovary(1)	1	all_neural(327;0.117)					AATAAAAACCAAAAAAAAAAA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123050597	123050597	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123050597delA								SLC13A1 (210572 upstream) : IQUB (41641 downstream)																							GTTCCAAAGGAAAAAAGGTGG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123781072	123781073	+	Intron	INS	-	T	T	rs138379781	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123781072_123781073insT	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																		tttgatttttcttttttttgat	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124872149	124872149	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124872149delT	uc010lky.1	-											Homo sapiens chromosome 7 isolate HA_003154 mRNA sequence.																		ttagtagaaattttttttttc	0.000													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126228364	126228364	+	Intron	DEL	A	-	-	rs75502814		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126228364delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	TAGAAAGTTGAAAAGTGTTTT	0.229										HNSCC(24;0.065)			4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126249040	126249040	+	Intron	DEL	T	-	-	rs17610771	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126249040delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	agATGTGACCTTTTTTTAAGC	0.189										HNSCC(24;0.065)			4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126266156	126266157	+	Intron	INS	-	TGTA	TGTA	rs72248910		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126266156_126266157insTGTA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	TATGAGAGAAgtgtgtgtgtgt	0.248										HNSCC(24;0.065)			2	5	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126545582	126545582	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126545582delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	ataaacagtatttttttttag	0.149										HNSCC(24;0.065)			4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126584370	126584371	+	Intron	INS	-	G	G	rs148474447	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126584370_126584371insG	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	GAGGTGGACCTGGGCTGCATGC	0.450										HNSCC(24;0.065)			3	6	---	---	---	---	
FSCN3	29999	broad.mit.edu	37	7	127232060	127232060	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127232060delT	uc003vmd.1	+						FSCN3_uc003vmc.1_Intron|FSCN3_uc011kog.1_5'Flank|FSCN3_uc011koh.1_5'Flank|FSCN3_uc010llc.1_5'Flank	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3							actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1						AATGTTTGCCTTACACATTAA	0.274													4	2	---	---	---	---	
FSCN3	29999	broad.mit.edu	37	7	127234334	127234335	+	Intron	DEL	GC	-	-	rs2696064		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127234334_127234335delGC	uc003vmd.1	+						FSCN3_uc003vmc.1_Intron|FSCN3_uc011kog.1_Intron|FSCN3_uc011koh.1_Intron|FSCN3_uc010llc.1_Intron	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3							actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1						gtgtgtgtgtgCGCACTTGCCT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128331671	128331671	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128331671delA								FAM71F2 (7372 upstream) : FAM71F1 (17444 downstream)																							agatggtgataaaagggacct	0.010													4	2	---	---	---	---	
AHCYL2	23382	broad.mit.edu	37	7	129059588	129059588	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129059588delA	uc011kov.1	+						AHCYL2_uc003vot.2_Intron|AHCYL2_uc003vov.2_Intron|AHCYL2_uc011kow.1_Intron|AHCYL2_uc011kox.1_Intron	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						AAAAAAAAACAAAAAAAAACC	0.373													4	2	---	---	---	---	
FLJ43663	378805	broad.mit.edu	37	7	130661391	130661391	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130661391delA	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0						acagcaaaggaaaaaaaaata	0.000													3	3	---	---	---	---	
MKLN1	4289	broad.mit.edu	37	7	130915186	130915186	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130915186delG	uc011kpl.1	+							NM_001145354	NP_001138826	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					TCCCAGTGGTGGGGATGATGA	0.219													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	131936411	131936411	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131936411delA	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						TTCAAACCACAAAAAAACAGT	0.502													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133644459	133644459	+	Intron	DEL	A	-	-	rs77306463		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133644459delA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				ctgtcagaagaaaaaaaaaat	0.000													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133728364	133728367	+	Intron	DEL	GATA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133728364_133728367delGATA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				GTCCTCCAGGGATAGCAGTTTCTT	0.475													6	3	---	---	---	---	
SLC35B4	84912	broad.mit.edu	37	7	133991264	133991265	+	Intron	INS	-	CTTA	CTTA	rs112358351		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133991264_133991265insCTTA	uc003vrn.2	-						SLC35B4_uc010lmk.2_Intron|SLC35B4_uc010lml.1_Intron|SLC35B4_uc003vro.3_Intron	NM_032826	NP_116215	Q969S0	S35B4_HUMAN	solute carrier family 35, member B4							Golgi membrane|integral to membrane	UDP-N-acetylglucosamine transmembrane transporter activity|UDP-xylose transmembrane transporter activity			skin(1)	1						TCTCTTTTTGCCTTCTCAGATG	0.351													13	7	---	---	---	---	
CHRM2	1129	broad.mit.edu	37	7	136586960	136586963	+	Intron	DEL	ATCC	-	-	rs147700166		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136586960_136586963delATCC	uc003vtf.1	+						CHRM2_uc003vtg.1_Intron|CHRM2_uc003vtj.1_Intron|CHRM2_uc003vtk.1_Intron|CHRM2_uc003vtl.1_Intron|CHRM2_uc003vtm.1_Intron|CHRM2_uc003vti.1_Intron|CHRM2_uc003vto.1_Intron|CHRM2_uc003vtn.1_Intron|uc003vtp.1_Intron|MIR490_hsa-mir-490|MI0003125_5'Flank	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2						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)	cgatctatctatccatccatccat	0.157													2	5	---	---	---	---	
DGKI	9162	broad.mit.edu	37	7	137441807	137441807	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137441807delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						TTCTCCAGGATTTTTTTTTTA	0.333													4	2	---	---	---	---	
CREB3L2	64764	broad.mit.edu	37	7	137568497	137568497	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137568497delT	uc003vtw.2	-						CREB3L2_uc003vtv.2_Intron	NM_194071	NP_919047	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like						chondrocyte differentiation|positive regulation of transcription, DNA-dependent|response to endoplasmic reticulum stress|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	cAMP response element binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L2(158)	soft_tissue(158)|upper_aerodigestive_tract(1)|ovary(1)	160						tattcagctattttaaggtaa	0.090			T	FUS	fibromyxoid sarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	137906785	137906785	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137906785delC								AKR1D1 (103735 upstream) : TRIM24 (238294 downstream)																							ttagtcactgcccatcaaggg	0.000													4	2	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139350305	139350308	+	Intron	DEL	CATC	-	-	rs72181046		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139350305_139350308delCATC	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)					CTCCTGGCCAcatccatccatcca	0.343													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141556508	141556508	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141556508delT								PRSS37 (15223 upstream) : OR9A4 (62168 downstream)																							gctgactttatttttttgtag	0.000													4	2	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	144027120	144027121	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144027120_144027121insA	uc003wec.1	-											SubName: Full=Seven transmembrane helix receptor;												0						ccctgtctcagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146846876	146846877	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146846876_146846877insA	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)			tgagaacagggaaaatgagata	0.040										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147963694	147963695	+	Intron	DEL	GT	-	-	rs71838472		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147963694_147963695delGT	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)			CAGCATTTGAgtgtgtgtgtgt	0.381										HNSCC(39;0.1)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148341179	148341179	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148341179delC								C7orf33 (28228 upstream) : CUL1 (53827 downstream)																							atctccatgtccccccaacaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148964887	148964887	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148964887delA	uc003wfr.3	+											Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																		gacttcatctaaaaaaaaaaa	0.244													4	3	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151531149	151531150	+	Intron	INS	-	A	A	rs138194213	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151531149_151531150insA	uc003wkk.2	-						PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		GTTTCTGGAGGAAAAAAAAAAT	0.490													15	9	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152033915	152033915	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152033915delA	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)		AACCTGACCTAAAATACAGGC	0.358			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152155303	152155304	+	IGR	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152155303_152155304delAC								FABP5L3 (15205 upstream) : LOC100128822 (5905 downstream)																							AAGAACACGAACACACACACAC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153306537	153306537	+	IGR	DEL	A	-	-	rs35052879		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153306537delA								ACTR3B (754074 upstream) : DPP6 (277882 downstream)																							aaacttaagcaaaagtaagta	0.035													1	5	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154216216	154216216	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154216216delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.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)			TCTAATTGACTAGACTTTCTC	0.428													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154665585	154665586	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154665585_154665586delCA	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)			cacccacaggcacacacatgca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155120316	155120317	+	IGR	INS	-	CT	CT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155120316_155120317insCT								INSIG1 (18374 upstream) : EN2 (130507 downstream)																							CTCATCTCTCCCTCCCCAAAGA	0.564													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2233184	2233185	+	IGR	INS	-	A	A	rs146202510	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2233184_2233185insA								MYOM2 (139805 upstream) : CSMD1 (559691 downstream)																							AGGTAGTTCCTAAAATCTTCTC	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4863001	4863004	+	IGR	DEL	TTTG	-	-	rs113560734		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4863001_4863004delTTTG								CSMD1 (10673 upstream) : None (None downstream)																							TGAGGGTGTTtttgtttgtttgtt	0.338													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4918816	4918816	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4918816delA								CSMD1 (66488 upstream) : None (None downstream)																							TTAATTTCGGAAAAAAAAAAT	0.318													5	4	---	---	---	---	
MTMR9	66036	broad.mit.edu	37	8	11153008	11153011	+	Intron	DEL	ACTC	-	-	rs149766910		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11153008_11153011delACTC	uc003wtm.2	+						MTMR9_uc010lrx.2_Intron|MTMR9_uc011kxa.1_Intron	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9							cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		GTCTGGTGTTACTCACGTTATATG	0.392													8	4	---	---	---	---	
BLK	640	broad.mit.edu	37	8	11411895	11411895	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11411895delG	uc003wty.2	+						BLK_uc003wtz.2_Intron	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		TCACTCCAACGAGACTAGATT	0.502											OREG0018557	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12407297	12407297	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12407297delT	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_RNA|uc003wvw.1_Intron|uc003wvx.1_Intron|uc003wvy.3_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						ACCTGCTCCCTTCACCAGGAG	0.264													4	2	---	---	---	---	
VPS37A	137492	broad.mit.edu	37	8	17112142	17112142	+	Intron	DEL	T	-	-	rs79989258		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17112142delT	uc003wxj.2	+						VPS37A_uc003wxk.2_Intron	NM_152415	NP_689628	Q8NEZ2	VP37A_HUMAN	hepatocellular carcinoma related protein 1						cellular membrane organization|endosome transport|protein transport	centrosome|late endosome membrane|nucleus					0				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		ctttttcttcttttttttttA	0.284													4	2	---	---	---	---	
PCM1	5108	broad.mit.edu	37	8	17885372	17885372	+	3'UTR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17885372delT	uc003wyi.3	+	39					PCM1_uc011kyh.1_3'UTR|PCM1_uc003wyj.3_3'UTR|PCM1_uc011kyi.1_3'UTR|PCM1_uc011kyj.1_3'UTR|PCM1_uc003wyk.3_3'UTR|PCM1_uc011kyk.1_3'UTR	NM_006197	NP_006188	Q15154	PCM1_HUMAN	pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)		ACACACTGTGTTTTTTTTTTT	0.333			T	RET|JAK2	papillary thyroid|CML|MPD								20	10	---	---	---	---	
SLC18A1	6570	broad.mit.edu	37	8	20029215	20029216	+	Intron	DEL	GC	-	-	rs2132700	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20029215_20029216delGC	uc011kyq.1	-						SLC18A1_uc003wzl.2_Intron|SLC18A1_uc003wzm.2_Intron|SLC18A1_uc011kyr.1_Intron|SLC18A1_uc003wzn.2_Intron|SLC18A1_uc010ltf.2_Intron|SLC18A1_uc003wzo.2_Intron	NM_001135691	NP_001129163	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine),						neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)		gtgtgtgtgtgcgcgcgcgtgt	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20248693	20248693	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20248693delT								LZTS1 (135890 upstream) : None (None downstream)																							TCTCTCGTTCTTTTTTTTCTG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21183511	21183511	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21183511delC								None (None upstream) : GFRA2 (366019 downstream)																							TCTCAATCCTCCCCCCACACA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24759104	24759104	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24759104delG								ADAM7 (374623 upstream) : NEFM (12170 downstream)																							GGAGAGAGGAGGCAATGAAGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26279262	26279263	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26279262_26279263insT								BNIP3L (8618 upstream) : PNMA2 (82933 downstream)																							ttgaggaaggatttttttttaa	0.000													4	2	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27740533	27740533	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27740533delA	uc003xgj.2	-						SCARA5_uc010luz.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		caacaaagctaaaagggctct	0.075													4	2	---	---	---	---	
ELP3	55140	broad.mit.edu	37	8	28000806	28000807	+	Intron	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28000806_28000807insC	uc003xgo.3	+						ELP3_uc003xgn.3_Intron|ELP3_uc011laq.1_Intron|ELP3_uc011lar.1_Intron|ELP3_uc011las.1_Intron|ELP3_uc011lat.1_Intron	NM_018091	NP_060561	Q9H9T3	ELP3_HUMAN	elongation protein 3 homolog						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GATTTTATACTCCCCCCCAACA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	28920740	28920740	+	IGR	DEL	G	-	-	rs112983954	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28920740delG								HMBOX1 (10500 upstream) : KIF13B (4056 downstream)																							ACACGGGTGTGGGGGCAGCGC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40327981	40327981	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40327981delA								C8orf4 (315160 upstream) : ZMAT4 (60135 downstream)																							attatcccccaccggcaaatc	0.174													1	5	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	59759451	59759452	+	Intron	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59759451_59759452delTG	uc003xtw.1	-							NM_014729	NP_055544	O94900	TOX_HUMAN	thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				TTCCCTTGTATGTGACCTCCCA	0.421													4	2	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63699054	63699055	+	Intron	INS	-	A	A	rs139596816	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63699054_63699055insA	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				TCTCCTCATATAAAGGATTCAT	0.436													2	6	---	---	---	---	
ARMC1	55156	broad.mit.edu	37	8	66539812	66539822	+	Intron	DEL	AGTTTGAGAAA	-	-	rs35778954		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66539812_66539822delAGTTTGAGAAA	uc003xvl.2	-						ARMC1_uc011leo.1_Intron	NM_018120	NP_060590	Q9NVT9	ARMC1_HUMAN	armadillo repeat-containing protein						metal ion transport		metal ion binding			skin(1)	1			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			GCAACTCTACAGTTTGAGAAAAGTAAAATGA	0.299													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66841804	66841804	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66841804delT								PDE7A (88049 upstream) : DNAJC5B (91987 downstream)																							CTTAAAACCATTTTTTTTTTC	0.438													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68482335	68482335	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68482335delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAACAAGAACTTTTTTTTTTC	0.313													6	7	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69532928	69532928	+	Intron	DEL	A	-	-	rs4993631	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69532928delA	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			GTTTACTGGGAAAAAAAAAAA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	69809550	69809550	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69809550delA								C8orf34 (78294 upstream) : SULF1 (569309 downstream)																							ctgtcttaagaaaaaaaaaac	0.119													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72316198	72316198	+	RNA	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72316198delT	uc003xyw.2	-	4		c.1274delA								Homo sapiens cDNA clone IMAGE:5264099.																		TACATACTTGTTTTTCGTGAC	0.289													4	2	---	---	---	---	
STAU2	27067	broad.mit.edu	37	8	74538310	74538311	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74538310_74538311delAC	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			AAGTacacatacacacacacac	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78153492	78153493	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78153492_78153493insC								PEX2 (240968 upstream) : None (None downstream)																							tctctgtatttccttGTGTGTC	0.267													4	2	---	---	---	---	
STMN2	11075	broad.mit.edu	37	8	80577225	80577225	+	Intron	DEL	A	-	-	rs78006622		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80577225delA	uc011lfn.1	+						STMN2_uc003ybk.2_RNA	NM_007029	NP_008960	Q93045	STMN2_HUMAN	superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			AACTCATTATaaaaaaaaaaa	0.303													33	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81243771	81243771	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81243771delT								TPD52 (159935 upstream) : ZBTB10 (154083 downstream)																							CTTCTTCTTCTTTTTTTTTTA	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81831111	81831111	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81831111delT								ZNF704 (44095 upstream) : PAG1 (48937 downstream)																							CAATATCGTATTTACTATCCT	0.408													4	2	---	---	---	---	
RALYL	138046	broad.mit.edu	37	8	85132097	85132098	+	Intron	INS	-	ATAG	ATAG	rs141153228	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85132097_85132098insATAG	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						ACAGAAGACGTatagatagata	0.292													2	4	---	---	---	---	
CNGB3	54714	broad.mit.edu	37	8	87698881	87698882	+	Intron	INS	-	A	A	rs145194299	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87698881_87698882insA	uc003ydx.2	-							NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						GGGTGTTCTGCATTGATAAGAG	0.386													2	5	---	---	---	---	
MMP16	4325	broad.mit.edu	37	8	89271961	89271961	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89271961delA	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8						ATGCGGACATAAAAAATACTG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93199503	93199503	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93199503delA								RUNX1T1 (91797 upstream) : C8orf83 (696362 downstream)																							CTTGTGGTAGAAAAAAATAGT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93490485	93490486	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93490485_93490486delTC								RUNX1T1 (382779 upstream) : C8orf83 (405379 downstream)																							cagatctcaatctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93661520	93661520	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93661520delC								RUNX1T1 (553814 upstream) : C8orf83 (234345 downstream)																							CCTTTTTTTTCCCCCAATTTT	0.348													4	2	---	---	---	---	
RAD54B	25788	broad.mit.edu	37	8	95416106	95416107	+	Intron	DEL	TA	-	-	rs150995806		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95416106_95416107delTA	uc003ygk.2	-						RAD54B_uc010may.1_Intron|RAD54B_uc003ygl.1_Intron	NM_012415	NP_036547	O95073	FSBP_HUMAN	RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			CTCCTAGCAGTATGTTTGGCAC	0.396								Direct_reversal_of_damage|Homologous_recombination					5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96692630	96692631	+	IGR	INS	-	G	G	rs140851623	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96692630_96692631insG								C8orf37 (411193 upstream) : GDF6 (461929 downstream)																							ATGTTAATTCAAAATGTCattt	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96703820	96703820	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96703820delT								C8orf37 (422383 upstream) : GDF6 (450740 downstream)																							CTTTTATTGCTTTTTTTTTCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	113150049	113150049	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113150049delT								None (None upstream) : CSMD3 (85112 downstream)																							ccactttggctttttttgtgt	0.000													4	2	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116499625	116499625	+	Intron	DEL	C	-	-	rs35098703		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116499625delC	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			agcctgtggaccccaggagta	0.000									Langer-Giedion_syndrome				2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117323237	117323237	+	IGR	DEL	T	-	-	rs80278776		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117323237delT								TRPS1 (642009 upstream) : EIF3H (333819 downstream)																							tttcaagttgttttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119798538	119798538	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119798538delA								SAMD12 (164304 upstream) : TNFRSF11B (137259 downstream)																							TTTCATCCACAAAATGAACCT	0.433													4	2	---	---	---	---	
COL14A1	7373	broad.mit.edu	37	8	121298403	121298403	+	Intron	DEL	T	-	-	rs77603140	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121298403delT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			gaaatgtgcatttttTTTTTT	0.279													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122096286	122096286	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122096286delT								SNTB1 (271977 upstream) : HAS2 (528985 downstream)																							CTTAGCTCTATTTTTTACTTT	0.289													4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123909412	123909412	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123909412delA	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CATGAGAGGCAAAACAGCATG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126393587	126393587	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126393587delC								NSMCE2 (14220 upstream) : TRIB1 (48976 downstream)																							aaataaaaaacccacagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126626589	126626590	+	IGR	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126626589_126626590delGT								TRIB1 (175947 upstream) : FAM84B (938097 downstream)																							agggagagtcgtgtgtgtgtat	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129953271	129953272	+	IGR	INS	-	TG	TG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129953271_129953272insTG								MIR1208 (790837 upstream) : GSDMC (807171 downstream)																							gtgtgtgtgtctgtgtgtgtgt	0.000													2	4	---	---	---	---	
OC90	729330	broad.mit.edu	37	8	133064147	133064147	+	5'Flank	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133064147delT	uc003ytg.2	-						OC90_uc011lix.1_Intron	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90						lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			ttttcaaaaattttttttgaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137846270	137846270	+	IGR	DEL	A	-	-	rs72095983		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137846270delA								None (None upstream) : None (None downstream)																							CTGGAAAAACAAAAAAAACTA	0.453													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139848868	139848868	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139848868delC	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						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)			ACACCAATATCCtgtgatcct	0.284										HNSCC(7;0.00092)			4	2	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140627496	140627497	+	Intron	INS	-	CTT	CTT	rs141735792	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140627496_140627497insCTT	uc003yvf.1	-						KCNK9_uc003yve.1_Intron	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)			taagtgttcgccttctctgaac	0.168													2	4	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141117975	141117976	+	Intron	INS	-	A	A	rs146527628	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141117975_141117976insA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						GTGAAACATTTAAGTCTGGCAG	0.535													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142557695	142557695	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142557695delG								FLJ43860 (40365 upstream) : MIR1302-7 (309908 downstream)																							ATGTGGcagtggaagtggctg	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142679012	142679012	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142679012delA								FLJ43860 (161682 upstream) : MIR1302-7 (188591 downstream)																							cccactcaggaaatggttgct	0.303													4	2	---	---	---	---	
ADCK5	203054	broad.mit.edu	37	8	145600940	145600940	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145600940delT	uc003zch.2	+						ADCK5_uc003zcg.2_Intron	NM_174922	NP_777582	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5							integral to membrane	protein serine/threonine kinase activity			stomach(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GTTTTCTTTCTTTTTTTTAAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2901641	2901641	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2901641delC								KIAA0020 (57511 upstream) : RFX3 (323008 downstream)																							cagatctcctccaccaatcct	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	4479604	4479604	+	IGR	DEL	C	-	-	rs5896075		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4479604delC								GLIS3 (179569 upstream) : SLC1A1 (10840 downstream)																							CAAGTCAGCACCCCTGCCTCC	0.527													4	4	---	---	---	---	
KIAA2026	158358	broad.mit.edu	37	9	5979525	5979525	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5979525delA	uc003zjq.3	-							NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358											ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		acccacaaacaaaaaaaaaaT	0.129													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6991692	6991692	+	Intron	DEL	T	-	-	rs78016005		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6991692delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						CTTTCACAGATTTTTTCCCCC	0.269													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11501903	11501906	+	IGR	DEL	AAAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11501903_11501906delAAAC								PTPRD (889180 upstream) : None (None downstream)																							aagataggaaaaacaaacaaacaa	0.152													3	3	---	---	---	---	
NFIB	4781	broad.mit.edu	37	9	14275817	14275818	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14275817_14275818insT	uc003zle.2	-						NFIB_uc003zlf.2_Intron|NFIB_uc011lmo.1_Intron	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		CCCTATCTCTATTTTTCTTTTA	0.342			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								4	2	---	---	---	---	
ADAMTSL1	92949	broad.mit.edu	37	9	18681708	18681708	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18681708delC	uc003zne.3	+						ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		GGGGGGGGGGCGGGGAAAAAG	0.443													6	3	---	---	---	---	
DENND4C	55667	broad.mit.edu	37	9	19305459	19305459	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19305459delA	uc003znq.2	+	6	746	c.713delA	c.(712-714)TATfs	p.Y238fs	DENND4C_uc011lnc.1_5'UTR	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	238	DENN.					integral to membrane				ovary(1)|skin(1)	2						GACTCAAGGTATTTTGATCTT	0.383													482	239	---	---	---	---	
UNC13B	10497	broad.mit.edu	37	9	35275037	35275037	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35275037delT	uc003zwq.2	+						UNC13B_uc010mkl.1_Intron|UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TTTTGAATTCTTTTTTTTTCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35998104	35998104	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35998104delG								OR2S2 (39953 upstream) : RECK (38806 downstream)																							aagttttgttggggtaggcaa	0.000													4	2	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67272725	67272726	+	Intron	DEL	GG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67272725_67272726delGG	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_RNA|AQP7P1_uc004aep.1_RNA					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						GTGAAGATGCGGGGGGGGGGGG	0.579													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68406573	68406573	+	IGR	DEL	G	-	-	rs112666148		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68406573delG								FAM27B (612384 upstream) : MIR1299 (595666 downstream)																							tatagaatgaggaaaaaatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68416069	68416070	+	IGR	INS	-	T	T	rs144623635		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68416069_68416070insT								FAM27B (621880 upstream) : MIR1299 (586169 downstream)																							ctacaatatagtttaagcataa	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68421945	68421945	+	IGR	DEL	A	-	-	rs74488106		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68421945delA								FAM27B (627756 upstream) : MIR1299 (580294 downstream)																							ccagctaattaaaaaatatat	0.000													3	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430426	68430427	+	IGR	INS	-	AT	AT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430426_68430427insAT								FAM27B (636237 upstream) : MIR1299 (571812 downstream)																							GTTTTTACTTCATATATATAAT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68450124	68450124	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68450124delA								FAM27B (655935 upstream) : MIR1299 (552115 downstream)																							tagattctacagacattaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70836724	70836724	+	IGR	DEL	T	-	-	rs143594975		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70836724delT								CBWD3 (336661 upstream) : FOXD4L3 (81059 downstream)																							AAATCAGGTGTCGGGGAGTGT	0.219													6	3	---	---	---	---	
RORB	6096	broad.mit.edu	37	9	77239948	77239948	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77239948delA	uc004aji.2	+						RORB_uc004ajh.2_Intron	NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						TCCTTAAGGCAAAAAAAAAAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81441407	81441407	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81441407delG								PSAT1 (496400 upstream) : TLE4 (745471 downstream)																							ATTTCGGCAAGGATATTCAGG	0.338													4	2	---	---	---	---	
GKAP1	80318	broad.mit.edu	37	9	86357843	86357843	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86357843delG	uc004amy.2	-						GKAP1_uc004amz.2_Intron	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0						aggccaaggtgggcagatcac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	89136480	89136480	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89136480delT								ZCCHC6 (167102 upstream) : GAS1 (422799 downstream)																							aaagggggaattttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93686899	93686899	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93686899delC								SYK (26066 upstream) : AUH (289200 downstream)																							AAAACAACCACCACCACACCA	0.493													4	2	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94616290	94616291	+	Intron	INS	-	G	G	rs139874392	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94616290_94616291insG	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						cagggggccctgaagtggagta	0.064													25	17	---	---	---	---	
SPTLC1	10558	broad.mit.edu	37	9	94853008	94853008	+	Intron	DEL	A	-	-	rs3858090	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94853008delA	uc004arl.1	-						SPTLC1_uc011ltv.1_Intron|SPTLC1_uc004arm.1_Intron|SPTLC1_uc004arn.1_Intron	NM_006415	NP_006406	O15269	SPTC1_HUMAN	serine palmitoyltransferase subunit 1 isoform a							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)	AAGGCAAGGGAAAAAAAAAAG	0.403													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	97108767	97108768	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97108767_97108768insT	uc004auq.1	+											Homo sapiens cDNA FLJ37869 fis, clone BRSSN2017422.																		TTTTTTACAAGTTTTTTTTTTT	0.213													5	3	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101155784	101155785	+	Intron	INS	-	CCAT	CCAT	rs148265954	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101155784_101155785insCCAT	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	agcccacccacccatccatcca	0.015													4	2	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101423693	101423694	+	Intron	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101423693_101423694insC	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CTTTTCCCCCACCCCCCCgata	0.114													4	2	---	---	---	---	
CYLC2	1539	broad.mit.edu	37	9	105763572	105763572	+	Intron	DEL	A	-	-	rs79082433		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105763572delA	uc004bbs.2	+							NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2						cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)				atacacacacaatacatataa	0.179													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111546827	111546827	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111546827delT								None (None upstream) : ACTL7B (70044 downstream)																							taacaagttctttttttaaaa	0.000													4	2	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112606712	112606712	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112606712delA	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						cttgtgggggaaaaaaaatag	0.085													4	2	---	---	---	---	
C9orf84	158401	broad.mit.edu	37	9	114450036	114450036	+	Intron	DEL	T	-	-	rs66866615		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114450036delT	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfq.2_Intron|C9orf84_uc010mug.2_Intron	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1											ovary(2)	2						cttcttcttcttttttttttt	0.333													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126985112	126985113	+	IGR	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126985112_126985113delCA								LHX2 (189670 upstream) : NEK6 (34773 downstream)																							CACAGGCATGCACACACACACA	0.495													4	2	---	---	---	---	
PTGES2	80142	broad.mit.edu	37	9	130893424	130893443	+	5'Flank	DEL	AGCCAGTGGTTGCAGTAGGC	-	-	rs72466106		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130893424_130893443delAGCCAGTGGTTGCAGTAGGC	uc004bti.2	-						PTGES2_uc004btj.2_5'Flank|PTGES2_uc004btk.2_5'Flank|PTGES2_uc004btl.2_5'Flank|PTGES2_uc004btm.2_5'Flank	NM_025072	NP_079348	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2						cell redox homeostasis|prostaglandin biosynthetic process	Golgi membrane|integral to membrane|mitochondrion|perinuclear region of cytoplasm	electron carrier activity|prostaglandin-E synthase activity|protein binding|protein disulfide oxidoreductase activity				0						GTCTTTTGAAAGCCAGTGGTTGCAGTAGGCACATCCTCTC	0.477													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133407319	133407320	+	IGR	INS	-	A	A	rs139488112	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133407319_133407320insA								ASS1 (30659 upstream) : LOC100272217 (45419 downstream)																							AGGAAAGGATGATGCCAGGGCT	0.208													4	4	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1424090	1424091	+	Intron	DEL	AT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1424090_1424091delAT	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)		acttccagtgataggatgaatg	0.000													4	2	---	---	---	---	
PITRM1	10531	broad.mit.edu	37	10	3185253	3185256	+	Intron	DEL	ATTC	-	-	rs146381838		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3185253_3185256delATTC	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igs.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|uc001igv.1_RNA			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						CTCAGCCTAAATTCATTCGATTTT	0.417													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6980291	6980292	+	IGR	DEL	TA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6980291_6980292delTA								PRKCQ (358053 upstream) : SFMBT2 (223957 downstream)																							tggtgaacattatatatatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10636810	10636810	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10636810delG								None (None upstream) : SFTA1P (189592 downstream)																							TGGGCTGGTTGGGTACTAAGT	0.458													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11303439	11303439	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11303439delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						AAGTATTTTTAAAATCCCATC	0.448													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14048566	14048567	+	Intron	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14048566_14048567delTG	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CGACTGGATTTGTGTGTGTGTG	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16351805	16351806	+	IGR	INS	-	A	A	rs147967994	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16351805_16351806insA								FAM188A (449286 upstream) : PTER (127161 downstream)																							TGTGCAACTCCAAAAAAAAACA	0.416													4	2	---	---	---	---	
TRDMT1	1787	broad.mit.edu	37	10	17197009	17197010	+	Intron	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17197009_17197010delAG	uc001iop.2	-						TRDMT1_uc001ioq.2_Intron|TRDMT1_uc001ior.2_Intron|TRDMT1_uc001ios.2_Intron|TRDMT1_uc009xjt.2_Intron|TRDMT1_uc010qcc.1_Intron|TRDMT1_uc010qcd.1_Intron	NM_004412	NP_004403	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1 isoform						tRNA processing	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding			ovary(1)	1						acctgaggtcagaggagttcga	0.040													2	8	---	---	---	---	
STAM	8027	broad.mit.edu	37	10	17710178	17710178	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17710178delA	uc001ipj.1	+						STAM_uc010qcf.1_Intron	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						tccagtagctaaaataattga	0.000													4	2	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	18116345	18116345	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18116345delA	uc001ipm.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						aaaaataaccaaaaaaaaaaa	0.343													4	2	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	18145099	18145099	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18145099delA	uc001ipm.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						acactgtctcaaaaaaaaaaa	0.204													23	13	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24014947	24014948	+	Intron	INS	-	A	A	rs139471466	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24014947_24014948insA	uc001irs.2	+							NM_001098500	NP_001091970	Q5T5P2	SKT_HUMAN	sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						TTTCCTCACTCAAAAAGGGACC	0.297													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27609443	27609443	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27609443delA								LOC387646 (68208 upstream) : PTCHD3 (77674 downstream)																							GCGTGTTTCTAACAGAAAATA	0.443													4	2	---	---	---	---	
MTPAP	55149	broad.mit.edu	37	10	30632981	30632982	+	Intron	INS	-	TT	TT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30632981_30632982insTT	uc001iva.3	-						MTPAP_uc001ivb.3_Intron|MTPAP_uc001ivc.2_Intron	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						ataaaatggtctttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42622646	42622647	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42622646_42622647insT								None (None upstream) : LOC441666 (204668 downstream)																							CTGTCCTTTTGTTTTGCTCTTA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43238084	43238084	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43238084delA								ZNF33B (104092 upstream) : BMS1 (39870 downstream)																							CAGCAATTCTAGCATCCAGAT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43368950	43368950	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43368950delG								BMS1 (38567 upstream) : RET (203567 downstream)																							ATTTGGATGAGGTTGAGGTGA	0.463													4	2	---	---	---	---	
SYT15	83849	broad.mit.edu	37	10	46968899	46968908	+	Intron	DEL	CACACACACA	-	-	rs72038340		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46968899_46968908delCACACACACA	uc001jea.2	-						SYT15_uc001jdz.2_Intron|SYT15_uc001jeb.2_Intron|SYT15_uc010qfp.1_5'Flank	NM_031912	NP_114118	Q9BQS2	SYT15_HUMAN	synaptotagmin XV isoform a							integral to membrane|plasma membrane					0						cacacacacgcacacacacacacacacaca	0.276													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47063315	47063319	+	Intron	DEL	ACTTT	-	-	rs144530575		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47063315_47063319delACTTT	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						gcatattataactttactttagaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	48443293	48443296	+	IGR	DEL	TGTG	-	-	rs9421806		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48443293_48443296delTGTG								GDF10 (4127 upstream) : FRMPD2L1 (400747 downstream)																							tgtgtgtgtatgtgtgtgtgtgtg	0.338													4	2	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50151644	50151644	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50151644delT	uc001jha.3	+						WDFY4_uc009xob.2_Intron|WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						CTCAGATCTCttttttttttt	0.269													6	4	---	---	---	---	
AGAP6	414189	broad.mit.edu	37	10	51768242	51768242	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51768242delT	uc001jix.3	+							NM_001077665	NP_001071133	Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			skin(1)	1						tttttttttcttttttttttt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	52444482	52444483	+	IGR	INS	-	TTTA	TTTA	rs147667479		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52444482_52444483insTTTA								SGMS1 (59559 upstream) : ASAH2B (55213 downstream)																							TAAAGCCCAGCTGCCTCAGGCT	0.639													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	52444485	52444486	+	IGR	DEL	CC	-	-	rs61857066		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52444485_52444486delCC								SGMS1 (59562 upstream) : ASAH2B (55210 downstream)																							AGCCCAGCTGCCTCAGGCTTCC	0.644													9	5	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53150936	53150937	+	Intron	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53150936_53150937delTT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AACAGAACTCTTTTTTCTGCTT	0.228													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56940480	56940480	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56940480delA	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				CCTTCATGGCAAAAATATCAT	0.294										HNSCC(58;0.16)			4	2	---	---	---	---	
IPMK	253430	broad.mit.edu	37	10	59975732	59975732	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59975732delA	uc001jkb.2	-							NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase							nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1						atcagtgaacaaaaaaaaaaa	0.090													9	6	---	---	---	---	
TMEM26	219623	broad.mit.edu	37	10	63172939	63172939	+	Intron	DEL	G	-	-	rs1915431	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63172939delG	uc001jlo.2	-						TMEM26_uc010qij.1_Intron|TMEM26_uc001jlq.2_Intron|TMEM26_uc001jlp.1_Intron	NM_178505	NP_848600	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26							integral to membrane					0	Prostate(12;0.0112)					tacctggtttgcaggaggtct	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64669634	64669635	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64669634_64669635insC								EGR2 (90707 upstream) : NRBF2 (223372 downstream)																							GCCCATTAAAAAAACCTACCCA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67534126	67534127	+	IGR	DEL	CA	-	-	rs112514425		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67534126_67534127delCA								ANXA2P3 (947492 upstream) : CTNNA3 (145598 downstream)																							tgattgtgtccacacacacaca	0.000													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68040587	68040587	+	Intron	DEL	T	-	-	rs71879341		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68040587delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						ATTAAAGGCATTTTTTTTTTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77152269	77152269	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77152269delA								COMTD1 (156499 upstream) : ZNF503 (5336 downstream)																							GTAGAAAGGGAAAAAGGAAGG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79958029	79958029	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79958029delA								RPS24 (141459 upstream) : LOC283050 (745055 downstream)																							AAGTGTTGACAAAACAAGGAA	0.443													4	2	---	---	---	---	
ZMIZ1	57178	broad.mit.edu	37	10	80981027	80981028	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80981027_80981028delGT	uc001kaf.2	+							NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			gcatgcatgcgtgtgtgtgtgt	0.520													4	2	---	---	---	---	
ZCCHC24	219654	broad.mit.edu	37	10	81197985	81197986	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81197985_81197986delCA	uc001kak.2	-						ZCCHC24_uc010qlr.1_Intron|ZCCHC24_uc009xrw.2_Intron	NM_153367	NP_699198	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24								nucleic acid binding|zinc ion binding			breast(1)	1						CAGACACGCGCACACACACACG	0.540													4	2	---	---	---	---	
OPN4	94233	broad.mit.edu	37	10	88413633	88413634	+	5'Flank	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88413633_88413634delCA	uc001kdq.2	+						OPN4_uc001kdp.2_5'Flank|OPN4_uc010qmk.1_5'Flank	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 1						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1						cacacactctcacacacacaca	0.287													4	2	---	---	---	---	
BMPR1A	657	broad.mit.edu	37	10	88666063	88666064	+	Intron	INS	-	GT	GT	rs146956565	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88666063_88666064insGT	uc001kdy.2	+							NM_004329	NP_004320	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8						catttagaagcgtgtgtgtgtg	0.000			Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				3	3	---	---	---	---	
GLUD1	2746	broad.mit.edu	37	10	88819234	88819234	+	Intron	DEL	A	-	-	rs35013042		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88819234delA	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	TCTATTTAGGAAAAAAAAAAA	0.328													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91410696	91410696	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91410696delT								PANK1 (5481 upstream) : FLJ37201 (40361 downstream)																							AGGTTCCTAGTTCCTGGCTCA	0.229													4	2	---	---	---	---	
RPP30	10556	broad.mit.edu	37	10	92648409	92648409	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92648409delG	uc009xtx.2	+						RPP30_uc001khd.2_Intron|RPP30_uc010qnj.1_Intron	NM_006413	NP_006404	P78346	RPP30_HUMAN	ribonuclease P/MRP 30kDa subunit isoform b						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0						TGAGGGAAGTGGGGCAGTGGG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	95313453	95313454	+	IGR	DEL	TG	-	-	rs71864034		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95313453_95313454delTG								CEP55 (24606 upstream) : GPR120 (12968 downstream)																							CTCTCTTGCTtgtgtgtgtgtg	0.401													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	95427646	95427647	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95427646_95427647insA								PDE6C (2219 upstream) : C10orf4 (682 downstream)																							GTAGTGAGGTGAAAAAAAACAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	100126125	100126126	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100126125_100126126delTG								LOXL4 (98118 upstream) : PYROXD2 (17197 downstream)																							CCACGTGTCCTGTGTGTGTGTA	0.485													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100802757	100802757	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100802757delC	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		cacaaacagaccccacacaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	106282213	106282213	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106282213delT								CCDC147 (67374 upstream) : SORCS3 (118646 downstream)																							GATGTAAACATTTTTTTTTTA	0.473													4	4	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108808519	108808519	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108808519delC	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CTGTATTCAGCCCAAAGGAAA	0.423													4	2	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112344318	112344319	+	Intron	INS	-	TC	TC	rs148794272	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112344318_112344319insTC	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)		ATACATATAGTTCTTTTTTAAA	0.208													11	11	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114711672	114711673	+	Intron	INS	-	T	T	rs143225562	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114711672_114711673insT	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	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)		ATCCGAAGAACTTTCCTTTGCG	0.490													4	3	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115351797	115351797	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115351797delT	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGTAAAGCCCTTTTTTTTTTC	0.383													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119368600	119368601	+	IGR	INS	-	AAAAC	AAAAC	rs113534254		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119368600_119368601insAAAAC								EMX2 (59544 upstream) : RAB11FIP2 (395828 downstream)																							aaataaaaacaaaaacaaaaca	0.173													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119490248	119490248	+	IGR	DEL	T	-	-	rs17096705	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119490248delT								EMX2 (181192 upstream) : RAB11FIP2 (274181 downstream)																							TGCTCTGAGATTTTTTTCTCC	0.423													4	2	---	---	---	---	
PLEKHA1	59338	broad.mit.edu	37	10	124186772	124186772	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124186772delT	uc001lge.1	+						PLEKHA1_uc001lgf.1_Intron|PLEKHA1_uc001lgg.1_Intron|PLEKHA1_uc001lgh.2_Intron	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A						B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AATGCACAAGTAGGGCAACTA	0.318													4	2	---	---	---	---	
GLRX3	10539	broad.mit.edu	37	10	131953903	131953903	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131953903delT	uc001lkm.1	+						GLRX3_uc001lkn.1_Intron|GLRX3_uc001lko.2_Intron	NM_006541	NP_006532	O76003	GLRX3_HUMAN	glutaredoxin 3						cell redox homeostasis|negative regulation of cardiac muscle hypertrophy|regulation of the force of heart contraction	cell cortex	electron carrier activity|iron-sulfur cluster binding|metal ion binding|protein disulfide oxidoreductase activity				0		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		gtgagaggtgtttgatagagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132593036	132593036	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132593036delC								GLRX3 (610252 upstream) : TCERG1L (297620 downstream)																							TGGCACACTACCATCACTAGT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132724314	132724315	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132724314_132724315delTG								GLRX3 (741530 upstream) : TCERG1L (166341 downstream)																							tgagggagcatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
HBG2	3048	broad.mit.edu	37	11	5275268	5275271	+	Intron	DEL	AAAG	-	-	rs111945382		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5275268_5275271delAAAG	uc001mai.1	-						HBG2_uc001maj.1_Intron	NM_000559	NP_000550	P69892	HBG2_HUMAN	A-gamma globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAATCTAATAAAGAAAAGTCATT	0.368													4	2	---	---	---	---	
STK33	65975	broad.mit.edu	37	11	8584161	8584161	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8584161delT	uc001mgj.1	-						STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron	NM_030906	NP_112168	Q9BYT3	STK33_HUMAN	serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GTTTCACAGATTTTTTTTTTG	0.308													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11596321	11596322	+	Intron	INS	-	T	T	rs138133622	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11596321_11596322insT	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		TTTAATATCTCTCCCAGCAAAG	0.470													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11626496	11626496	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11626496delA	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		CTGCGGAGGTAAAAAAAAAGA	0.408													7	4	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	20087549	20087549	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20087549delG	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron|NAV2_uc009yhz.2_Intron|NAV2_uc001mpu.2_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						ctgtgaccctggacaaatgac	0.050													4	2	---	---	---	---	
SVIP	258010	broad.mit.edu	37	11	22849830	22849830	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22849830delA	uc001mqp.3	-						uc001mqq.1_5'Flank	NM_148893	NP_683691	Q8NHG7	SVIP_HUMAN	small VCP/p97-interacting protein							Golgi membrane|plasma membrane|smooth endoplasmic reticulum membrane					0						CTCAGTGTGTAGGAGGGAAGG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25395503	25395503	+	IGR	DEL	G	-	-	rs5790475		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25395503delG								LUZP2 (291321 upstream) : ANO3 (815326 downstream)																							TATGTGGACAGGAAGATGATT	0.274													4	2	---	---	---	---	
IMMP1L	196294	broad.mit.edu	37	11	31464300	31464300	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31464300delT	uc001msy.1	-						IMMP1L_uc001msz.1_Intron	NM_144981	NP_659418	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane						proteolysis	mitochondrial inner membrane	serine-type peptidase activity				0	Lung SC(675;0.225)					TTTAGAATCCTTTTTTTAATG	0.274													4	2	---	---	---	---	
EIF3M	10480	broad.mit.edu	37	11	32616779	32616779	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32616779delT	uc001mtu.2	+						EIF3M_uc010ref.1_Intron	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					TCTTAAtttcttttttttttt	0.174													8	5	---	---	---	---	
LDLRAD3	143458	broad.mit.edu	37	11	35993961	35993962	+	Intron	INS	-	T	T	rs113805702		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35993961_35993962insT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				ACAGCTTAAACTTTTTTTTTTT	0.366													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37282144	37282144	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37282144delA								C11orf74 (585754 upstream) : None (None downstream)																							TTGTATACTCAAAAAATAATG	0.254													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40448473	40448473	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40448473delT	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)				TCTGGTCAAGTTTTTTCCTTC	0.373													4	2	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48160685	48160685	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48160685delA	uc001ngp.3	+						PTPRJ_uc010rhr.1_Intron	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						actccgtctcaaaaaaaaaaG	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55310595	55310596	+	IGR	INS	-	G	G	rs138302887	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55310595_55310596insG								OR4A15 (174202 upstream) : OR4C15 (11187 downstream)																							cagtctctccttttcttctttg	0.000													5	4	---	---	---	---	
PRG3	10394	broad.mit.edu	37	11	57145026	57145027	+	Intron	INS	-	T	T	rs148016647	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57145026_57145027insT	uc001njv.1	-							NM_006093	NP_006084	Q9Y2Y8	PRG3_HUMAN	proteoglycan 3 precursor						basophil activation|histamine biosynthetic process|immune response|leukotriene biosynthetic process|negative regulation of translation|neutrophil activation|positive regulation of interleukin-8 biosynthetic process|superoxide anion generation		sugar binding				0						CTATCACCTGGTTTTGCTTTGA	0.500													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59397031	59397031	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59397031delT								OSBP (13414 upstream) : PATL1 (7163 downstream)																							CAAGGAGCTCTTTTTTTTCCC	0.343													4	2	---	---	---	---	
SCGB1D1	10648	broad.mit.edu	37	11	61959294	61959294	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61959294delA	uc001nsz.1	+							NM_006552	NP_006543	O95968	SG1D1_HUMAN	lipophilin A precursor							extracellular space	binding			skin(1)	1						AGTGTGCTTTAAaaaaaaaac	0.184													4	3	---	---	---	---	
TMEM223	79064	broad.mit.edu	37	11	62558503	62558503	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62558503delT	uc001nve.2	-							NM_001080501	NP_001073970	A0PJW6	TM223_HUMAN	transmembrane protein 223							integral to membrane					0						TACTGAGCGCttttttttttg	0.264													6	3	---	---	---	---	
SLC22A6	9356	broad.mit.edu	37	11	62745013	62745013	+	Intron	DEL	T	-	-	rs77512817		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62745013delT	uc001nwk.2	-						SLC22A6_uc001nwl.2_Intron|SLC22A6_uc001nwj.2_Intron|SLC22A6_uc001nwm.2_Intron	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a						alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0						AATTTGGCGAttttttttttt	0.343													4	3	---	---	---	---	
SLC22A25	387601	broad.mit.edu	37	11	62932393	62932393	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62932393delT	uc001nwr.1	-						SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_Intron|SLC22A25_uc001nws.1_Intron	NM_199352	NP_955384	Q6T423	S22AP_HUMAN	putative UST1-like organic anion transporter						transmembrane transport	integral to membrane				ovary(3)|skin(1)	4						AGCTAAAGAGTTTTTTTTTTG	0.398													4	2	---	---	---	---	
SLC22A25	387601	broad.mit.edu	37	11	62948537	62948537	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62948537delA	uc001nwr.1	-						SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_Intron|SLC22A25_uc001nws.1_Intron|SLC22A25_uc001nwt.1_Intron	NM_199352	NP_955384	Q6T423	S22AP_HUMAN	putative UST1-like organic anion transporter						transmembrane transport	integral to membrane				ovary(3)|skin(1)	4						CAGGATGGGGAAAAAAATGAA	0.378													4	2	---	---	---	---	
NRXN2	9379	broad.mit.edu	37	11	64427407	64427407	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64427407delC	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						aggcttagcacccactaggcg	0.244													4	2	---	---	---	---	
RBM14	10432	broad.mit.edu	37	11	66393249	66393253	+	Intron	DEL	TCTTC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66393249_66393253delTCTTC	uc001oit.2	+						RBM14_uc009yrh.2_Intron|RBM14_uc009yri.2_Intron|RBM4_uc009yrj.2_Intron|RBM4_uc009yrk.2_Intron	NM_006328	NP_006319	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14						DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|histone deacetylation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus	mediator complex|ribonucleoprotein complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|protein binding, bridging|RNA binding|RNA polymerase II transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						CCTCCCTCGGTCTTCTCTTCTCTAT	0.610													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69042854	69042857	+	IGR	DEL	CATC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69042854_69042857delCATC								TPCN2 (112947 upstream) : MYEOV (18765 downstream)																							tccatgtacacatccatccatcca	0.000													5	3	---	---	---	---	
NUMA1	4926	broad.mit.edu	37	11	71730234	71730234	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71730234delA	uc001orl.1	-						NUMA1_uc009ysw.1_5'Flank|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001orn.2_5'Flank|NUMA1_uc009ysx.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc009ysy.1_Intron|NUMA1_uc001orp.2_Intron|NUMA1_uc001orq.2_Intron	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						tctttgtcagaaaaaAAAAAA	0.199			T	RARA	APL								6	3	---	---	---	---	
C11orf51	25906	broad.mit.edu	37	11	71817517	71817517	+	3'UTR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71817517delC	uc009ytc.1	-	4					LRTOMT_uc010rqv.1_Intron|LRTOMT_uc010rqw.1_Intron|LRTOMT_uc001ors.3_Intron			P60006	CK051_HUMAN	Homo sapiens HSPC020 mRNA, complete cds.							intracellular					0						gccacaaatgctggcctcaaa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74379810	74379810	+	IGR	DEL	T	-	-	rs67090561		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74379810delT								POLD3 (26045 upstream) : CHRDL2 (27665 downstream)																							TTCTGTTGTGTTTTTTTTACA	0.353													4	2	---	---	---	---	
CHRDL2	25884	broad.mit.edu	37	11	74430427	74430428	+	Intron	DEL	AC	-	-	rs34404319		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74430427_74430428delAC	uc001ovi.2	-						CHRDL2_uc001ovg.2_5'Flank|CHRDL2_uc001ovh.2_Intron|CHRDL2_uc001ovk.1_Intron			Q6WN34	CRDL2_HUMAN	RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;						cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)					cctcccctGTacacacacacac	0.218													2	4	---	---	---	---	
RNF169	254225	broad.mit.edu	37	11	74512929	74512929	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74512929delC	uc001ovl.3	+							NM_001098638	NP_001092108	Q8NCN4	RN169_HUMAN	ring finger protein 169								zinc ion binding			ovary(1)	1						gcttgtgaaaccccccttaga	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76557480	76557481	+	IGR	INS	-	TTGG	TTGG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76557480_76557481insTTGG								TSKU (48283 upstream) : ACER3 (14436 downstream)																							tgattgattgattgCTTCACCT	0.282													4	2	---	---	---	---	
ALG8	79053	broad.mit.edu	37	11	77837992	77837992	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77837992delT	uc001oza.1	-						ALG8_uc001oyz.1_Intron|ALG8_uc009yux.1_Intron|ALG8_uc009yuy.1_Intron	NM_024079	NP_076984	Q9BVK2	ALG8_HUMAN	dolichyl pyrophosphate Glc1Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GAGACCACAATTTTTATAAAG	0.239													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78612147	78612147	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78612147delA	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						aaaaggcatgaaagGGCCTCG	0.065													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78729498	78729501	+	Intron	DEL	CACA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78729498_78729501delCACA	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						cacacacatgcacacacacacaca	0.382													4	2	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86308385	86308385	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86308385delT	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)	ATAGAGACAGTTAGCAGCTTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87679442	87679456	+	IGR	DEL	TACAGATACAGACAA	-	-	rs73537226	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87679442_87679456delTACAGATACAGACAA								TMEM135 (644874 upstream) : RAB38 (166975 downstream)																							GCTTCAAGTGTACAGATACAGACAATAATTCTATc	0.135													3	3	---	---	---	---	
GRM5	2915	broad.mit.edu	37	11	88736164	88736165	+	Intron	INS	-	T	T	rs143535327	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88736164_88736165insT	uc001pcq.2	-						GRM5_uc009yvm.2_Intron|GRM5_uc009yvn.1_Intron	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	CCTTTATaggattttttttgtg	0.134													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91603367	91603368	+	IGR	DEL	TG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91603367_91603368delTG								None (None upstream) : FAT3 (481894 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.054													4	2	---	---	---	---	
MMP20	9313	broad.mit.edu	37	11	102479422	102479423	+	Intron	INS	-	AAA	AAA	rs5794187		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102479422_102479423insAAA	uc001phc.2	-							NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		AAAACATAAACCGACAAATGAC	0.332													5	3	---	---	---	---	
MMP20	9313	broad.mit.edu	37	11	102479423	102479424	+	Intron	INS	-	A	A	rs72986033		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102479423_102479424insA	uc001phc.2	-							NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		AAACATAAACCGACAAATGACT	0.332													5	3	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103006871	103006871	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103006871delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATGGGAAAGATTTTTTTTTTG	0.229													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111099609	111099609	+	IGR	DEL	A	-	-	rs67637503		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111099609delA								ARHGAP20 (515697 upstream) : C11orf53 (27098 downstream)																							TTAATAAAAGAAAAAAAAAAA	0.239													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112168361	112168361	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112168361delA								PTS (27684 upstream) : NCAM1 (663634 downstream)																							ATGTGACAGGAAAAGCAAAAG	0.279													4	2	---	---	---	---	
USP28	57646	broad.mit.edu	37	11	113711062	113711065	+	Intron	DEL	CTCA	-	-	rs142754847		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113711062_113711065delCTCA	uc001poh.2	-						USP28_uc010rwy.1_Intron|USP28_uc001poi.2_Intron|USP28_uc001poj.3_Intron|USP28_uc010rwz.1_Intron	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28						cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|breast(2)|ovary(1)|large_intestine(1)|kidney(1)	7		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		cttattcactctcacTGCTATAAT	0.152													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116478111	116478111	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116478111delC								None (None upstream) : BUD13 (140777 downstream)																							tcccccttttccttctcctgt	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118002202	118002202	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118002202delT								TMPRSS4 (6161 upstream) : SCN4B (1892 downstream)																							tgccttgcccttgggtgcttc	0.095													4	2	---	---	---	---	
PVRL1	5818	broad.mit.edu	37	11	119573900	119573900	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119573900delC	uc001pwv.2	-						PVRL1_uc001pwu.1_Intron|PVRL1_uc001pww.2_Intron	NM_002855	NP_002846	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 1						adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CTCAAAGCTTCCCCAGCTCCA	0.438													4	2	---	---	---	---	
OR6M1	390261	broad.mit.edu	37	11	123677273	123677274	+	5'Flank	INS	-	TT	TT	rs71833479		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123677273_123677274insTT	uc010rzz.1	-							NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		ttttttgtttgtttgtttgttt	0.030													8	4	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125149999	125149999	+	Intron	DEL	T	-	-	rs35541174		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125149999delT	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)		ttttttttccttttttttttt	0.328													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130368290	130368291	+	IGR	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130368290_130368291delTT								ADAMTS15 (24575 upstream) : SNX19 (377476 downstream)																							ttttcttgtatttttttttttt	0.000													2	4	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131630239	131630239	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131630239delA	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						ACTGAGTATTAAAAATGATGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134858930	134858931	+	IGR	INS	-	T	T	rs142572867	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134858930_134858931insT								B3GAT1 (577118 upstream) : None (None downstream)																							CATTTGATGTCTCTTTTTTTTT	0.228													4	2	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	625449	625452	+	Intron	DEL	AGAA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:625449_625452delAGAA	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)			atacagagttagaaagagagtgat	0.000													2	7	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	1010305	1010305	+	Intron	DEL	G	-	-	rs13313205	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1010305delG	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron|WNK1_uc009zdm.1_Intron|WNK1_uc009zdn.1_Intron|uc009zdo.1_5'Flank	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CTGTTTATTAGTGATTGCTGA	0.308													4	2	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3307765	3307766	+	Intron	INS	-	C	C	rs11373287		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3307765_3307766insC	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			agcacAGGTCACACcagcacag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	9725479	9725479	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9725479delA	uc001qwb.1	+											Homo sapiens mRNA; cDNA DKFZp686A1124 (from clone DKFZp686A1124).																		TTCTCTCTTCAGCTTTTACCT	0.363													5	12	---	---	---	---	
PLBD1	79887	broad.mit.edu	37	12	14659645	14659645	+	Intron	DEL	T	-	-	rs78906132		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14659645delT	uc001rcc.1	-							NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0						TTACAGATGATTTTTTTTTTT	0.274													5	3	---	---	---	---	
PLEKHA5	54477	broad.mit.edu	37	12	19307921	19307921	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19307921delG	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc001rdz.3_Intron	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTACACTGGTGGGGCTCAGGC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22127356	22127357	+	IGR	DEL	CT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22127356_22127357delCT								ABCC9 (33020 upstream) : CMAS (71802 downstream)																							gggaagtttcctcctaacccca	0.000													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24449864	24449865	+	Intron	INS	-	AC	AC	rs141010418	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24449864_24449865insAC	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TAGacagacagacacacacaca	0.307													3	3	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24464976	24464977	+	Intron	INS	-	A	A	rs143803002	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24464976_24464977insA	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TGGTAGTTGAGAAATTAAGGCC	0.223													2	6	---	---	---	---	
PPFIBP1	8496	broad.mit.edu	37	12	27735054	27735054	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27735054delT	uc001ric.1	+						PPFIBP1_uc001rhy.1_Intron|PPFIBP1_uc001rhz.1_Intron|PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					ATGACTTTGATTTTTTTTTTC	0.378													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38914022	38914023	+	IGR	INS	-	TG	TG	rs138265479	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38914022_38914023insTG								ALG10B (190495 upstream) : CPNE8 (131979 downstream)																							CTATATCTCTTtgtgtgtgtgt	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40767545	40767545	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40767545delT								LRRK2 (4461 upstream) : CNTN1 (318813 downstream)																							GAATTAATCCTTTTTTTTTTT	0.219													4	2	---	---	---	---	
ADAMTS20	80070	broad.mit.edu	37	12	43860813	43860813	+	Intron	DEL	G	-	-	rs35870813		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43860813delG	uc010skx.1	-							NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCTGGCATCTGAATCTACACA	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45999517	45999517	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45999517delT								ANO6 (165330 upstream) : LOC400027 (120293 downstream)																							tcaaatattatttttggctca	0.000													4	2	---	---	---	---	
SMARCD1	6602	broad.mit.edu	37	12	50489043	50489043	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50489043delA	uc001rvx.3	+						SMARCD1_uc001rvy.3_Intron|SMARCD1_uc009zlp.2_Intron	NM_003076	NP_003067	Q96GM5	SMRD1_HUMAN	SWI/SNF-related matrix-associated						chromatin-mediated maintenance of transcription|nervous system development|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	protein complex scaffold|transcription coactivator activity			ovary(1)	1						AAATAAAGCCAAAAGTGCTTT	0.129													6	4	---	---	---	---	
LIMA1	51474	broad.mit.edu	37	12	50634695	50634696	+	Intron	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50634695_50634696delAG	uc001rwj.3	-						LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1						ctgacaaggaagagagagagag	0.000													4	2	---	---	---	---	
KRT82	3888	broad.mit.edu	37	12	52795073	52795075	+	In_Frame_Del	DEL	CTT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52795073_52795075delCTT	uc001sai.1	-	3	794_796	c.679_681delAAG	c.(679-681)AAGdel	p.K227del		NM_033033	NP_149022	Q9NSB4	KRT82_HUMAN	keratin 82	227	Coil 1B.|Rod.					keratin filament	protein binding|structural constituent of epidermis			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.193)		TCCTCCTTACCTTCTTCAAGGCA	0.552													116	51	---	---	---	---	
KRT74	121391	broad.mit.edu	37	12	52961207	52961207	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52961207delA	uc001sap.1	-							NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4							keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)		CATGTCCACCAACCCTTTCTC	0.299													4	2	---	---	---	---	
ESPL1	9700	broad.mit.edu	37	12	53666172	53666173	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53666172_53666173delGT	uc001sck.2	+						ESPL1_uc001scj.2_Intron	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						cattgagagggtgacatgagca	0.000													4	2	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64269058	64269059	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64269058_64269059delGT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		ttattgtttggtgTGTGTGTGT	0.243													3	4	---	---	---	---	
HMGA2	8091	broad.mit.edu	37	12	66320680	66320680	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66320680delA	uc001ssx.2	+						HMGA2_uc001ssw.1_Intron	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		CCAGGAAAGGAAAAAAAAAGT	0.458			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								3	3	---	---	---	---	
TMBIM4	51643	broad.mit.edu	37	12	66539381	66539381	+	Intron	DEL	T	-	-	rs75009871		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66539381delT	uc001stc.2	-						LLPH_uc010ssx.1_Intron|TMBIM4_uc001std.2_Intron|TMBIM4_uc009zqr.2_Intron|TMBIM4_uc001ste.2_Intron|TMBIM4_uc001stf.2_Intron|TMBIM4_uc009zqs.2_Intron	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4							integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)		GGAAAGCTTATTTTTTTTTTT	0.343													2	4	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66904559	66904560	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66904559_66904560delCA	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		ACACATACACCACACACACACA	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69842171	69842171	+	IGR	DEL	T	-	-	rs113875095		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69842171delT								YEATS4 (57596 upstream) : FRS2 (21958 downstream)																							ttttgtcccctttttttttgt	0.000													3	3	---	---	---	---	
BEST3	144453	broad.mit.edu	37	12	70040718	70040719	+	Intron	INS	-	T	T	rs148039653	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70040718_70040719insT	uc001svd.1	-						BEST3_uc001sve.1_Intron	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform							chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			TCCTTGGGGAATAAAAAAAAAG	0.416													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70426929	70426929	+	IGR	DEL	A	-	-	rs34320606		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70426929delA								RAB3IP (209947 upstream) : CNOT2 (209848 downstream)																							aataggacataaaaaaaaaat	0.000													2	4	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78560211	78560212	+	Intron	INS	-	AAG	AAG	rs149695892	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78560211_78560212insAAG	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						CTTTTTAATCAAAGACTATGGA	0.277										HNSCC(70;0.22)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80623429	80623429	+	IGR	DEL	T	-	-	rs76461131		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80623429delT								PPP1R12A (294194 upstream) : PTPRQ (214697 downstream)																							TCTCTCTCTCTTTTTTTTTTT	0.343													4	2	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83361862	83361863	+	Intron	DEL	CT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83361862_83361863delCT	uc001szt.2	+						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						GGCTGGAGTACTAGACAGTAAA	0.351													4	2	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86204699	86204700	+	Intron	INS	-	TG	TG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86204699_86204700insTG	uc001taf.1	-							NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						CTGTTTTACTTTGTGTGTGTGT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88660645	88660645	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88660645delC								TMTC3 (66982 upstream) : KITLG (225924 downstream)																							CTGTGTGTGGCCCAGGCTGAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92258031	92258031	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92258031delT								DCN (681225 upstream) : BTG1 (120835 downstream)																							TCATTTATTCTACCACCCTCC	0.458													4	2	---	---	---	---	
EEA1	8411	broad.mit.edu	37	12	93171332	93171332	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93171332delT	uc001tck.2	-	27	4266	c.4001delA	c.(4000-4002)AACfs	p.N1334fs		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	1334	Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3						AAGTGATTGGTTTTCTCTGCC	0.358													630	319	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94567963	94567963	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94567963delT	uc001tdc.2	+							NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						cttttgtttatttttttttct	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96558468	96558469	+	IGR	INS	-	AC	AC	rs145814025	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96558468_96558469insAC								LTA4H (121170 upstream) : ELK3 (29738 downstream)																							tcacacacactacacacacaca	0.178													5	3	---	---	---	---	
CDK17	5128	broad.mit.edu	37	12	96686622	96686622	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96686622delA	uc001tep.1	-						CDK17_uc009ztk.2_Intron|CDK17_uc010svb.1_Intron	NM_002595	NP_002586	Q00537	CDK17_HUMAN	PCTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7						CAGATTAGCTAAAAAAAAAAT	0.299													3	3	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100520233	100520233	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100520233delA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						GTGAGAGGAGAAAAAAAAAAA	0.403													5	4	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101270369	101270369	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101270369delA	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						aattacagggaaagtacgtaa	0.070										HNSCC(74;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102340336	102340337	+	IGR	INS	-	C	C	rs146916097	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102340336_102340337insC								DRAM1 (22937 upstream) : CCDC53 (66381 downstream)																							aaatgatgtgattttttttctt	0.000													6	3	---	---	---	---	
TXNRD1	7296	broad.mit.edu	37	12	104676397	104676398	+	Intron	INS	-	TG	TG	rs138149408	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104676397_104676398insTG	uc010swk.1	+							NM_001093771	NP_001087240	Q16881	TRXR1_HUMAN	thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0						cagaaaagctttgtgtgtgtgt	0.040													6	3	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111514656	111514657	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111514656_111514657insA	uc001tsa.1	+							NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						TGTGTGTCCTTAAAAAAAAATC	0.391													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111595198	111595198	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111595198delT	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						agttggcatcttattctgaat	0.000													4	2	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	112036115	112036115	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112036115delC	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsm.1_5'UTR	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						CCTAACTTCTCCCCTCCAGAG	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114220283	114220283	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114220283delT								LHX5 (310406 upstream) : RBM19 (34260 downstream)																							TCCTTTGTCATTTTCTGTTAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115696203	115696203	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115696203delA								TBX3 (574234 upstream) : MED13L (700180 downstream)																							tgctgatgggaaaaggtaact	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116030218	116030222	+	IGR	DEL	GATCT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116030218_116030222delGATCT								TBX3 (908249 upstream) : MED13L (366161 downstream)																							tggcagggaggatctgttccctgct	0.000													4	3	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117290182	117290183	+	3'UTR	INS	-	TTCCCC	TTCCCC	rs140709252	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117290182_117290183insTTCCCC	uc009zwn.2	+	12					RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_3'UTR|RNFT2_uc001twd.2_RNA	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		AAACCAGGACTTTCCCCTTGGC	0.564													5	3	---	---	---	---	
KDM2B	84678	broad.mit.edu	37	12	121955699	121955699	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121955699delT	uc001uat.2	-						KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						CTTAAAACACtttttttgagg	0.254													4	2	---	---	---	---	
AACS	65985	broad.mit.edu	37	12	125622294	125622295	+	Intron	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125622294_125622295delGT	uc001uhc.2	+						AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Intron	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		gtgtgtgtgagtgtgtgtgtgt	0.396													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127953042	127953044	+	IGR	DEL	CTA	-	-	rs142696904		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127953042_127953044delCTA								LOC100128554 (995712 upstream) : TMEM132C (946247 downstream)																							ATTCTAACTTCTACTCAGTGGGG	0.389													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128893790	128893790	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128893790delT								None (None upstream) : TMEM132C (5501 downstream)																							CTTGTGGTCCTTCTGTTGATG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130479730	130479731	+	IGR	INS	-	TGT	TGT	rs142830430	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130479730_130479731insTGT								TMEM132D (91518 upstream) : LOC100190940 (38268 downstream)																							tgtggccaccctgttgttgttg	0.099													3	4	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	131122511	131122512	+	Intron	INS	-	A	A	rs139579918	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131122511_131122512insA	uc001uim.2	-									O15034	RIMB2_HUMAN	RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		AGCCTTCTTGGAATGCAAACTT	0.401													2	5	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133363960	133363960	+	Intron	DEL	T	-	-	rs1564644	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133363960delT	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CTCCAAACCCTCAGGACCCAG	0.602													4	2	---	---	---	---	
LOC100101938	100101938	broad.mit.edu	37	13	19906538	19906538	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19906538delT	uc010tck.1	-							NR_027248				Homo sapiens cDNA clone IMAGE:5265638.												0						tctgccatcatttttTAATGT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22962755	22962758	+	IGR	DEL	TAAT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22962755_22962758delTAAT								FGF9 (684115 upstream) : SGCG (792302 downstream)																							TGTTGGTAAATAATTAATGATTAT	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24931625	24931626	+	IGR	INS	-	CA	CA	rs71676732		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24931625_24931626insCA								C1QTNF9 (34960 upstream) : PARP4 (63449 downstream)																							atcacacacaccacacacacaa	0.203													4	2	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26323502	26323502	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26323502delG	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AAGCATCAGAGGACCCCGCCA	0.592													4	2	---	---	---	---	
CCDC122	160857	broad.mit.edu	37	13	44423623	44423623	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44423623delT	uc010acf.2	-							NM_144974	NP_659411	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122												0		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		aggcaaactgtttagggaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	48425064	48425065	+	IGR	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48425064_48425065delGA								HTR2A (954014 upstream) : SUCLA2 (91727 downstream)																							tAAAGTGTGTGAGAGAGAGGAA	0.297													4	2	---	---	---	---	
FNDC3A	22862	broad.mit.edu	37	13	49741846	49741846	+	Intron	DEL	A	-	-	rs76309481		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49741846delA	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		tgtctcaaacaaaaaaaaaaa	0.119													4	2	---	---	---	---	
WDFY2	115825	broad.mit.edu	37	13	52286880	52286880	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52286880delA	uc001vfp.2	+						WDFY2_uc010ads.1_Intron|WDFY2_uc010adt.1_Intron	NM_052950	NP_443182	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2								metal ion binding				0		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		gttaacagggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	52446536	52446537	+	IGR	DEL	AG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52446536_52446537delAG								CCDC70 (6165 upstream) : ATP7B (60269 downstream)																							aagtttaagaagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63289871	63289871	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63289871delG								None (None upstream) : None (None downstream)																							gtgctattctggaataaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73810215	73810216	+	IGR	INS	-	C	C	rs151301565	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73810215_73810216insC								KLF5 (158540 upstream) : KLF12 (449934 downstream)																							TGTGTCCCACTCTTTCTTCATA	0.490													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85936796	85936796	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85936796delT								None (None upstream) : SLITRK6 (430126 downstream)																							GAAGATTTCGttttttttttt	0.070													3	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94464641	94464641	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94464641delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				tctgtctcggaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	98081820	98081820	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98081820delC								MBNL2 (35448 upstream) : RAP2A (4655 downstream)																							ctgtaagatgcagaaaacctt	0.134													4	2	---	---	---	---	
SLC15A1	6564	broad.mit.edu	37	13	99405376	99405377	+	5'Flank	INS	-	GT	GT			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99405376_99405377insGT	uc001vno.2	-							NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)	attgtgtgtgagtgtgtgtgtg	0.119													4	2	---	---	---	---	
A2LD1	87769	broad.mit.edu	37	13	101220787	101220787	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101220787delC	uc001vor.2	-							NM_033110	NP_149101	Q9BVM4	A2LD1_HUMAN	AIG2-like domain 1						cellular modified amino acid catabolic process		acyltransferase activity|gamma-glutamylcyclotransferase activity				0						tcaattatctccaccaggtgc	0.000													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102542693	102542693	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102542693delA	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTCTTACCTGAAAAAAAAAAC	0.418													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106834820	106834821	+	IGR	DEL	CA	-	-	rs71114990	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106834820_106834821delCA								DAOA (691438 upstream) : EFNB2 (307277 downstream)																							CTCTCTCTCTcacacacacaca	0.376													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108102614	108102617	+	Intron	DEL	AGAT	-	-	rs76420428		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108102614_108102617delAGAT	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						GAATTGAGAAAGATAGAAAAGGAG	0.485													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110376731	110376731	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110376731delA								MYO16 (516376 upstream) : IRS2 (29455 downstream)																							ATCTGCTATGAAAAGAAGTGG	0.408													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110812276	110812276	+	Intron	DEL	G	-	-	rs35304611		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110812276delG	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)			aaagtagaatggggggtcacc	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112633453	112633453	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112633453delT								C13orf16 (636860 upstream) : SOX1 (88460 downstream)																							GCCCCAATGCTTTTTTTTAAa	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	113089069	113089069	+	IGR	DEL	A	-	-	rs80170871		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113089069delA								C13orf28 (68 upstream) : TUBGCP3 (50259 downstream)																							GGTTTTTTTTAAAAAAAAGAA	0.318													8	7	---	---	---	---	
PARP2	10038	broad.mit.edu	37	14	20820034	20820035	+	Intron	DEL	AG	-	-	rs138419981		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20820034_20820035delAG	uc001vxc.2	+						PARP2_uc001vxd.2_Intron|PARP2_uc001vxb.1_Intron|PARP2_uc010tle.1_5'Flank	NM_005484	NP_005475	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase family, member 2						protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity			ovary(1)|pancreas(1)	2	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		aaagaaAAAAAGAGAATATTCA	0.149								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26067385	26067385	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26067385delT								STXBP6 (548214 upstream) : NOVA1 (847705 downstream)																							ATGAtttcaattttttgactg	0.249													2	4	---	---	---	---	
PRKD1	5587	broad.mit.edu	37	14	30057411	30057411	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30057411delT	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)		AATGGGGTTATTTTTTTGTTT	0.368													4	2	---	---	---	---	
PRKD1	5587	broad.mit.edu	37	14	30156763	30156763	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30156763delA	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)		GATTGTCTGGAAGGGGGGCCT	0.458													4	2	---	---	---	---	
EGLN3	112399	broad.mit.edu	37	14	34399023	34399024	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34399023_34399024insA	uc001wsa.3	-						EGLN3_uc001wry.2_Intron|EGLN3_uc001wrz.2_Intron	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3						apoptosis	cytoplasm|nucleus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding				0	Breast(36;0.0303)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.000246)|Lung(238;0.000959)|Epithelial(34;0.155)	GBM - Glioblastoma multiforme(112;0.0118)	Vitamin C(DB00126)	gtttttgacttaaaaaaaaatg	0.228													4	2	---	---	---	---	
SFTA3	253970	broad.mit.edu	37	14	36978896	36978896	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36978896delT	uc001wtr.2	-						SFTA3_uc001wtq.2_Intron|SFTA3_uc001wts.2_Intron	NM_001101341	NP_001094811	P0C7M3	SFTA3_HUMAN	surfactant associated 3												0						CTCTTCTGTCTTTCCAATGAG	0.463													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37343242	37343242	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37343242delT	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		CCTACCTCTATTAGAAATGTA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38074674	38074677	+	IGR	DEL	GTGA	-	-	rs144608849		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38074674_38074677delGTGA								FOXA1 (10185 upstream) : SSTR1 (602527 downstream)																							TGGTATGTGGGTGAGTGAGTATGG	0.407													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45965846	45965847	+	IGR	INS	-	G	G	rs74221563	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45965846_45965847insG								C14orf106 (243241 upstream) : None (None downstream)																							gcagtttcagcgggggagtagg	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49416851	49416852	+	IGR	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49416851_49416852delGT								None (None upstream) : SDCCAG1 (616175 downstream)																							AAGTGGTAAGGTGTACTTAGTA	0.342													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50244330	50244330	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50244330delA	uc010anj.1	-						KLHDC2_uc001wwx.2_Intron|KLHDC2_uc001wwy.2_Intron|KLHDC2_uc010anp.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TGTGActatgaaaaaaaaaat	0.015													4	3	---	---	---	---	
FRMD6	122786	broad.mit.edu	37	14	52188464	52188464	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52188464delG	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron|FRMD6_uc001wze.2_Intron|FRMD6_uc001wzf.2_Intron|FRMD6_uc001wzg.2_Intron	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					gaggaaggaagggaggaagga	0.184													5	5	---	---	---	---	
FRMD6	122786	broad.mit.edu	37	14	52188469	52188471	+	Intron	DEL	GAA	-	-	rs149590944	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52188469_52188471delGAA	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron|FRMD6_uc001wze.2_Intron|FRMD6_uc001wzf.2_Intron|FRMD6_uc001wzg.2_Intron	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					aggaagggaggaaggaaggaggg	0.187													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	52287511	52287511	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52287511delT								FRMD6 (90069 upstream) : GNG2 (26441 downstream)																							ttacaagttgttgcaaataac	0.000													4	2	---	---	---	---	
C14orf166	51637	broad.mit.edu	37	14	52453931	52453931	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52453931delA	uc010aod.2	+							NM_016039	NP_057123	Q9Y224	CN166_HUMAN	homeobox prox 1							microtubule organizing center|nucleus|perinuclear region of cytoplasm|tRNA-splicing ligase complex	identical protein binding				0	Breast(41;0.0639)|all_epithelial(31;0.101)					AAATTCAGAGAAAAAAAAAGA	0.333													4	2	---	---	---	---	
SAMD4A	23034	broad.mit.edu	37	14	55181918	55181918	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55181918delA	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbf.1_Intron	NM_015589	NP_056404	Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0						TATTTGAAAGAAAAAAAAAAT	0.408													4	2	---	---	---	---	
DACT1	51339	broad.mit.edu	37	14	59107927	59107928	+	Intron	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59107927_59107928delTT	uc001xdw.2	+						DACT1_uc010trv.1_Intron|DACT1_uc001xdx.2_Intron|DACT1_uc010trw.1_Intron	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1						multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5						ACTTCAAAAGTTTTTTTTTTTT	0.342													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66367476	66367477	+	IGR	INS	-	G	G	rs144165616	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66367476_66367477insG								FUT8 (157515 upstream) : C14orf53 (585632 downstream)																							tgactttttttgggGGGGGTGG	0.168													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66384147	66384148	+	IGR	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66384147_66384148delTT								FUT8 (174186 upstream) : C14orf53 (568961 downstream)																							TTTCCTTCTCTTTTTTTTTTTT	0.421													4	2	---	---	---	---	
RDH11	51109	broad.mit.edu	37	14	68149832	68149832	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68149832delT	uc001xjv.3	-						RDH11_uc001xjw.3_Intron|RDH11_uc001xjx.3_Intron	NM_016026	NP_057110	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11						retinol metabolic process|steroid metabolic process	endoplasmic reticulum membrane|integral to membrane	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(1)	1				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	ATCAAAAGACTTTTATGTTCA	0.294													4	2	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	73031696	73031696	+	3'UTR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73031696delT	uc001xna.3	+	17					RGS6_uc010ttn.1_3'UTR|RGS6_uc001xmx.3_3'UTR|RGS6_uc010tto.1_RNA|RGS6_uc001xmy.3_3'UTR	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		AGGCTGCCTATCCAAGGTCCA	0.502													4	2	---	---	---	---	
C14orf115	55237	broad.mit.edu	37	14	74814199	74814199	+	5'Flank	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74814199delC	uc001xpw.3	+							NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	hypothetical protein LOC55237						transposition, DNA-mediated		DNA binding|transposase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00147)		GGAGCTGGAGCATAATGGATG	0.483													4	2	---	---	---	---	
LTBP2	4053	broad.mit.edu	37	14	74969103	74969103	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74969103delA	uc001xqa.2	-							NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding						protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		TCCCCACAGGAAGCTTGTAGG	0.522											OREG0022805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FLVCR2	55640	broad.mit.edu	37	14	76106749	76106750	+	Intron	DEL	TG	-	-	rs138889356		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76106749_76106750delTG	uc001xrs.2	+						FLVCR2_uc010tvd.1_Intron	NM_017791	NP_060261	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular						transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)		TATGAgtgtttgtgtgtgtgtg	0.342													3	3	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76190359	76190360	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76190359_76190360insT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		TAAGCTAGTTGTTTTTTTTTTT	0.376													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	76985350	76985350	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76985350delC								ESRRB (17172 upstream) : VASH1 (242885 downstream)																							CTAATCCCCACCACAACCTTG	0.537													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79501788	79501788	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79501788delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TTGACAGCCATTCACGTGAAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82498690	82498690	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82498690delT								SEL1L (498485 upstream) : None (None downstream)																							TCAAAGTCCATTTTTTAAATA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87761595	87761596	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87761595_87761596insA								None (None upstream) : GALC (542568 downstream)																							CTCCCAAAGTGAAAAAATACGG	0.465													4	2	---	---	---	---	
GALC	2581	broad.mit.edu	37	14	88354198	88354198	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88354198delA	uc010tvw.1	-							NM_000153		P54803	GALC_HUMAN	galactosylceramidase isoform a precursor						carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0						tgttcccatgaaaaaggaaag	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	91549867	91549868	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91549867_91549868delAA								RPS6KA5 (22874 upstream) : C14orf159 (30489 downstream)																							attccgtctcaaaaaaaaaaaa	0.223													3	3	---	---	---	---	
TC2N	123036	broad.mit.edu	37	14	92268372	92268372	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92268372delA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)		AAGGGAAATTAAATGGAATTT	0.164													4	2	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95662150	95662150	+	Intron	DEL	A	-	-	rs35172170		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95662150delA	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		TGACGATGAGAGAGGGGAGAG	0.473													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96427977	96427977	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96427977delA								TCL1A (247444 upstream) : C14orf132 (77685 downstream)																							ccagctaaccaaagcaagggc	0.189													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97244115	97244116	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97244115_97244116delAA								PAPOLA (210669 upstream) : VRK1 (19568 downstream)																							CCTCCACACTAAAAAATATTTG	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97362864	97362864	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97362864delG								VRK1 (14914 upstream) : None (None downstream)																							tgggaaaactgggacatctag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99070368	99070368	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99070368delT								C14orf64 (625907 upstream) : C14orf177 (107582 downstream)																							CTGAATACTGTTTTTTTTGCG	0.323													4	2	---	---	---	---	
YY1	7528	broad.mit.edu	37	14	100744094	100744094	+	3'UTR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100744094delA	uc001ygy.1	+	5					uc001ygz.1_5'Flank	NM_003403	NP_003394	P25490	TYY1_HUMAN	YY1 transcription factor						cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)				AGTAAAAATTAAAAAAAAAAA	0.303													5	3	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102472943	102472943	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102472943delT	uc001yks.2	+							NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						ACTACTTTGAttttttttttt	0.090													2	4	---	---	---	---	
RCOR1	23186	broad.mit.edu	37	14	103077310	103077310	+	Intron	DEL	A	-	-	rs11357036		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103077310delA	uc001ymb.2	+							NM_015156	NP_055971	Q9UKL0	RCOR1_HUMAN	REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1						GAATTCCTCTAGGGGTGTATT	0.338													1	5	---	---	---	---	
TNFAIP2	7127	broad.mit.edu	37	14	103595852	103595852	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103595852delT	uc001ymm.1	+						TNFAIP2_uc010awo.1_Intron|TNFAIP2_uc010txz.1_Intron	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2						angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)			ggggggggggtggtgagagag	0.045													4	2	---	---	---	---	
KIAA0125	9834	broad.mit.edu	37	14	106371713	106371713	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106371713delT	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0						CCTTTATCTCTTTAAAGTCGT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20128011	20128014	+	IGR	DEL	TAAT	-	-	rs145049235		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20128011_20128014delTAAT								None (None upstream) : GOLGA6L6 (609080 downstream)																							AAGTTTAAAATAATTAACCAGAAG	0.289													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20448943	20448943	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20448943delA								None (None upstream) : GOLGA6L6 (288151 downstream)																							ctaaaaatacaaaaaattagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20463602	20463604	+	IGR	DEL	AAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20463602_20463604delAAC								None (None upstream) : GOLGA6L6 (273490 downstream)																							gggtgacaATAACAACAACAACA	0.202													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20510735	20510735	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20510735delT								None (None upstream) : GOLGA6L6 (226359 downstream)																							TATCAATATGTAAATATGTGA	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20861860	20861860	+	IGR	DEL	T	-	-	rs116027405		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20861860delT								GOLGA8C (80834 upstream) : BCL8 (8196 downstream)																							TGAGTTTTCGTTTTTTTTGTA	0.303													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20865614	20865614	+	IGR	DEL	T	-	-	rs150729021		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20865614delT								GOLGA8C (84588 upstream) : BCL8 (4442 downstream)																							CTAATAAGCCTTTTTTTTCAC	0.299													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20866952	20866953	+	IGR	DEL	TG	-	-	rs146033076		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20866952_20866953delTG								GOLGA8C (85926 upstream) : BCL8 (3103 downstream)																							CTGTAATCTCTGTCTCAGGCCT	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21156319	21156320	+	Intron	INS	-	TT	TT	rs142796279	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21156319_21156320insTT	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																		AATATAAAAAATTAAGTCTGGT	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25032180	25032180	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25032180delA								C15orf2 (103588 upstream) : SNRPN (36614 downstream)																							aatctggtctaaaaagcttcc	0.169													4	2	---	---	---	---	
DNAJC17	55192	broad.mit.edu	37	15	41060469	41060470	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41060469_41060470delAC	uc001zms.1	-						C15orf62_uc010bby.2_5'Flank	NM_018163	NP_060633	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCCGGCTTCTACCCAGCCAGCT	0.649													4	2	---	---	---	---	
UBR1	197131	broad.mit.edu	37	15	43398407	43398407	+	5'Flank	DEL	T	-	-	rs78412725		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43398407delT	uc001zqq.2	-						UBR1_uc010udk.1_5'Flank	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GGACTGGAGATTTTTTTTTTC	0.512													6	4	---	---	---	---	
EIF3J	8669	broad.mit.edu	37	15	44853660	44853660	+	3'UTR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44853660delA	uc001ztv.2	+	8					EIF3J_uc010ueg.1_3'UTR|EIF3J_uc001ztw.2_3'UTR	NM_003758	NP_003749	O75822	EIF3J_HUMAN	eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity				0		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		GCAACGTGACAAAAAAAATTG	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48069433	48069433	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48069433delT								SEMA6D (3014 upstream) : SLC24A5 (343736 downstream)																							gcatatgtggttactgagtac	0.204													4	2	---	---	---	---	
GALK2	2585	broad.mit.edu	37	15	49462884	49462886	+	Intron	DEL	CTC	-	-	rs148297516		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49462884_49462886delCTC	uc001zxj.1	+						GALK2_uc001zxi.1_Intron|GALK2_uc010ufb.1_Intron|GALK2_uc001zxk.2_Intron|GALK2_uc010ufc.1_Intron	NM_002044	NP_002035	Q01415	GALK2_HUMAN	galactokinase 2 isoform 1						galactose metabolic process	cytoplasm	ATP binding|galactokinase activity|N-acetylgalactosamine kinase activity			breast(1)	1		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		CCACACTGAACTCCTCTCTTTGT	0.365													3	4	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50407861	50407861	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50407861delG	uc001zxu.2	-						ATP8B4_uc010ber.2_5'Flank|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		atatggggctggcaaggcagg	0.085													4	2	---	---	---	---	
KIAA1370	56204	broad.mit.edu	37	15	52938158	52938158	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52938158delT	uc002acg.3	-						KIAA1370_uc002ach.3_Intron|KIAA1370_uc010bfg.1_Intron|KIAA1370_uc010ugf.1_Intron	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204												0				all cancers(107;0.0803)		CCCAGTGCTGTTTTTTTCCCC	0.358													4	2	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54627179	54627179	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54627179delA	uc002ack.2	+						UNC13C_uc002acl.2_Intron	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)		tatttcaatgaaaaaaaaaat	0.050													3	3	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58371872	58371872	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58371872delA	uc010ugw.1	-							NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	atgttcaaagaaaaaaaaaca	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62534763	62534764	+	RNA	DEL	TA	-	-	rs2414766	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62534763_62534764delTA	uc002ain.1	-	11		c.2883_2884delTA			uc002aio.2_5'Flank|uc002aip.2_5'Flank|uc002air.1_5'Flank|uc002ais.2_5'Flank|uc002ait.2_5'Flank|uc002aiu.2_5'Flank|uc002aiv.2_5'Flank|uc002aix.1_5'Flank|uc002aiy.2_5'Flank|uc002aiz.1_5'Flank|uc002aja.2_5'Flank|uc002ajb.2_5'Flank|uc002ajc.2_5'Flank|uc002ajd.2_5'Flank|uc002aje.2_5'Flank|uc002ajf.2_5'Flank|uc010uhn.1_5'Flank|uc002ajg.1_5'Flank					Homo sapiens cDNA FLJ38723 fis, clone KIDNE2010137, weakly similar to GOLGIN-95.																		TTTTTTTTTTTAAATTTGGTGG	0.332													5	3	---	---	---	---	
RAB8B	51762	broad.mit.edu	37	15	63543514	63543514	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63543514delA	uc002alz.2	+						RAB8B_uc010uih.1_Intron	NM_016530	NP_057614	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)|kidney(1)	2						AGAACATCATAACAGGGATGA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70417525	70417526	+	IGR	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70417525_70417526delGA								TLE3 (27269 upstream) : UACA (529369 downstream)																							TAGAAATATTGAGAGAGAGAGA	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70517887	70517888	+	IGR	DEL	AT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70517887_70517888delAT								TLE3 (127631 upstream) : UACA (429007 downstream)																							AGCACCAGAGATAGCCCATAAG	0.525													4	2	---	---	---	---	
NPTN	27020	broad.mit.edu	37	15	73857920	73857920	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73857920delA	uc002avs.2	-						NPTN_uc010bjc.2_Intron|NPTN_uc002avt.2_Intron|NPTN_uc002avr.2_Intron|NPTN_uc010ula.1_Intron	NM_012428	NP_036560	Q9Y639	NPTN_HUMAN	neuroplastin isoform b precursor						elevation of cytosolic calcium ion concentration|homophilic cell adhesion|long-term synaptic potentiation|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of long-term neuronal synaptic plasticity|positive regulation of neuron projection development|positive regulation of protein phosphorylation	integral to membrane|plasma membrane|presynaptic membrane	cell adhesion molecule binding|type 1 fibroblast growth factor receptor binding				0						TTGAGGGGGGAAAAAAAAGAA	0.418													4	2	---	---	---	---	
ETFA	2108	broad.mit.edu	37	15	76539941	76539942	+	Intron	INS	-	T	T	rs146829525	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76539941_76539942insT	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117	P13804	ETFA_HUMAN	electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0						TAATCAGTACATTTTTTTTTAC	0.297													4	2	---	---	---	---	
ISL2	64843	broad.mit.edu	37	15	76628277	76628277	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76628277delA	uc002bbw.1	+							NM_145805	NP_665804	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						ACAAAACAACAAAAAAAagga	0.274													4	2	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	76646649	76646649	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76646649delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						AAAAGAGCAGAAAAAAAAAAT	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78663715	78663715	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78663715delT								CRABP1 (23143 upstream) : IREB2 (66803 downstream)																							aagtgaaagatttttttaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78675656	78675656	+	IGR	DEL	T	-	-	rs112849950		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78675656delT								CRABP1 (35084 upstream) : IREB2 (54862 downstream)																							ATAAGGAGAAttttttttttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79832505	79832506	+	IGR	DEL	TT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79832505_79832506delTT								KIAA1024 (67863 upstream) : MTHFS (304814 downstream)																							ATAGGCATTATTAGCATATCCC	0.322													4	3	---	---	---	---	
KIAA1199	57214	broad.mit.edu	37	15	81120726	81120726	+	Intron	DEL	A	-	-	rs113892730		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81120726delA	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						gtctcaaaagaaaaaaaaaaa	0.204													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81306768	81306768	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81306768delC								MESDC1 (10424 upstream) : C15orf26 (84981 downstream)																							GCACTCATCTCCCACCACCCC	0.512													4	2	---	---	---	---	
FSD2	123722	broad.mit.edu	37	15	83458106	83458107	+	Intron	INS	-	ATA	ATA	rs143796502	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83458106_83458107insATA	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing											central_nervous_system(1)	1						TCTAGAAGGATataataataat	0.030													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87859320	87859322	+	IGR	DEL	CTC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87859320_87859322delCTC								AGBL1 (287037 upstream) : NCRNA00052 (260838 downstream)																							TTGCAGAAGTCTCCACCACTGAT	0.251													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89039621	89039621	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89039621delT								MRPS11 (18127 upstream) : DET1 (15167 downstream)																							cagctcaggcttcagaatcag	0.199													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	90943393	90943394	+	Intron	DEL	TT	-	-	rs137887693		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90943393_90943394delTT	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ataatgtctcttgtttgtttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98853683	98853685	+	IGR	DEL	GAT	-	-	rs147762951	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98853683_98853685delGAT								ARRDC4 (336616 upstream) : FAM169B (126706 downstream)																							cagatggatagatgatagataga	0.232													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98952668	98952669	+	IGR	DEL	TG	-	-	rs68010149		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98952668_98952669delTG								ARRDC4 (435601 upstream) : FAM169B (27722 downstream)																							TCTGTACCATtgtgtgtgtgtg	0.272													3	4	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99487110	99487111	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99487110_99487111insT	uc002bul.2	+						IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	GACTGACATCATTTTTTTTTTA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	99630416	99630417	+	IGR	INS	-	G	G	rs145138353	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99630416_99630417insG								PGPEP1L (79392 upstream) : SYNM (14869 downstream)																							TGTTTTCATCTGGGGAACCACC	0.515													3	5	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101914492	101914493	+	Intron	INS	-	T	T	rs144407744	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101914492_101914493insT	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxf.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCCTCCTCCTATTTTTTTTTCC	0.500													7	6	---	---	---	---	
NMRAL1	57407	broad.mit.edu	37	16	4523926	4523926	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4523926delA	uc002cwm.2	-						NMRAL1_uc002cwn.2_Intron|NMRAL1_uc002cwo.2_Intron|NMRAL1_uc002cwp.2_Intron|HMOX2_uc010bts.2_5'Flank|HMOX2_uc002cwr.3_5'Flank|HMOX2_uc002cwq.3_5'Flank|HMOX2_uc002cws.3_5'Flank	NM_020677	NP_065728	Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1							nucleus|perinuclear region of cytoplasm	binding			kidney(1)	1						aactccgtccaaaaaaaaaaa	0.279													9	4	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4938714	4938714	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4938714delT	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						ttatcctgcattttttttttt	0.000													15	7	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7679014	7679014	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7679014delA	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_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		CTACCCAGAGAAGGTTAGTTA	0.398													4	2	---	---	---	---	
C16orf72	29035	broad.mit.edu	37	16	9207962	9207962	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9207962delT	uc002czm.2	+							NM_014117	NP_054836	Q14CZ0	CP072_HUMAN	hypothetical protein LOC29035											large_intestine(1)	1						TAGCTCAAGATTTTTTTTTGG	0.383													6	3	---	---	---	---	
TEKT5	146279	broad.mit.edu	37	16	10777014	10777014	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10777014delT	uc002czz.1	-							NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						ctgagctgggttttcacaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11622433	11622434	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11622433_11622434delAA								C16orf75 (176816 upstream) : LITAF (19148 downstream)																							tttgttttttaaagatgggctc	0.168													4	2	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12094979	12094979	+	Intron	DEL	T	-	-	rs75119546		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12094979delT	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						GCTGCTGCTGtttttttttag	0.199			T	CIITA	PMBL|Hodgkin Lymphona|								4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12660559	12660560	+	Intron	DEL	CC	-	-	rs67122432		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12660559_12660560delCC	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						TAAGTGGGGTCCCCCATCCTTT	0.525													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13875423	13875423	+	IGR	DEL	T	-	-	rs113672519		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13875423delT								SHISA9 (541151 upstream) : ERCC4 (138591 downstream)																							CTCTCAATGATTTTTTTTCTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13878057	13878057	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13878057delG								SHISA9 (543785 upstream) : ERCC4 (135957 downstream)																							ccagaatgctgggatgacagg	0.000													4	2	---	---	---	---	
NDE1	54820	broad.mit.edu	37	16	15744606	15744607	+	Intron	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15744606_15744607delTC	uc010uzy.1	+						NDE1_uc002dds.2_Intron	NM_001143979	NP_001137451	Q9NXR1	NDE1_HUMAN	nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1						TCGTTTCTTTTCTCTCTCTCTC	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17613015	17613016	+	IGR	INS	-	TTT	TTT	rs76852269		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17613015_17613016insTTT								XYLT1 (48277 upstream) : NOMO2 (898167 downstream)																							TTCTTGTTTGATTTTTTTTTTT	0.381													2	5	---	---	---	---	
SYT17	51760	broad.mit.edu	37	16	19182538	19182538	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19182538delT	uc002dfw.2	+						SYT17_uc002dfx.2_5'Flank|SYT17_uc002dfy.2_5'Flank|SYT17_uc002dfv.1_Intron	NM_016524	NP_057608	Q9BSW7	SYT17_HUMAN	B/K protein							membrane|synaptic vesicle	transporter activity			ovary(1)	1						CCTTTGACTATTTCCCAAGCT	0.368													4	2	---	---	---	---	
TMEM159	57146	broad.mit.edu	37	16	21186046	21186046	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21186046delT	uc002dif.3	+						TMEM159_uc002dig.3_Intron|TMEM159_uc010vbf.1_Intron|TMEM159_uc002dih.3_Intron	NM_020422	NP_065155	Q96B96	TM159_HUMAN	transmembrane protein 159							integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0972)		TATTGATTCCTTTTAAAAGAT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21538105	21538107	+	Intron	DEL	GGA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21538105_21538107delGGA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		GGGAGGAAGCGGAGGAGGAGGAG	0.522													4	2	---	---	---	---	
HS3ST2	9956	broad.mit.edu	37	16	22846617	22846618	+	Intron	INS	-	TTTG	TTTG	rs140810929	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22846617_22846618insTTTG	uc002dli.2	+						HS3ST2_uc002dlj.2_Intron	NM_006043	NP_006034	Q9Y278	HS3S2_HUMAN	heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)		tttctgttctttttgtTTGTTT	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22929699	22929700	+	IGR	DEL	GT	-	-	rs71151686	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22929699_22929700delGT								HS3ST2 (2042 upstream) : USP31 (143029 downstream)																							GCTCCTCAGGGTGTGTGTGTGT	0.119													4	2	---	---	---	---	
USP31	57478	broad.mit.edu	37	16	23101729	23101730	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23101729_23101730insA	uc002dll.2	-							NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)		aacaaacaaacaacaacaacaa	0.168													2	5	---	---	---	---	
SCNN1B	6338	broad.mit.edu	37	16	23386364	23386364	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23386364delG	uc002dln.2	+							NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	actcgccctaggacacatagc	0.154											OREG0031416	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26285229	26285231	+	IGR	DEL	GTG	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26285229_26285231delGTG								HS3ST4 (136221 upstream) : C16orf82 (792988 downstream)																							ggtgataatagtggtggtggtcg	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26659613	26659614	+	IGR	INS	-	TGGCTCAT	TGGCTCAT	rs138580761	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26659613_26659614insTGGCTCAT								HS3ST4 (510605 upstream) : C16orf82 (418605 downstream)																							CTCAGCTGCTATGGCCCATTAG	0.485													4	3	---	---	---	---	
ATXN2L	11273	broad.mit.edu	37	16	28845028	28845035	+	Intron	DEL	GATCAGGG	-	-	rs141681863		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28845028_28845035delGATCAGGG	uc002drc.2	+						uc010vct.1_Intron|ATXN2L_uc002drb.2_Intron|ATXN2L_uc002dqy.2_Intron|ATXN2L_uc002dra.2_Intron|ATXN2L_uc002dqz.2_Intron|ATXN2L_uc010vdb.1_Intron|ATXN2L_uc002dre.2_Intron|ATXN2L_uc002drf.2_Intron|ATXN2L_uc002drg.2_5'Flank	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A							membrane				upper_aerodigestive_tract(1)|ovary(1)	2						AGGTTTGGGTGATCAGGGGATCAGGGAT	0.423													6	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	30641216	30641216	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30641216delT								ZNF689 (19534 upstream) : PRR14 (21025 downstream)																							tatgctacactttttttgttg	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32122709	32122710	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32122709_32122710insT								ZNF267 (194083 upstream) : HERC2P4 (39900 downstream)																							tgtgtttgtaggggggggtctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32543613	32543614	+	IGR	DEL	TG	-	-	rs143680542		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32543613_32543614delTG								HERC2P4 (379739 upstream) : TP53TG3B (141227 downstream)																							ggtataattctgtgtgttgaat	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32817084	32817088	+	IGR	DEL	CTTTC	-	-	rs58625443		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32817084_32817088delCTTTC								TP53TG3B (128206 upstream) : SLC6A10P (71709 downstream)																							tcatttcattctttcatttcatttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33482740	33482741	+	IGR	INS	-	AAAAC	AAAAC	rs150640455	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33482740_33482741insAAAAC								SLC6A10P (586277 upstream) : MIR1826 (482767 downstream)																							ctctgtctcaaaaaacaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33492738	33492738	+	IGR	DEL	T	-	-	rs71378056		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33492738delT								SLC6A10P (596275 upstream) : MIR1826 (472770 downstream)																							cacccagggatcccccagcag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33995422	33995422	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33995422delG								MIR1826 (29830 upstream) : UBE2MP1 (408380 downstream)																							tccttttccagcataggcctc	0.000													4	2	---	---	---	---	
C16orf87	388272	broad.mit.edu	37	16	46858579	46858580	+	Intron	INS	-	T	T	rs143280053		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46858579_46858580insT	uc002eek.1	-							NM_001001436	NP_001001436	Q6PH81	CP087_HUMAN	hypothetical protein LOC388272												0						TATTCACAttcttttttttttt	0.139													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47889085	47889086	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47889085_47889086delAC	uc002eex.1	-											Homo sapiens cDNA clone IMAGE:5303550.																		ttcaacacagacacacacacac	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48863081	48863081	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48863081delT								N4BP1 (218961 upstream) : CBLN1 (449130 downstream)																							CATCCTCCTGTTTTTTTCCAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49056247	49056247	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49056247delC								N4BP1 (412127 upstream) : CBLN1 (255964 downstream)																							CCAATGTATTCCCCCAAATGA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50055598	50055599	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50055598_50055599insC								ZNF423 (194680 upstream) : TMEM188 (3590 downstream)																							AAACTTGCACACCCCCCTCAGG	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50927951	50927951	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50927951delC								CYLD (92105 upstream) : SALL1 (241935 downstream)																							tggataaataccccagcttcc	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51531393	51531394	+	IGR	INS	-	A	A	rs143501742	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51531393_51531394insA								SALL1 (346210 upstream) : TOX3 (940524 downstream)																							acccattaagtatttctcatca	0.079													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55005874	55005875	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55005874_55005875delTC								IRX5 (37481 upstream) : IRX6 (352596 downstream)																							tttctttctttctctctttctt	0.000													10	5	---	---	---	---	
CES7	221223	broad.mit.edu	37	16	55950756	55950756	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55950756delT	uc002eir.2	-						CES7_uc002eiq.2_Intron			Q6NT32	EST5A_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000383269; Flags: Fragment;							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		aggccttctcttccactccag	0.114													4	2	---	---	---	---	
GNAO1	2775	broad.mit.edu	37	16	56377907	56377907	+	3'UTR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56377907delC	uc002eit.3	+	8					GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)				TGGCCTGCCGCCCCCCCTCCC	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59760423	59760423	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59760423delA								GOT2 (992177 upstream) : None (None downstream)																							AGAGGAAGGTAAAAAAAAAAA	0.254													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61348082	61348082	+	IGR	DEL	A	-	-	rs147356718		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61348082delA								None (None upstream) : CDH8 (339153 downstream)																							catgggggggaaaaaaaagaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65317648	65317649	+	IGR	DEL	TC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65317648_65317649delTC								CDH11 (161729 upstream) : LOC283867 (753 downstream)																							CTGctttctgtctctctctctc	0.267													4	2	---	---	---	---	
LRRC29	26231	broad.mit.edu	37	16	67242174	67242174	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67242174delG	uc002esd.2	-						LRRC29_uc002ese.2_Intron|LRRC29_uc002esf.2_Intron|LRRC29_uc002esg.2_Intron	NM_012163	NP_036295	Q8WV35	LRC29_HUMAN	F-box and leucine-rich repeat protein 9												0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		CCTGACTTCAGCCCCCAGATC	0.577													42	35	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	68614859	68614860	+	IGR	INS	-	A	A	rs111613798		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68614859_68614860insA								ZFP90 (13821 upstream) : CDH3 (63291 downstream)																							gtctcaaaaagaaaaaaaaaaa	0.040													4	2	---	---	---	---	
PDPR	55066	broad.mit.edu	37	16	70175439	70175441	+	Intron	DEL	GAA	-	-	rs72232114		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70175439_70175441delGAA	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		CAGGCACAATGAAGAATCGAATG	0.414													5	3	---	---	---	---	
AARS	16	broad.mit.edu	37	16	70305440	70305441	+	Intron	DEL	AA	-	-	rs75942139		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70305440_70305441delAA	uc002eyn.1	-						AARS_uc010vlu.1_Intron	NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)	tcaaaaaaacaaaaaaaaaaaa	0.183													5	3	---	---	---	---	
FUK	197258	broad.mit.edu	37	16	70501069	70501069	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70501069delC	uc002eyy.2	+						FUK_uc010vmb.1_3'UTR|FUK_uc010cft.2_Intron|FUK_uc002eyz.2_Intron	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase							cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)				agcagccctgccccttctgtc	0.368													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73417147	73417147	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73417147delT								HTA (289477 upstream) : PSMD7 (913534 downstream)																							AGGAAGTGGGTTTGGAAACTC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74419892	74419892	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74419892delT	uc010vmt.1	+											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cctttctctcttttttttttt	0.169													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76254581	76254584	+	IGR	DEL	AAAC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76254581_76254584delAAAC								TERF2IP (563253 upstream) : CNTNAP4 (56592 downstream)																							AACTAAGCAAAAACAAACAAATAA	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76803326	76803326	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76803326delT								CNTNAP4 (210191 upstream) : MON1B (421510 downstream)																							GTTGTTTTTCTTTTTTTTTTC	0.502													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77359576	77359576	+	Intron	DEL	A	-	-	rs36036462		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77359576delA	uc002ffc.3	-						ADAMTS18_uc010chc.1_Intron|ADAMTS18_uc002ffe.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						TTATAGGGGGAAAAAAAAAAA	0.378													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77744378	77744378	+	IGR	DEL	T	-	-	rs72107335		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77744378delT								ADAMTS18 (275367 upstream) : NUDT7 (12033 downstream)																							ATTTATAATGTTTTTTTTTTT	0.303													5	3	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77940335	77940335	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77940335delA	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						cgattgatggacagatgtcaa	0.159													3	3	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78791223	78791230	+	Intron	DEL	ACCCCAGC	-	-	rs112499853		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78791223_78791230delACCCCAGC	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)		CTTACCACCTaccccagcaccccagcac	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80476479	80476479	+	IGR	DEL	T	-	-	rs111848660		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80476479delT								MAF (841857 upstream) : DYNLRB2 (98375 downstream)																							TTACTTTTCCTTTTTTTTTTT	0.353													3	3	---	---	---	---	
CENPN	55839	broad.mit.edu	37	16	81046081	81046082	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81046081_81046082insT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094	Q96H22	CENPN_HUMAN	centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0						TTTCATGTGTATTTATCTCTTT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	81778127	81778127	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81778127delA								CMIP (32762 upstream) : PLCG2 (34803 downstream)																							acttgtaaccaaaaaaattcC	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	83881766	83881767	+	IGR	DEL	TC	-	-	rs449254	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83881766_83881767delTC								HSBP1 (35172 upstream) : MLYCD (50963 downstream)																							CGTTGAAGGGTCTTTTTTTTTT	0.356													4	2	---	---	---	---	
GGT6	124975	broad.mit.edu	37	17	4466554	4466555	+	5'Flank	INS	-	AT	AT	rs9903122	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4466554_4466555insAT	uc002fyd.3	-						GGT6_uc002fyc.3_5'Flank|GGT6_uc010vsc.1_5'Flank	NM_001122890	NP_001116362	Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6 isoform a						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			skin(1)	1						cacacacacacacacacgcaAA	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5966092	5966092	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5966092delC								NLRP1 (478260 upstream) : WSCD1 (6345 downstream)																							TTTATGTGCTCCAACAGAAAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10381071	10381071	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10381071delG	uc002gml.1	+											Homo sapiens cDNA FLJ40181 fis, clone TESTI2018178.																		AAAAATGAGTGGAAGAGACAA	0.313													4	2	---	---	---	---	
ELAC2	60528	broad.mit.edu	37	17	12906626	12906627	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12906626_12906627insT	uc002gnz.3	-						ELAC2_uc002gnu.3_5'Flank|ELAC2_uc002gnv.3_Intron|ELAC2_uc002gnw.3_Intron|ELAC2_uc002gnx.3_Intron|ELAC2_uc010vvo.1_Intron|ELAC2_uc010vvp.1_Intron|ELAC2_uc010vvq.1_Intron|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1						tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						TTCTTCACGAGTGTAGCACAGA	0.505									Hereditary_Prostate_Cancer		OREG0024189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16791073	16791075	+	IGR	DEL	GGT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16791073_16791075delGGT								LOC162632 (83254 upstream) : TNFRSF13B (41774 downstream)																							GGGACAGCGAGGTGGTGGTGGCT	0.557													4	2	---	---	---	---	
CCDC144B	284047	broad.mit.edu	37	17	18457651	18457651	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18457651delA	uc002gua.3	-											Homo sapiens cDNA FLJ36492 fis, clone THYMU2018455.											ovary(1)|skin(1)	2						AAAAACTAATAtttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21227696	21227697	+	IGR	DEL	AG	-	-	rs149665353		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21227696_21227697delAG								MAP2K3 (9147 upstream) : KCNJ12 (52002 downstream)																							acacagaaacagagagtcacat	0.084													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21250069	21250069	+	IGR	DEL	C	-	-	rs66672846		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21250069delC								MAP2K3 (31520 upstream) : KCNJ12 (29630 downstream)																							GTTCTTTGTGCTGTAGCTGCA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21522035	21522035	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21522035delT								C17orf51 (44304 upstream) : FAM27L (303335 downstream)																							tcctcccaccttggcctcctg	0.065													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21560338	21560339	+	IGR	INS	-	G	G	rs147837000		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21560338_21560339insG								C17orf51 (82607 upstream) : FAM27L (265031 downstream)																							GGTGAATATAAGCCACAGATAG	0.525													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21792720	21792720	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21792720delA								C17orf51 (314989 upstream) : FAM27L (32650 downstream)																							CTCTTTCGGGAAGGGAGTCAG	0.557													4	2	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29533686	29533700	+	Intron	DEL	TTTTGAACAAAAATA	-	-	rs3216935		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29533686_29533700delTTTTGAACAAAAATA	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCCTTAAAACTTTTGAACAAAAATATTTTGATTAG	0.321			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	4	---	---	---	---	
UTP6	55813	broad.mit.edu	37	17	30216089	30216089	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30216089delA	uc002hgr.2	-						UTP6_uc002hgq.2_5'Flank|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_Intron	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				agactgtctcaaaaaaaaaaa	0.005													7	4	---	---	---	---	
MYO1D	4642	broad.mit.edu	37	17	31112948	31112948	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31112948delC	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ACAAGAATAACAAAAACAGAA	0.333													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31606568	31606569	+	Intron	DEL	CG	-	-	rs7211739	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31606568_31606569delCG	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	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)	ACGTGGAGCACGAGAGAGAGGC	0.376													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32020633	32020633	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32020633delA	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)	ACCAGGTCTGAGGAGCTCAAA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35240141	35240141	+	IGR	DEL	G	-	-	rs34331874		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35240141delG								MRM1 (274735 upstream) : LHX1 (54358 downstream)																							ttcccctgatggggggacaga	0.139													2	5	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	35993686	35993686	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35993686delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron|DDX52_uc002hoj.1_Intron	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				accttgtctcaaaaaaaaaaa	0.144													3	3	---	---	---	---	
CISD3	284106	broad.mit.edu	37	17	36888228	36888229	+	Intron	DEL	CC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36888228_36888229delCC	uc010wds.1	+							NM_001136498	NP_001129970	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3 precursor							mitochondrion	2 iron, 2 sulfur cluster binding|metal ion binding				0						TCCCAGCCTTCCCCTGTGCCCC	0.411													4	2	---	---	---	---	
CACNB1	782	broad.mit.edu	37	17	37347528	37347529	+	Intron	INS	-	ACTTATTAT	ACTTATTAT	rs138131266	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37347528_37347529insACTTATTAT	uc002hrm.1	-						CACNB1_uc002hrl.1_Intron|CACNB1_uc002hrn.2_Intron|CACNB1_uc002hro.2_Intron|CACNB1_uc002hrp.1_Intron|CACNB1_uc010web.1_Intron	NM_000723	NP_000714	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1						axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)	taataacacgcacttattatac	0.000													6	6	---	---	---	---	
KRT39	390792	broad.mit.edu	37	17	39124164	39124165	+	5'Flank	INS	-	T	T	rs35330880		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39124164_39124165insT	uc002hvo.1	-						KRT39_uc010wfm.1_5'Flank	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35							intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)				ccttttcatcCTTTTTTTTTTT	0.025													4	2	---	---	---	---	
KAT2A	2648	broad.mit.edu	37	17	40270120	40270123	+	Intron	DEL	GAGA	-	-	rs150172215		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40270120_40270123delGAGA	uc002hyx.2	-							NM_021078	NP_066564	Q92830	KAT2A_HUMAN	general control of amino acid synthesis 5-like						chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity			upper_aerodigestive_tract(1)|lung(1)	2						TGAAGCTGAGGAGAGAGAGAGTCA	0.623													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41545904	41545904	+	IGR	DEL	T	-	-	rs112368255		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41545904delT								MIR2117 (23651 upstream) : DHX8 (15430 downstream)																							GTGGTATTCATTTTTTTTTTT	0.408													2	4	---	---	---	---	
LOC100128977	100128977	broad.mit.edu	37	17	43966910	43966911	+	Intron	INS	-	AGG	AGG	rs140819255	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43966910_43966911insAGG	uc010wjz.1	-							NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0						gtggggaaggaaggactgagca	0.000													4	2	---	---	---	---	
STXBP4	252983	broad.mit.edu	37	17	53059956	53059957	+	Intron	DEL	TG	-	-	rs71361747		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53059956_53059957delTG	uc002iuf.1	+						STXBP4_uc010dcc.1_Intron|STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1						GAGGGTGGTTtgtgtgtgtgtg	0.238													2	4	---	---	---	---	
MTMR4	9110	broad.mit.edu	37	17	56591058	56591059	+	Intron	DEL	GA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56591058_56591059delGA	uc002iwj.2	-						MTMR4_uc010dcx.1_Intron	NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4							cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACAGCCAGGGGAGAGAGAGAGA	0.668													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	57588165	57588166	+	IGR	INS	-	TGT	TGT	rs141859677	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57588165_57588166insTGT								YPEL2 (109070 upstream) : DHX40 (54720 downstream)																							tggatgacagatggtgtctagg	0.000													3	4	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59019432	59019433	+	Intron	INS	-	AGG	AGG	rs142016905	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59019432_59019433insAGG	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AGCAAAAAAGTAGGAGTGGCAA	0.297													0	6	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59402357	59402357	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59402357delA	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron|BCAS3_uc002izc.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			GAGTTCTTGCAAAGGAGATGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61082843	61082843	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61082843delA								MIR633 (61170 upstream) : TANC2 (4055 downstream)																							aaaaaataacaaaaaaaaaag	0.000													4	2	---	---	---	---	
FAM20A	54757	broad.mit.edu	37	17	66545747	66545747	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66545747delT	uc002jho.2	-						FAM20A_uc010wqp.1_Intron|PRKAR1A_uc002jhm.2_Intron|FAM20A_uc002jhn.2_Intron	NM_017565	NP_060035	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A							extracellular region					0	Breast(10;1.64e-13)					ttatcattacttttatgcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67691905	67691906	+	IGR	DEL	TG	-	-	rs34753510		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67691905_67691906delTG								MAP2K6 (153443 upstream) : KCNJ16 (379520 downstream)																							aggggctgactgtgaggagacg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68469518	68469518	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68469518delC								KCNJ2 (293337 upstream) : None (None downstream)																							ccaccaccagcacatacacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71963609	71963609	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71963609delA								C17orf54 (138933 upstream) : RPL38 (236186 downstream)																							TATCTTCCATAAAAGGCAACC	0.438													4	2	---	---	---	---	
GRIN2C	2905	broad.mit.edu	37	17	72840014	72840014	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72840014delT	uc002jlt.1	-						GRIN2C_uc010wrh.1_Intron	NM_000835	NP_000826	Q14957	NMDE3_HUMAN	N-methyl-D-aspartate receptor subunit 2C						glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)	GGACGTTGGCttttttttttt	0.308													5	4	---	---	---	---	
RHBDF2	79651	broad.mit.edu	37	17	74492840	74492840	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74492840delT	uc002jrq.1	-						RHBDF2_uc002jrp.1_Intron	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1						negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						TCCAGAtctcttttttttttc	0.274													3	3	---	---	---	---	
NPLOC4	55666	broad.mit.edu	37	17	79562978	79562980	+	Intron	DEL	GTT	-	-	rs145761561		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79562978_79562980delGTT	uc002kat.3	-						NPLOC4_uc002kau.3_Intron|NPLOC4_uc010wur.1_Intron	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4						cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ATGCTGTTAAGTTGTTCAGAATT	0.365													5	7	---	---	---	---	
ASPSCR1	79058	broad.mit.edu	37	17	79967497	79967497	+	Intron	DEL	G	-	-	rs111699244		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79967497delG	uc002kcx.2	+						ASPSCR1_uc002kcw.1_Intron|ASPSCR1_uc002kcy.2_Intron|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Intron	NM_024083	NP_076988	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region,								protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGGGCCCCCCGTGAGGTCTGT	0.652			T	TFE3	alveolar soft part sarcoma								10	9	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80773723	80773723	+	Intron	DEL	T	-	-	rs77575615		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80773723delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CCTGCAGTTCTTTTTTTTAAT	0.338													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4379300	4379300	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4379300delT	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TTCCCCAGGCTTTTTAGCTCT	0.269													4	2	---	---	---	---	
SEH1L	81929	broad.mit.edu	37	18	12979075	12979076	+	Intron	INS	-	T	T	rs71370922		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12979075_12979076insT	uc002krr.2	+						SEH1L_uc002krq.2_Intron	NM_031216	NP_112493	Q96EE3	SEH1_HUMAN	sec13-like protein isoform 2						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0						TTttttctttcttttttttttt	0.104													10	6	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13490410	13490410	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13490410delA	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)		ttcaagatccaaaaaagttca	0.050													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13609028	13609028	+	Intron	DEL	A	-	-	rs67040657		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13609028delA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron|C18orf1_uc002kse.2_5'Flank|C18orf1_uc002ksf.2_5'Flank|C18orf1_uc002ksg.1_5'Flank	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)		GTGACTGCACAAAACTCATAT	0.463													5	5	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	18975681	18975681	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18975681delT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						TAGTAACTTCttttttttttt	0.119													10	5	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	19065309	19065309	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19065309delA	uc010xam.1	+						GREB1L_uc010dlp.1_Intron|GREB1L_uc010xan.1_Intron|GREB1L_uc010dlr.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						GTATCCCAACAAAAAAAAAAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25271308	25271309	+	IGR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25271308_25271309insA								C18orf16 (500658 upstream) : CDH2 (259621 downstream)																							TGCaaaaaaataaaaaaaaaaa	0.347													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	31062401	31062401	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31062401delT								C18orf34 (41716 upstream) : ASXL3 (96140 downstream)																							CCCCCACCTCTTTTTtttttc	0.214													3	3	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32335641	32335641	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32335641delA	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_5'Flank	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						CGAGTCACCTAACAGATGGTA	0.189													4	2	---	---	---	---	
RPRD1A	55197	broad.mit.edu	37	18	33649971	33649971	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33649971delA	uc002kzf.1	-						RPRD1A_uc002kze.1_5'Flank|RPRD1A_uc002kzg.2_5'Flank|RPRD1A_uc010dmw.2_5'Flank|RPRD1A_uc010dmx.2_5'Flank	NM_018170	NP_060640	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2						ttttttttttaaaaggagaca	0.119													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35139480	35139480	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35139480delT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						CAACTTTCACTTTTTTTTTTC	0.448													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41351874	41351874	+	IGR	DEL	C	-	-	rs34996475		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41351874delC								SYT4 (494259 upstream) : SETBP1 (908264 downstream)																							acaggctttaccctaccattg	0.050													3	3	---	---	---	---	
SLC14A2	8170	broad.mit.edu	37	18	42962275	42962276	+	Intron	INS	-	T	T	rs35489604		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42962275_42962276insT	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						ACTTAATATAAGCTCTAGTTTC	0.272													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44770549	44770550	+	Intron	DEL	CT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44770549_44770550delCT	uc010dnt.1	-											RecName: Full=Ladybird homeobox corepressor 1-like protein; AltName: Full=LBX1 corepressor 1-like protein; AltName: Full=Functional Smad-suppressing element on chromosome 18;          Short=Fussel-18;																		ctctacaccactctctctctct	0.228													4	2	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46911088	46911089	+	Intron	INS	-	A	A	rs144952541	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46911088_46911089insA	uc002ldi.1	-						DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						caataacagctaaaacatacac	0.054													1	5	---	---	---	---	
POLI	11201	broad.mit.edu	37	18	51824236	51824236	+	3'UTR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51824236delG	uc002lfj.3	+	10					POLI_uc010xds.1_3'UTR|POLI_uc002lfk.3_3'UTR|POLI_uc010dpg.2_3'UTR	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota						DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		GGGACATGGTGGGGGCTTACC	0.294								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
TCF4	6925	broad.mit.edu	37	18	53125301	53125301	+	Intron	DEL	A	-	-	rs34050038		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53125301delA	uc002lfz.2	-						TCF4_uc002lfy.2_Intron|TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron|TCF4_uc002lgc.3_Intron	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		CAAAAAAAGGAAAAAAAAAAA	0.318													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54800009	54800010	+	IGR	INS	-	C	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54800009_54800010insC								WDR7 (102973 upstream) : ST8SIA3 (219711 downstream)																							TTCTTGAACCACCCCCAAAACT	0.416													4	2	---	---	---	---	
PMAIP1	5366	broad.mit.edu	37	18	57568707	57568707	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57568707delC	uc002lic.2	+						PMAIP1_uc002lid.2_Intron	NM_021127	NP_066950	Q13794	APR_HUMAN	phorbol-12-myristate-13-acetate-induced protein						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to glucose starvation|cellular response to hypoxia|negative regulation of mitochondrial membrane potential|positive regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of glucose metabolic process|positive regulation of protein oligomerization|positive regulation of release of cytochrome c from mitochondria|proteasomal protein catabolic process|reactive oxygen species metabolic process|regulation of mitochondrial membrane permeability|response to dsRNA|signal transduction by p53 class mediator resulting in induction of apoptosis|T cell homeostasis|virus-infected cell apoptosis	cytosol|mitochondrial outer membrane|nucleus	protein binding				0		Colorectal(73;0.0946)				GATCTTGTAGCCCATAAAGAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61679824	61679825	+	IGR	INS	-	GC	GC	rs141866778	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61679824_61679825insGC								SERPINB8 (23217 upstream) : C18orf20 (67418 downstream)																							tgtgtgtgtgtgcgtgtgtgtg	0.243													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62165961	62165962	+	IGR	INS	-	T	T	rs113093203		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62165961_62165962insT								C18orf20 (349701 upstream) : None (None downstream)																							TCCCCAAACAATTTTTTTTTTA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65162899	65162899	+	IGR	DEL	A	-	-	rs34841616		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65162899delA								CDH19 (891683 upstream) : DSEL (10920 downstream)																							cttaaggcagaaaaaaatgag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69786715	69786716	+	IGR	INS	-	A	A	rs140229758	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69786715_69786716insA								None (None upstream) : CBLN2 (417199 downstream)																							ccgcaacagatatttttctact	0.000													2	7	---	---	---	---	
ZNF407	55628	broad.mit.edu	37	18	72704485	72704485	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72704485delG	uc002llw.2	+							NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GATTGAAGGTGGGGAAATCCG	0.308													4	2	---	---	---	---	
ADNP2	22850	broad.mit.edu	37	18	77865094	77865094	+	5'Flank	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77865094delA	uc002lnw.2	+							NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2						cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		gaaaatgcagaaaaaaatgaa	0.249													4	2	---	---	---	---	
GZMM	3004	broad.mit.edu	37	19	544961	544963	+	Intron	DEL	ACC	-	-	rs59558746		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:544961_544963delACC	uc002low.1	+							NM_005317	NP_005308	P51124	GRAM_HUMAN	granzyme M precursor						apoptosis|cytolysis|innate immune response|proteolysis	extracellular region	serine-type endopeptidase activity				0		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cctcctttcaacctccctccttc	0.113													4	2	---	---	---	---	
ADAMTSL5	339366	broad.mit.edu	37	19	1508023	1508023	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1508023delA	uc002ltd.2	-	7	1019	c.575delT	c.(574-576)TTCfs	p.F192fs	ADAMTSL5_uc010dsl.2_5'UTR|ADAMTSL5_uc010xgq.1_Frame_Shift_Del_p.F202fs	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor	192						proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGCTGCACGAAAAGGCACGA	0.652													4	2	---	---	---	---	
TBXA2R	6915	broad.mit.edu	37	19	3605964	3605965	+	Intron	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3605964_3605965delAC	uc002lyg.1	-							NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha						platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	agacagaaaaacacagacacac	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5355203	5355203	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5355203delC								PTPRS (14389 upstream) : ZNRF4 (100223 downstream)																							TTAGCAGGAGCCCCCAGAGGG	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9378522	9378522	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9378522delG								OR7E24 (15783 upstream) : ZNF699 (27464 downstream)																							ACAGAGTTCAGGGAAATGGGC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11481790	11481790	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11481790delT								LPPR2 (5418 upstream) : C19orf39 (3593 downstream)																							atttcttttctttttttttct	0.000													4	2	---	---	---	---	
LPHN1	22859	broad.mit.edu	37	19	14286177	14286178	+	Intron	DEL	AA	-	-	rs150665041		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14286177_14286178delAA	uc010xnn.1	-						LPHN1_uc010xno.1_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5						ttaaatacacaaagacacagcc	0.059													7	4	---	---	---	---	
C19orf42	79086	broad.mit.edu	37	19	16752991	16752991	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16752991delG	uc002neo.1	-						C19orf42_uc002nep.1_Intron			Q9BQ49	CS042_HUMAN	Homo sapiens cDNA: FLJ21949 fis, clone HEP04922.							integral to membrane					0						cacaaaatctgaacacaaacc	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	17557011	17557014	+	Intron	DEL	ATCT	-	-	rs71162135		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17557011_17557014delATCT	uc002ngr.2	-											Homo sapiens cDNA clone IMAGE:5300504.																		ccatccatccatctatccatccat	0.103													6	3	---	---	---	---	
PGLS	25796	broad.mit.edu	37	19	17628819	17628822	+	Intron	DEL	AAAA	-	-	rs67260410		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17628819_17628822delAAAA	uc002ngw.2	+							NM_012088	NP_036220	O95336	6PGL_HUMAN	6-phosphogluconolactonase							cytosol	6-phosphogluconolactonase activity				0						GAAAAAAAGGAAAAAAaaaaaaaa	0.181													6	3	---	---	---	---	
ELL	8178	broad.mit.edu	37	19	18613367	18613367	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18613367delC	uc002njh.2	-						ELL_uc010ebq.2_Intron	NM_006532	NP_006523	P55199	ELL_HUMAN	elongation factor RNA polymerase II						positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	Cajal body|nuclear speck|transcription elongation factor complex	protein binding			lung(1)	1				GBM - Glioblastoma multiforme(1328;7.81e-07)		GATCAAATATCCCCAACCACA	0.498			T	MLL	AL								4	2	---	---	---	---	
GATAD2A	54815	broad.mit.edu	37	19	19505759	19505759	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19505759delT	uc010xqt.1	+						GATAD2A_uc010xqu.1_Intron	NM_017660	NP_060130	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A						DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCTGGTTGTCTTTTTTTTTCC	0.547													4	2	---	---	---	---	
GATAD2A	54815	broad.mit.edu	37	19	19508552	19508552	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19508552delT	uc010xqt.1	+						GATAD2A_uc010xqu.1_Intron	NM_017660	NP_060130	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A						DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CAGttttttgttttttttgag	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20946142	20946142	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20946142delA								ZNF626 (101740 upstream) : ZNF85 (159938 downstream)																							aacctgtctcaaaaaaaagct	0.020													4	2	---	---	---	---	
ZNF493	284443	broad.mit.edu	37	19	21604656	21604657	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21604656_21604657insT	uc002npx.2	+						ZNF493_uc002npw.2_Intron|ZNF493_uc002npy.2_Intron	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AATTATTCATCtttttttttgg	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22051142	22051143	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22051142_22051143insT								ZNF43 (16312 upstream) : ZNF208 (64617 downstream)																							TCAGGAACCTGTTTTTTTTTTT	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24556909	24556909	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24556909delA								LOC100101266 (210660 upstream) : None (None downstream)																							gcctatggtgaaaaaagaaat	0.000													4	2	---	---	---	---	
MAG	4099	broad.mit.edu	37	19	35788231	35788232	+	Intron	DEL	CA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35788231_35788232delCA	uc002nyy.1	+						MAG_uc002nyx.1_Intron|MAG_uc010eds.1_Intron|MAG_uc002nyz.1_Intron	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a						blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			breast(3)|lung(2)|central_nervous_system(1)|skin(1)	7	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			acacacacaccacacacacacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36913800	36913800	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36913800delA								ZFP82 (4250 upstream) : ZNF566 (22222 downstream)																							CTTTGTCATTAAAAAAAAAAA	0.194													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42318470	42318470	+	IGR	DEL	C	-	-	rs35918720		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42318470delC								CEACAM3 (2879 upstream) : LYPD4 (22680 downstream)																							GTGGAAGGGTCCACTCAGGTC	0.567													3	4	---	---	---	---	
MARK4	57787	broad.mit.edu	37	19	45780931	45780931	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45780931delT	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron			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;						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)		TGGCCAAGAATTTTTTTTTTT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46968266	46968266	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46968266delA								CCDC8 (51347 upstream) : PNMAL1 (1483 downstream)																							ATCTTCCTGCAAACACTCCGG	0.587													4	2	---	---	---	---	
MEIS3	56917	broad.mit.edu	37	19	47916988	47916988	+	Intron	DEL	T	-	-	rs112493679		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47916988delT	uc002pgu.2	-						MEIS3_uc002pgo.2_5'Flank|MEIS3_uc002pgp.2_Intron|MEIS3_uc002pgq.2_Intron|MEIS3_uc002pgr.2_Intron|MEIS3_uc002pgt.2_Intron|MEIS3_uc002pgv.2_Intron|MEIS3_uc002pgs.2_Intron|MEIS3_uc010eld.2_Intron	NM_001009813	NP_001009813	Q99687	MEIS3_HUMAN	Meis1, myeloid ecotropic viral integration site							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		GGTTTGAttcttttttttttt	0.234													4	2	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49851747	49851755	+	Intron	DEL	CAGCTGCAT	-	-	rs33974425		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49851747_49851755delCAGCTGCAT	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						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)		gtccccagaccagctgcatcaacgcacct	0.158													4	5	---	---	---	---	
ZNF577	84765	broad.mit.edu	37	19	52374140	52374140	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52374140delG	uc010ydd.1	-							NR_024181		Q9BSK1	ZN577_HUMAN	Homo sapiens cDNA FLJ32291 fis, clone PROST2000572.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		tttctgtcatggaaagctgtc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53529953	53529953	+	IGR	DEL	A	-	-	rs75753639		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53529953delA								ZNF702P (33169 upstream) : ZNF160 (39915 downstream)																							cacaaaaagcaaaaaaaaaAA	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54844234	54844234	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54844234delG								LILRA5 (19825 upstream) : LILRA4 (459 downstream)																							tgcccatgaagggagtgttta	0.318													4	2	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55502269	55502269	+	Intron	DEL	T	-	-	rs66496541		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55502269delT	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGTTTTCGGGttttttttttc	0.194													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57209250	57209251	+	IGR	INS	-	TTCT	TTCT	rs149807795	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57209250_57209251insTTCT								ZNF835 (25004 upstream) : ZIM2 (76672 downstream)																							tcctctctcccttggctgtcca	0.000													2	6	---	---	---	---	
FKBP1A	2280	broad.mit.edu	37	20	1348280	1348280	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1348280delA	uc010gac.2	-						uc002wew.2_Intron|uc002wex.2_Intron			P62942	FKB1A_HUMAN	Homo sapiens FKBP12-Exip2 mRNA for FK506 binding protein12, complete cds.						'de novo' protein folding|beta-amyloid formation|fibril organization|heart trabecula formation|negative regulation of protein phosphatase type 2B activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein binding|positive regulation of protein ubiquitination|protein maturation by protein folding|protein refolding|regulation of activin receptor signaling pathway|regulation of immune response|regulation of ryanodine-sensitive calcium-release channel activity|SMAD protein complex assembly|T cell activation|ventricular cardiac muscle tissue morphogenesis	axon|cytosol|sarcoplasmic reticulum membrane|terminal cisterna	activin binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity|signal transducer activity|SMAD binding|type I transforming growth factor beta receptor binding				0					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	taatcctcctatctcagggtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7084485	7084485	+	IGR	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7084485delG								BMP2 (323575 upstream) : HAO1 (779146 downstream)																							TGCAATTTCTGGAGAGAGGGT	0.075													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8220801	8220802	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8220801_8220802insA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_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						TTTTTTTCATGAAAAAAAACAA	0.337													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15943920	15943921	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15943920_15943921insT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GTGTATAGCAGTTTTTTTTTGG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25910266	25910267	+	IGR	INS	-	T	T	rs149342775		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25910266_25910267insT								FAM182B (61480 upstream) : LOC100134868 (80168 downstream)																							TGTGAGGACAGTTTTTTTTAAT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074256	26074257	+	IGR	INS	-	TC	TC	rs141028126	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074256_26074257insTC								FAM182A (6704 upstream) : C20orf191 (9796 downstream)																							GCACATGTGGTCCCCCAAAGAA	0.243													4	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29624894	29624894	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29624894delG	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TGACAAATGAGGAAAATATTT	0.289													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29638538	29638538	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29638538delT	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						AGAGCAAGAATTTTTAAAGAA	0.378													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29909247	29909247	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29909247delT								DEFB116 (12859 upstream) : DEFB118 (47181 downstream)																							TTGTGGGGGGTTTTTTTTGTG	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31776104	31776104	+	IGR	DEL	T	-	-	rs67745079		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31776104delT								C20orf70 (6881 upstream) : BASE (5307 downstream)																							TATAAGTGGGTTtttttttgt	0.209													6	4	---	---	---	---	
ACSS2	55902	broad.mit.edu	37	20	33502693	33502693	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33502693delG	uc002xbd.2	+						ACSS2_uc002xbc.2_Intron|ACSS2_uc010zum.1_Intron|ACSS2_uc010gey.2_Intron|ACSS2_uc002xbe.2_Intron|ACSS2_uc002xbf.2_Intron	NM_018677	NP_061147	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2						ethanol oxidation|lipid biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	acetate-CoA ligase activity|ATP binding|protein binding				0					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCAGGCTTCTGGTGGGAATGG	0.552													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	35049859	35049860	+	Intron	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35049859_35049860delAA	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				agactgtctcaaaaaaaaaaaa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38005540	38005540	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38005540delT								LOC339568 (152149 upstream) : None (None downstream)																							TTTCTCCATCTTTTTTTTTCC	0.393													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41577256	41577256	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41577256delA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				cagctcacacaaaaaaaaatg	0.000													4	3	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45766375	45766375	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45766375delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				CACCACCAAATTTTTTTTTCT	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48994003	48994004	+	IGR	DEL	GT	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48994003_48994004delGT								CEBPB (184791 upstream) : PTPN1 (132887 downstream)																							ttgtgcacaggtgtgtgtgtgt	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53086486	53086486	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53086486delA								PFDN4 (249995 upstream) : DOK5 (5771 downstream)																							TGAGGAACTGAAGCAGAACTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55320895	55320895	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55320895delA								TFAP2C (106559 upstream) : BMP7 (422914 downstream)																							gattttctccaaaaactaacc	0.159													4	2	---	---	---	---	
TAF4	6874	broad.mit.edu	37	20	60586256	60586256	+	Intron	DEL	T	-	-	rs28382063		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60586256delT	uc002ybs.2	-							NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			TAAGCATGGATTTTTTTTTTA	0.463											OREG0026102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10141190	10141191	+	IGR	DEL	AA	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10141190_10141191delAA								None (None upstream) : TPTE (765552 downstream)																							aaatatgtctaaaatgtaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10734173	10734174	+	IGR	INS	-	TGA	TGA	rs138115959		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10734173_10734174insTGA								None (None upstream) : TPTE (172569 downstream)																							tagtatttatgtgatatttcct	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11066268	11066268	+	Intron	DEL	C	-	-	rs4009908		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11066268delC	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)		aaaacaaaaacaaaaacaaaG	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11120163	11120164	+	IGR	DEL	TT	-	-	rs112214687		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11120163_11120164delTT								BAGE (21226 upstream) : None (None downstream)																							ctttggaaactttgaactcttc	0.000													5	3	---	---	---	---	
C21orf81	391267	broad.mit.edu	37	21	15343195	15343196	+	Intron	INS	-	A	A	rs149164878		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15343195_15343196insA	uc002yji.2	-							NR_027270				Homo sapiens C21orf81 protein (C21orf81) mRNA, complete cds.												0						gattgcatctcaaaaaaaaCTT	0.119													5	5	---	---	---	---	
JAM2	58494	broad.mit.edu	37	21	27081522	27081523	+	Intron	INS	-	G	G	rs140445207	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27081522_27081523insG	uc002ylp.1	+						JAM2_uc011ace.1_Intron|JAM2_uc002ylq.1_Intron|JAM2_uc011acf.1_Intron|JAM2_uc010glh.1_Intron|JAM2_uc002ylr.1_Intron|JAM2_uc010gli.1_Intron	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						gctctcttgttacttaagtacc	0.015													12	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29582597	29582597	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29582597delT	uc002yml.2	-											Homo sapiens cDNA clone IMAGE:5541115, partial cds.																		CTTACAGATATTTTTTTAATG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29828794	29828794	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29828794delA								C21orf94 (433266 upstream) : NCRNA00161 (82846 downstream)																							tcagggctgcaaatgatactc	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30182285	30182285	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30182285delT								NCRNA00161 (269609 upstream) : N6AMT1 (62228 downstream)																							TCTCACTGCCTTACTCTGCTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34467686	34467686	+	IGR	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34467686delC								OLIG1 (22959 upstream) : C21orf54 (70091 downstream)																							GACTCACCATCCAAAACAGTT	0.418													4	2	---	---	---	---	
CLIC6	54102	broad.mit.edu	37	21	36045533	36045533	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36045533delT	uc010gmt.1	+						CLIC6_uc002yuf.1_Intron	NM_053277	NP_444507	Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6							chloride channel complex|cytoplasm|plasma membrane	voltage-gated chloride channel activity			ovary(1)|central_nervous_system(1)	2						AGTTGCTAACTTTTTTTTTTC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	36112821	36112822	+	IGR	INS	-	ATCC	ATCC	rs143812091	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36112821_36112822insATCC								NCRNA00160 (3342 upstream) : RUNX1 (47277 downstream)																							cacatctacaaatccatccatc	0.045													4	2	---	---	---	---	
DSCR8	84677	broad.mit.edu	37	21	39519890	39519890	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39519890delA	uc002ywt.3	+						DSCR8_uc010gnp.2_Intron|DSCR8_uc010gnq.2_Intron|DSCR8_uc010gnr.2_Intron|DSCR8_uc010gns.2_Intron	NR_026838				Homo sapiens down syndrome critical region protein DSCR8 (DSCR8) mRNA, complete cds.												0						actctttaccaaaaaaACCCC	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39593064	39593064	+	IGR	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39593064delA								DSCR10 (12328 upstream) : KCNJ15 (35600 downstream)																							TTCCCAGAGGAAAAAAAACGG	0.517													4	2	---	---	---	---	
NCRNA00114	400866	broad.mit.edu	37	21	40114925	40114926	+	Intron	INS	-	TC	TC	rs13053122		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40114925_40114926insTC	uc010goa.2	-						NCRNA00114_uc011aen.1_Intron|NCRNA00114_uc002yxd.3_Intron	NR_027067				Homo sapiens chromosome 21 open reading frame 24 isoform 1 (C21orf24) mRNA, complete sequence.												0						ctctctctctgtctctctctct	0.099													4	2	---	---	---	---	
MX1	4599	broad.mit.edu	37	21	42820854	42820874	+	Intron	DEL	GTTTTGTGTGTGTGTGTGTGT	-	-	rs34045368		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42820854_42820874delGTTTTGTGTGTGTGTGTGTGT	uc002yzh.2	+						MX1_uc002yzi.2_Intron|MX1_uc010goq.2_Intron	NM_001144925	NP_001138397	P20591	MX1_HUMAN	myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				TTCAGATCTGGTTTtgtgtgtgtgtgtgtgtgtgtgtgtgt	0.312													2	4	---	---	---	---	
SIK1	150094	broad.mit.edu	37	21	44836039	44836040	+	3'UTR	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44836039_44836040insA	uc002zdf.2	-	14						NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1						anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7						ACTAAAATAAGAAAAAAAAGTC	0.416													4	2	---	---	---	---	
HSF2BP	11077	broad.mit.edu	37	21	45022914	45022915	+	Intron	INS	-	A	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45022914_45022915insA	uc002zdi.2	-						HSF2BP_uc011aey.1_Intron	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding						spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)		GGGCAGTGAGGAAAAAAAATAA	0.421													6	3	---	---	---	---	
MCM3AP	8888	broad.mit.edu	37	21	47700726	47700727	+	Intron	INS	-	T	T	rs111306908		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47700726_47700727insT	uc002zir.1	-							NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3						DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					CTCTTTCCCCCttttttttttt	0.267													5	3	---	---	---	---	
DIP2A	23181	broad.mit.edu	37	21	47947171	47947171	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47947171delT	uc002zjo.2	+						DIP2A_uc011afy.1_Intron|DIP2A_uc011afz.1_Intron|DIP2A_uc002zjl.2_Intron|DIP2A_uc002zjm.2_Intron|DIP2A_uc010gql.2_Intron|DIP2A_uc002zjn.2_Intron|DIP2A_uc002zjp.1_Intron	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		AAATTCTTTATGCATTACAAT	0.114													4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26249224	26249224	+	Intron	DEL	C	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26249224delC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						TGCCTGAGATCATCAGCACTG	0.443													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27116790	27116790	+	IGR	DEL	G	-	-	rs36069489		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27116790delG								MIAT (1841 upstream) : None (None downstream)																							aggtagacaagatccttggct	0.000													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27858647	27858647	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27858647delT								MIAT (743698 upstream) : MN1 (285619 downstream)																							ctttcttttcttttttttttA	0.383													5	3	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29521778	29521778	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29521778delT	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						CTTTTGACTGTTTTTTTTTTA	0.333													3	3	---	---	---	---	
CCDC157	550631	broad.mit.edu	37	22	30768671	30768671	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30768671delG	uc011aku.1	+						CCDC157_uc011akv.1_Intron	NM_001017437	NP_001017437	Q569K6	CC157_HUMAN	coiled-coil domain containing 157											central_nervous_system(1)	1						gccaggggaaggacagggcag	0.179													4	2	---	---	---	---	
C22orf30	253143	broad.mit.edu	37	22	32082728	32082728	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32082728delT	uc003alp.3	-						C22orf30_uc003alo.1_Intron|C22orf30_uc010gwj.1_Intron	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143												0						cTCTGATTCGTTTTTTTTAAA	0.134													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33158858	33158859	+	Intron	INS	-	G	G	rs150628273	by1000genomes	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33158858_33158859insG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						gagaatgcacagggaagagctt	0.094													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	34306760	34306760	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34306760delA	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				TGGAtccagcaaaaaaagcag	0.224													4	2	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40409371	40409371	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40409371delT	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						ctaaagggcattttttttctc	0.000													4	2	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41747815	41747819	+	Intron	DEL	ATTTT	-	-	rs71803158		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41747815_41747819delATTTT	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						GTTGTGTCTCattttattttatttt	0.171													13	6	---	---	---	---	
TOB2	10766	broad.mit.edu	37	22	41831483	41831484	+	3'UTR	DEL	AC	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41831483_41831484delAC	uc003azz.1	-	2						NM_016272	NP_057356	Q14106	TOB2_HUMAN	transducer of ERBB2, 2						female gamete generation|negative regulation of cell proliferation	cytoplasm|nucleus				ovary(1)	1						CAAACCAAATACACACACACAC	0.490													4	2	---	---	---	---	
FGD1	2245	broad.mit.edu	37	X	54505448	54505448	+	Intron	DEL	A	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54505448delA	uc004dtg.2	-							NM_004463	NP_004454	P98174	FGD1_HUMAN	faciogenital dysplasia protein						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|skin(2)|central_nervous_system(1)	6						TACAAACCAGAAAAAAACTGT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	57758787	57758787	+	IGR	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57758787delT								ZXDB (134881 upstream) : ZXDA (175411 downstream)																							tctaaccaggtttttttacct	0.000													4	2	---	---	---	---	
SH3BGRL	6451	broad.mit.edu	37	X	80502145	80502145	+	Intron	DEL	T	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80502145delT	uc004eef.2	+						SH3BGRL_uc011mqs.1_Intron|SH3BGRL_uc010nml.2_Intron|SH3BGRL_uc010nmm.2_Intron|SH3BGRL_uc010nmn.2_Intron	NM_003022	NP_003013	O75368	SH3L1_HUMAN	SH3 domain binding glutamic acid-rich protein							cytoplasm|nucleus	SH3 domain binding|SH3/SH2 adaptor activity			ovary(1)	1		all_lung(315;5.94e-05)				gggttctctatttttttttta	0.000													5	4	---	---	---	---	
CENPI	2491	broad.mit.edu	37	X	100356525	100356526	+	Intron	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100356525_100356526insT	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1						acctttTTTTCTTTTTTTTTTT	0.094													8	4	---	---	---	---	
DOCK11	139818	broad.mit.edu	37	X	117630826	117630826	+	Intron	DEL	G	-	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117630826delG	uc004eqp.2	+							NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3						TGGAGGACCTGGGGTCAGAGC	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9952378	9952379	+	IGR	INS	-	T	T	rs78434293		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9952378_9952379insT								TTTY22 (301524 upstream) : None (None downstream)																							tagtattaccctgatatcaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13265412	13265413	+	IGR	INS	-	T	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13265412_13265413insT								None (None upstream) : None (None downstream)																							acactgattgattttttatatg	0.000													4	3	---	---	---	---	
