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
Unknown	0	broad.mit.edu	37	1	13418	13418	+	RNA	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13418G>A	uc001aaa.3	+	3		c.661G>A			uc010nxq.1_Missense_Mutation_p.E61K|uc010nxr.1_RNA					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		CCACCACCCCGAGATCACATT	0.562													6	9	---	---	---	---	PASS
ESPN	83715	broad.mit.edu	37	1	6504722	6504722	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6504722A>G	uc001amy.2	+	6	1340	c.1172A>G	c.(1171-1173)AAG>AGG	p.K391R		NM_031475	NP_113663	B1AK53	ESPN_HUMAN	espin	391					sensory perception of sound	brush border|cytoplasm|filamentous actin|stereocilium	actin filament binding|SH3 domain binding				0	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TCCAGCATCAAGGGCCAGCAC	0.617													15	30	---	---	---	---	PASS
LOC440563	440563	broad.mit.edu	37	1	13183480	13183480	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13183480A>G	uc010obg.1	-	1	488	c.393T>C	c.(391-393)CCT>CCC	p.P131P		NM_001136561	NP_001130033	B2RXH8	B2RXH8_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	131						ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0						GAGGAGGAGGAGGTACACGTG	0.507													41	240	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19523668	19523668	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19523668C>T	uc001bbi.2	-	8	989	c.985G>A	c.(985-987)GTG>ATG	p.V329M		NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	329					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AGGACTGTCACATCTTGTAGA	0.408													5	329	---	---	---	---	PASS
ZMYM6	9204	broad.mit.edu	37	1	35453715	35453715	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35453715A>C	uc001byh.2	-	16	3196	c.2968T>G	c.(2968-2970)TAT>GAT	p.Y990D	uc001byd.3_5'Flank|uc001bye.2_5'Flank|ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Missense_Mutation_p.Y893D	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	990					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				aaaccagaatacctgccagtc	0.000													5	28	---	---	---	---	PASS
ZC3H12A	80149	broad.mit.edu	37	1	37947235	37947235	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37947235A>G	uc001cbb.3	+	4	767	c.617A>G	c.(616-618)AAG>AGG	p.K206R	ZC3H12A_uc001cbc.1_5'UTR	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	206					angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GAGAAGAAGAAGATCCTGGTG	0.607													6	286	---	---	---	---	PASS
FAF1	11124	broad.mit.edu	37	1	50941196	50941196	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50941196T>C	uc009vyx.1	-	19	1872	c.1809A>G	c.(1807-1809)GTA>GTG	p.V603V	FAF1_uc009vyw.1_RNA|FAF1_uc001cse.1_Silent_p.V603V|FAF1_uc010onc.1_Silent_p.V361V	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1	603	UBX.				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			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CTTTGGAAGCTACAAAATCAA	0.507													4	208	---	---	---	---	PASS
WLS	79971	broad.mit.edu	37	1	68659760	68659760	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68659760T>C	uc001def.1	-	2	528	c.257A>G	c.(256-258)GAA>GGA	p.E86G	uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Missense_Mutation_p.E84G|WLS_uc001deg.1_Intron|WLS_uc001deh.1_Missense_Mutation_p.E86G|WLS_uc009wbf.1_Missense_Mutation_p.E41G	NM_024911	NP_079187	Q5T9L3	WLS_HUMAN	G protein-coupled receptor 177 isoform 1	86	Lumenal (Potential).				multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0						GTCATTGGCTTCAATTTCCCT	0.478													6	262	---	---	---	---	PASS
LMO4	8543	broad.mit.edu	37	1	87805819	87805819	+	Silent	SNP	A	G	G	rs150946026	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87805819A>G	uc001dmi.2	+	4	1203	c.423A>G	c.(421-423)AGA>AGG	p.R141R	LMO4_uc001dmj.2_Silent_p.R141R	NM_006769	NP_006760	P61968	LMO4_HUMAN	LIM domain only 4	141	LIM zinc-binding 2.				neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		AACATGATAGACCTACAGCTC	0.433													7	408	---	---	---	---	PASS
KIAA1107	23285	broad.mit.edu	37	1	92643949	92643949	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92643949G>C	uc010otd.1	+	7	1306	c.1208G>C	c.(1207-1209)GGA>GCA	p.G403A	KIAA1107_uc001dop.2_Missense_Mutation_p.G328A	NM_015237	NP_056052	Q9UPP5	K1107_HUMAN	hypothetical protein LOC23285	458											0						ACTAGCAATGGATGTACTGCA	0.368													103	250	---	---	---	---	PASS
HAO2	51179	broad.mit.edu	37	1	119929445	119929445	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119929445T>C	uc001ehq.1	+	6	1114	c.762T>C	c.(760-762)GTT>GTC	p.V254V	HAO2_uc001ehr.1_Silent_p.V254V	NM_001005783	NP_001005783	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2	254	FMN hydroxy acid dehydrogenase.				fatty acid alpha-oxidation	peroxisome	(S)-2-hydroxy-acid oxidase activity			ovary(2)|skin(2)	4	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		TTGATGAGGTTCTTGCTTCAG	0.363													7	629	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293269	145293269	+	5'Flank	SNP	G	A	A	rs61350760	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293269G>A	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'UTR|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001emq.1_5'UTR	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTTCACAACAGTAAGTTAAGA	0.423													7	54	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145297661	145297661	+	Missense_Mutation	SNP	C	A	A	rs4068083	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145297661C>A	uc001end.3	+	4	571	c.536C>A	c.(535-537)GCT>GAT	p.A179D	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.A179D|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	179											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTTGAGGAGGCTGAGAAAGTA	0.433													4	203	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145438828	145438828	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145438828C>A	uc001enn.3	+	1	367	c.26C>A	c.(25-27)TCT>TAT	p.S9Y	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_5'Flank	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	9					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAGATCAAGTCTTTTGAGGTG	0.458													24	249	---	---	---	---	PASS
TCHH	7062	broad.mit.edu	37	1	152084846	152084846	+	Silent	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152084846G>T	uc001ezp.2	-	2	847	c.847C>A	c.(847-849)CGG>AGG	p.R283R	TCHH_uc009wne.1_Silent_p.R283R	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	283					keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTCTTGCCGCTCCAGCTTC	0.403													22	80	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158622267	158622267	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158622267T>C	uc001fst.1	-	23	3564	c.3365A>G	c.(3364-3366)GAG>GGG	p.E1122G		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1122	Spectrin 11.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CTTTTGGAACTCATCAAACTT	0.393													6	322	---	---	---	---	PASS
PRDX6	9588	broad.mit.edu	37	1	173454603	173454603	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173454603C>T	uc001giy.1	+	3	407	c.356C>T	c.(355-357)CCA>CTA	p.P119L		NM_004905	NP_004896	P30041	PRDX6_HUMAN	peroxiredoxin 6	119	Thioredoxin.				cell redox homeostasis|phospholipid catabolic process	cytoplasmic membrane-bounded vesicle|cytosol|lysosome	peroxiredoxin activity|phospholipase A2 activity|protein binding			central_nervous_system(1)	1						ATGCTGGATCCAGCAGAGAAG	0.458													6	263	---	---	---	---	PASS
CFHR3	10878	broad.mit.edu	37	1	196759211	196759211	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196759211G>A	uc001gtl.2	+	5	737	c.650G>A	c.(649-651)AGC>AAC	p.S217N	CFHR3_uc010poy.1_Missense_Mutation_p.S156N|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	217	Sushi 4.					extracellular space					0						CCACCTATTAGCAATGGTGAT	0.373													5	203	---	---	---	---	PASS
DYRK3	8444	broad.mit.edu	37	1	206822222	206822222	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206822222G>T	uc001hej.2	+	3	1847	c.1679G>T	c.(1678-1680)GGA>GTA	p.G560V	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Missense_Mutation_p.G540V	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	560					erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CCAGTTGTTGGAATAGCCAAT	0.448													17	126	---	---	---	---	PASS
SMC6	79677	broad.mit.edu	37	2	17906608	17906608	+	Silent	SNP	C	T	T	rs144198428	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17906608C>T	uc002rco.2	-	9	938	c.642G>A	c.(640-642)ACG>ACA	p.T214T	SMC6_uc010exo.2_Silent_p.T214T|SMC6_uc002rcn.2_Silent_p.T214T|SMC6_uc002rcp.1_Silent_p.T240T|SMC6_uc002rcq.2_Silent_p.T240T|SMC6_uc002rcr.1_Silent_p.T214T	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	214					DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTTCAAGTTGCGTTGCTTTCA	0.299													5	619	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61493258	61493258	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61493258A>G	uc002sbe.2	-	42	5500	c.5478T>C	c.(5476-5478)AGT>AGC	p.S1826S	USP34_uc002sbf.2_5'UTR	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	1826					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			GGTCCTTTAGACTTGGCAACA	0.378													6	463	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89076056	89076056	+	RNA	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89076056C>T	uc002stf.2	+	3		c.406C>T			FLJ40330_uc010fhf.2_RNA|FLJ40330_uc010fhg.2_RNA|FLJ40330_uc010fhh.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						CAAAAGTAGCCATAAGAAGGA	0.328													4	65	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89104384	89104384	+	RNA	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89104384G>A	uc010fhg.2	+	15		c.1417G>A			FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_RNA	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						ATCCTGCAGCGTTCAAGTTTG	0.289													6	263	---	---	---	---	PASS
ACTR3	10096	broad.mit.edu	37	2	114709129	114709129	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114709129T>C	uc002tkx.1	+	9	1252	c.932T>C	c.(931-933)GTC>GCC	p.V311A	ACTR3_uc010yyc.1_Missense_Mutation_p.V249A|ACTR3_uc010yyd.1_Missense_Mutation_p.V260A	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog	311					cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						CCTATTGATGTCAGACGTCCT	0.299													8	418	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138421031	138421031	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138421031C>A	uc002tva.1	+	25	4450	c.4450C>A	c.(4450-4452)CCA>ACA	p.P1484T	THSD7B_uc010zbj.1_RNA	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)		CATGAAAGTACCAGGCTCAGA	0.363													73	564	---	---	---	---	PASS
PLA2R1	22925	broad.mit.edu	37	2	160824141	160824141	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160824141T>C	uc002ube.1	-	20	3020	c.2813A>G	c.(2812-2814)AAG>AGG	p.K938R	PLA2R1_uc010zcp.1_Missense_Mutation_p.K938R|PLA2R1_uc002ubf.2_Missense_Mutation_p.K938R	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	938	Extracellular (Potential).|C-type lectin 5.				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3						CTTTTTTCGCTTACAGATACT	0.398													6	459	---	---	---	---	PASS
CASP10	843	broad.mit.edu	37	2	202093848	202093848	+	3'UTR	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202093848C>T	uc002uxl.1	+	10					CASP10_uc002uxm.1_3'UTR	NM_032974	NP_116756	Q92851	CASPA_HUMAN	caspase 10 isoform b preproprotein						apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6						CCAGCCACATCGCCTGAGATT	0.572													3	73	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188205	10188205	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188205T>C	uc003bvc.2	+	2	561	c.348T>C	c.(346-348)CTT>CTC	p.L116L	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	116	Involved in binding to CCT complex.		L -> V (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(2)|p.L116V(1)|p.W117fs*40(1)|p.L116fs*43(1)|p.H115fs*41(1)|p.H115fs*42(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TAGGTCACCTTTGGCTCTTCA	0.348		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				62	135	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188208	10188208	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188208G>C	uc003bvc.2	+	2	564	c.351G>C	c.(349-351)TGG>TGC	p.W117C	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	117	Involved in binding to CCT complex.		W -> C (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.W117*(5)|p.W117R(5)|p.W117fs*42(3)|p.W117C(2)|p.W117L(1)|p.?(1)|p.W117G(1)|p.W117fs*14(1)|p.W117fs*40(1)|p.H115fs*41(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTCACCTTTGGCTCTTCAGAG	0.348		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				63	141	---	---	---	---	PASS
LRRC3B	116135	broad.mit.edu	37	3	26751198	26751198	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26751198T>C	uc003cdp.2	+	2	624	c.35T>C	c.(34-36)CTC>CCC	p.L12P	LRRC3B_uc003cdq.2_Missense_Mutation_p.L12P	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B precursor	12						integral to membrane				pancreas(2)|ovary(1)|skin(1)	4						ACCCGTTCCCTCTCCATGTGT	0.473													6	376	---	---	---	---	PASS
CYP8B1	1582	broad.mit.edu	37	3	42916230	42916230	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42916230A>G	uc003cmh.2	-	1	1404	c.1079T>C	c.(1078-1080)GTT>GCT	p.V360A	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Missense_Mutation_p.V360A	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	360					bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		GTCTTCATGAACCAACCTGAG	0.572													13	15	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47158115	47158115	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47158115T>A	uc003cqs.2	-	4	4637	c.4584A>T	c.(4582-4584)GAA>GAT	p.E1528D	SETD2_uc003cqv.2_Missense_Mutation_p.E1517D	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1528	AWS.				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)		TTACTTACCATTCAATCATGA	0.338			N|F|S|Mis		clear cell renal carcinoma								135	195	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52610695	52610695	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52610695G>A	uc003des.2	-	22	3565	c.3553C>T	c.(3553-3555)CGA>TGA	p.R1185*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.R1185*|PBRM1_uc003der.2_Nonsense_Mutation_p.R1153*|PBRM1_uc003det.2_Nonsense_Mutation_p.R1200*|PBRM1_uc003deu.2_Nonsense_Mutation_p.R1200*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.R1185*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.R1160*|PBRM1_uc003dey.2_Nonsense_Mutation_p.R1160*|PBRM1_uc003dez.1_Nonsense_Mutation_p.R1184*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1185	BAH 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.R1185*(1)		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)		GCTCCATCTCGAACCCATACT	0.338			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								65	314	---	---	---	---	PASS
GNL3	26354	broad.mit.edu	37	3	52728434	52728434	+	3'UTR	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52728434A>G	uc003dfd.2	+	15					GNL3_uc003dfe.2_3'UTR|GNL3_uc003dff.2_3'UTR	NM_014366	NP_055181	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3						regulation of cell proliferation	nucleolus	GTP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		GGAATCCCTAAATTCTGTAAA	0.303													6	5	---	---	---	---	PASS
LMOD3	56203	broad.mit.edu	37	3	69169050	69169050	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69169050A>T	uc003dns.2	-	2	665	c.456T>A	c.(454-456)GAT>GAA	p.D152E	LMOD3_uc003dnt.2_Missense_Mutation_p.D152E	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	152	Glu-rich.					cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		catcatcatcatcttcttctt	0.249													5	662	---	---	---	---	PASS
IMPG2	50939	broad.mit.edu	37	3	101038458	101038458	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101038458C>A	uc003duq.1	-	2	507	c.304G>T	c.(304-306)GCA>TCA	p.A102S	IMPG2_uc011bhe.1_5'UTR	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	102	Extracellular (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						ACATGATTTGCCACAGCCTCT	0.388													91	298	---	---	---	---	PASS
IMPG2	50939	broad.mit.edu	37	3	101038459	101038459	+	Silent	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101038459C>A	uc003duq.1	-	2	506	c.303G>T	c.(301-303)GTG>GTT	p.V101V	IMPG2_uc011bhe.1_5'UTR	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	101	Extracellular (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						CATGATTTGCCACAGCCTCTG	0.388													94	300	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122418399	122418399	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122418399T>C	uc003efq.3	+	6	1057	c.998T>C	c.(997-999)TTC>TCC	p.F333S	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Missense_Mutation_p.F50S|PARP14_uc003efs.1_Missense_Mutation_p.F50S	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	333					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		TTATGGAAGTTCTTACAGAAA	0.448													5	201	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130454836	130454836	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130454836T>C	uc003enj.2	-	3	1325	c.744A>G	c.(742-744)ATA>ATG	p.I248M		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	248	Protein kinase.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						AAAGCTCAGCTATCACACAAC	0.318													5	390	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182554141	182554141	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182554141T>C	uc003flb.2	+	6	692	c.435T>C	c.(433-435)ATT>ATC	p.I145I	ATP11B_uc003fla.2_Silent_p.I145I	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	145	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TGGGTGATATTGTTCGAATAG	0.398													6	478	---	---	---	---	PASS
PCGF3	10336	broad.mit.edu	37	4	755156	755156	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:755156T>C	uc011bva.1	+	10	1027	c.552T>C	c.(550-552)CAT>CAC	p.H184H	PCGF3_uc003gbd.1_RNA|PCGF3_uc003gbe.2_Silent_p.H184H|PCGF3_uc010ibh.2_Silent_p.H184H|PCGF3_uc003gbg.1_Silent_p.H150H|PCGF3_uc003gbh.2_Silent_p.H150H	NM_006315	NP_006306	Q3KNV8	PCGF3_HUMAN	ring finger protein 3	184					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0						CCGTCTTGCATCTGAAGAAGT	0.493													4	106	---	---	---	---	PASS
OCIAD1	54940	broad.mit.edu	37	4	48862838	48862838	+	3'UTR	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48862838G>T	uc003gyo.2	+	9					OCIAD1_uc003gyr.2_3'UTR|OCIAD1_uc003gyp.2_3'UTR|OCIAD1_uc003gys.2_3'UTR|OCIAD1_uc003gyq.2_3'UTR|OCIAD1_uc010igk.2_3'UTR	NM_017830	NP_060300	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1 isoform 1							endosome	protein binding				0						AGGTGGTCATGATTACCTGCA	0.373													69	154	---	---	---	---	PASS
PAICS	10606	broad.mit.edu	37	4	57318153	57318153	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57318153A>G	uc003hbs.1	+	8	1118	c.887A>G	c.(886-888)GAA>GGA	p.E296G	PAICS_uc011cac.1_Missense_Mutation_p.E296G|PAICS_uc003hbt.1_Missense_Mutation_p.E303G|PAICS_uc003hbu.1_Missense_Mutation_p.E296G|PAICS_uc010ihd.1_Missense_Mutation_p.E297G	NM_006452	NP_006443	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase,	296	AIR carboxylase.				'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|identical protein binding|phosphoribosylaminoimidazole carboxylase activity|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	ATTCCATGTGAACTTCGAGTA	0.408													6	409	---	---	---	---	PASS
MRPL1	65008	broad.mit.edu	37	4	78783945	78783945	+	5'UTR	SNP	A	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78783945A>C	uc003hku.2	+	1						NM_020236	NP_064621	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1 precursor								RNA binding				0						ACCTTTTTTTAATTCTTCCCA	0.527													56	134	---	---	---	---	PASS
LIN54	132660	broad.mit.edu	37	4	83849233	83849233	+	3'UTR	SNP	T	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83849233T>G	uc003hnx.3	-	13					LIN54_uc003hnz.3_3'UTR|LIN54_uc003hny.3_3'UTR|LIN54_uc010ijt.2_3'UTR|LIN54_uc010iju.2_3'UTR|LIN54_uc010ijv.2_3'UTR	NM_194282	NP_919258	Q6MZP7	LIN54_HUMAN	lin-54 homolog isoform a						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)				ACAGTTCCATTTATCAGTCTT	0.373													78	196	---	---	---	---	PASS
DNAJB14	79982	broad.mit.edu	37	4	100824888	100824888	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100824888T>C	uc003hvl.2	-	7	1161	c.1010A>G	c.(1009-1011)CAA>CGA	p.Q337R	DNAJB14_uc003hvk.2_Missense_Mutation_p.Q252R|DNAJB14_uc010ili.2_Missense_Mutation_p.Q270R	NM_001031723	NP_001026893	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	337					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)		CTTACTTTGTTGTCTTTCTTT	0.303													6	476	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104097155	104097155	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104097155C>A	uc003hxb.1	-	15	1531	c.1441G>T	c.(1441-1443)GAG>TAG	p.E481*	CENPE_uc003hxc.1_Nonsense_Mutation_p.E481*	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	481	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CATTCTATCTCACTTAATGTA	0.279													138	519	---	---	---	---	PASS
GSTCD	79807	broad.mit.edu	37	4	106639196	106639196	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106639196A>G	uc003hxz.3	+	2	498	c.426A>G	c.(424-426)GAA>GAG	p.E142E	GSTCD_uc003hxx.2_Silent_p.E142E|GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron|GSTCD_uc010ils.1_Silent_p.E142E	NM_001031720	NP_001026890	Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain	142	GST C-terminal.					cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		CCTGTGCTGAAGTAAGTATAA	0.328													5	154	---	---	---	---	PASS
SEC24B	10427	broad.mit.edu	37	4	110412565	110412565	+	Splice_Site	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110412565T>C	uc003hzk.2	+	5	1301	c.1246_splice	c.e5+2	p.D416_splice	SEC24B_uc003hzl.2_Splice_Site_p.D381_splice|SEC24B_uc011cfp.1_Splice_Site_p.D447_splice|SEC24B_uc011cfq.1_Splice_Site_p.D416_splice|SEC24B_uc011cfr.1_Splice_Site_p.D381_splice	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		GTTACCCAGGTAATTTGTTTT	0.393													7	560	---	---	---	---	PASS
PRSS12	8492	broad.mit.edu	37	4	119256798	119256798	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119256798C>T	uc003ica.1	-	3	697	c.650G>A	c.(649-651)GGA>GAA	p.G217E		NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor	217	SRCR 1.					membrane	scavenger receptor activity			skin(1)	1						TTTTGCTATTCCTTTTCCTCT	0.338													5	352	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16783480	16783480	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16783480T>C	uc003jft.3	-	5	1034	c.566A>G	c.(565-567)AAG>AGG	p.K189R	MYO10_uc003jfu.2_Missense_Mutation_p.K156R	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	189	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ACAGGATGTCTTCTCCTTTAA	0.378													6	445	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35806973	35806973	+	Silent	SNP	C	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35806973C>G	uc003jjo.2	+	35	5286	c.5175C>G	c.(5173-5175)CTC>CTG	p.L1725L	SPEF2_uc003jjp.1_Silent_p.L1211L|SPEF2_uc003jjr.2_Silent_p.L780L	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	1725					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)			AAACACTACTCAAAGTGTTCA	0.383													7	321	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54579409	54579409	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54579409C>T	uc003jpx.2	-	11	1707	c.1587G>A	c.(1585-1587)TCG>TCA	p.S529S	DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	529							ATP binding|ATP-dependent helicase activity|translation initiation factor activity	p.S529L(1)		ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AATCCTCATCCGAAACTAAAT	0.393													8	653	---	---	---	---	PASS
MAP3K1	4214	broad.mit.edu	37	5	56177007	56177007	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56177007T>C	uc003jqw.3	+	13	2778	c.2277T>C	c.(2275-2277)TGT>TGC	p.C759C		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	759					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GCCGCCTTTGTCTTATAGATA	0.363													9	813	---	---	---	---	PASS
GPBP1	65056	broad.mit.edu	37	5	56526737	56526737	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56526737A>G	uc003jrh.3	+	4	1402	c.128A>G	c.(127-129)AAC>AGC	p.N43S	GPBP1_uc010iwg.2_Missense_Mutation_p.N43S|GPBP1_uc003jri.3_5'UTR|GPBP1_uc003jrj.3_Missense_Mutation_p.N50S|GPBP1_uc003jrk.3_Missense_Mutation_p.N50S|GPBP1_uc003jrl.3_RNA	NM_022913	NP_075064	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 1	43					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		TATGATGTGAACCGTCGACGA	0.353													8	744	---	---	---	---	PASS
TMEM232	642987	broad.mit.edu	37	5	110002980	110002980	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110002980A>G	uc011cvh.1	-	2	140	c.68T>C	c.(67-69)CTC>CCC	p.L23P	TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Missense_Mutation_p.L25P|TMEM232_uc003koy.3_5'UTR			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;	25						integral to membrane					0						TAATTTCCAGAGCTCTTCATG	0.284													7	603	---	---	---	---	PASS
SLC12A2	6558	broad.mit.edu	37	5	127488499	127488499	+	Splice_Site	SNP	T	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127488499T>G	uc003kus.2	+	15	2527	c.2363_splice	c.e15+2	p.R788_splice	SLC12A2_uc010jdf.2_Splice_Site|SLC12A2_uc010jdg.2_Splice_Site_p.R788_splice	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	AAACTTTAGGTAAGTGATAAA	0.393													44	156	---	---	---	---	PASS
SLC12A2	6558	broad.mit.edu	37	5	127493693	127493693	+	Intron	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127493693T>C	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron|SLC12A2_uc003kut.1_5'UTR	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	AAAATCTTGTTGCCAGAAACA	0.363													6	414	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140803191	140803191	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140803191T>C	uc003lkq.1	+	1	2655	c.2397T>C	c.(2395-2397)GCT>GCC	p.A799A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Silent_p.A799A|PCDHGA11_uc003lkp.1_Intron|PCDHGB8P_uc011daz.1_5'Flank	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	799	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGACTCAGCTATCATTTTAG	0.463													4	86	---	---	---	---	PASS
ARHGAP26	23092	broad.mit.edu	37	5	142393677	142393677	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142393677A>G	uc011dbj.1	+	12	1175	c.1140A>G	c.(1138-1140)GAA>GAG	p.E380E	ARHGAP26_uc003lmt.2_Silent_p.E380E|ARHGAP26_uc003lmw.2_Silent_p.E380E	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	380					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)			GCCAGAGTGAAGGGAGTAAGT	0.453													7	537	---	---	---	---	PASS
ZKSCAN4	387032	broad.mit.edu	37	6	28212765	28212765	+	3'UTR	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28212765T>C	uc003nks.1	-	5					ZKSCAN4_uc011dlb.1_3'UTR	NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						CCAGACTACATTTTCTAATAC	0.418													15	43	---	---	---	---	PASS
GRM4	2914	broad.mit.edu	37	6	33996013	33996013	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33996013C>T	uc003oir.3	-	9	2743	c.2573G>A	c.(2572-2574)CGC>CAC	p.R858H	GRM4_uc011dsn.1_Missense_Mutation_p.R811H|GRM4_uc010jvh.2_Missense_Mutation_p.R858H|GRM4_uc010jvi.2_Missense_Mutation_p.R550H|GRM4_uc003oio.2_Missense_Mutation_p.R550H|GRM4_uc003oip.2_RNA|GRM4_uc011dsl.1_Missense_Mutation_p.R718H|GRM4_uc003oiq.2_Missense_Mutation_p.R725H|GRM4_uc011dsm.1_Missense_Mutation_p.R689H	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	858	Cytoplasmic (Potential).				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)	TTTGAGGCTGCGCTTGCGCTT	0.602													9	27	---	---	---	---	PASS
GPR110	266977	broad.mit.edu	37	6	46967976	46967976	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46967976A>G	uc003oyt.2	-	15	2915	c.2716T>C	c.(2716-2718)TTT>CTT	p.F906L	GPR110_uc011dwl.1_Missense_Mutation_p.F594L	NM_153840	NP_722582	Q5T601	GP110_HUMAN	G-protein coupled receptor 110 isoform 1	906	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3						TTTGAGACAAACTGAGTTAGC	0.333													6	476	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93979281	93979281	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93979281C>A	uc003poe.2	-	7	1788	c.1547G>T	c.(1546-1548)CGG>CTG	p.R516L	EPHA7_uc003pof.2_Missense_Mutation_p.R516L|EPHA7_uc011eac.1_Missense_Mutation_p.R516L	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	516	Extracellular (Potential).|Fibronectin type-III 2.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		AGTAAAAGCCCGAATCTGGAA	0.403													5	471	---	---	---	---	PASS
GTF3C6	112495	broad.mit.edu	37	6	111281660	111281660	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111281660T>C	uc003pum.2	+	3	392	c.182T>C	c.(181-183)GTC>GCC	p.V61A		NM_138408	NP_612417	Q969F1	TF3C6_HUMAN	general transcription factor IIIC, polypeptide	61						transcription factor TFIIIC complex	DNA binding|protein binding				0		all_cancers(87;0.00328)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|Colorectal(196;0.0466)|all_epithelial(87;0.0575)		OV - Ovarian serous cystadenocarcinoma(136;0.105)|all cancers(137;0.179)|Epithelial(106;0.186)		GACAGCTGTGTCTTTGCTGGG	0.403													8	785	---	---	---	---	PASS
KPNA5	3841	broad.mit.edu	37	6	117026266	117026266	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117026266A>G	uc003pxh.2	+	7	730	c.599A>G	c.(598-600)GAC>GGC	p.D200G		NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5	197	ARM 3.|NLS binding site (major) (By similarity).				NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		ATTGCTGGTGACAATGCAGAA	0.289													7	722	---	---	---	---	PASS
C6orf170	221322	broad.mit.edu	37	6	121452795	121452795	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121452795T>C	uc003pyo.1	-	25	2945	c.2877A>G	c.(2875-2877)AAA>AAG	p.K959K	C6orf170_uc003pyq.1_RNA|C6orf170_uc010kej.1_Silent_p.K58K|C6orf170_uc003pyp.1_Silent_p.K519K	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	959					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		TTATATCAGGTTTGGCTTTCA	0.308													7	678	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158331037	158331037	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158331037T>C	uc003qqv.1	+	9	1102	c.929T>C	c.(928-930)CTT>CCT	p.L310P		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	310	PX.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		ATCCCTTCTCTTCCAGACAAA	0.428													7	582	---	---	---	---	PASS
TYW1	55253	broad.mit.edu	37	7	66532334	66532334	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66532334C>T	uc003tvn.2	+	10	1367	c.1218C>T	c.(1216-1218)CGC>CGT	p.R406R	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Silent_p.R20R	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	406					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				AGAGCCATCGCTGCATGGAAA	0.418													181	589	---	---	---	---	PASS
MCM7	4176	broad.mit.edu	37	7	99695528	99695528	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99695528T>C	uc003usw.1	-	8	1424	c.914A>G	c.(913-915)AAG>AGG	p.K305R	MCM7_uc003usv.1_Missense_Mutation_p.K129R|MCM7_uc003usx.1_Missense_Mutation_p.K129R	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	305					cell cycle checkpoint|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|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)	CTTGTTCATCTTCACAATCCG	0.522													7	379	---	---	---	---	PASS
SDR16C5	195814	broad.mit.edu	37	8	57214061	57214061	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57214061A>G	uc003xsy.1	-	7	1546	c.908T>C	c.(907-909)GTT>GCT	p.V303A	SDR16C5_uc010lyk.1_3'UTR|SDR16C5_uc010lyl.1_Missense_Mutation_p.V259A	NM_138969	NP_620419	Q8N3Y7	RDHE2_HUMAN	epidermal retinal dehydrogenase 2	303					detection of light stimulus involved in visual perception|keratinocyte proliferation|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3						CTTTTGGTCAACAAAGCCATC	0.383													102	298	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95530150	95530150	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95530150G>A	uc003ygo.1	-	10	2547	c.2534C>T	c.(2533-2535)TCA>TTA	p.S845L	KIAA1429_uc003ygp.2_Missense_Mutation_p.S845L|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	845					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ATAAGCTACTGACTTCTTAGA	0.313													103	249	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113484888	113484888	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113484888G>T	uc003ynu.2	-	32	5486	c.5327C>A	c.(5326-5328)CCA>CAA	p.P1776Q	CSMD3_uc003yns.2_Missense_Mutation_p.P1048Q|CSMD3_uc003ynt.2_Missense_Mutation_p.P1736Q|CSMD3_uc011lhx.1_Missense_Mutation_p.P1672Q	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1776	Extracellular (Potential).|CUB 10.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TGGATAGTTTGGTGATAGAAC	0.333										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			6	351	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116426789	116426789	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116426789T>C	uc003ynz.2	-	6	3767	c.3308A>G	c.(3307-3309)GAC>GGC	p.D1103G	TRPS1_uc011lhy.1_Missense_Mutation_p.D1107G|TRPS1_uc003yny.2_Missense_Mutation_p.D1116G|TRPS1_uc010mcy.2_Missense_Mutation_p.D1103G	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	1103	Mediates interaction with RNF4 (By similarity).				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)			ACTCTGGAAGTCATTATGTAC	0.468									Langer-Giedion_syndrome				7	602	---	---	---	---	PASS
TEK	7010	broad.mit.edu	37	9	27109633	27109633	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27109633C>T	uc003zqi.3	+	1	487	c.45C>T	c.(43-45)CTC>CTT	p.L15L	TEK_uc010mjc.1_Silent_p.L15L|TEK_uc011lnn.1_Silent_p.L15L|TEK_uc011lno.1_Silent_p.L15L|TEK_uc011lnp.1_Silent_p.L15L	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	15					angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)		TCAGCTTGCTCCTTTCTGGTA	0.413													57	583	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66454921	66454921	+	RNA	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66454921C>T	uc010mng.1	-	2		c.376G>A			uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		TGTGGGGCCCCAGAAACTTCC	0.517													2	1	---	---	---	---	PASS
AGTPBP1	23287	broad.mit.edu	37	9	88190270	88190270	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88190270A>G	uc011ltd.1	-	24	3496	c.3463T>C	c.(3463-3465)TTT>CTT	p.F1155L	AGTPBP1_uc004aod.3_Missense_Mutation_p.F781L|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Missense_Mutation_p.F1115L|AGTPBP1_uc011lte.1_Missense_Mutation_p.F1167L	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1155					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						TCATTTTCAAAGTCAAGCAGG	0.318													6	322	---	---	---	---	PASS
AKR1E2	83592	broad.mit.edu	37	10	4873010	4873010	+	Silent	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4873010G>T	uc001ihi.2	+	2	298	c.183G>T	c.(181-183)CGG>CGT	p.R61R	AKR1E2_uc001ihl.1_RNA|AKR1E2_uc010qam.1_Silent_p.R61R|AKR1E2_uc001ihh.1_Silent_p.R61R|AKR1E2_uc009xhw.2_Silent_p.R61R|AKR1E2_uc001ihj.2_RNA|AKR1E2_uc001ihk.2_Silent_p.R61R	NM_001040177	NP_001035267	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	61						cytoplasm	1,5-anhydro-D-fructose reductase activity				0						CTGTAAGACGGGAGGATCTGT	0.512													4	305	---	---	---	---	PASS
PLXDC2	84898	broad.mit.edu	37	10	20335841	20335841	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20335841C>T	uc001iqg.1	+	3	1005	c.368C>T	c.(367-369)CCA>CTA	p.P123L	PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	123	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						ATATATGGTCCATCTGATTCT	0.358													6	358	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55755498	55755498	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55755498T>C	uc001jju.1	-	21	3174	c.2779A>G	c.(2779-2781)AGT>GGT	p.S927G	PCDH15_uc010qhq.1_Missense_Mutation_p.S932G|PCDH15_uc010qhr.1_Missense_Mutation_p.S927G|PCDH15_uc010qhs.1_Missense_Mutation_p.S939G|PCDH15_uc010qht.1_Missense_Mutation_p.S934G|PCDH15_uc010qhu.1_Missense_Mutation_p.S927G|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.S927G|PCDH15_uc010qhw.1_Missense_Mutation_p.S890G|PCDH15_uc010qhx.1_Missense_Mutation_p.S856G|PCDH15_uc010qhy.1_Missense_Mutation_p.S932G|PCDH15_uc010qhz.1_Missense_Mutation_p.S927G|PCDH15_uc010qia.1_Missense_Mutation_p.S905G|PCDH15_uc010qib.1_Missense_Mutation_p.S905G|PCDH15_uc001jjw.2_Missense_Mutation_p.S927G	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	927	Extracellular (Potential).|Cadherin 9.				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)				ATTCGTTTACTAAAGACAGGA	0.413										HNSCC(58;0.16)			30	249	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55755499	55755499	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55755499A>T	uc001jju.1	-	21	3173	c.2778T>A	c.(2776-2778)TTT>TTA	p.F926L	PCDH15_uc010qhq.1_Missense_Mutation_p.F931L|PCDH15_uc010qhr.1_Missense_Mutation_p.F926L|PCDH15_uc010qhs.1_Missense_Mutation_p.F938L|PCDH15_uc010qht.1_Missense_Mutation_p.F933L|PCDH15_uc010qhu.1_Missense_Mutation_p.F926L|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.F926L|PCDH15_uc010qhw.1_Missense_Mutation_p.F889L|PCDH15_uc010qhx.1_Missense_Mutation_p.F855L|PCDH15_uc010qhy.1_Missense_Mutation_p.F931L|PCDH15_uc010qhz.1_Missense_Mutation_p.F926L|PCDH15_uc010qia.1_Missense_Mutation_p.F904L|PCDH15_uc010qib.1_Missense_Mutation_p.F904L|PCDH15_uc001jjw.2_Missense_Mutation_p.F926L	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	926	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)				TTCGTTTACTAAAGACAGGAG	0.408										HNSCC(58;0.16)			30	246	---	---	---	---	PASS
TMEM20	159371	broad.mit.edu	37	10	95658339	95658339	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95658339A>G	uc001kjg.1	+	2	251	c.190A>G	c.(190-192)AAA>GAA	p.K64E	TMEM20_uc001kji.2_Intron|TMEM20_uc001kjf.1_Missense_Mutation_p.K63E|TMEM20_uc001kjh.2_Intron|TMEM20_uc010qnw.1_Missense_Mutation_p.K47E|TMEM20_uc001kjj.2_Intron	NM_001134658	NP_001128130	Q2M3R5	TMM20_HUMAN	transmembrane protein 20 isoform 1	64						integral to membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;3.46e-05)|Renal(717;0.018)|Ovarian(717;0.0228)|all_hematologic(284;0.189)		STAD - Stomach adenocarcinoma(243;0.00345)		AGCCAAGAAGAAAGCACCCTG	0.388													7	644	---	---	---	---	PASS
MMS19	64210	broad.mit.edu	37	10	99229886	99229886	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99229886C>T	uc001kns.3	-	10	1071	c.846G>A	c.(844-846)CTG>CTA	p.L282L	MMS19_uc009xvs.2_5'Flank|MMS19_uc009xvt.2_Silent_p.L124L|MMS19_uc001knr.2_Silent_p.L124L|MMS19_uc010qox.1_Silent_p.L260L|MMS19_uc001knt.2_Silent_p.L282L|MMS19_uc001knu.1_RNA	NM_022362	NP_071757	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog	282	HEAT 2.				chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AATCACTCACCAGAGTCTGTA	0.463								Direct_reversal_of_damage|NER					40	289	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104119230	104119230	+	Intron	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104119230C>A	uc001kux.1	+						GBF1_uc001kuw.2_3'UTR|GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TCACCTCCCCCATCCTACCTA	0.498													15	59	---	---	---	---	PASS
KCNC1	3746	broad.mit.edu	37	11	17793557	17793557	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17793557G>A	uc001mnk.3	+	2	971	c.916G>A	c.(916-918)GTG>ATG	p.V306M	KCNC1_uc009yhc.1_Missense_Mutation_p.V306M	NM_004976	NP_004967	P48547	KCNC1_HUMAN	Shaw-related voltage-gated potassium channel	306						voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)	1						AGCCAAGGACGTGCTGGGCTT	0.617													22	60	---	---	---	---	PASS
TMEM86A	144110	broad.mit.edu	37	11	18722527	18722527	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18722527C>T	uc001moz.1	+	2	152	c.69C>T	c.(67-69)TGC>TGT	p.C23C		NM_153347	NP_699178	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	23	Helical; (Potential).					integral to membrane				ovary(1)	1						AGGCCACCTGCGTGTATTTTG	0.572													40	120	---	---	---	---	PASS
TCP11L1	55346	broad.mit.edu	37	11	33076188	33076188	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33076188A>G	uc001mud.2	+	3	613	c.213A>G	c.(211-213)AGA>AGG	p.R71R	TCP11L1_uc009yju.2_5'UTR|TCP11L1_uc010rei.1_Silent_p.R71R|TCP11L1_uc001mue.2_Silent_p.R71R	NM_018393	NP_060863	Q9NUJ3	T11L1_HUMAN	t-complex 11 (mouse) like 1	71											0						AGACAGCGAGAGGTGTCACCA	0.418													6	318	---	---	---	---	PASS
CD44	960	broad.mit.edu	37	11	35226122	35226122	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35226122A>G	uc001mvu.2	+	10	1651	c.1217A>G	c.(1216-1218)AAC>AGC	p.N406S	CD44_uc001mvv.2_Missense_Mutation_p.N363S|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron|CD44_uc010res.1_Intron|CD44_uc010ret.1_Intron|CD44_uc010reu.1_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor	406	Extracellular (Potential).|Stem.				cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	TGGTTTGGCAACAGATGGCAT	0.448													6	304	---	---	---	---	PASS
CKAP5	9793	broad.mit.edu	37	11	46766093	46766093	+	Silent	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46766093G>C	uc001ndi.1	-	43	5849	c.5739C>G	c.(5737-5739)CCC>CCG	p.P1913P	CKAP5_uc009ylg.1_Silent_p.P1806P|CKAP5_uc001ndj.1_Silent_p.P1853P|CKAP5_uc001ndh.1_Silent_p.P842P	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1913					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						TTGTGGGCGTGGGCACACATG	0.488													12	232	---	---	---	---	PASS
PGM2L1	283209	broad.mit.edu	37	11	74054422	74054422	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74054422T>C	uc001ovb.1	-	10	1554	c.1258A>G	c.(1258-1260)ATA>GTA	p.I420V		NM_173582	NP_775853	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	420					glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)					AGGAGGTCTATTATCCTACTT	0.328													5	228	---	---	---	---	PASS
ACAT1	38	broad.mit.edu	37	11	108013318	108013318	+	Intron	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108013318C>T	uc001pjy.2	+						ACAT1_uc001pjx.2_3'UTR	NM_000019	NP_000010	P24752	THIL_HUMAN	acetyl-Coenzyme A acetyltransferase 1 precursor						acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	aatcccagcactttcggaggt	0.149													17	28	---	---	---	---	PASS
C11orf34	349633	broad.mit.edu	37	11	112131327	112131327	+	5'UTR	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112131327T>C	uc009yyp.2	-	1					PTS_uc009yyo.2_Intron	NM_001145024	NP_001138496	Q6UQ28	PLET1_HUMAN	hypothetical protein LOC349633 precursor							integral to membrane					0						TCAGTCTGTTTGGAAAGTGCT	0.498													19	124	---	---	---	---	PASS
C11orf63	79864	broad.mit.edu	37	11	122817268	122817268	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122817268A>T	uc001pym.2	+	6	1994	c.1697A>T	c.(1696-1698)CAG>CTG	p.Q566L		NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1	566										ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		TGGCTCACCCAGATAATGGAG	0.468													14	99	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4747326	4747326	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4747326C>A	uc001qnb.3	-	3	266	c.37G>T	c.(37-39)GGA>TGA	p.G13*		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	13					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						TTGCATACTCCATTTTGGCTT	0.408													143	310	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6091108	6091108	+	Silent	SNP	C	T	T	rs61750632		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6091108C>T	uc001qnn.1	-	42	7381	c.7131G>A	c.(7129-7131)CCG>CCA	p.P2377P	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	2377					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GCAAACGGTGCGGGGGGCAGG	0.607													17	51	---	---	---	---	PASS
CLEC4E	26253	broad.mit.edu	37	12	8693431	8693431	+	5'UTR	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8693431C>T	uc001quo.1	-	1						NM_014358	NP_055173	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E							integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)					ctctctctctctttttctctc	0.269													8	803	---	---	---	---	PASS
LRP6	4040	broad.mit.edu	37	12	12397536	12397536	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12397536T>C	uc001rah.3	-	2	251	c.109A>G	c.(109-111)ACA>GCA	p.T37A	LRP6_uc010shl.1_Missense_Mutation_p.T37A	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	37	Extracellular (Potential).|Beta-propeller 1.				cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				TTGCCATTTGTAGCATCAACC	0.423													5	360	---	---	---	---	PASS
SFRS2IP	9169	broad.mit.edu	37	12	46321158	46321158	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46321158T>C	uc001rox.2	-	11	2613	c.2326A>G	c.(2326-2328)AGC>GGC	p.S776G	SFRS2IP_uc001row.2_Missense_Mutation_p.S461G|SFRS2IP_uc001roy.1_Missense_Mutation_p.S850G	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,	776					spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		TCTTTTGGGCTTTCAGATGGT	0.383													7	666	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49442511	49442511	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49442511T>C	uc001rta.3	-	13	4062	c.4062A>G	c.(4060-4062)GAA>GAG	p.E1354E		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1354	Poly-Glu.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CATCATCTTCTTCCTCCTCCT	0.478			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			7	341	---	---	---	---	PASS
SMARCD1	6602	broad.mit.edu	37	12	50482450	50482450	+	Intron	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50482450T>C	uc001rvx.3	+						SMARCD1_uc010smo.1_3'UTR|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						AGGCTTTGACTCTGATTGGAG	0.463													48	159	---	---	---	---	PASS
KRT6A	3853	broad.mit.edu	37	12	52884653	52884653	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52884653A>G	uc001sam.2	-	4	1110	c.901T>C	c.(901-903)TTG>CTG	p.L301L		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	301	Coil 1B.|Rod.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCATCATACAAGGCTCTCAGG	0.483													7	537	---	---	---	---	PASS
ZFC3H1	196441	broad.mit.edu	37	12	72036246	72036246	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72036246T>C	uc001swo.2	-	6	1956	c.1597A>G	c.(1597-1599)ATG>GTG	p.M533V		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	533					RNA processing	intracellular	metal ion binding	p.M533V(1)		ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						TCTGTATCCATAGCAACTTCT	0.373													6	683	---	---	---	---	PASS
E2F7	144455	broad.mit.edu	37	12	77424037	77424037	+	Silent	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77424037G>T	uc001sym.3	-	10	1694	c.1458C>A	c.(1456-1458)CTC>CTA	p.L486L	E2F7_uc009zse.2_5'UTR	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	486					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						GGTCAACAGAGAGGACAGGGA	0.473													49	169	---	---	---	---	PASS
C12orf75	387882	broad.mit.edu	37	12	105764547	105764547	+	3'UTR	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105764547T>C	uc001tlh.3	+	6					C12orf75_uc001tli.3_RNA	NM_001145199	NP_001138671	Q8TAD7	OCC1_HUMAN	hypothetical protein LOC387882												0						AAACCCTGGGTACATATTGTT	0.393													6	584	---	---	---	---	PASS
TESC	54997	broad.mit.edu	37	12	117477015	117477015	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117477015T>A	uc001twh.2	-	8	732	c.727A>T	c.(727-729)ATC>TTC	p.I243F	TESC_uc001twi.2_RNA	NM_017899	NP_060369	Q96BS2	TESC_HUMAN	tescalcin	190					negative regulation of cell proliferation|positive regulation of megakaryocyte differentiation|positive regulation of transcription, DNA-dependent|regulation of cell adhesion mediated by integrin	cytoplasm|lamellipodium|nucleus|plasma membrane|ruffle	calcium ion binding|magnesium ion binding|phosphatase inhibitor activity|protein binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		CCCTGCCAGATCTGGAAGGGA	0.642													39	93	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19419613	19419613	+	RNA	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19419613G>C	uc010tcj.1	-	1		c.26497C>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						CAAGATAATTGTGAAAAATTC	0.284													5	27	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19419620	19419620	+	RNA	SNP	A	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19419620A>T	uc010tcj.1	-	1		c.26490T>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						ATTGTGAAAAATTCTTGCCTC	0.284													5	24	---	---	---	---	PASS
ZMYM2	7750	broad.mit.edu	37	13	20579312	20579312	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20579312A>G	uc001umr.2	+	6	1530	c.1232A>G	c.(1231-1233)GAC>GGC	p.D411G	ZMYM2_uc001umq.2_Missense_Mutation_p.D324G|ZMYM2_uc001ums.2_Missense_Mutation_p.D411G|ZMYM2_uc001umt.2_Missense_Mutation_p.D411G|ZMYM2_uc010tco.1_RNA	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	411	MYM-type 2.			DK -> EQ (in Ref. 1; CAA73875).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		CTCTATGAAGACAAACAGAAT	0.323													6	425	---	---	---	---	PASS
ZAR1L	646799	broad.mit.edu	37	13	32884860	32884860	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32884860T>C	uc010abc.1	-	2	692	c.663A>G	c.(661-663)GAA>GAG	p.E221E		NM_001136571	NP_001130043	A6NP61	ZAR1L_HUMAN	zygote arrest 1-like	221						membrane	bile acid:sodium symporter activity				0						CATATTTTGGTTCCAAAAACT	0.353											OREG0022356	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	298	---	---	---	---	PASS
SLC25A15	10166	broad.mit.edu	37	13	41381591	41381591	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41381591A>G	uc001uxn.2	+	5	936	c.614A>G	c.(613-615)GAT>GGT	p.D205G	SUGT1L1_uc001uxp.1_Intron|SLC25A15_uc010tfb.1_Missense_Mutation_p.D111G|SUGT1L1_uc001uxo.1_RNA	NM_014252	NP_055067	Q9Y619	ORNT1_HUMAN	mitochondrial ornithine transporter 1	205					cellular amino acid metabolic process|mitochondrial ornithine transport|urea cycle	integral to membrane|mitochondrial inner membrane	L-ornithine transmembrane transporter activity				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	AGATCAAAAGATGAATTAGGT	0.468													6	413	---	---	---	---	PASS
C13orf18	80183	broad.mit.edu	37	13	46935706	46935706	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46935706A>G	uc010acl.2	-	8	1594	c.989T>C	c.(988-990)GTC>GCC	p.V330A	C13orf18_uc001vbf.3_Missense_Mutation_p.V263A|C13orf18_uc001vbg.3_Missense_Mutation_p.V58A|C13orf18_uc010tfz.1_Missense_Mutation_p.V173A|C13orf18_uc010acm.2_Missense_Mutation_p.V195A|C13orf18_uc010acn.2_Missense_Mutation_p.V115A|C13orf18_uc001vbe.3_Missense_Mutation_p.V330A|C13orf18_uc001vbh.3_Missense_Mutation_p.V330A|C13orf18_uc001vbi.3_Missense_Mutation_p.V173A|C13orf18_uc010aco.1_Missense_Mutation_p.V330A	NM_025113	NP_079389	Q9H714	CM018_HUMAN	hypothetical protein LOC80183	330											0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)		CTCATAAGTGACACTGAAATG	0.428													5	196	---	---	---	---	PASS
SUGT1	10910	broad.mit.edu	37	13	53261959	53261959	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53261959A>T	uc001vhc.2	+	14	1312	c.1087A>T	c.(1087-1089)AAA>TAA	p.K363*	SUGT1_uc001vhb.2_Nonsense_Mutation_p.K331*|SUGT1_uc010thb.1_Nonsense_Mutation_p.K275*|SUGT1_uc001vhd.2_Nonsense_Mutation_p.K220*	NM_001130912	NP_001124384	Q9Y2Z0	SUGT1_HUMAN	suppressor of G2 allele of SKP1 isoform a	363	SGS.				mitosis	kinetochore|ubiquitin ligase complex	binding				0		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		TATGGAATGGAAAAAGTACTA	0.348													10	402	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77785318	77785318	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77785318A>G	uc001vkf.2	-	24	3377	c.3286T>C	c.(3286-3288)TAT>CAT	p.Y1096H	MYCBP2_uc010aev.2_Missense_Mutation_p.Y500H	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	1096					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATTACATCATATACAGGATCA	0.323													67	175	---	---	---	---	PASS
SLC15A1	6564	broad.mit.edu	37	13	99371510	99371510	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99371510A>G	uc001vno.2	-	8	698	c.621T>C	c.(619-621)GCT>GCC	p.A207A		NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide	207	Helical; (Potential).				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)	CAGCCATGAGAGCAGCAGGAA	0.428													6	298	---	---	---	---	PASS
TUBGCP3	10426	broad.mit.edu	37	13	113201891	113201891	+	Intron	SNP	T	A	A	rs112103679	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113201891T>A	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron|TUBGCP3_uc001vsg.1_Missense_Mutation_p.D404V	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					CGTGGGAAAGTCGCGCGTGGG	0.597													6	47	---	---	---	---	PASS
TUBGCP3	10426	broad.mit.edu	37	13	113201894	113201894	+	Intron	SNP	C	T	T	rs112767817	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113201894C>T	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron|TUBGCP3_uc001vsg.1_Missense_Mutation_p.R403H	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					GGGAAAGTCGCGCGTGGGAAA	0.602													6	55	---	---	---	---	PASS
EIF2B2	8892	broad.mit.edu	37	14	75475938	75475938	+	3'UTR	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75475938A>G	uc001xrc.1	+	8						NM_014239	NP_055054	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B,						cellular response to stimulus|myelination|oligodendrocyte development|ovarian follicle development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	ATP binding|GTP binding|protein binding|translation initiation factor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00661)		ATACAGAATGAAGAGGAGACT	0.453													49	109	---	---	---	---	PASS
SERPINA4	5267	broad.mit.edu	37	14	95029883	95029883	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95029883C>T	uc001ydk.2	+	2	130	c.64C>T	c.(64-66)CTG>TTG	p.L22L	SERPINA4_uc010avd.2_Silent_p.L59L|SERPINA4_uc001ydl.2_Silent_p.L22L	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade	22					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)|skin(1)	4				COAD - Colon adenocarcinoma(157;0.211)		TCATGGCCAGCTGCACGTTGA	0.562													16	47	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106372754	106372754	+	Splice_Site	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106372754C>T	uc010tyt.1	-	2763		c.46358_splice	c.e2763-1		KIAA0125_uc001ysq.2_Intron|KIAA0125_uc001ysr.2_Intron|KIAA0125_uc001yss.2_5'Flank					Parts of antibodies, mostly variable regions.												0						TGATCTCGAACACCAGTTTAT	0.547													5	7	---	---	---	---	PASS
GOLGA6L6	727832	broad.mit.edu	37	15	20740040	20740040	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20740040A>C	uc001ytk.2	-	8	1801	c.1710T>G	c.(1708-1710)GAT>GAG	p.D570E	uc010tzb.1_5'Flank	NM_001145004	NP_001138476	A8MZA4	GG6L6_HUMAN	golgi autoantigen, golgin subfamily a, 6-like 6	570	Potential.|Glu-rich.|Gln-rich.										0						tccacatcttatcctcctgct	0.050													14	169	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22383016	22383016	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22383016C>T	uc001yuc.1	+	7	1525	c.544C>T	c.(544-546)CGA>TGA	p.R182*	LOC727924_uc001yub.1_Intron|OR4N4_uc010tzv.1_Nonsense_Mutation_p.R182*	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTGTGATGTCCGACAGGTCAT	0.527													4	190	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	42984191	42984191	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42984191C>T	uc010udj.1	+	1	2399	c.1397C>T	c.(1396-1398)CCG>CTG	p.P466L	uc010bcw.2_RNA					Homo sapiens mRNA for KIAA1300 protein, partial cds.																		TATGCGCTGCCGTGGCGTCCG	0.557													4	89	---	---	---	---	PASS
GOLGA6L10	647042	broad.mit.edu	37	15	82635163	82635163	+	RNA	SNP	C	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82635163C>G	uc002bgx.2	-	5		c.417G>C						A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						CCCTGTTCTCCGCAGCCCGAA	0.478													16	56	---	---	---	---	PASS
MRPL28	10573	broad.mit.edu	37	16	418395	418395	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:418395T>C	uc002cgr.1	-	4	612	c.596A>G	c.(595-597)GAG>GGG	p.E199G	MRPL28_uc010bqu.1_Intron|MRPL28_uc002cgs.1_Missense_Mutation_p.E199G|MRPL28_uc002cgt.1_Missense_Mutation_p.E199G	NM_006428	NP_006419	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28 precursor	199					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				CTCTGCCTCCTCCTCTGGGAT	0.627													4	68	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24231490	24231490	+	3'UTR	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24231490G>T	uc002dmd.2	+	17					PRKCB_uc002dme.2_3'UTR	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	CCAAGCGTATGTATCAATTCT	0.443													44	144	---	---	---	---	PASS
SLC6A10P	386757	broad.mit.edu	37	16	32890950	32890950	+	Missense_Mutation	SNP	A	G	G	rs151263854	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32890950A>G	uc002edh.1	-	3	280	c.104T>C	c.(103-105)GTC>GCC	p.V35A	SLC6A10P_uc002edi.1_RNA					RecName: Full=Transporter;												0						ATACACCCAGACCACCACCAC	0.637													5	66	---	---	---	---	PASS
CDH16	1014	broad.mit.edu	37	16	66944295	66944295	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66944295G>A	uc002eql.2	-	15	2108	c.2035C>T	c.(2035-2037)CGC>TGC	p.R679C	CDH16_uc010cdy.2_Missense_Mutation_p.R657C|CDH16_uc002eqm.2_Missense_Mutation_p.R582C	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	679	Extracellular (Potential).|Ectodomain G.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|upper_aerodigestive_tract(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		TGGTCTTGGCGGGGTGTGCAG	0.632													4	222	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													3	28	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7667223	7667223	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7667223C>T	uc002giu.1	+	18	3067	c.3053C>T	c.(3052-3054)TCG>TTG	p.S1018L		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1018	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGGACTGTTCGCACCTCAAG	0.562													33	81	---	---	---	---	PASS
TRPV2	51393	broad.mit.edu	37	17	16329580	16329580	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16329580C>T	uc002gpy.2	+	6	1459	c.1092C>T	c.(1090-1092)AGC>AGT	p.S364S	TRPV2_uc002gpz.2_Intron	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	364	Cytoplasmic (Potential).|Required for interaction with SLC50A1 (By similarity).				sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATTGCAAGAGCCCGGTGAGCC	0.582													4	193	---	---	---	---	PASS
SYNRG	11276	broad.mit.edu	37	17	35937489	35937489	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35937489A>G	uc002hoa.2	-	7	895	c.812T>C	c.(811-813)ATT>ACT	p.I271T	SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Missense_Mutation_p.I271T|SYNRG_uc002hof.2_5'Flank|SYNRG_uc010cvd.1_Intron|SYNRG_uc002hog.1_Missense_Mutation_p.I405T|SYNRG_uc010wdh.1_Intron	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	271					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						ACTCTCTTCAATTGACAGGTT	0.408													7	394	---	---	---	---	PASS
PIP4K2B	8396	broad.mit.edu	37	17	36935738	36935738	+	Silent	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36935738C>A	uc002hqs.2	-	5	1033	c.552G>T	c.(550-552)CTG>CTT	p.L184L	PIP4K2B_uc010wdt.1_Silent_p.L184L|PIP4K2B_uc010wdu.1_Silent_p.L120L	NM_003559	NP_003550	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	184	PIPK.				cell surface receptor linked signaling pathway	endoplasmic reticulum membrane|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|receptor signaling protein activity			ovary(1)	1						GGTACATGCCCAGGAACTGTG	0.517													39	58	---	---	---	---	PASS
C17orf57	124989	broad.mit.edu	37	17	45473242	45473242	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45473242A>G	uc002iln.2	+	17	2255	c.1844A>G	c.(1843-1845)GAG>GGG	p.E615G	C17orf57_uc002ilm.2_Missense_Mutation_p.E519G	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	615							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						CTCAGAAAGGAGACGATGAGT	0.363													7	533	---	---	---	---	PASS
DHX40P1	653645	broad.mit.edu	37	17	58066651	58066651	+	Silent	SNP	C	T	T	rs144367363	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58066651C>T	uc002iyf.2	-	9	721	c.486G>A	c.(484-486)CAG>CAA	p.Q162Q	uc002iye.1_Intron	NR_002924				Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263).												0						ACTGGTAAAGCTGTTTAAGAG	0.333													5	332	---	---	---	---	PASS
WBP2	23558	broad.mit.edu	37	17	73851365	73851365	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73851365T>A	uc002jps.2	-	1	137	c.14A>T	c.(13-15)AAG>ATG	p.K5M	WBP2_uc002jpr.2_Translation_Start_Site|WBP2_uc010wsl.1_Translation_Start_Site|WBP2_uc002jpt.2_Missense_Mutation_p.K5M|WBP2_uc002jpu.1_RNA|WBP2_uc010wsm.1_Missense_Mutation_p.K5M|WBP2_uc010wsn.1_Missense_Mutation_p.K5M	NM_012478	NP_036610	Q969T9	WBP2_HUMAN	WW domain binding protein 2	5	GRAM.						protein binding				0			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGAGTGATTCTTGTTGAGCGC	0.562													24	97	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3188908	3188908	+	Silent	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3188908T>C	uc002klp.2	-	4	943	c.609A>G	c.(607-609)ACA>ACG	p.T203T	MYOM1_uc002klq.2_Silent_p.T203T	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	203	4.|6 X 6 AA tandem repeats.					striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GCTTGGATGCTGTGGACTGCT	0.532													9	726	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14542798	14542798	+	Silent	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14542798G>A	uc010dln.2	-	1	802	c.348C>T	c.(346-348)AAC>AAT	p.N116N	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	116										skin(3)	3						AAGCGCCCACGTTGCTCTTGC	0.602													5	110	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31320355	31320355	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31320355C>A	uc010dmg.1	+	11	3042	c.2987C>A	c.(2986-2988)CCA>CAA	p.P996Q	ASXL3_uc002kxq.2_Missense_Mutation_p.P703Q	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	996					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TCTAGCAGCCCACCTGAGAAA	0.443													38	89	---	---	---	---	PASS
ELAC1	55520	broad.mit.edu	37	18	48510776	48510776	+	Silent	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48510776C>A	uc002lez.2	+	3	574	c.468C>A	c.(466-468)ATC>ATA	p.I156I	ELAC1_uc010dpe.2_Silent_p.I156I|SMAD4_uc010xdo.1_Intron	NM_018696	NP_061166	Q9H777	RNZ1_HUMAN	elaC homolog 1	156					tRNA 3'-trailer cleavage	nucleus	endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GAAGAACTATCCTGTTAGACT	0.398													39	169	---	---	---	---	PASS
CDH19	28513	broad.mit.edu	37	18	64211439	64211439	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64211439T>C	uc002lkc.1	-	7	1121	c.983A>G	c.(982-984)AAC>AGC	p.N328S	CDH19_uc010dql.1_RNA|CDH19_uc010xey.1_Missense_Mutation_p.N328S|CDH19_uc002lkd.2_Missense_Mutation_p.N328S	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein	328	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				ACCGTAGTGGTTCTGGTGCTC	0.388													6	389	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9049931	9049931	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9049931G>T	uc002mkp.2	-	5	31904	c.31700C>A	c.(31699-31701)ACC>AAC	p.T10567N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10569	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGAGGCTGTGGTCTCTGATTC	0.493													9	579	---	---	---	---	PASS
ZNF442	79973	broad.mit.edu	37	19	12461589	12461589	+	Silent	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12461589A>G	uc002mtr.1	-	6	1421	c.810T>C	c.(808-810)TGT>TGC	p.C270C	ZNF442_uc010xmk.1_Silent_p.C201C	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	270	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4						AGGCTTTGGAACAGTGCTTGC	0.403													5	225	---	---	---	---	PASS
CHST8	64377	broad.mit.edu	37	19	34180166	34180166	+	5'UTR	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34180166G>A	uc002nus.3	+	3					CHST8_uc002nut.3_5'UTR|CHST8_uc002nuu.2_5'UTR	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)					AGCCAGCCCCGGATGACCCTG	0.632													12	33	---	---	---	---	PASS
SRRM5	100170229	broad.mit.edu	37	19	44117603	44117603	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44117603T>A	uc002oxb.2	+	3	1683	c.1330T>A	c.(1330-1332)TAC>AAC	p.Y444N	ZNF428_uc002oxa.2_Intron|SRRM5_uc010xwr.1_Missense_Mutation_p.Y444N	NM_001145641	NP_001139113	B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	444	Ser-rich.										0						TAGAAGTCCCTACAAGGCGAG	0.537													8	181	---	---	---	---	PASS
CCDC155	147872	broad.mit.edu	37	19	49912528	49912528	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49912528G>C	uc002pnm.1	+	14	1308	c.1134G>C	c.(1132-1134)GAG>GAC	p.E378D	CCDC155_uc010emx.1_Missense_Mutation_p.E351D	NM_144688	NP_653289	Q8N6L0	CC155_HUMAN	coiled-coil domain containing 155	378						integral to membrane	calcium ion binding			ovary(1)|central_nervous_system(1)	2						TGGAGATCGAGGCCATTCGAC	0.602													16	62	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57642538	57642538	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57642538T>C	uc002qny.2	+	4	2851	c.2495T>C	c.(2494-2496)ATC>ACC	p.I832T		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	832					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTCAGCCATATCGGGAGCTCC	0.473													5	164	---	---	---	---	PASS
ZNF343	79175	broad.mit.edu	37	20	2465254	2465254	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2465254A>G	uc002wge.1	-	6	841	c.353T>C	c.(352-354)TTC>TCC	p.F118S	ZNF343_uc010gao.1_Missense_Mutation_p.F118S|ZNF343_uc002wgd.1_Missense_Mutation_p.F28S	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	118	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CTGACAGGAGAAGGCCAGAAG	0.468													5	115	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21307196	21307196	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21307196T>C	uc002wsf.1	+	3	367	c.272T>C	c.(271-273)ATT>ACT	p.I91T	XRN2_uc002wsg.1_Missense_Mutation_p.I15T|XRN2_uc010zsk.1_Missense_Mutation_p.I37T	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	91					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						CTTTTCAGTATTGTAAGACCA	0.328													6	505	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29632643	29632643	+	Intron	SNP	T	C	C	rs143379667	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29632643T>C	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.L75P					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GACCACAAACTTAAAATAAGT	0.294													12	63	---	---	---	---	PASS
RALGAPB	57148	broad.mit.edu	37	20	37169704	37169704	+	Silent	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37169704G>A	uc002xiw.2	+	18	2840	c.2583G>A	c.(2581-2583)CTG>CTA	p.L861L	RALGAPB_uc002xix.2_Silent_p.L857L|RALGAPB_uc002xiy.1_Silent_p.L861L|RALGAPB_uc002xiz.2_Silent_p.L639L|RALGAPB_uc002xja.1_Silent_p.L588L	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	861					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						AGGAAGTACTGGAGATTGTGG	0.368													5	483	---	---	---	---	PASS
SPINLW1	57119	broad.mit.edu	37	20	44166690	44166690	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44166690T>C	uc010zxc.1	-	4	467	c.435A>G	c.(433-435)ATA>ATG	p.I145M	WFDC6_uc002xos.1_Missense_Mutation_p.I45M	NM_020398	NP_065131	O95925	EPPI_HUMAN	serine peptidase inhibitor-like, with Kunitz and	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						extracellular region	serine-type endopeptidase inhibitor activity			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				TACACTGGTCTATTTCTTCCA	0.478													5	539	---	---	---	---	PASS
ARFGEF2	10564	broad.mit.edu	37	20	47612391	47612391	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47612391T>C	uc002xtx.3	+	23	3345	c.3193T>C	c.(3193-3195)TCG>CCG	p.S1065P	ARFGEF2_uc010zyf.1_Missense_Mutation_p.S358P	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1065					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TGAGACCAGCTCGCAGAGTGT	0.468													6	492	---	---	---	---	PASS
PEX26	55670	broad.mit.edu	37	22	18566476	18566476	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18566476G>C	uc002znp.3	+	4	854	c.645G>C	c.(643-645)GAG>GAC	p.E215D	TUBA8_uc002znr.2_Intron|PEX26_uc002znq.3_Missense_Mutation_p.E215D|PEX26_uc002znt.2_Missense_Mutation_p.E215D	NM_017929	NP_060399	Q7Z412	PEX26_HUMAN	peroxisome biogenesis factor 26	215	Cytoplasmic (Potential).				protein import into peroxisome matrix|protein import into peroxisome membrane	integral to peroxisomal membrane	protein C-terminus binding|protein complex binding			skin(1)	1						GCTCTGAGGAGGCCCAGAAGC	0.567													36	115	---	---	---	---	PASS
TOP3B	8940	broad.mit.edu	37	22	22323060	22323060	+	Silent	SNP	T	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22323060T>A	uc002zvs.2	-	7	1104	c.669A>T	c.(667-669)GGA>GGT	p.G223G	TOP3B_uc010gtm.1_5'Flank|TOP3B_uc002zvr.2_5'UTR|TOP3B_uc010gtl.2_Silent_p.G223G|TOP3B_uc002zvt.3_Silent_p.G223G	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	223					DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CCACACAGAATCCCAGGGTTG	0.502													5	285	---	---	---	---	PASS
SCUBE1	80274	broad.mit.edu	37	22	43614319	43614319	+	Silent	SNP	C	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43614319C>T	uc003bdt.1	-	15	1921	c.1833G>A	c.(1831-1833)AAG>AAA	p.K611K		NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	611					adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				CCTCCAGCGCCTTGGCTGGCC	0.632													14	16	---	---	---	---	PASS
VCX3B	425054	broad.mit.edu	37	X	8433461	8433461	+	5'UTR	SNP	T	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8433461T>C	uc010ndo.2	+	2					VCX3B_uc011mht.1_5'UTR|VCX3B_uc004csd.1_5'UTR	NM_001001888	NP_001001888	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B							nucleolus					0						CTGGAGTTAGTCGACCGTTGC	0.592													5	71	---	---	---	---	PASS
LPAR4	2846	broad.mit.edu	37	X	78011061	78011061	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78011061G>A	uc010nme.2	+	2	1100	c.695G>A	c.(694-696)CGC>CAC	p.R232H		NM_005296	NP_005287	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	232	Cytoplasmic (Potential).					integral to plasma membrane	lipid binding|purinergic nucleotide receptor activity, G-protein coupled			ovary(3)	3						AGAACTCTTCGCAAGCCTGCT	0.373													4	166	---	---	---	---	PASS
IL9R	3581	broad.mit.edu	37	X	155233148	155233148	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155233148C>A	uc004fnv.1	+	3	356	c.177C>A	c.(175-177)AAC>AAA	p.N59K	IL9R_uc010nvn.2_Missense_Mutation_p.N38K|IL9R_uc004fnu.1_Missense_Mutation_p.N106K	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	59	Extracellular (Potential).				cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCCTCACCAACAACATTCTCA	0.607													82	189	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2008	2008	+	5'Flank	SNP	G	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2008G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CCTACCGAGCCTGGTGATAGC	0.418													5	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13270	13270	+	RNA	SNP	C	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13270C>A	uc004cox.3	+	1		c.934C>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		GTCAACTAGGACTCATAATAG	0.458													89	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	10390	10390	+	5'Flank	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10390delC	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		ctaaccctaacccctaacccc	0.000													7	4	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3131653	3131653	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3131653delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGACACCATCCCATCTGCTT	0.507			T	EVI1	MDS|AML								4	2	---	---	---	---	
WDR8	49856	broad.mit.edu	37	1	3563513	3563513	+	Intron	DEL	C	-	-	rs34514629		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3563513delC	uc001ako.2	-						WDR8_uc001akn.3_Intron|WDR8_uc010nzi.1_Intron	NM_017818	NP_060288	Q9P2S5	WRP73_HUMAN	WD repeat domain 8							centrosome	protein binding				0	all_cancers(77;0.0128)|all_epithelial(69;0.00526)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-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;4.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.16e-22)|GBM - Glioblastoma multiforme(42;1.05e-14)|Colorectal(212;1.19e-05)|BRCA - Breast invasive adenocarcinoma(365;2.67e-05)|COAD - Colon adenocarcinoma(227;5.82e-05)|Kidney(185;0.000364)|KIRC - Kidney renal clear cell carcinoma(229;0.00223)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		TTAAAACCAGCAGAGACCCGA	0.512													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11607674	11607675	+	IGR	DEL	AG	-	-	rs34399641		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11607674_11607675delAG								PTCHD2 (10035 upstream) : FBXO2 (100775 downstream)																							agacagaggcagagagagagag	0.020													4	8	---	---	---	---	
MAD2L2	10459	broad.mit.edu	37	1	11750579	11750579	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11750579delG	uc009vnc.2	-						MAD2L2_uc001asq.3_Intron|C1orf187_uc001asr.1_5'Flank	NM_001127325	NP_001120797	Q9UI95	MD2L2_HUMAN	MAD2 homolog						cell division|DNA damage response, signal transduction resulting in transcription|double-strand break repair|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of transcription, DNA-dependent|regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleoplasm|spindle|zeta DNA polymerase complex	JUN kinase binding				0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		cgaggtcataggggacggcat	0.219								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
PLOD1	5351	broad.mit.edu	37	1	12004289	12004290	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12004289_12004290insA	uc001atm.2	+						PLOD1_uc010obb.1_Intron	NM_000302	NP_000293	Q02809	PLOD1_HUMAN	lysyl hydroxylase 1 precursor						epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)	gactctgtctcaaaaaaaaaaa	0.099													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15171409	15171409	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15171409delG	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						ttggtgttttggtgggtgggG	0.005													4	2	---	---	---	---	
CTRC	11330	broad.mit.edu	37	1	15772454	15772455	+	Intron	INS	-	ATTT	ATTT	rs150994793	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15772454_15772455insATTT	uc001awi.1	+						CTRC_uc001awj.1_Intron	NM_007272	NP_009203	Q99895	CTRC_HUMAN	chymotrypsin C preproprotein						proteolysis		serine-type endopeptidase activity				0		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ttcactcatgcattcattcatt	0.000													5	3	---	---	---	---	
FBLIM1	54751	broad.mit.edu	37	1	16087232	16087232	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16087232delA	uc001axd.1	+						FBLIM1_uc001axe.1_Intron|FBLIM1_uc001axf.2_Intron	NM_017556	NP_060026	Q8WUP2	FBLI1_HUMAN	filamin-binding LIM protein-1 isoform a						cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytoskeleton|cytosol|focal adhesion|intracellular membrane-bounded organelle	zinc ion binding			skin(1)	1		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		TCCTTTGGACAGGAAATGACT	0.582													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16929805	16929808	+	Intron	DEL	CTTC	-	-	rs140610974		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16929805_16929808delCTTC	uc009vos.1	-						NBPF1_uc001aza.3_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		gtctctggatcttccTTGATGGGA	0.025													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17053517	17053521	+	IGR	DEL	AAAAG	-	-	rs67944636		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17053517_17053521delAAAAG								ESPNP (6865 upstream) : CROCC (13247 downstream)																							AAGATTAGAAAAAAGAAACATGAAT	0.327													4	2	---	---	---	---	
IFFO2	126917	broad.mit.edu	37	1	19252276	19252276	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19252276delA	uc001bbd.2	-							NM_001136265	NP_001129737	Q5TF58	IFFO2_HUMAN	intermediate filament family orphan 2												0						ggatggatggattggttggat	0.000													4	2	---	---	---	---	
HSPG2	3339	broad.mit.edu	37	1	22179402	22179403	+	Intron	INS	-	C	C	rs142340642	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22179402_22179403insC	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	GTCCCGGGGGGCTGCCATACCT	0.698													4	2	---	---	---	---	
HMGCL	3155	broad.mit.edu	37	1	24142941	24142942	+	Intron	INS	-	CCT	CCT			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24142941_24142942insCCT	uc001bib.2	-						HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Intron|HMGCL_uc009vqs.1_Intron|HMGCL_uc001bid.1_Intron	NM_000191	NP_000182	P35914	HMGCL_HUMAN	3-hydroxy-3-methylglutaryl CoA lyase isoform 1						acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		ttctgaaatgctcacaacttca	0.030													4	2	---	---	---	---	
RUNX3	864	broad.mit.edu	37	1	25258683	25258683	+	5'Flank	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25258683delG	uc001bjq.2	-						RUNX3_uc010oen.1_5'Flank|RUNX3_uc009vrj.2_Intron|RUNX3_uc001bjr.2_Intron|RUNX3_uc009vrk.2_Intron|RUNX3_uc009vrl.1_Intron	NM_004350	NP_004341	Q13761	RUNX3_HUMAN	runt-related transcription factor 3 isoform 2						cell proliferation|induction of apoptosis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|protein phosphorylation|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		CGCTTACGATGGGTTCACAGA	0.587													4	2	---	---	---	---	
PTPRU	10076	broad.mit.edu	37	1	29560961	29560961	+	5'Flank	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29560961delA	uc001bru.2	+						PTPRU_uc001brv.2_5'Flank|PTPRU_uc001brw.2_5'Flank|PTPRU_uc009vtq.2_5'Flank|PTPRU_uc009vtr.2_5'Flank	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U						canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CTGGAGCTGTaaaaaaaaaaa	0.308													3	3	---	---	---	---	
HCRTR1	3061	broad.mit.edu	37	1	32085626	32085627	+	Intron	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32085626_32085627delGT	uc009vtx.2	+						HCRTR1_uc001btb.2_Intron|HCRTR1_uc001btc.3_Intron|HCRTR1_uc001btd.2_Intron|HCRTR1_uc010ogl.1_Intron	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1						feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		ACAGCCCACAGTGACACATACA	0.569													4	2	---	---	---	---	
ADC	113451	broad.mit.edu	37	1	33563269	33563269	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33563269delG	uc001bwr.2	+						ADC_uc001bws.2_Intron|ADC_uc009vue.2_Intron|ADC_uc001bwt.1_Intron|ADC_uc001bwu.2_Intron|ADC_uc001bwv.2_Intron|ADC_uc001bww.2_Intron|ADC_uc001bwx.1_Intron|ADC_uc001bwz.1_Intron|ADC_uc009vuf.1_Intron|ADC_uc001bwy.1_Intron|ADC_uc009vug.2_Intron	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2						polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)	TTATAGACCTGGGGGATTGTC	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34837356	34837356	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34837356delG								C1orf94 (152627 upstream) : MIR552 (297844 downstream)																							tagatagatagatagatagat	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35596379	35596380	+	IGR	DEL	TT	-	-	rs76536607		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35596379_35596380delTT								ZMYM1 (14925 upstream) : SFPQ (45602 downstream)																							TTATTGAGTGTTTTTTTTTTTT	0.188													3	3	---	---	---	---	
HPCAL4	51440	broad.mit.edu	37	1	40148562	40148562	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40148562delT	uc001cdr.2	-						HPCAL4_uc010oix.1_Intron	NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	hippocalcin-like protein 4						central nervous system development	intracellular	calcium ion binding			central_nervous_system(1)	1	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGAGCAACtcttttttttttt	0.234													2	5	---	---	---	---	
EIF2B3	8891	broad.mit.edu	37	1	45418928	45418928	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45418928delA	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TTTTTCATTGAAAAAAAAGAA	0.129													4	2	---	---	---	---	
EIF2B3	8891	broad.mit.edu	37	1	45418937	45418937	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45418937delA	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GAAAAAAAAGAAAAaaaaaag	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	50684288	50684288	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50684288delC								ELAVL4 (16748 upstream) : DMRTA2 (198941 downstream)																							AGTCCAGTGGCCCAGCAGCGC	0.468													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51058610	51058610	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51058610delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.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			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		actctgtttcaaaaaaaaaaa	0.070													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56382747	56382748	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56382747_56382748delGA								USP24 (701985 upstream) : PPAP2B (577685 downstream)																							ttaacactgcgagagagagaga	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	77168788	77168789	+	IGR	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77168788_77168789delCT								ST6GALNAC3 (72119 upstream) : ST6GALNAC5 (164397 downstream)																							AAGAGGGCAACTCTCTCTCTCT	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	77177626	77177626	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77177626delT								ST6GALNAC3 (80957 upstream) : ST6GALNAC5 (155560 downstream)																							tgacaattactttGTTTCAAA	0.194													4	2	---	---	---	---	
TTLL7	79739	broad.mit.edu	37	1	84413169	84413169	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84413169delA	uc001djc.2	-						TTLL7_uc001djb.2_Intron|TTLL7_uc001djd.2_Intron|TTLL7_uc001dje.2_Intron|TTLL7_uc001djf.2_Intron|TTLL7_uc001djg.2_Intron	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		ttcatcagtgaaaaaaaaaaa	0.035													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95274052	95274053	+	Intron	INS	-	T	T	rs148794556	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95274052_95274053insT	uc001dqu.2	-											Homo sapiens cDNA clone IMAGE:4795773.																		AGCATTTTAGGTACATTAATCA	0.396													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96578763	96578764	+	IGR	DEL	AG	-	-	rs140517181		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96578763_96578764delAG								RWDD3 (865990 upstream) : PTBP2 (608411 downstream)																							GTGAATGTTCAGAGTCTTTACT	0.307													4	3	---	---	---	---	
VAV3	10451	broad.mit.edu	37	1	108463820	108463820	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108463820delA	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGCTGCAGATATCCGAAAGCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110496525	110496525	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110496525delG								CSF1 (24171 upstream) : AHCYL1 (30783 downstream)																							TGACCCCCCAGTGAGTCATTG	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	112687244	112687245	+	IGR	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112687244_112687245delCT								KCND3 (155467 upstream) : CTTNBP2NL (251555 downstream)																							tttttagttcctctctctctcc	0.040													4	2	---	---	---	---	
TSPAN2	10100	broad.mit.edu	37	1	115602826	115602826	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115602826delT	uc001eft.2	-							NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TTAGAGATCCTTTTTTTTTTG	0.373													5	7	---	---	---	---	
PTGFRN	5738	broad.mit.edu	37	1	117529859	117529860	+	3'UTR	INS	-	T	T	rs138984974	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117529859_117529860insT	uc001egv.1	+	9						NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		CCTTCATCTAATTTTTTTTCTC	0.446													3	3	---	---	---	---	
HAO2	51179	broad.mit.edu	37	1	119935343	119935344	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119935343_119935344insA	uc001ehq.1	+						HAO2_uc001ehr.1_Intron	NM_001005783	NP_001005783	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2						fatty acid alpha-oxidation	peroxisome	(S)-2-hydroxy-acid oxidase activity			ovary(2)|skin(2)	4	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		ATTTGGAACTTAAAGCAGGATG	0.431													164	71	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142608175	142608176	+	IGR	DEL	TG	-	-	rs141317539		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142608175_142608176delTG								None (None upstream) : None (None downstream)																							tgacaaaaactgcatgattatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143425098	143425099	+	5'Flank	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143425098_143425099insA	hsa-mir-3118-3|MI0014133	-						uc001ejn.1_RNA																							ccagtaatgctaaaaaccaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143495448	143495449	+	IGR	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143495448_143495449insC								None (None upstream) : LOC100286793 (152190 downstream)																							CTTAGCATTTACCCCCATTTCT	0.248													10	5	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145031540	145031540	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145031540delG	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	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)		ttacaatacagggatTCAGGT	0.159			T	PDGFRB	MPD								4	2	---	---	---	---	
PMVK	10654	broad.mit.edu	37	1	154910321	154910321	+	5'Flank	DEL	T	-	-	rs12045997	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154910321delT	uc001ffq.2	-							NM_006556	NP_006547	Q15126	PMVK_HUMAN	phosphomevalonate kinase						cholesterol biosynthetic process|protein phosphorylation	cytosol|peroxisome	ATP binding|phosphomevalonate kinase activity|protein binding				0	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TTTTTTGGGGTTTTTTTTGTT	0.423													4	2	---	---	---	---	
GPATCH4	54865	broad.mit.edu	37	1	156573009	156573009	+	5'Flank	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156573009delT	uc001fpm.2	-						GPATCH4_uc001fpl.2_5'Flank	NM_015590	NP_056405	Q5T3I0	GPTC4_HUMAN	G patch domain containing 4 isoform 1							intracellular	nucleic acid binding			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTTGAACAAttttttttttt	0.209													3	3	---	---	---	---	
ARHGEF11	9826	broad.mit.edu	37	1	157014457	157014457	+	5'UTR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157014457delA	uc001fqo.2	-	1					ARHGEF11_uc001fqn.2_5'UTR	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CACTATGGCCAAAAAAAAATG	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163949149	163949149	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163949149delT								NUF2 (623596 upstream) : PBX1 (579653 downstream)																							CAAGCTTTTCTTTTTTTTAAG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	164445863	164445863	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164445863delA								None (None upstream) : PBX1 (82939 downstream)																							ATTCTCAGGGAAAAAAAAAAG	0.279													4	3	---	---	---	---	
ADCY10	55811	broad.mit.edu	37	1	167863667	167863667	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167863667delC	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron|ADCY10_uc009wvl.2_Intron|ADCY10_uc009wvm.2_Intron	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10						intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3						cctcctatttcctcacctggg	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175003755	175003755	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175003755delC								MRPS14 (11194 upstream) : TNN (33239 downstream)																							TTCCTTTTTTCCTCATTTACC	0.338													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175516701	175516704	+	Intron	DEL	GAAA	-	-	rs71808077		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175516701_175516704delGAAA	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					aagatagaaggaaagaaagaaaga	0.000													4	2	---	---	---	---	
FAM163A	148753	broad.mit.edu	37	1	179711246	179711246	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179711246delA	uc009wxj.2	+						FAM163A_uc001gnj.2_5'Flank|FAM163A_uc009wxk.2_5'Flank	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753							integral to membrane				ovary(1)	1						GAGTTAGAGTAAAAAGTGGAG	0.403													4	2	---	---	---	---	
RGS13	6003	broad.mit.edu	37	1	192602629	192602629	+	5'Flank	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192602629delT	uc001gsj.2	+						RGS13_uc001gsk.2_5'Flank	NM_002927	NP_002918	O14921	RGS13_HUMAN	regulator of G-protein signalling 13							plasma membrane	GTPase activator activity|signal transducer activity				0						GAGTGTCTCCTTTTTTTTTTC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193658513	193658513	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193658513delT								CDC73 (434573 upstream) : None (None downstream)																							tgggttgttgttacatacact	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196612411	196612411	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196612411delA								KCNT2 (34912 upstream) : CFH (8597 downstream)																							cccatttaggaaaaaaaagta	0.000													4	2	---	---	---	---	
CACNA1S	779	broad.mit.edu	37	1	201017076	201017076	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201017076delC	uc001gvv.2	-							NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	GGCCCAAATACCCCCAGGCAG	0.527													4	2	---	---	---	---	
CACNA1S	779	broad.mit.edu	37	1	201019881	201019881	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201019881delA	uc001gvv.2	-							NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TAACCAAAACAAAAAAAAAAA	0.289													8	4	---	---	---	---	
NAV1	89796	broad.mit.edu	37	1	201677385	201677386	+	Intron	INS	-	CT	CT	rs141310076	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201677385_201677386insCT	uc001gwu.2	+							NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						GTTGGGAGAGACTTGCATCTGT	0.525													4	4	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202173341	202173342	+	Intron	INS	-	CA	CA	rs111964081		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202173341_202173342insCA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						CCTCCTTCAAGcacacacacac	0.277													5	4	---	---	---	---	
MDM4	4194	broad.mit.edu	37	1	204511693	204511695	+	Intron	DEL	GAT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204511693_204511695delGAT	uc001hba.2	+						MDM4_uc001hbd.1_Intron|MDM4_uc010pqw.1_Intron|MDM4_uc010pqx.1_Intron|MDM4_uc001hay.1_Intron|MDM4_uc001hbb.2_Intron|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_Intron|MDM4_uc009xbe.1_Intron	NM_002393	NP_002384	O15151	MDM4_HUMAN	mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			CTTGATAAACGATGATCTGTTTG	0.345			A		GBM|bladder|retinoblastoma								6	3	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206634174	206634175	+	Intron	INS	-	A	A	rs143386629	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206634174_206634175insA	uc001hdy.2	+						SRGAP2_uc010pru.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TTTTCTAAAGGAAAAAAAAAAT	0.218													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215814185	215814186	+	Intron	DEL	AC	-	-	rs2995518		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215814185_215814186delAC	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)		ACCAATCCaaacaaaaaaaaaa	0.317										HNSCC(13;0.011)			8	5	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217155756	217155756	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217155756delT	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CATTCTTTGATTTTTTTTCTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221502321	221502322	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221502321_221502322delTG								HLX (443923 upstream) : LOC400804 (948 downstream)																							tctctctctctgtgtgtgtgtg	0.267													2	4	---	---	---	---	
DNAH14	127602	broad.mit.edu	37	1	225525299	225525300	+	Intron	INS	-	A	A	rs149594225	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225525299_225525300insA	uc001how.2	+						DNAH14_uc001hox.2_Intron	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						AACTGTCAGGGAAAAAATAATA	0.386													8	7	---	---	---	---	
H3F3A	3020	broad.mit.edu	37	1	226252976	226252976	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226252976delT	uc001hpw.2	+						H3F3A_uc010pvl.1_Intron	NM_005324	NP_005315	P84243	H33_HUMAN	H3 histone, family 3B						blood coagulation|nucleosome assembly	nucleoplasm|nucleosome	DNA binding				0	Breast(184;0.179)			GBM - Glioblastoma multiforme(131;0.203)		GTTGGTCATCTTTAAGGGCTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	233716360	233716360	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233716360delC								KIAA1804 (195467 upstream) : KCNK1 (33390 downstream)																							gaccataacacctctggcaag	0.000													4	2	---	---	---	---	
GNG4	2786	broad.mit.edu	37	1	235780026	235780027	+	Intron	INS	-	TG	TG	rs144780891	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235780026_235780027insTG	uc001hxe.3	-						GNG4_uc009xfz.2_Intron|GNG4_uc001hxh.3_Intron	NM_001098722	NP_001092192	P50150	GBG4_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|negative regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)			GTGCTGAAAGAtgtgtgtgtgt	0.238													2	4	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236693816	236693816	+	Intron	DEL	G	-	-	rs2794788	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236693816delG	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ATCACTCATAGATTTTTTTTT	0.358													4	2	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240376405	240376405	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240376405delT	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ATCATCAAACTTCACATTAAA	0.363													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246032465	246032465	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246032465delT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		AGTCCTGGAATTTTTTTTTAG	0.294													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246109039	246109040	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246109039_246109040insA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		atagactggataaaaaaatcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2513892	2513892	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2513892delA								MYT1L (178847 upstream) : TSSC1 (678849 downstream)																							tcccaacagcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3194061	3194061	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3194061delA	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CCCATTTCACAAAAAAATTCC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	3971144	3971145	+	IGR	INS	-	C	C	rs35852570		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3971144_3971145insC								ALLC (220886 upstream) : None (None downstream)																							tgtgcttatgggggggggtctt	0.000													4	2	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11451476	11451476	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11451476delC	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		AAGAAGTGAACCTAAAGTTGA	0.119													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15600750	15600750	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15600750delC	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						TGGAAGACTACCAGGTGGTAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17267233	17267233	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17267233delA								FAM49A (420137 upstream) : RAD51AP2 (424753 downstream)																							TTATCTACATAAAAAGATTTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18039968	18039968	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18039968delT								MSGN1 (41602 upstream) : KCNS3 (19146 downstream)																							TGGGGATGCATTTTTTTTCTT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18458581	18458581	+	IGR	DEL	C	-	-	rs74323736		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18458581delC								KCNS3 (344357 upstream) : NT5C1B (277410 downstream)																							CTGAATTCCACCCCCATTCCC	0.388													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23230092	23230092	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23230092delC								None (None upstream) : KLHL29 (525363 downstream)																							AAAGCCAGATCCCACAAGGTA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23674226	23674227	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23674226_23674227insT								None (None upstream) : KLHL29 (81228 downstream)																							CTTGTCCTGTGTTCCCTGAAGG	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23707744	23707745	+	IGR	DEL	CC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23707744_23707745delCC								None (None upstream) : KLHL29 (47710 downstream)																							GTGTTCATATCCCACCTTGGGG	0.584													4	2	---	---	---	---	
MAPRE3	22924	broad.mit.edu	37	2	27216401	27216401	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27216401delA	uc002rhw.2	+						MAPRE3_uc002rhx.2_Intron	NM_012326	NP_036458	Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family,						cell division|mitosis|positive regulation of transcription, DNA-dependent	cytoplasm|cytoplasmic microtubule|microtubule|midbody|perinuclear region of cytoplasm	microtubule binding|protein binding|small GTPase regulator activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACTTAGAGCTAAGTCCTTCTC	0.453													4	2	---	---	---	---	
PPM1G	5496	broad.mit.edu	37	2	27605697	27605697	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27605697delT	uc002rkl.2	-						ZNF513_uc002rkj.2_5'Flank|ZNF513_uc002rkk.2_5'Flank|PPM1G_uc002rkm.2_Intron	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G						cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					gtcttttttgttttttttttt	0.025													11	5	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28346278	28346278	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28346278delC	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					TATCTTTCCTCCCATTTTAGC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36379468	36379468	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36379468delC								None (None upstream) : CRIM1 (203929 downstream)																							attgtgtaatccagaaaccaa	0.000													4	2	---	---	---	---	
CRIM1	51232	broad.mit.edu	37	2	36681685	36681686	+	Intron	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36681685_36681686delTT	uc002rpd.2	+							NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				ctagctgctcttaacagcttga	0.272													4	2	---	---	---	---	
FEZ2	9637	broad.mit.edu	37	2	36817798	36817798	+	Intron	DEL	A	-	-	rs146856068		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36817798delA	uc002rph.2	-						FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093	Q9UHY8	FEZ2_HUMAN	zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)				agactccgtcaaaaaaaaaaa	0.199													7	4	---	---	---	---	
HEATR5B	54497	broad.mit.edu	37	2	37260028	37260028	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37260028delT	uc002rpp.1	-							NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				ttttgttttgttttttttttt	0.095													11	5	---	---	---	---	
C2orf56	55471	broad.mit.edu	37	2	37465158	37465161	+	Intron	DEL	TTAC	-	-	rs72221409		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37465158_37465161delTTAC	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron	NM_144736	NP_653337	Q7L592	MIDA_HUMAN	hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)				TAATCAGTCATTACTTACTGTTGT	0.319													19	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37810766	37810767	+	IGR	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37810766_37810767delGT								QPCT (210302 upstream) : CDC42EP3 (59976 downstream)																							gtgcgtgcacgtgtgtgtgtgt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37970359	37970359	+	IGR	DEL	T	-	-	rs62842460		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37970359delT								CDC42EP3 (71033 upstream) : FAM82A1 (182103 downstream)																							gtagtggcagtgatggtggtg	0.164													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42604688	42604689	+	IGR	DEL	AC	-	-	rs66888425		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42604688_42604689delAC								COX7A2L (8538 upstream) : KCNG3 (64470 downstream)																							TGCTCTCTTTACACACACACAC	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43349669	43349669	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43349669delA								HAAO (329918 upstream) : ZFP36L2 (99873 downstream)																							ttcagacggtaaaaaaaaatg	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56912690	56912690	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56912690delA								CCDC85A (299382 upstream) : None (None downstream)																							TTGCAAAATGAAAAAAAAACC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58687298	58687298	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58687298delT								FANCL (218783 upstream) : None (None downstream)																							TCTGTGTTTCTTTTTTTTTTC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58937265	58937265	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58937265delC	uc002rzy.2	+											Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		taaacacagtccccaccattc	0.000													4	2	---	---	---	---	
BCL11A	53335	broad.mit.edu	37	2	60695687	60695688	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60695687_60695688delGA	uc002sae.1	-						BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_Intron|BCL11A_uc002saf.1_Intron	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1						negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AAAGGGGAGGGAAGAAGTCCCT	0.505			T	IGH@	B-CLL								4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60805324	60805325	+	IGR	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60805324_60805325delCT								BCL11A (24691 upstream) : PAPOLG (178058 downstream)																							GAGGACCCACCTCTCTCTCTAT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64523253	64523254	+	IGR	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64523253_64523254delAA								PELI1 (151648 upstream) : HSPC159 (158073 downstream)																							AGATAGCTTTAAAAAAAAAAAT	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64618884	64618884	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64618884delA								PELI1 (247279 upstream) : HSPC159 (62443 downstream)																							CGAGTGATACAAAAAAAAAAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66328747	66328749	+	IGR	DEL	ATG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66328747_66328749delATG								SPRED2 (669091 upstream) : MEIS1 (333783 downstream)																							aaggaataaaatgatgatgatga	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67813580	67813580	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67813580delT								ETAA1 (176047 upstream) : C1D (455753 downstream)																							gtctaacaggtttttttttct	0.000													2	4	---	---	---	---	
ASPRV1	151516	broad.mit.edu	37	2	70238650	70238650	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70238650delG	uc002sga.2	-									Q53RT3	APRV1_HUMAN	Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1						agccagataaggggaggagga	0.000													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72860432	72860434	+	Intron	DEL	TGT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72860432_72860434delTGT	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						ATACACTGTAtgttgttgttgtt	0.345													4	2	---	---	---	---	
SMYD5	10322	broad.mit.edu	37	2	73448561	73448561	+	Intron	DEL	T	-	-	rs112717194		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73448561delT	uc002siw.2	+						SMYD5_uc010yre.1_Intron|SMYD5_uc002six.1_5'Flank	NM_006062	NP_006053	Q6GMV2	SMYD5_HUMAN	SMYD family member 5								metal ion binding				0						GCCTGTAGTCTTTTTTTTTTT	0.403													6	3	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74477888	74477888	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74477888delG	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						AAAGTCTGATGGGAATATGTC	0.532											OREG0014716	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
TACR1	6869	broad.mit.edu	37	2	75277046	75277046	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75277046delA	uc002sng.2	-							NM_001058	NP_001049	P25103	NK1R_HUMAN	tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CCAAGACTAGAAAAAAAAAAT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76519006	76519006	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76519006delT								C2orf3 (580895 upstream) : LRRTM4 (455852 downstream)																							ggtcataatcttttttttcat	0.000													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77360876	77360876	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77360876delT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		AATAGCTGCCTCCTCACTGTA	0.373													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79974365	79974366	+	Intron	INS	-	TCT	TCT	rs147822778	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79974365_79974366insTCT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						GCAGTGCCAAATCTAAGTTTTC	0.317													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83000741	83000741	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83000741delA								None (None upstream) : None (None downstream)																							aacccagcagaaaaaaaaaat	0.000													4	2	---	---	---	---	
IMMT	10989	broad.mit.edu	37	2	86408714	86408714	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86408714delA	uc002sqz.3	-						IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002srd.2_Intron|IMMT_uc002sre.3_Intron|IMMT_uc010ytf.1_Intron|IMMT_uc010fgs.1_Intron	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1						ttttaatattaaaaaaaaatt	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91738192	91738194	+	IGR	DEL	TCA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738192_91738194delTCA								None (None upstream) : LOC654342 (66998 downstream)																							tcatttcatctcatcatttttca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91762557	91762558	+	IGR	INS	-	C	C	rs147674439		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91762557_91762558insC								None (None upstream) : LOC654342 (42634 downstream)																							GGCCCAAGAGACCCCTCACCCA	0.584													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92117663	92117663	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92117663delT								GGT8P (147510 upstream) : FKSG73 (11496 downstream)																							TCATTCCTCCTTTATTTATAA	0.194													4	2	---	---	---	---	
VWA3B	200403	broad.mit.edu	37	2	98748735	98748735	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98748735delG	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6						CACGAGTAGTGCCCCTGCCTT	0.577													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100432273	100432274	+	Intron	DEL	TC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100432273_100432274delTC	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						cctggttccttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101832690	101832690	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101832690delG								TBC1D8 (64844 upstream) : C2orf29 (36655 downstream)																							gacagagtgagGGGAAAAAAA	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105313582	105313582	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105313582delT								LOC150568 (184368 upstream) : POU3F3 (158387 downstream)																							tcagggttgctttttgaaaat	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106082273	106082273	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106082273delA								FHL2 (27043 upstream) : NCK2 (279081 downstream)																							actccatctcaaaaaaaaaaa	0.050													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108115873	108115873	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108115873delA								ST6GAL2 (612310 upstream) : LOC729121 (323647 downstream)																							CTCAACTGAGAACCAGGCCAG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	115105182	115105182	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115105182delA								ACTR3 (389015 upstream) : DPP10 (94717 downstream)																							tcaagcaaataaaaaaaaaac	0.000													4	2	---	---	---	---	
CCDC93	54520	broad.mit.edu	37	2	118687867	118687867	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118687867delG	uc002tlj.2	-							NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93											large_intestine(1)|ovary(1)	2						GAAACCACATGGATTTAGGTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119577480	119577481	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119577480_119577481delAC								INSIG2 (709884 upstream) : EN1 (22267 downstream)																							acacacacatacacacacacac	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120485149	120485149	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120485149delA								TMEM177 (3958 upstream) : PTPN4 (32058 downstream)																							aaatggaaagaaaggggaaaa	0.005													4	2	---	---	---	---	
TFCP2L1	29842	broad.mit.edu	37	2	121997404	121997406	+	Intron	DEL	GAA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121997404_121997406delGAA	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)					AGGGCCACATGAAGGAAACCAGC	0.453													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123957956	123957957	+	IGR	DEL	TC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123957956_123957957delTC								None (None upstream) : CNTNAP5 (824907 downstream)																							aagagtgttttcaggaagaagc	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124566328	124566328	+	IGR	DEL	A	-	-	rs138367030		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124566328delA								None (None upstream) : CNTNAP5 (216536 downstream)																							cattaaatagaaaaaaaaaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126140715	126140715	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126140715delG								CNTNAP5 (467854 upstream) : None (None downstream)																							cagccttgatggggaaagttt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131009759	131009760	+	IGR	INS	-	CCG	CCG	rs138344915	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131009759_131009760insCCG								TUBA3E (53725 upstream) : CCDC115 (86056 downstream)																							GGGATGGCGCACCAGAACTTCA	0.653													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131388744	131388745	+	IGR	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131388744_131388745insC								LOC150527 (81273 upstream) : C2orf14 (48878 downstream)																							TGAATTATTTTTCACATGTTAG	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133104413	133104413	+	IGR	DEL	T	-	-	rs76243010		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133104413delT								NCRNA00164 (88871 upstream) : GPR39 (69734 downstream)																							TCTGTAATTCTTTTTTTTTCT	0.353													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133116248	133116249	+	IGR	INS	-	T	T	rs147563539	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133116248_133116249insT								NCRNA00164 (100706 upstream) : GPR39 (57898 downstream)																							gggaaaaagacttttatttaat	0.000													2	4	---	---	---	---	
YSK4	80122	broad.mit.edu	37	2	135779605	135779606	+	Intron	INS	-	T	T	rs145301787	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135779605_135779606insT	uc002tue.1	-						YSK4_uc010fne.1_Intron|YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron|YSK4_uc002tui.3_Intron	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)		ATGGCTTACTATTTTTTTTTAA	0.351													5	3	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141021738	141021739	+	Intron	INS	-	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141021738_141021739insG	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		cttcttacaaagacaccagtca	0.000										TSP Lung(27;0.18)			4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141403855	141403855	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141403855delA	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		acaatccattaaaaacctggc	0.129										TSP Lung(27;0.18)			4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142862584	142862584	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142862584delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		agtctaagagaaaaaatgtca	0.139										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	148585566	148585566	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148585566delC								None (None upstream) : ACVR2A (16520 downstream)																							agcgagaccacaaacccacca	0.000													4	2	---	---	---	---	
ACVR2A	92	broad.mit.edu	37	2	148604526	148604527	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148604526_148604527delGA	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Intron	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor						activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGTTATTCTTGAGCAGTCTCAA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151809223	151809223	+	IGR	DEL	T	-	-	rs73006872	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151809223delT								RND3 (465043 upstream) : RBM43 (295506 downstream)																							aggatacatctttttttcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157041259	157041259	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157041259delA	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																		CAAATAAACTAAAAAAACTTA	0.353													4	2	---	---	---	---	
CSRNP3	80034	broad.mit.edu	37	2	166467371	166467371	+	Intron	DEL	C	-	-	rs78701497		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166467371delC	uc002udf.2	+						CSRNP3_uc002udg.2_Intron	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5						CATGTGAGAGCTTTTATGAGT	0.393													4	2	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166909129	166909130	+	Intron	INS	-	T	T	rs140499279		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166909129_166909130insT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	GGTGAAAAAAAAAAAAACCCAT	0.317													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168459141	168459142	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168459141_168459142insT								XIRP2 (342882 upstream) : B3GALT1 (216040 downstream)																							TACTAGCCACATTTTTTAAAGA	0.307													4	2	---	---	---	---	
LASS6	253782	broad.mit.edu	37	2	169367738	169367738	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169367738delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						gatttaattctacattttgtt	0.000													4	2	---	---	---	---	
TLK1	9874	broad.mit.edu	37	2	172046704	172046705	+	Intron	INS	-	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172046704_172046705insG	uc002ugp.2	-							NM_001136554	NP_001130026	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 2						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						gatgaagctaaggggaaattca	0.000													4	2	---	---	---	---	
METTL8	79828	broad.mit.edu	37	2	172263506	172263506	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172263506delG	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046	B3KW44	B3KW44_HUMAN	methyltransferase like 8								methyltransferase activity			ovary(1)	1						CCTAGTTTGTGGGGCGAAATA	0.254													4	2	---	---	---	---	
NFE2L2	4780	broad.mit.edu	37	2	178192566	178192566	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178192566delA	uc002uli.3	-						LOC100130691_uc002ulk.1_Intron	NM_001145412	NP_001138884	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			tatgtgggggaaaaaaaatca	0.000			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			4	2	---	---	---	---	
PLEKHA3	65977	broad.mit.edu	37	2	179362668	179362668	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179362668delT	uc002umn.2	+							NM_019091	NP_061964	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AATCTTCATGtttttttttta	0.194													4	2	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182934181	182934181	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182934181delT	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			CTAAGGTATCTTTTTTTTTTT	0.378													7	4	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183872663	183872663	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183872663delT	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ttttgttttctttttttttga	0.005													4	2	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	198032264	198032264	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198032264delT	uc002uuc.2	-						ANKRD44_uc002uua.1_Intron|ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron|ANKRD44_uc002uud.1_Intron	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GAATAATTTCTACAGTTAAAG	0.383													4	2	---	---	---	---	
PLCL1	5334	broad.mit.edu	37	2	198917250	198917250	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198917250delA	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	ATAGAGGTTGAAAAAAAAAAA	0.363													4	3	---	---	---	---	
PLCL1	5334	broad.mit.edu	37	2	198917262	198917263	+	Intron	DEL	AC	-	-	rs57265854	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198917262_198917263delAC	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	AAAAAAAAAAACCATTACCTTA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200938899	200938900	+	IGR	INS	-	A	A	rs112469437		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200938899_200938900insA								C2orf47 (110054 upstream) : SPATS2L (231704 downstream)																							aaaaaaaagttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
AOX1	316	broad.mit.edu	37	2	201457272	201457273	+	Intron	INS	-	C	C	rs72542094	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201457272_201457273insC	uc002uvx.2	+							NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CTGCTGCTATGTGCCAGGCTGC	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	202954984	202954984	+	Intron	DEL	A	-	-	rs35496514		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202954984delA	uc010ftp.2	+						uc010zhu.1_Intron					SubName: Full=cDNA FLJ39061 fis, clone NT2RP7013764; Flags: Fragment;																		ACTTTGGCAGATAGGTTCCCA	0.313													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204989366	204989367	+	IGR	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204989366_204989367delAG								ICOS (163070 upstream) : PARD3B (421149 downstream)																							AGGAGGGCAAAGAGAGAGGGGC	0.421													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	205538909	205538910	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205538909_205538910insA	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		cagactaagccataaaattaac	0.129													4	2	---	---	---	---	
PTH2R	5746	broad.mit.edu	37	2	209332687	209332687	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209332687delA	uc002vdb.2	+						PTH2R_uc010zjb.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		agggagaatgaagactcttat	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210065416	210065416	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210065416delA								PTH2R (360598 upstream) : MAP2 (223355 downstream)																							agatctttttatctctattct	0.000													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210486951	210486951	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210486951delA	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TGTGCTGAGTAAAAAAAGTAC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210606789	210606789	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210606789delA								MAP2 (7955 upstream) : UNC80 (29928 downstream)																							TTCCAACCACAAAAAAATGGT	0.318													4	2	---	---	---	---	
SMARCAL1	50485	broad.mit.edu	37	2	217286429	217286429	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217286429delA	uc002vgc.3	+						SMARCAL1_uc010fvf.2_Intron|SMARCAL1_uc002vgd.3_Intron|SMARCAL1_uc010fvg.2_Intron	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated						chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		ATTGTTTTTTAAAAACGATGT	0.393									Schimke_Immuno-Osseous_Dysplasia				4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218704775	218704775	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218704775delG	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GAAGAAAGGAGGGAGGGGCGG	0.592													4	2	---	---	---	---	
TUBA4B	80086	broad.mit.edu	37	2	220119769	220119770	+	Intron	DEL	TC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220119769_220119770delTC	uc002vkv.1	+						TUBA4A_uc002vkt.1_5'Flank|TUBA4A_uc010zkz.1_5'Flank|TUBA4B_uc002vku.2_Intron	NR_003063				RecName: Full=Putative tubulin-like protein alpha-4B; AltName: Full=Alpha-tubulin 4B;												0						GCtttctctttctctctctctc	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228457743	228457744	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228457743_228457744delTG								AGFG1 (31805 upstream) : C2orf83 (17063 downstream)																							tgtgtatatatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228730970	228730970	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228730970delC								CCL20 (48690 upstream) : WDR69 (5357 downstream)																							GCAGACTGCTCCTGCCTGGCT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229726935	229726935	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229726935delT								SPHKAP (680574 upstream) : PID1 (161755 downstream)																							TGCTACTGCCTTTTTTCCATT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229854317	229854317	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229854317delT								SPHKAP (807956 upstream) : PID1 (34373 downstream)																							attgcctgacttcaaactgta	0.000													4	2	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230634174	230634174	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230634174delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.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)		ACCTCTTTCCaaaaaaaaaaa	0.333													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232239670	232239670	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232239670delG								ARMC9 (1064 upstream) : B3GNT7 (20665 downstream)																							AGCACAGCCTGGGGCTGGTGG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236196399	236196399	+	IGR	DEL	T	-	-	rs5839584		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236196399delT								SH3BP4 (232043 upstream) : AGAP1 (206337 downstream)																							AAATAATGGATTTTTTTTTTG	0.428													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	237013548	237013548	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237013548delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						tgtctcaaggaaaaaaaaaaG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105181	105181	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105181delT								None (None upstream) : CHL1 (133469 downstream)																							ACAAGAAATCTTTTTCTTGTT	0.423													4	2	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2354408	2354408	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2354408delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		AAAAATAAACTTTTTTTTCCA	0.303													4	2	---	---	---	---	
NR2C2	7182	broad.mit.edu	37	3	14996941	14996941	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14996941delT	uc003bzj.3	+						NR2C2_uc003bzi.2_Intron	NM_003298	NP_003289	P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2						cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0						TTCCTGTCACTTTTTTTTTTC	0.219													4	2	---	---	---	---	
TBC1D5	9779	broad.mit.edu	37	3	17544485	17544485	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17544485delC	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						tcgatggcttccgaaatgatt	0.000													4	2	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25304416	25304417	+	Intron	DEL	TC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25304416_25304417delTC	uc011awl.1	+							NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	atttgtatgttctctctctgac	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	28577444	28577447	+	IGR	DEL	CATT	-	-	rs72204584		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28577444_28577447delCATT								ZCWPW2 (10814 upstream) : RBMS3 (745496 downstream)																							AAAATGAGGCCATTCAAATTATAA	0.255													3	3	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	29462056	29462057	+	Intron	INS	-	TTTTG	TTTTG	rs9816136	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29462056_29462057insTTTTG	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				GGtttgtttttttttgttttgt	0.198													6	3	---	---	---	---	
GPD1L	23171	broad.mit.edu	37	3	32181468	32181468	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32181468delA	uc003cew.2	+							NM_015141	NP_055956	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like						glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0						gggtagaaggaggatgaactt	0.000													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41853948	41853948	+	Intron	DEL	A	-	-	rs34831277		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41853948delA	uc003ckv.3	-						ULK4_uc003ckw.2_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ATAACTGTTCAAAAAAAAAGA	0.318													3	3	---	---	---	---	
SCAP	22937	broad.mit.edu	37	3	47502936	47502936	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47502936delA	uc003crh.1	-						SCAP_uc011baz.1_Intron|SCAP_uc003crg.2_Intron	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein						cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CAATTCTTCCAAATGTTCACA	0.363													4	3	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57897931	57897931	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57897931delT	uc003dje.1	+						SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		ATCACTTTGGTTTTTTTTTCC	0.333													4	2	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65794766	65794767	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65794766_65794767insA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TTATGGTCCACAGGGCCCATGG	0.396													4	2	---	---	---	---	
PDZRN3	23024	broad.mit.edu	37	3	73491940	73491940	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73491940delA	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron|PDZRN3_uc011bgg.1_Intron	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		gaagcagggtaaagctgtccc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73698259	73698259	+	IGR	DEL	A	-	-	rs111449319		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73698259delA								PDZRN3 (24187 upstream) : CNTN3 (613463 downstream)																							aagaaaaaagaaaaaaaaaaa	0.234													4	3	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	79672286	79672288	+	Intron	DEL	CAA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79672286_79672288delCAA	uc003dqe.2	-							NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		acaatggcatcaacaacaacaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80471004	80471004	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80471004delG								ROBO1 (653945 upstream) : None (None downstream)																							acgtcctaaaggtcctttctt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86535845	86535845	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86535845delC								CADM2 (417897 upstream) : VGLL3 (451280 downstream)																							TGCTTGGGCTCAAAAAGCTAC	0.308													4	2	---	---	---	---	
LOC100302640	100302640	broad.mit.edu	37	3	106748857	106748858	+	Intron	INS	-	AC	AC	rs147552368	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106748857_106748858insAC	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0						cacagacacaaacacacacaca	0.233													3	3	---	---	---	---	
MYH15	22989	broad.mit.edu	37	3	108225446	108225446	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108225446delA	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						ATATGATTTTAAGggcctggg	0.199													4	2	---	---	---	---	
PHLDB2	90102	broad.mit.edu	37	3	111622262	111622262	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111622262delG	uc010hqa.2	+						PHLDB2_uc003dyc.2_Intron|PHLDB2_uc003dyd.2_Intron|PHLDB2_uc003dyg.2_Intron|PHLDB2_uc003dyh.2_Intron|PHLDB2_uc003dyf.3_Intron	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						TATGGCAACTGGGCAGAGCTC	0.522													4	2	---	---	---	---	
KIAA2018	205717	broad.mit.edu	37	3	113371901	113371901	+	3'UTR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113371901delA	uc003eam.2	-	7					KIAA2018_uc003eal.2_3'UTR	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717						regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						acagagtctcaaaaaaaaaag	0.289													15	7	---	---	---	---	
GRAMD1C	54762	broad.mit.edu	37	3	113558801	113558802	+	Intron	INS	-	CA	CA			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113558801_113558802insCA	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3						actgatgatgccacacacacac	0.005													4	2	---	---	---	---	
DRD3	1814	broad.mit.edu	37	3	113847888	113847888	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113847888delT	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	acccacttacttttttttata	0.095													4	2	---	---	---	---	
DRD3	1814	broad.mit.edu	37	3	113886729	113886730	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113886729_113886730insT	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	taagaaaaggattttctctctt	0.050													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114242507	114242507	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114242507delA	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		tgcaggagagaaggcaaaata	0.000													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114334383	114334383	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114334383delT	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		AGATCCTGACTTTAAACTGAG	0.408													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114615683	114615683	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114615683delA	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		AAGGTCTTTTAGATTCAGTAC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117148072	117148072	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117148072delG								LOC285194 (712187 upstream) : None (None downstream)																							tgaaggaaatggatcaagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118010117	118010117	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118010117delT								None (None upstream) : IGSF11 (609364 downstream)																							ttcctgggtatttttttttaa	0.000													4	2	---	---	---	---	
PLA1A	51365	broad.mit.edu	37	3	119334672	119334672	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119334672delA	uc003ecu.2	+						PLA1A_uc003ecv.2_Intron|PLA1A_uc003ecw.2_Intron|PLA1A_uc011bjc.1_Intron	NM_015900	NP_056984	Q53H76	PLA1A_HUMAN	phospholipase A1 member A precursor						lipid catabolic process|phosphatidylserine metabolic process	extracellular region	phospholipase A1 activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						aaagcctcagaaaaaaaaaag	0.159													16	7	---	---	---	---	
PARP15	165631	broad.mit.edu	37	3	122349961	122349961	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122349961delC	uc003efm.2	+						PARP15_uc003efn.2_Intron|PARP15_uc003efo.1_Intron|PARP15_uc003efp.1_Intron|PARP15_uc011bjt.1_Intron	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		AGCAGCAGATCCAAAAGGACT	0.483													4	2	---	---	---	---	
PDIA5	10954	broad.mit.edu	37	3	122868431	122868431	+	Intron	DEL	C	-	-	rs34297598		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122868431delC	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801	Q14554	PDIA5_HUMAN	protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)		GACTGAGAAGCAATAACATTT	0.393													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124077233	124077233	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124077233delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GAAGGAAGTCTTTTTTTTTCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125128608	125128608	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125128608delT								ZNF148 (34410 upstream) : SNX4 (36887 downstream)																							tttcaatccattgcaattatc	0.000													4	2	---	---	---	---	
SNX4	8723	broad.mit.edu	37	3	125170478	125170479	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125170478_125170479insT	uc003eib.2	-						SNX4_uc011bkf.1_Intron	NM_003794	NP_003785	O95219	SNX4_HUMAN	sorting nexin 4						cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4						TCTACtttttcttttttttttg	0.124													6	3	---	---	---	---	
ACPP	55	broad.mit.edu	37	3	132073428	132073428	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132073428delA	uc010htp.2	+						ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Intron	NM_001099	NP_001090	P15309	PPAP_HUMAN	acid phosphatase, prostate short isoform							extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1						AATTCTGTCTAAGCCTGCTta	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135371798	135371798	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135371798delG								EPHB1 (392493 upstream) : PPP2R3A (312769 downstream)																							ccatcacaCTGGGCTGTCTTG	0.254													4	2	---	---	---	---	
TMEM22	80723	broad.mit.edu	37	3	136573162	136573162	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136573162delT	uc003erf.3	+						TMEM22_uc003erg.3_Intron|TMEM22_uc010hub.2_Intron	NM_001097600	NP_001091069	Q8TBE7	TMM22_HUMAN	transmembrane protein 22							Golgi apparatus|integral to membrane				ovary(1)	1						CTCTAATTTCTTTTTTTTCTG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137439392	137439392	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137439392delA								IL20RB (709472 upstream) : SOX14 (44187 downstream)																							GTACTTACTTAAAAAAGATTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141372541	141372542	+	IGR	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141372541_141372542delAG								RASA2 (41344 upstream) : RNF7 (84509 downstream)																							AGAGCAGAAAAGAGAGAGAGCT	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145606923	145606924	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145606923_145606924delTG								None (None upstream) : PLOD2 (180304 downstream)																							GAGTTTTTGATGTGTGTGTGTG	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146806106	146806106	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146806106delC								PLSCR5 (482103 upstream) : ZIC4 (297731 downstream)																							tttattccttccaactcttgt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147229387	147229387	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147229387delT								ZIC1 (94883 upstream) : None (None downstream)																							taaaatcatctttttttatgg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157627624	157627624	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157627624delA								C3orf55 (308605 upstream) : SHOX2 (186177 downstream)																							AGTAGCCTCCAAAAAAAAATC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	160215748	160215748	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160215748delA								IFT80 (48122 upstream) : KPNA4 (2215 downstream)																							CTTAGTAAACAAAAAAAATAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166133515	166133515	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166133515delG								BCHE (578262 upstream) : ZBBX (824566 downstream)																							GTATGCCTTTGAATAAGTTTG	0.294													4	2	---	---	---	---	
ZBBX	79740	broad.mit.edu	37	3	167064010	167064010	+	Intron	DEL	T	-	-	rs79612619		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167064010delT	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2						TAATTGCCTCTCATGCATTTA	0.308													2	4	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169068063	169068063	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169068063delG	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						cttggaacctggtctaagctc	0.080													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174825326	174825327	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174825326_174825327delAC	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		acacacacaaacacacacacac	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179768512	179768512	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179768512delC								PEX5L (13995 upstream) : TTC14 (551406 downstream)																							tgctgtctgaccctgcttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180128872	180128872	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180128872delT								PEX5L (374355 upstream) : TTC14 (191046 downstream)																							GTTTTCTTCATTTTTTTTGGA	0.333													4	2	---	---	---	---	
ATP11B	23200	broad.mit.edu	37	3	182596615	182596615	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182596615delT	uc003flb.2	+						ATP11B_uc003flc.2_Intron|ATP11B_uc011bqm.1_Intron|ATP11B_uc010hxf.1_Intron	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TTTCATAGAGTTTTTTTTTAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184132553	184132554	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184132553_184132554delTG								CHRD (24934 upstream) : EPHB3 (147033 downstream)																							ggtatatgtatgtgtgtgtgtg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184197637	184197638	+	IGR	INS	-	T	T	rs140295853	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184197637_184197638insT								CHRD (90018 upstream) : EPHB3 (81949 downstream)																							ttccaagactgtacttccagtc	0.168													5	7	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185379523	185379523	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185379523delG	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)			agacagtaatggtcactgtca	0.000													4	2	---	---	---	---	
MASP1	5648	broad.mit.edu	37	3	186937265	186937266	+	3'UTR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186937265_186937266insT	uc003frh.1	-	16						NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		AACCTTGTCTGTTTTACTTTTT	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193471282	193471282	+	IGR	DEL	T	-	-	rs79897100	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193471282delT								OPA1 (55683 upstream) : LOC100128023 (239602 downstream)																							cttgtccacatttaactctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193551393	193551393	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193551393delA								OPA1 (135794 upstream) : LOC100128023 (159491 downstream)																							ctctggtgataaggacacata	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197856329	197856330	+	IGR	INS	-	G	G	rs144208948		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197856329_197856330insG								LOC348840 (48787 upstream) : FAM157A (22907 downstream)																							CCCCAACGCCAGGGCTGTCCTG	0.460													4	2	---	---	---	---	
LETM1	3954	broad.mit.edu	37	4	1834801	1834801	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1834801delT	uc003gdv.2	-							NM_012318	NP_036450	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane						cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			CTACttcttcttttttttttt	0.299													5	4	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5405197	5405197	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5405197delC	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						ttccctgtctcccctgcccat	0.000													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7504531	7504531	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7504531delC	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						GCCGGCCTTGCCCCCACGGCA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12378818	12378819	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12378818_12378819insT								HS3ST1 (948281 upstream) : HSP90AB2P (956218 downstream)																							TTTAACTGATCTGTGAGTTTGT	0.307													4	2	---	---	---	---	
C1QTNF7	114905	broad.mit.edu	37	4	15353055	15353055	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15353055delT	uc003gno.2	+							NM_001135170	NP_001128642	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7							collagen					0						AACAACATCCTAAACAAGGTT	0.318													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21146319	21146319	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21146319delT	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				CATCTCCTCCTTATTTCTTCA	0.303													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21656121	21656121	+	Intron	DEL	T	-	-	rs74550997		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21656121delT	uc003gqh.1	-						KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				GATTAAAATGTTTTTTTTTTT	0.100													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24333733	24333734	+	IGR	INS	-	T	T	rs148626329	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24333733_24333734insT								PPARGC1A (442033 upstream) : MIR573 (188081 downstream)																							AGAACAGTGGgtttttttttgt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29448214	29448215	+	IGR	INS	-	T	T	rs140409456	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29448214_29448215insT								None (None upstream) : None (None downstream)																							gaaaaaGTTTCTTTTTTTTTAA	0.069													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32551884	32551885	+	IGR	INS	-	AA	AA	rs150379379	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32551884_32551885insAA								None (None upstream) : None (None downstream)																							AATCTTATAACAGAGAAAAAAA	0.257													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33487556	33487557	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33487556_33487557delAC								None (None upstream) : None (None downstream)																							GGATTTCcatacacacacacac	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35932097	35932097	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35932097delT								None (None upstream) : ARAP2 (17747 downstream)																							ttgatacaagtttttttttgt	0.000													4	2	---	---	---	---	
ARAP2	116984	broad.mit.edu	37	4	36002748	36002748	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36002748delT	uc003gso.2	-									Q8WZ64	ARAP2_HUMAN	Homo sapiens cDNA clone IMAGE:5296543.						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						tgcctgagtgtttgaccggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	44969011	44969015	+	IGR	DEL	GATAT	-	-	rs68022841		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44969011_44969015delGATAT								GNPDA2 (240399 upstream) : None (None downstream)																							gtatggggtagatatgatgattatt	0.083													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45084225	45084225	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45084225delA								GNPDA2 (355613 upstream) : GABRG1 (953564 downstream)																							AATGTGATTTAAATGCATCCG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45773339	45773340	+	IGR	INS	-	AA	AA	rs139960347	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45773339_45773340insAA								None (None upstream) : GABRG1 (264449 downstream)																							AAAAAAGTAGGGAGAGAGAGAG	0.416													2	4	---	---	---	---	
USP46	64854	broad.mit.edu	37	4	53462531	53462531	+	3'UTR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53462531delT	uc003gzn.2	-	9					USP46_uc003gzm.3_3'UTR|USP46_uc011bzr.1_3'UTR|USP46_uc011bzs.1_3'UTR	NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1						behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)			CAAATGACCCTTTTAAAGGTA	0.323													4	2	---	---	---	---	
KIT	3815	broad.mit.edu	37	4	55595036	55595036	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55595036delT	uc010igr.2	+						KIT_uc010igs.2_Intron|KIT_uc010igt.1_Intron	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCATTTTAGGTTTTCACTCAC	0.383		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61428778	61428778	+	IGR	DEL	T	-	-	rs35173829		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61428778delT								None (None upstream) : LPHN3 (638196 downstream)																							GAGTGAAGAATTTTTTTTTTC	0.378													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67967131	67967131	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67967131delG								MIR1269 (824485 upstream) : CENPC1 (370858 downstream)																							tgctcttcctggcttagtcct	0.050													4	2	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72125356	72125356	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72125356delT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hga.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			CCACTGTGCATTTTTTTTTTC	0.463													3	3	---	---	---	---	
MTHFD2L	441024	broad.mit.edu	37	4	75154810	75154810	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75154810delA	uc011cbk.1	+						MTHFD2L_uc003hhu.2_Intron|uc003hhv.1_Intron	NM_001144978	NP_001138450	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase 2-like						folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)			acagtgacctaaaaagacaaa	0.025													4	2	---	---	---	---	
MTHFD2L	441024	broad.mit.edu	37	4	75167277	75167280	+	Intron	DEL	TGTT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75167277_75167280delTGTT	uc011cbk.1	+						MTHFD2L_uc003hhu.2_Intron|uc003hhv.1_Intron	NM_001144978	NP_001138450	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase 2-like						folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)			tgtgtgtgtctgtTTATTACAGCC	0.221													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	75809993	75809993	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75809993delA								BTC (90111 upstream) : PARM1 (48305 downstream)																							GGTTCACAGTAAAAAAAACTT	0.328													4	2	---	---	---	---	
RCHY1	25898	broad.mit.edu	37	4	76407500	76407500	+	3'UTR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76407500delA	uc003hik.2	-	9					RCHY1_uc010iio.2_3'UTR|RCHY1_uc003hij.2_3'UTR|RCHY1_uc003hil.2_3'UTR|RCHY1_uc010iip.2_3'UTR|RCHY1_uc010iiq.2_RNA|RCHY1_uc010iir.2_3'UTR	NM_015436	NP_056251	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nuclear speck|ubiquitin ligase complex	electron carrier activity|p53 binding|protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ATTGGCTTCCAAAAAACTGAC	0.358													4	2	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77516725	77516725	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77516725delC	uc011cbx.1	+						uc011cby.1_Intron	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)			aatactttttcaaaaatcctc	0.000													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79363578	79363578	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79363578delA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc010ijj.1_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						gggaaggcagaaaagtctgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80365789	80365789	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80365789delT								GK2 (36417 upstream) : GDEP (382836 downstream)																							TAACATGttcttttttttttg	0.164													2	4	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81865476	81865476	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81865476delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						ggctcacggtaaccactcaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82328853	82328856	+	IGR	DEL	GGAT	-	-	rs35096672		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82328853_82328856delGGAT								PRKG2 (192635 upstream) : RASGEF1B (19363 downstream)																							AAGggatggaggatggatggatgg	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85424430	85424431	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85424430_85424431delGA								NKX6-1 (5043 upstream) : CDS1 (79626 downstream)																							TATCGTCAGTGAGAGAGAGGAT	0.495													4	2	---	---	---	---	
WDFY3	23001	broad.mit.edu	37	4	85880350	85880351	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85880350_85880351insA	uc003hpd.2	-							NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GATGTGACTGGAGAAGCTGGAG	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88770046	88770046	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88770046delT								MEPE (2104 upstream) : SPP1 (126756 downstream)																							AATGTTCATATTTTTTTCATC	0.383													4	2	---	---	---	---	
HERC3	8916	broad.mit.edu	37	4	89626015	89626015	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89626015delT	uc003hrw.1	+						HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron	NM_014606	NP_055421	Q15034	HERC3_HUMAN	hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		tctttctttcttttttttttt	0.174													4	3	---	---	---	---	
SNCA	6622	broad.mit.edu	37	4	90662097	90662098	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90662097_90662098delTG	uc003hsq.2	-						SNCA_uc010ikt.2_Intron|SNCA_uc003hso.2_Intron|SNCA_uc003hsp.2_Intron|SNCA_uc003hsr.2_Intron	NM_001146054	NP_001139526	P37840	SYUA_HUMAN	alpha-synuclein isoform NACP140						activation of caspase activity|anti-apoptosis|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)	tgtgtgtgtatgtgtgtgtgtg	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	98430383	98430383	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98430383delT								None (None upstream) : C4orf37 (49651 downstream)																							AGAATTTGACTTTTTTTTTTT	0.383													2	5	---	---	---	---	
MANBA	4126	broad.mit.edu	37	4	103582225	103582225	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103582225delC	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		atccaggagtcccttgctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105692628	105692629	+	IGR	DEL	TG	-	-	rs72400458		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105692628_105692629delTG								CXXC4 (276570 upstream) : TET2 (375314 downstream)																							catgccaagctgtgtgtgtgtg	0.059													4	2	---	---	---	---	
LOC285456	285456	broad.mit.edu	37	4	109510602	109510602	+	Intron	DEL	T	-	-	rs33950013		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109510602delT	uc011cfl.1	-						LOC285456_uc003hyy.2_Intron					SubName: Full=cDNA FLJ57077;												0						CAATTCCCTGTTTTTTTTTTT	0.313													2	4	---	---	---	---	
SEC24B	10427	broad.mit.edu	37	4	110385170	110385170	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110385170delT	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		GGGACAGTTGTTTTTTTAGCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118881452	118881454	+	IGR	DEL	TTG	-	-	rs2389473		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118881452_118881454delTTG								TRAM1L1 (874716 upstream) : NDST3 (73319 downstream)																							gaaaagggttttgtttttttttt	0.005													4	2	---	---	---	---	
PRDM5	11107	broad.mit.edu	37	4	121706488	121706488	+	Intron	DEL	T	-	-	rs80154434	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121706488delT	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2						AAAAAAAATATTCCTATTATC	0.328													4	2	---	---	---	---	
LOC285419	285419	broad.mit.edu	37	4	124780671	124780671	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124780671delT	uc011cgn.1	+						LOC285419_uc003ifd.2_Intron	NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0						TTTGACTTTCTTTTTACTGAG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125175090	125175090	+	IGR	DEL	A	-	-	rs67512643		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125175090delA								LOC285419 (323572 upstream) : ANKRD50 (410378 downstream)																							AAATTTTCTGAAAAAAAAAAA	0.303													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128287098	128287098	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128287098delA								None (None upstream) : INTU (267022 downstream)																							TTTGAACAGGAAAAAAAAAAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	133986671	133986672	+	IGR	INS	-	AG	AG	rs146653453	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133986671_133986672insAG								None (None upstream) : PCDH10 (83798 downstream)																							gcaaggcaaaagcaccgggaaa	0.000													3	3	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	140748083	140748087	+	Intron	DEL	AAATA	-	-	rs10561252		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140748083_140748087delAAATA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					ACTGCAAATGAAATAAAATAAGAAA	0.366													5	3	---	---	---	---	
ZNF330	27309	broad.mit.edu	37	4	142148270	142148271	+	Intron	INS	-	T	T	rs113845697		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142148270_142148271insT	uc003iiq.3	+						ZNF330_uc011chl.1_Intron	NM_014487	NP_055302	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330							chromosome, centromeric region|midbody|nucleolus	protein binding|zinc ion binding				0	all_hematologic(180;0.162)					TCAGTGGTACCTTTTTTTTTTT	0.188													4	2	---	---	---	---	
TTC29	83894	broad.mit.edu	37	4	147865138	147865139	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147865138_147865139insA	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)					GGCACCTCCTTAGGGTTCTCCC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	149444164	149444164	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149444164delC								NR3C2 (80521 upstream) : None (None downstream)																							CTTGAAATAACCAGCACACTC	0.398													4	2	---	---	---	---	
PET112L	5188	broad.mit.edu	37	4	152633794	152633794	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152633794delA	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	AGGTTTGACCAAAAAAAAAGC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153129694	153129695	+	IGR	DEL	CA	-	-	rs10560469		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153129694_153129695delCA								PET112L (447548 upstream) : FBXW7 (112716 downstream)																							ttgactctaccacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154070888	154070889	+	IGR	DEL	AA	-	-	rs71847599		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154070888_154070889delAA								FHDC1 (170040 upstream) : TRIM2 (3381 downstream)																							gcagagtaagaaaaaaaaaaag	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154874376	154874377	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154874376_154874377delAC								SFRP2 (164148 upstream) : DCHS2 (281150 downstream)																							AAGAGTGAGGACACACACACAA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	156335044	156335044	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156335044delG								MAP9 (36922 upstream) : GUCY1A3 (252818 downstream)																							ttcagcttttgacatgtcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165921931	165921931	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165921931delT								TRIM61 (23113 upstream) : TRIM60 (31220 downstream)																							taacagaaagtttagacaaac	0.000													4	2	---	---	---	---	
SH3RF1	57630	broad.mit.edu	37	4	170171470	170171470	+	Intron	DEL	A	-	-	rs34622708		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170171470delA	uc003isa.1	-							NM_020870	NP_065921	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		TCTTGGGTTTAAAAAAAAAAA	0.323													3	3	---	---	---	---	
MFAP3L	9848	broad.mit.edu	37	4	170944590	170944591	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170944590_170944591insT	uc003isp.3	-							NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform							integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		TAAACTACTTCTGATAGCTCTT	0.366													4	2	---	---	---	---	
GALNTL6	442117	broad.mit.edu	37	4	173312092	173312093	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173312092_173312093insA	uc003isv.2	+							NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						GCACTCTTATGAAAAAAAATAG	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	175406907	175406908	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175406907_175406908insA								KIAA1712 (152376 upstream) : HPGD (4420 downstream)																							gtgtgtaaaggaaaaaaaaact	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179365374	179365375	+	IGR	INS	-	CT	CT			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179365374_179365375insCT								LOC285501 (453471 upstream) : None (None downstream)																							TTTTATTGTGCCTCTCTCTCTC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182284794	182284794	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182284794delA								None (None upstream) : MGC45800 (775365 downstream)																							GACAAACTTTAAAAAAAATAG	0.413													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183313553	183313553	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183313553delA	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		AAGATGTAATAAAAAGTAAGC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188189813	188189814	+	IGR	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188189813_188189814delTT								FAT1 (541963 upstream) : ZFP42 (727111 downstream)																							GCTTGTCCTCTTTTGTCCTAAA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189039737	189039737	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189039737delT								TRIML2 (9315 upstream) : TRIML1 (20861 downstream)																							TACCACAAAGTTTTTGTGCCA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190596331	190596332	+	IGR	INS	-	A	A	rs79631982		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190596331_190596332insA								None (None upstream) : FRG1 (265642 downstream)																							TGTACTTTTTTTAAAAACTGTT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	11257	11258	+	IGR	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11257_11258insC								None (None upstream) : PLEKHG4B (129115 downstream)																							cctaaccctaaccctaacccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3070342	3070342	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3070342delC								C5orf38 (314830 upstream) : IRX1 (525826 downstream)																							TCCTGGAACACCCCAGTGGGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3745062	3745062	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3745062delC								IRX1 (143546 upstream) : None (None downstream)																							ATCCCTTCAGCCCCACTTGAA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4474425	4474425	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4474425delT								IRX1 (872909 upstream) : LOC340094 (560047 downstream)																							AATCTTTTTCTTTTTTTTCCA	0.328													4	2	---	---	---	---	
PAPD7	11044	broad.mit.edu	37	5	6756454	6756454	+	3'UTR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6756454delT	uc003jdx.1	+	13					PAPD7_uc010itl.1_3'UTR	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma						cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1						TGACTTCCTGTTTTTAAAACG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10553215	10553215	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10553215delT								ROPN1L (88078 upstream) : DAP (126128 downstream)																							CCACACCTGCttttttttttt	0.259													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11017429	11017429	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11017429delG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.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						ACTCTTTGGAGGTATGCGATA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12536938	12536938	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12536938delT								CTNND2 (632828 upstream) : None (None downstream)																							gatgaatccatttttttaaaa	0.000													4	2	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14360994	14360994	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14360994delG	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					CTAAACATGTGGCATGGTGAA	0.478													4	2	---	---	---	---	
LOC285696	285696	broad.mit.edu	37	5	17185933	17185933	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17185933delT	uc003jfw.2	-							NR_027253				Homo sapiens cDNA FLJ34047 fis, clone FCBBF3000001.												0						CCTAGGAGGCTTTTTTTTTTT	0.398													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20495918	20495919	+	IGR	DEL	AA	-	-	rs145924050		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20495918_20495919delAA								CDH18 (507611 upstream) : GUSBP1 (846023 downstream)																							CTCAGAAAATAAAGTCAAAAGA	0.317													6	3	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21551921	21551922	+	Intron	INS	-	CTC	CTC	rs148574802	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21551921_21551922insCTC	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						TAGAAAAAGGACTCTGTAAAAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23303407	23303407	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23303407delA								CDH12 (449676 upstream) : PRDM9 (204317 downstream)																							CAAATTCTATAAAATATAATG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23413029	23413029	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23413029delC								CDH12 (559298 upstream) : PRDM9 (94695 downstream)																							aagaaagaagccccccaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	26539388	26539388	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26539388delT								None (None upstream) : CDH9 (341321 downstream)																							CATAAGTTTATTTTTTTTCTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	26678910	26678910	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26678910delA								None (None upstream) : CDH9 (201799 downstream)																							TAGGGGAGATATTTACTAATA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27053569	27053569	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27053569delA								CDH9 (14880 upstream) : None (None downstream)																							ATAAACACTGAAAAAAAAAAA	0.299													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27192777	27192777	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27192777delA								CDH9 (154088 upstream) : None (None downstream)																							atacagccttaaaaaagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31585824	31585825	+	IGR	DEL	GT	-	-	rs113799912		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31585824_31585825delGT								C5orf22 (30660 upstream) : PDZD2 (53692 downstream)																							ATGTGTGACAgtgtgtgtgtgt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33154091	33154092	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33154091_33154092insA								C5orf23 (362272 upstream) : TARS (286710 downstream)																							CATACCCTTGTAAAAATCTAGG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33354936	33354936	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33354936delT								C5orf23 (563117 upstream) : TARS (85866 downstream)																							ATTTTTTCCCTTCAAAAACAG	0.318													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33827550	33827550	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33827550delG	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						agtctgtgctgccctaagcca	0.000										HNSCC(64;0.19)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34109932	34109934	+	IGR	DEL	TGT	-	-	rs78871010		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34109932_34109934delTGT								C1QTNF3 (66615 upstream) : RAI14 (546499 downstream)																							tgatacagactgttttctgagaa	0.128													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35283944	35283944	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35283944delA								PRLR (53150 upstream) : SPEF2 (334045 downstream)																							AGAGTGTCACAAAAAAGCATC	0.363													4	2	---	---	---	---	
FYB	2533	broad.mit.edu	37	5	39140548	39140548	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39140548delA	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)			ttcacataagaaaaaaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51969891	51969891	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51969891delT								None (None upstream) : ITGA1 (113883 downstream)																							TGGAGTTGAATTTTTTTTCTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53878501	53878501	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53878501delA								SNX18 (36086 upstream) : ESM1 (395195 downstream)																							gtgcacttgtaatctcagcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55230929	55230929	+	IGR	DEL	T	-	-	rs75976988		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55230929delT								IL31RA (12252 upstream) : IL6ST (5766 downstream)																							AGGGTTTTGGTTTTTTTTTGG	0.398													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55371640	55371642	+	IGR	DEL	TGT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55371640_55371642delTGT								IL6ST (80877 upstream) : ANKRD55 (23866 downstream)																							GAGAATTAAGTGTTGTTTGAAAA	0.463													2	4	---	---	---	---	
MAP3K1	4214	broad.mit.edu	37	5	56144344	56144344	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56144344delA	uc003jqw.3	+							NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CAGGACAAGGAAAAGGCCCTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63964128	63964129	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63964128_63964129delTG								RGS7BP (56009 upstream) : SFRS12IP1 (49851 downstream)																							ttttttgttttgtgtgtgtgtg	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	64342773	64342773	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64342773delT								CWC27 (28183 upstream) : ADAMTS6 (101791 downstream)																							tctaaagatatttggcattca	0.000													4	2	---	---	---	---	
NLN	57486	broad.mit.edu	37	5	65043023	65043023	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65043023delG	uc003juf.2	+						NLN_uc003jue.2_Intron	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		gggaagtggagggaatttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66823075	66823075	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66823075delT								CD180 (330458 upstream) : PIK3R1 (688529 downstream)																							gtacagggtatttttttttag	0.005													4	2	---	---	---	---	
TNPO1	3842	broad.mit.edu	37	5	72183586	72183586	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72183586delA	uc003kck.3	+						TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_Intron	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CCATTGCTTTAAAAAAAAATC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73423217	73423217	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73423217delG								RGNEF (185804 upstream) : ENC1 (500018 downstream)																							TAAGTGCACTGAATGATCCTG	0.493													4	2	---	---	---	---	
S100Z	170591	broad.mit.edu	37	5	76166432	76166432	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76166432delT	uc003kep.1	+						S100Z_uc003keq.3_Intron	NM_130772	NP_570128	Q8WXG8	S100Z_HUMAN	S100 calcium binding protein Z								calcium ion binding			ovary(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)		aaaagcttgattttttttttt	0.020													3	3	---	---	---	---	
PDE8B	8622	broad.mit.edu	37	5	76620997	76620998	+	Intron	INS	-	T	T	rs144041890	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76620997_76620998insT	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)		TGGGGGGATTGTTTTGGCtttg	0.099													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	76961052	76961053	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76961052_76961053insT								OTP (26530 upstream) : TBCA (25942 downstream)																							tagaacctcaatttttttgagg	0.109													4	2	---	---	---	---	
LHFPL2	10184	broad.mit.edu	37	5	77860729	77860729	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77860729delA	uc003kfo.2	-							NM_005779	NP_005770	Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2							integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		GTTAGATTTTAAAAACACATA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82293931	82293931	+	IGR	DEL	T	-	-	rs34526886		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82293931delT								ATP6AP1L (679785 upstream) : TMEM167A (54736 downstream)																							TGTACGTGTATTTTTAGAGAT	0.239													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	83136104	83136104	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83136104delA								HAPLN1 (119208 upstream) : EDIL3 (102022 downstream)																							GAGTGGGTCTAGGAGAAGAGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87404837	87404838	+	IGR	INS	-	TG	TG	rs142841971	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87404837_87404838insTG								CCNH (696001 upstream) : TMEM161B (86186 downstream)																							GGAAAAAGGGCTGTGTGGGATG	0.401													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87485960	87485960	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87485960delA								CCNH (777124 upstream) : TMEM161B (5064 downstream)																							aagaactagtaaatacttgtt	0.000													4	2	---	---	---	---	
MEF2C	4208	broad.mit.edu	37	5	88031890	88031890	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88031890delC	uc003kjj.2	-						MEF2C_uc003kji.2_Intron|MEF2C_uc003kjk.2_Intron|MEF2C_uc003kjm.2_Intron|MEF2C_uc003kjl.2_Intron	NM_002397	NP_002388	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C isoform 1						apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		CTTCTATTATCCCCTCTCCTC	0.378										HNSCC(66;0.2)			4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90397025	90397025	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90397025delA	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)		TAATTCAGGGAAAAAAAAACT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91373035	91373035	+	IGR	DEL	T	-	-	rs74947763		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91373035delT								LOC100129716 (656504 upstream) : None (None downstream)																							ttaaagtaggttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91997435	91997435	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91997435delA								None (None upstream) : FLJ42709 (747630 downstream)																							ATACATAACCAAAAGAATCAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95646180	95646180	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95646180delT								MIR583 (231264 upstream) : PCSK1 (79939 downstream)																							cttcctctaattttttgtaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96956613	96956613	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96956613delT								RIOK2 (437608 upstream) : None (None downstream)																							gtagtttttcttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97444903	97444903	+	IGR	DEL	T	-	-	rs150973876		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97444903delT								RIOK2 (925898 upstream) : RGMB (660096 downstream)																							AGATGTGAAGTTTTTTTTTTT	0.274													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	100031599	100031599	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100031599delA								FAM174A (109159 upstream) : ST8SIA4 (111041 downstream)																							TGATTTGAATAAAAAAAAAAA	0.323													4	3	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102342870	102342897	+	Intron	DEL	CACACACACACACACACACATATACATA	-	-	rs75082956	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102342870_102342897delCACACACACACACACACACATATACATA	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_5'Flank	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GCTTGTCTCTcacacacacacacacacacatatacatacacacacaca	0.281											OREG0005106	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106260155	106260155	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106260155delA								None (None upstream) : EFNA5 (452436 downstream)																							TAAATGTCTTAACCAGCTAGA	0.323													4	2	---	---	---	---	
TSLP	85480	broad.mit.edu	37	5	110405787	110405787	+	5'Flank	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110405787delT	uc003kpb.2	+						TSLP_uc003kpa.2_RNA	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1							extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		AAGAGTGGACTTTTTTTTCAA	0.428													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111535837	111535837	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111535837delT	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)		aacactggcctttttcgtttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	111814894	111814894	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111814894delC								FLJ11235 (58221 upstream) : APC (228324 downstream)																							tcagcatctaccagactttta	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115694890	115694890	+	IGR	DEL	C	-	-	rs11305907		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115694890delC								COMMD10 (65912 upstream) : SEMA6A (84362 downstream)																							CCCAGCACAACAGCTgctgcc	0.229													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115771421	115771422	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115771421_115771422insT								COMMD10 (142443 upstream) : SEMA6A (7830 downstream)																							caatttctatcttttttTTTCA	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116394488	116394488	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116394488delT								SEMA6A (483937 upstream) : None (None downstream)																							GTCTTTGTGCTTTTTTTATGC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117218580	117218580	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117218580delT								None (None upstream) : DTWD2 (953991 downstream)																							CAGTCTAAAGTTTTTTGTATC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	118083678	118083679	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118083678_118083679insA								None (None upstream) : DTWD2 (88892 downstream)																							tccaaaatctgaaaaaaaatcc	0.050													4	2	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118456958	118456958	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118456958delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CCTAtttttcttttttttttc	0.119													14	8	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118463045	118463045	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118463045delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TCCTTTATCCttttttttttt	0.318													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124323227	124323227	+	IGR	DEL	T	-	-	rs5871111		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124323227delT								ZNF608 (238727 upstream) : None (None downstream)																							ACAGAGAGGCTTGTGATTCCT	0.458													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124947179	124947180	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124947179_124947180delTG								ZNF608 (862679 upstream) : GRAMD3 (748608 downstream)																							ccttagtaACtgtgtgtgtgtg	0.059													4	2	---	---	---	---	
MARCH3	115123	broad.mit.edu	37	5	126335982	126335983	+	Intron	INS	-	CCTCTTGAT	CCTCTTGAT	rs140342993	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126335982_126335983insCCTCTTGAT	uc003kuf.2	-						MARCH3_uc011cxc.1_Intron	NM_178450	NP_848545	Q86UD3	MARH3_HUMAN	membrane-associated ring finger (C3HC4) 3						endocytosis	cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosome	ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.074)|OV - Ovarian serous cystadenocarcinoma(64;0.0793)		CTCACACTCTGCCTCTTGATGC	0.411													4	2	---	---	---	---	
ADAMTS19	171019	broad.mit.edu	37	5	128913293	128913293	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128913293delC	uc003kvb.1	+							NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		aaagaatgttccaggcaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131687839	131687839	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131687839delC	uc003kwr.3	-											Homo sapiens hypothetical LOC553103, mRNA (cDNA clone IMAGE:5288197).																		ttagccctcacctttcaccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133190747	133190747	+	IGR	DEL	T	-	-	rs33978538		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133190747delT								FSTL4 (242524 upstream) : C5orf15 (100452 downstream)																							CTACTCCCCCTGACTTCCCTA	0.323													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133782844	133782844	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133782844delA								CDKN2AIPNL (35255 upstream) : PHF15 (77222 downstream)																							GCAGAGTAGTAAAGGAAAGCT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134469451	134469452	+	Intron	DEL	GT	-	-	rs113707089		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134469451_134469452delGT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		GAGAGATTGAgtgtgtgtgtgt	0.426													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	136054421	136054421	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136054421delC								TRPC7 (361348 upstream) : SPOCK1 (256567 downstream)																							ATTCTTATTTCCCCAACCCAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	136080509	136080510	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136080509_136080510delGA								TRPC7 (387436 upstream) : SPOCK1 (230478 downstream)																							GTGAAAGTGTGAGAGAGAGAGA	0.426													4	2	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136324951	136324952	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136324951_136324952insC	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTTTCTTATTTCCCTGGGGGAG	0.391													4	2	---	---	---	---	
MYOT	9499	broad.mit.edu	37	5	137211346	137211346	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137211346delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412	Q9UBF9	MYOTI_HUMAN	myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			tgccaaaaggaaaaaaaaaag	0.129													12	6	---	---	---	---	
CDC25C	995	broad.mit.edu	37	5	137626152	137626155	+	Intron	DEL	AAGA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137626152_137626155delAAGA	uc003lcp.1	-						CDC25C_uc003lcq.1_Intron|CDC25C_uc003lcr.1_Intron|CDC25C_uc011cyp.1_Intron|CDC25C_uc003lcs.1_Intron	NM_001790	NP_001781	P30307	MPIP3_HUMAN	cell division cycle 25C isoform a						cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding			lung(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCAGAAGAATAAGAAATACTTTCT	0.368													7	12	---	---	---	---	
PCDHA1	56147	broad.mit.edu	37	5	140303492	140303492	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140303492delT	uc003lhb.2	+						PCDHA1_uc003lha.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_5'Flank|PCDHAC1_uc003lig.1_5'Flank	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor						homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGTGAAGATTTCCCATACT	0.408													4	2	---	---	---	---	
PRELID2	153768	broad.mit.edu	37	5	145175167	145175168	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145175167_145175168insA	uc003lnp.1	-						PRELID2_uc003lnq.1_Intron|PRELID2_uc003lno.1_Intron|PRELID2_uc003lnr.1_3'UTR	NM_182960	NP_892005	Q8N945	PRLD2_HUMAN	PRELI domain containing 2 isoform a												0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tcccacaAAACAAAATGAGGTA	0.129													4	2	---	---	---	---	
DPYSL3	1809	broad.mit.edu	37	5	146831597	146831597	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146831597delC	uc003lon.1	-						DPYSL3_uc003loo.2_Intron	NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCCTGCTGGCCTCAACTCTT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147678079	147678080	+	Intron	DEL	CC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147678079_147678080delCC	uc003lpb.1	-											Homo sapiens cDNA FLJ30191 fis, clone BRACE2001313.																		CTCATCTTCTCCACTATATAAT	0.386													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148416860	148416860	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148416860delT	uc003lpu.2	-						SH3TC2_uc003lpp.1_Intron|SH3TC2_uc003lps.2_Intron|SH3TC2_uc003lpt.2_Intron|SH3TC2_uc010jgx.2_Intron|SH3TC2_uc003lpv.1_Intron|SH3TC2_uc011dbz.1_Intron	NM_024577	NP_078853	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)			CTTGATATCCTTTTCTTCCTT	0.388													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149100713	149100713	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149100713delG								ARHGEF37 (86186 upstream) : PPARGC1B (9151 downstream)																							CAGTCTTCCTGGCTGCTCTAG	0.547													4	2	---	---	---	---	
NDST1	3340	broad.mit.edu	37	5	149881953	149881953	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149881953delG	uc011dcj.1	+							NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan						heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tttctggcttgaggaactgga	0.035													4	2	---	---	---	---	
CCDC69	26112	broad.mit.edu	37	5	150593472	150593473	+	Intron	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150593472_150593473delCA	uc003ltq.2	-						CCDC69_uc010jhu.2_Intron	NM_015621	NP_056436	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69											ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTAGTTCTATCACACCTATCCT	0.337													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154283046	154283046	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154283046delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCTTTGCTTCAAAAAAAAAGT	0.318													2	5	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155824228	155824229	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155824228_155824229insT	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGAAAGAAAACTTTTTTTTTCT	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157316532	157316532	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157316532delG								CLINT1 (30364 upstream) : EBF1 (806392 downstream)																							ACATTGTGGTGGAGCTGGAAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157855406	157855406	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157855406delC								CLINT1 (569238 upstream) : EBF1 (267518 downstream)																							GGATGTGCTGCCTCCTTGCCT	0.483													4	2	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158272713	158272714	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158272713_158272714insA	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTACaaaaagaaaaaaaaaaa	0.307			T	HMGA2	lipoma								5	4	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160739026	160739027	+	Intron	DEL	TG	-	-	rs72149262		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160739026_160739027delTG	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AGTAATGTTTtgtgtgtgtgtg	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163133678	163133679	+	IGR	INS	-	A	A	rs150402474	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163133678_163133679insA								MAT2B (187345 upstream) : None (None downstream)																							taattttctacaaaaaaggaaa	0.069													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163655304	163655304	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163655304delA								MAT2B (708971 upstream) : None (None downstream)																							aaaaaaaaacaaaaaaaaaaa	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164601983	164601983	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164601983delC								None (None upstream) : None (None downstream)																							TTATTCGTCTCCCAGTTTACT	0.398													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166917403	166917404	+	Intron	INS	-	AACC	AACC	rs144284198		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166917403_166917404insAACC	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		atgttactactaactCCATCTA	0.163													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167610388	167610388	+	Intron	DEL	A	-	-	rs113892292		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167610388delA	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)		ggcccagcacaaaaaaaaaaa	0.100													4	2	---	---	---	---	
PANK3	79646	broad.mit.edu	37	5	167990685	167990685	+	Intron	DEL	A	-	-	rs11336922		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167990685delA	uc003lzz.1	-						uc003maa.1_5'Flank|MIR103-1_hsa-mir-103-1|MI0000109_5'Flank	NM_024594	NP_078870	Q9H999	PANK3_HUMAN	pantothenate kinase 3						coenzyme A biosynthetic process	cytoplasm|nucleus	ATP binding|pantothenate kinase activity			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CTCAAAAATTAAAAAAAAAAA	0.279													5	3	---	---	---	---	
KCNIP1	30820	broad.mit.edu	37	5	169812744	169812744	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169812744delG	uc003map.2	+						KCNMB1_uc003maq.1_Intron|KCNMB1_uc003mar.2_Intron	NM_001034838	NP_001030010	Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1 isoform 3						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			gctcagtaatggccccccaag	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171244197	171244197	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171244197delG								FGF18 (360035 upstream) : FBXW11 (44359 downstream)																							agagttcccagggggatcagc	0.000													4	2	---	---	---	---	
STK10	6793	broad.mit.edu	37	5	171530665	171530665	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171530665delT	uc003mbo.1	-							NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGAAATTTGCTTTCAAATACG	0.488													4	2	---	---	---	---	
ERGIC1	57222	broad.mit.edu	37	5	172349085	172349085	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172349085delC	uc003mbw.3	+						ERGIC1_uc003mby.3_Intron|ERGIC1_uc011dfa.1_Intron	NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGCTCATCTCCCCAGTTCCG	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172634984	172634985	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172634984_172634985delTG								BNIP1 (43595 upstream) : NKX2-5 (24153 downstream)																							TGTGTGCAtatgtgtgtgtgtg	0.163													3	3	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177719234	177719235	+	Intron	INS	-	C	C	rs143960765	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177719234_177719235insC	uc003mje.2	-							NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	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)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GCCCGCACCTGCCCCTGCACCT	0.594													4	4	---	---	---	---	
ZNF879	345462	broad.mit.edu	37	5	178448973	178448973	+	5'Flank	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178448973delG	uc003mjt.3	+							NM_001136116	NP_001129588	B4DU55	ZN879_HUMAN	zinc finger protein 879						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1						TATTTTTTATGGGCCATCCCT	0.398													4	2	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179442665	179442666	+	Intron	INS	-	G	G	rs67220158		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179442665_179442666insG	uc003mll.1	-						RNF130_uc003mlm.1_Intron|MIR340_hsa-mir-340|MI0000802_5'Flank|uc003mln.2_5'Flank	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ggaaaggagtaggaaaggagta	0.000													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180562245	180562246	+	IGR	DEL	AC	-	-	rs33996681		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180562245_180562246delAC								BTNL9 (73723 upstream) : OR2V2 (19697 downstream)																							aggcttttcaacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	6987336	6987336	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6987336delT								LY86 (332120 upstream) : RREB1 (120852 downstream)																							ACATAGCTAATTTATGAGGCT	0.388													4	2	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11778597	11778597	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11778597delT	uc003nab.2	-						C6orf105_uc011dip.1_Intron	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			CAAGATGAGATTTTTTTTTTC	0.353													10	5	---	---	---	---	
GFOD1	54438	broad.mit.edu	37	6	13408142	13408145	+	Intron	DEL	CCAA	-	-	rs68037309		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13408142_13408145delCCAA	uc003nat.1	-						GFOD1_uc003nas.1_Intron	NM_018988	NP_061861	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain							extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			CTGTACTCACCCAACCAACTGACT	0.475													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14844656	14844656	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14844656delT								CD83 (707510 upstream) : JARID2 (401078 downstream)																							TACGGTTGTGTTTTTTTTTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19761922	19761922	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19761922delA								None (None upstream) : ID4 (75695 downstream)																							TAAAGTAAGTAAACAAAACTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31433605	31433606	+	IGR	DEL	TG	-	-	rs114857430	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31433605_31433606delTG								HCP5 (21 upstream) : HCG26 (5400 downstream)																							TATCCACTTTTGTGTGTGTGTG	0.109													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34419864	34419864	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34419864delG								RPS10 (25988 upstream) : PACSIN1 (14041 downstream)																							cacaggttctggggattcgga	0.085													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38848907	38848907	+	Intron	DEL	A	-	-	rs34216575		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38848907delA	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						gccgtaatagagcacctagag	0.015													3	3	---	---	---	---	
GPR110	266977	broad.mit.edu	37	6	46975336	46975336	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46975336delT	uc003oyt.2	-						GPR110_uc011dwl.1_Intron	NM_153840	NP_722582	Q5T601	GP110_HUMAN	G-protein coupled receptor 110 isoform 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3						AATAGCATCCTTTTTTGTCTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47174260	47174260	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47174260delA								GPR110 (164178 upstream) : TNFRSF21 (25009 downstream)																							ttagccaattaaaaaaaagga	0.100													4	2	---	---	---	---	
CRISP3	10321	broad.mit.edu	37	6	49699944	49699944	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49699944delC	uc003ozs.2	-							NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CCTCTAATGACCAGGCATTTG	0.393													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57304140	57304141	+	Intron	INS	-	TG	TG	rs113443807		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57304140_57304141insTG	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)		TTGAATTATTTTACTACCTTTG	0.292													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57375548	57375549	+	Intron	INS	-	TTA	TTA	rs150899802		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57375548_57375549insTTA	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)		CTGCTGTTGCTTTATTATTATT	0.396													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57435808	57435811	+	Intron	DEL	AAAC	-	-	rs10552360		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57435808_57435811delAAAC	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)		AAAATTAAGTAAACAATATTGATT	0.275													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57540277	57540278	+	IGR	INS	-	G	G	rs141654716		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57540277_57540278insG								PRIM2 (26902 upstream) : GUSBL2 (705881 downstream)																							CATGCAAGGCAGGCTACGTTAA	0.381													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	66440836	66440836	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66440836delT								EYS (23718 upstream) : MCART3P (56936 downstream)																							CACTTAAGTGTTGCCTATATC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	70294522	70294522	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70294522delA								BAI3 (195120 upstream) : LMBRD1 (91229 downstream)																							TCATAAAATGAAAAAGAGTCA	0.418													3	3	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73625465	73625465	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73625465delA	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)		AAGTACTGTCAAAAAAAAAAT	0.264													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82126943	82126943	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82126943delA								None (None upstream) : FAM46A (328505 downstream)																							ATTAGCTGAGAAAAAAAAAAA	0.303													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83574017	83574018	+	IGR	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83574017_83574018delCA								TPBG (497403 upstream) : UBE2CBP (28168 downstream)																							cacacacactcacacacacaca	0.000													4	2	---	---	---	---	
UBE2CBP	90025	broad.mit.edu	37	6	83631466	83631466	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83631466delT	uc003pjp.2	-						UBE2CBP_uc011dyx.1_Intron	NM_198920	NP_944602	Q7Z6J8	UB2CB_HUMAN	ubiquitin-conjugating enzyme E2C binding							cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)		CAGGAACATATTTTCATCCAG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	84736228	84736228	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84736228delG								CYB5R4 (66084 upstream) : MRAP2 (7192 downstream)																							GAGGGGGCATGAGTATGTGTG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85159057	85159057	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85159057delG								KIAA1009 (221722 upstream) : TBX18 (238024 downstream)																							TAATCTAACTGGCACATTGTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86074204	86074204	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86074204delA								TBX18 (600305 upstream) : NT5E (85098 downstream)																							TCAGCCTTACAAAAAATCCAG	0.388													4	2	---	---	---	---	
C6orf162	57150	broad.mit.edu	37	6	88050928	88050928	+	3'UTR	DEL	T	-	-	rs9362422		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88050928delT	uc003plp.1	+	4					C6orf164_uc003plr.2_Intron|C6orf162_uc003plq.1_3'UTR	NM_001042493	NP_001035958	Q96KF7	CF162_HUMAN	hypothetical protein LOC57150							integral to membrane					0		all_cancers(76;3.81e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.3e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0164)		GGCCTTTTTGTTTTTTTCCTT	0.328													4	2	---	---	---	---	
RNGTT	8732	broad.mit.edu	37	6	89635604	89635604	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89635604delA	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	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)		cctgtctcttaaaaaaaaaTC	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92320490	92320491	+	IGR	INS	-	ACAGG	ACAGG	rs143533468	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92320490_92320491insACAGG								None (None upstream) : None (None downstream)																							GAAAACAAAGAGTCCCAAGGAA	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	94930436	94930436	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94930436delT								TSG1 (444237 upstream) : None (None downstream)																							TGTAATTGAATTTTTTAGAAA	0.289													4	2	---	---	---	---	
PRDM13	59336	broad.mit.edu	37	6	100053891	100053891	+	5'Flank	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100053891delA	uc003pqg.1	+							NM_021620	NP_067633	Q9H4Q3	PRD13_HUMAN	PR domain containing 13						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		ACCCACTGGTAGAACTTCTTC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	103299512	103299512	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103299512delA								GRIK2 (781555 upstream) : None (None downstream)																							ggagaccagCAAAAAAATAGA	0.129													4	2	---	---	---	---	
ATG5	9474	broad.mit.edu	37	6	106760499	106760510	+	Intron	DEL	ACACACACACAC	-	-	rs147487015		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106760499_106760510delACACACACACAC	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		aaaaaagactacacacacacacacacacacac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113290645	113290645	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113290645delA								RFPL4B (618147 upstream) : MARCKS (887882 downstream)																							atagaactggaaaaaaacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113885484	113885484	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113885484delT								None (None upstream) : MARCKS (293043 downstream)																							ATTTAAGTGATTTTTTTTTTT	0.274													3	3	---	---	---	---	
C6orf170	221322	broad.mit.edu	37	6	121559117	121559117	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121559117delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc010kej.1_5'Flank|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		agagtacattaaaaaataaat	0.000													4	2	---	---	---	---	
PKIB	5570	broad.mit.edu	37	6	122793121	122793121	+	5'UTR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122793121delG	uc003pyz.2	+	1					SERINC1_uc003pyy.1_5'Flank	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)		AATTTCTCAAGGACTGCTGGC	0.517													4	2	---	---	---	---	
RNF217	154214	broad.mit.edu	37	6	125358919	125358920	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125358919_125358920insC	uc003pzs.2	+						RNF217_uc003pzr.2_Intron|RNF217_uc003pzt.2_Intron	NM_152553	NP_689766	Q8TC41	RN217_HUMAN	ring finger protein 217						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)		GTTACTGCTTTCGTTGCAATAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	126476189	126476189	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126476189delT								TRMT11 (115771 upstream) : CENPW (185064 downstream)																							tattaggctgtttgagttgtt	0.219													4	2	---	---	---	---	
LAMA2	3908	broad.mit.edu	37	6	129637525	129637525	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129637525delA	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		cgttaaagggaaaaaaaaata	0.060													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	132736980	132736980	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132736980delG								MOXD1 (14316 upstream) : STX7 (41683 downstream)																							gtgagggAGTGGGGAAGTGTT	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138303738	138303741	+	IGR	DEL	CTAG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138303738_138303741delCTAG								TNFAIP3 (99293 upstream) : PERP (105901 downstream)																							TCAGGAAATTCTAGACTAGACTTC	0.466													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142973359	142973359	+	IGR	DEL	T	-	-	rs113674176		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142973359delT								LOC153910 (14333 upstream) : HIVEP2 (99246 downstream)																							GGATTTTCTCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
HIVEP2	3097	broad.mit.edu	37	6	143125138	143125138	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143125138delC	uc003qjd.2	-							NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CTGTTTATCACCTGTTTTCAC	0.348													4	2	---	---	---	---	
HIVEP2	3097	broad.mit.edu	37	6	143250601	143250601	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143250601delA	uc003qjd.2	-							NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		AAACCAGAACAAAAAAAAAGG	0.303													2	4	---	---	---	---	
SASH1	23328	broad.mit.edu	37	6	148823491	148823491	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148823491delA	uc003qme.1	+							NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GTGATAAAAGAAAAAAAAAAC	0.343													5	3	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149132584	149132584	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149132584delA	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		gtcttatagcaaaaagtatgg	0.020													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149132771	149132771	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149132771delT	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		tgggagtcacttggctcaccc	0.000													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149246344	149246344	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149246344delA	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		TTGCCCCCATAAAAAAGTCCA	0.433													4	2	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152786902	152786903	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152786902_152786903delAC	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qow.2_5'Flank|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AAGAacacatacacacacacac	0.297										HNSCC(10;0.0054)			11	5	---	---	---	---	
IPCEF1	26034	broad.mit.edu	37	6	154660709	154660710	+	Intron	INS	-	TTTG	TTTG	rs149945811	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154660709_154660710insTTTG	uc003qpx.2	-						IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0						gcctggcgttttttgtttgttt	0.000													4	2	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155211446	155211447	+	Intron	DEL	AT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155211446_155211447delAT	uc003qqb.2	+						uc003qqc.1_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GATTTCATTCATATATATATAT	0.252													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157691545	157691546	+	IGR	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157691545_157691546insC								ARID1B (161144 upstream) : C6orf35 (18509 downstream)																							cagcagcagcaccattgctacc	0.020													2	7	---	---	---	---	
RSPH3	83861	broad.mit.edu	37	6	159411682	159411682	+	Intron	DEL	T	-	-	rs112960170		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159411682delT	uc003qrx.2	-						RSPH3_uc010kju.2_Intron|RSPH3_uc003qry.1_Intron	NM_031924	NP_114130	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog											ovary(1)|skin(1)	2		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		tttcaaaatgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165554822	165554822	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165554822delC								None (None upstream) : C6orf118 (138333 downstream)																							CCACAGCTTTCCCATCGTCTA	0.468													4	2	---	---	---	---	
C6orf118	168090	broad.mit.edu	37	6	165720404	165720405	+	Intron	INS	-	TG	TG	rs145859741	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165720404_165720405insTG	uc003qum.3	-						C6orf118_uc011egi.1_Intron	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090												0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		TCTGAAAACATTGTGTGTGTCT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168666515	168666515	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168666515delT								FRMD1 (186676 upstream) : DACT2 (41071 downstream)																							TTCACTCTCCTTCCCACCCTT	0.453													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3458158	3458158	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3458158delA	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)		CAGGTGGCATAAAAAAAAAAG	0.388													3	3	---	---	---	---	
WIPI2	26100	broad.mit.edu	37	7	5240936	5240936	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5240936delG	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		TTCCCTTGCTGGGGGCCAGTG	0.438													4	2	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8500924	8500924	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8500924delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CCAGGTTGTATTTTTTTTCCT	0.378													4	2	---	---	---	---	
TRA2A	29896	broad.mit.edu	37	7	23572707	23572708	+	5'Flank	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23572707_23572708insT	uc003swi.2	-						TRA2A_uc011jzb.1_5'Flank|TRA2A_uc011jzc.1_5'Flank|TRA2A_uc011jzd.1_5'Flank|TRA2A_uc010kuo.1_5'Flank	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						CAGCCGTGTAGTTTTTTTTTTA	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23585318	23585318	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23585318delT								TRA2A (13662 upstream) : CLK2P (39017 downstream)																							cattaggTAGTGAGTGATAAT	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	27503284	27503284	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27503284delT								EVX1 (217092 upstream) : HIBADH (61779 downstream)																							TTGGGTGAAGTTTAGAAGCAT	0.393													4	2	---	---	---	---	
JAZF1	221895	broad.mit.edu	37	7	28102249	28102249	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28102249delT	uc003szn.2	-							NM_175061	NP_778231	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131						gccagcaaacttctgtgacat	0.000			T	SUZ12	endometrial stromal tumours								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31547239	31547239	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31547239delC								NEUROD6 (166701 upstream) : CCDC129 (6446 downstream)																							tcagagtgcacccaaaattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	34287778	34287778	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34287778delG								BMPER (93667 upstream) : AAA1 (102257 downstream)																							cacggtgcttggggcagtacc	0.104													4	2	---	---	---	---	
NPSR1	387129	broad.mit.edu	37	7	34884071	34884071	+	Intron	DEL	T	-	-	rs111592093		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34884071delT	uc003teg.1	+						AAA1_uc010kwq.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron	NM_207172	NP_997055	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)	tgtttttttgttttttttttG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35509196	35509196	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35509196delT								TBX20 (215954 upstream) : HERPUD2 (163076 downstream)																							TCAGCTGCCATTTGCTGGGGC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35985727	35985727	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35985727delA								SEPT7 (40812 upstream) : EEPD1 (207109 downstream)																							TTACAGTTTTAAAAAAAAAAG	0.289													2	5	---	---	---	---	
EEPD1	80820	broad.mit.edu	37	7	36207247	36207247	+	Intron	DEL	A	-	-	rs140102096		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36207247delA	uc003tfa.2	+							NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0						ATGTTGATGCATAAGTTTGCC	0.448													2	4	---	---	---	---	
KIAA0895	23366	broad.mit.edu	37	7	36399918	36399918	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36399918delA	uc003tfd.2	-						KIAA0895_uc003tfc.2_Intron|KIAA0895_uc011kaw.1_Intron|KIAA0895_uc003tfb.2_Intron|KIAA0895_uc011kax.1_Intron|KIAA0895_uc003tfe.2_Intron|KIAA0895_uc011kay.1_Intron	NM_001100425	NP_001093895	Q8NCT3	K0895_HUMAN	hypothetical protein LOC23366 isoform 1												0						TCCAGATACTAAAAAAAAACG	0.423													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37110102	37110103	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37110102_37110103delTG	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						ATTTGTGAACTGTGTGTGTGTG	0.351													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37861358	37861359	+	Intron	INS	-	A	A	rs151118719	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37861358_37861359insA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																		CTTTATTGGGGAAAAAAAATAG	0.252													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	38298763	38298764	+	5'Flank	INS	-	T	T	rs141065618	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38298763_38298764insT	uc003tfv.2	-						uc003tfw.2_5'Flank|uc003tfx.1_Intron|uc003tfz.1_Intron					SubName: Full=TARP protein;																		acatgaggagattatggcacat	0.000													3	3	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38590868	38590868	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38590868delA	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						CATCATTAACAATGAACCAAT	0.398													4	2	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40393406	40393406	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40393406delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						TTTCATCAACTTTTTTTTCCA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42634094	42634094	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42634094delT								GLI3 (357476 upstream) : C7orf25 (314780 downstream)																							CTACTTTTTATTTTTTTTTGT	0.383													4	2	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43550330	43550331	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43550330_43550331delAA	uc003tid.1	+						HECW1_uc011kbi.1_Intron|uc003tig.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						TGAATCTTTCAAAAAGAGGAGA	0.460													4	2	---	---	---	---	
RASA4P	401331	broad.mit.edu	37	7	44073273	44073274	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44073273_44073274insC	uc011kbk.1	-						RASA4P_uc003tji.2_RNA|RASA4P_uc010kxx.2_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1												0						aacaacaacaaaaaaaaacaag	0.005													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46735706	46735706	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46735706delA	uc003tnu.1	-											Homo sapiens cDNA FLJ43321 fis, clone NT2RI2027396.																		tctggctctcaaaaaaaaaag	0.000													3	4	---	---	---	---	
PKD1L1	168507	broad.mit.edu	37	7	47851996	47851996	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47851996delT	uc003tny.1	-						C7orf69_uc003tnz.3_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						TTCATTGTTCTTTTTTTTTCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48772560	48772560	+	IGR	DEL	C	-	-	rs11185613	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48772560delC								ABCA13 (85469 upstream) : CDC14C (191597 downstream)																							aACAAACAAACAAAAAAAACA	0.169													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	50921544	50921544	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50921544delC								GRB10 (60385 upstream) : COBL (162366 downstream)																							tctccttctgcccacagagcc	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52754390	52754390	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52754390delT								None (None upstream) : POM121L12 (348959 downstream)																							atttgcttgctttttttttca	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57128262	57128262	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57128262delC								DKFZp434L192 (563285 upstream) : ZNF479 (59066 downstream)																							CCCCACCTGGCCCCCAGCCCT	0.627													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57498589	57498589	+	IGR	DEL	T	-	-	rs75462970		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57498589delT								ZNF479 (291018 upstream) : ZNF716 (11294 downstream)																							CCCTGCCTCCTTTTTTTTTTC	0.343													4	3	---	---	---	---	
TYW1	55253	broad.mit.edu	37	7	66635953	66635954	+	Intron	INS	-	T	T	rs149721131	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66635953_66635954insT	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				ttcctctgctattttttttgga	0.000													4	2	---	---	---	---	
PMS2L4	5382	broad.mit.edu	37	7	66762433	66762433	+	Intron	DEL	A	-	-	rs68053451		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66762433delA	uc003tvo.2	-						PMS2L4_uc003tvq.2_Intron|PMS2L4_uc003tvr.3_Intron|PMS2L4_uc003tvs.3_Intron					Homo sapiens cDNA clone IMAGE:4081618.												0						tctcaaaaagaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68415452	68415452	+	IGR	DEL	C	-	-	rs62460291	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68415452delC								None (None upstream) : AUTS2 (648453 downstream)																							ATATCTGCTTCCCTGTCTTCT	0.473													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69065039	69065040	+	Intron	INS	-	CTGT	CTGT	rs113411804		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69065039_69065040insCTGT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CGCGCTCCGGGctgtctgtctg	0.589													3	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69114501	69114501	+	Intron	DEL	T	-	-	rs74531286		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69114501delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CACTGTATGCTTTTTTTTTTG	0.458													4	5	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73432999	73433000	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73432999_73433000insC	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						CAGGGGGACCACCCCACTGAGC	0.554													4	2	---	---	---	---	
GTF2IP1	2970	broad.mit.edu	37	7	74615675	74615675	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74615675delA	uc003ubw.2	-						GTF2IP1_uc003ubx.3_Intron					SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0						TGTTTTTTTTAAAAAAAAAAA	0.338													2	4	---	---	---	---	
POR	5447	broad.mit.edu	37	7	75590188	75590188	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75590188delG	uc003udy.2	+							NM_000941	NP_000932	P16435	NCPR_HUMAN	cytochrome P450 reductase						cellular organofluorine metabolic process|positive regulation of monooxygenase activity	endoplasmic reticulum membrane	iron ion binding|NADPH-hemoprotein reductase activity			central_nervous_system(1)	1					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Lipoic Acid(DB00166)|Menadione(DB00170)|Methoxyflurane(DB01028)|Mitomycin(DB00305)|Nilutamide(DB00665)	GGAAACCTGTGGCCTCCAGGC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	79879263	79879263	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79879263delG								GNAI1 (30538 upstream) : CD36 (119628 downstream)																							cagagcagctggggatggatg	0.085													4	2	---	---	---	---	
CACNA2D1	781	broad.mit.edu	37	7	81871342	81871342	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81871342delA	uc003uhr.1	-							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)	TAAACTTCCTAAATTGTTTCA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82831058	82831061	+	IGR	DEL	TTTG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82831058_82831061delTTTG								PCLO (38861 upstream) : SEMA3E (162161 downstream)																							ccttctcttttttgtttgtttgtt	0.000													4	2	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88755446	88755446	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88755446delT	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TGTTAATGGATTTTTTTTTTA	0.294										HNSCC(36;0.09)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	90890032	90890033	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90890032_90890033insA								CDK14 (50128 upstream) : FZD1 (3750 downstream)																							aaaagaaaaagaaaaaaaaaGG	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98912197	98912198	+	IGR	INS	-	G	G	rs138025142	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98912197_98912198insG								MYH16 (16605 upstream) : ARPC1A (11312 downstream)																							ctgaagcttaaggtgagtagga	0.163													4	2	---	---	---	---	
PILRB	29990	broad.mit.edu	37	7	99943553	99943553	+	5'UTR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99943553delT	uc003uuk.2	+	4					PILRB_uc003uul.2_5'UTR	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGTGAAGGGATTTTTTTTTTT	0.413													4	2	---	---	---	---	
LRWD1	222229	broad.mit.edu	37	7	102106858	102106861	+	Intron	DEL	TTTA	-	-	rs66463732		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102106858_102106861delTTTA	uc003uzn.2	+						ALKBH4_uc003uzl.2_5'Flank|ALKBH4_uc003uzm.2_5'Flank|LRWD1_uc003uzo.2_Intron	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain						chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1						GATGTGCTACtttatttatttatt	0.260													6	6	---	---	---	---	
DNAJC2	27000	broad.mit.edu	37	7	102963381	102963381	+	Intron	DEL	T	-	-	rs75138416		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102963381delT	uc003vbo.2	-						PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Intron|DNAJC2_uc010lix.2_Intron|DNAJC2_uc003vbp.2_Intron	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2						'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						TAAACAATGAttttttttttt	0.129													6	6	---	---	---	---	
SRPK2	6733	broad.mit.edu	37	7	104991417	104991417	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104991417delC	uc003vcv.2	-						SRPK2_uc003vcw.1_Intron	NM_182692	NP_872634	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						CTATTTGCTACCACCCTGtga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117797158	117797159	+	IGR	INS	-	TC	TC			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117797158_117797159insTC								CTTNBP2 (283597 upstream) : NAA38 (26927 downstream)																							cctggaagttttctctctattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121276769	121276769	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121276769delT								FAM3C (240347 upstream) : PTPRZ1 (236390 downstream)																							ATATTCTTTGTTTTCAGGGAG	0.333													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122111213	122111213	+	Intron	DEL	G	-	-	rs28390321	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122111213delG	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						TCTCTCTTTCGAGTGGCTTTA	0.348													4	2	---	---	---	---	
SPAM1	6677	broad.mit.edu	37	7	123569950	123569950	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123569950delT	uc003vld.2	+						SPAM1_uc003vle.2_Intron|SPAM1_uc003vlf.3_Intron|SPAM1_uc010lku.2_Intron	NM_153189	NP_694859	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 2						binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)	tgtttagggattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123685577	123685578	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123685577_123685578delAA	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																		CAGGCTGCCTAAACCTGCTGTC	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124649782	124649782	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124649782delT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																		atgagactcatttttttaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124704408	124704408	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124704408delG	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																		gggtgagggtggatcttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125780966	125780966	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125780966delA								None (None upstream) : GRM8 (297686 downstream)																							ATGTGAGGCCAAAAAAAATGT	0.254													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126803669	126803669	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126803669delT	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)	actgtgattattttttcaagt	0.070										HNSCC(24;0.065)			4	2	---	---	---	---	
IMPDH1	3614	broad.mit.edu	37	7	128052380	128052380	+	5'Flank	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128052380delA	uc003vmu.2	-						IMPDH1_uc003vmw.2_5'Flank|IMPDH1_uc011kon.1_5'Flank|IMPDH1_uc003vmv.2_5'Flank|IMPDH1_uc003vmx.2_5'Flank|IMPDH1_uc003vmy.2_5'Flank	NM_000883	NP_000874	P20839	IMDH1_HUMAN	inosine monophosphate dehydrogenase 1 isoform a						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)	AAATCCAAATAAAGTTACCAG	0.328													4	2	---	---	---	---	
TNPO3	23534	broad.mit.edu	37	7	128636192	128636192	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128636192delG	uc003vol.1	-						TNPO3_uc003vom.1_Intron|TNPO3_uc010lly.1_Intron|TNPO3_uc010llz.1_Intron	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3						splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5						AACAGCACGTGGGATTTAATT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129621209	129621209	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129621209delA								UBE2H (28420 upstream) : ZC3HC1 (36918 downstream)																							ttctgtcttgaaaaaaagaaa	0.065													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133018190	133018190	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133018190delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_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)				ggagatctggtttttttttta	0.000													2	4	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138352275	138352275	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138352275delT	uc011kqh.1	-							NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						ttactctcccttttttcttcc	0.000													4	2	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138763121	138763121	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138763121delA	uc003vun.2	-						ZC3HAV1_uc003vuo.2_Intron|ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						atagttcctcaaaaaaaaaaa	0.000													8	5	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139331866	139331866	+	Intron	DEL	T	-	-	rs5887933		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139331866delT	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)					gcactgatagttttttttttt	0.000													5	3	---	---	---	---	
RAB19	401409	broad.mit.edu	37	7	140122189	140122189	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140122189delA	uc010lni.2	+						RAB19_uc011krc.1_Intron	NM_001008749	NP_001008749	A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0	Melanoma(164;0.0142)					acgctgtctcaaaaaaaaaag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144766332	144766332	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144766332delT								TPK1 (233186 upstream) : None (None downstream)																							attctttttctttttttTTTA	0.025													3	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152075521	152075522	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152075521_152075522insT	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)		gatcagtagcattttttagcaa	0.000			N		medulloblastoma								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152978429	152978429	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152978429delT								ACTR3B (425966 upstream) : DPP6 (605990 downstream)																							GGAGACTGCATTATCTTCAGG	0.388													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154109767	154109767	+	Intron	DEL	C	-	-	rs286849	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154109767delC	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_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)			CTTTTTTTTTCAACTTTAGAA	0.338													5	3	---	---	---	---	
LMBR1	64327	broad.mit.edu	37	7	156497296	156497297	+	Intron	INS	-	A	A	rs34052800		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156497296_156497297insA	uc003wmw.3	-						LMBR1_uc003wmv.3_Intron|LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		gatcctaactgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157841853	157841853	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157841853delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		accatcaccatcaatcatcat	0.070													3	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157841855	157841857	+	Intron	DEL	AAT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157841855_157841857delAAT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		catcaccatcaatcatcattgcc	0.079													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1140398	1140412	+	IGR	DEL	GGGGCATCTGCTGTT	-	-	rs67665105		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1140398_1140412delGGGGCATCTGCTGTT								ERICH1 (459172 upstream) : DLGAP2 (309157 downstream)																							AGTCAGGGTCGGGGCATCTGCTGTTGGGGCATCTG	0.567													13	8	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3874310	3874310	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3874310delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TATAGTTGGGTTTTTTTGGTC	0.348													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4617100	4617100	+	Intron	DEL	T	-	-	rs36026476		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4617100delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		accatccccctgtcaggtccc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4863001	4863004	+	IGR	DEL	TTTG	-	-	rs113560734		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4863001_4863004delTTTG								CSMD1 (10673 upstream) : None (None downstream)																							TGAGGGTGTTtttgtttgtttgtt	0.338													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6756876	6756876	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6756876delT								DEFB1 (21347 upstream) : DEFA6 (25345 downstream)																							GCGGATCTTCTTTTTTTTTTG	0.527													4	3	---	---	---	---	
MSRA	4482	broad.mit.edu	37	8	10043405	10043406	+	Intron	INS	-	T	T	rs145953101	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10043405_10043406insT	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc011kwy.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	atttccattcattttttttttc	0.208													4	2	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12307515	12307515	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12307515delT	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						cacaccaatatttttttttgt	0.000													4	2	---	---	---	---	
PDGFRL	5157	broad.mit.edu	37	8	17478915	17478915	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17478915delT	uc003wxr.2	+							NM_006207	NP_006198	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like							extracellular region	platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity				0				Colorectal(111;0.0752)		attattcctgttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19260665	19260666	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19260665_19260666insA								SH2D4A (7351 upstream) : CSGALNACT1 (1007 downstream)																							agttggaaaggaaaaaaATTCT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23477816	23477816	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23477816delT								SLC25A37 (47755 upstream) : NKX3-1 (58391 downstream)																							CTCCCCATCATTATTACAGGG	0.433													4	2	---	---	---	---	
DPYSL2	1808	broad.mit.edu	37	8	26395423	26395423	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26395423delG	uc003xfa.2	+							NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		ccttctatctggaagcgttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29694627	29694627	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29694627delG								C8orf75 (89002 upstream) : LOC286135 (84402 downstream)																							ACCAGTGGGAGGGCGGCACAG	0.562													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	31983360	31983360	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31983360delT	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		AGTTTCTACATTTTTTTGAAA	0.333													4	2	---	---	---	---	
HTRA4	203100	broad.mit.edu	37	8	38834466	38834466	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38834466delT	uc003xmj.2	+							NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor						proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			cttttctttctttttttttga	0.149													10	6	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40741944	40741945	+	Intron	INS	-	T	T	rs71546317		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40741944_40741945insT	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			ttgacatttcattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55763611	55763612	+	IGR	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55763611_55763612delGT								RP1 (81080 upstream) : XKR4 (251405 downstream)																							GTACACGTACgtgtgtgtgtgt	0.198													4	2	---	---	---	---	
IMPAD1	54928	broad.mit.edu	37	8	57895468	57895469	+	Intron	DEL	AT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57895468_57895469delAT	uc003xte.3	-							NM_017813	NP_060283	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1							Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				ttactcagccatatatacgaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58094436	58094436	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58094436delT								IMPAD1 (188009 upstream) : C8orf71 (97666 downstream)																							TTGTGATAACttttttttttt	0.119													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60301240	60301240	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60301240delT								TOX (269473 upstream) : CA8 (800183 downstream)																							AGTATACTTGTTTTTTTCTGA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61051557	61051557	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61051557delT								None (None upstream) : CA8 (49866 downstream)																							AATTCTTCAATTTTTCTGTAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71690038	71690038	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71690038delT								XKR9 (41862 upstream) : EYA1 (419632 downstream)																							tttgatgaggtttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73202695	73202696	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73202695_73202696delAA	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																		tcacacttttaatggcttgtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79797483	79797483	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79797483delG								IL7 (79725 upstream) : STMN2 (725897 downstream)																							GTTTCTTTTTGGGGGGATGAA	0.294													4	2	---	---	---	---	
PTDSS1	9791	broad.mit.edu	37	8	97280863	97280863	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97280863delT	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	GAGTGCAAACttttttttttt	0.383													7	4	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97831678	97831679	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97831678_97831679insA	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					gattaggaaacaaaaaaaaatc	0.000													4	2	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97853166	97853166	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97853166delC	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					cttgtatgttccattgggcaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98363451	98363451	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98363451delT								TSPYL5 (73275 upstream) : MTDH (292956 downstream)																							TAAGTTCTGCTTTTTTGGCCC	0.219													4	2	---	---	---	---	
SPAG1	6674	broad.mit.edu	37	8	101206174	101206174	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101206174delT	uc003yjh.1	+						SPAG1_uc003yjg.1_Intron|SPAG1_uc003yji.1_Intron	NM_172218	NP_757367	Q07617	SPAG1_HUMAN	sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		TGTGTGTGTGTTTTTTTTTTA	0.204													8	4	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	103065305	103065305	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103065305delG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			TCCTTCTACTGGAGTGAACTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104277738	104277738	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104277738delG	uc003ylf.2	-											Homo sapiens cDNA FLJ43745 fis, clone TESTI2019648.																		tccatttggtgggggagaaga	0.045													4	2	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106359773	106359774	+	Intron	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106359773_106359774delTT	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CTACTAAAGGTTTTAACATCTA	0.297													4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107360436	107360436	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107360436delG	uc003ymf.2	+							NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			CACGAGGGGTGGGAAAGTTTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108635405	108635405	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108635405delA								ANGPT1 (125151 upstream) : RSPO2 (276140 downstream)																							GAGTTTAAAGAAAAATCTGGG	0.323													4	2	---	---	---	---	
RSPO2	340419	broad.mit.edu	37	8	109013980	109013980	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109013980delA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			TCAGTGAGGGAAAAAAAAAAT	0.279													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	113165529	113165529	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113165529delA								None (None upstream) : CSMD3 (69632 downstream)																							cagaacttccaaaacaatgct	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122590347	122590347	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122590347delG								SNTB1 (766038 upstream) : HAS2 (34924 downstream)																							TTCAGCAAGTGGGGTGGTATG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125791000	125791001	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125791000_125791001insT								MTSS1 (50270 upstream) : LOC157381 (160883 downstream)																							GGAGTTACCTATTTTTTAAACA	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128652054	128652054	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128652054delA								LOC727677 (157670 upstream) : MYC (95711 downstream)																							CTTCTAAATTAAAAAAAAAGA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136338392	136338392	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136338392delA								LOC286094 (26433 upstream) : KHDRBS3 (131324 downstream)																							GACAGGTGTGAAAGGAGGCAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138848819	138848820	+	IGR	INS	-	TCA	TCA	rs149041801	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138848819_138848820insTCA								None (None upstream) : FAM135B (293448 downstream)																							aaacattgaagtcatcattatg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140130703	140130703	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140130703delA								COL22A1 (204467 upstream) : KCNK9 (482379 downstream)																							AAAGCAAAGGAAAAAAAAAAA	0.358													4	2	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140635457	140635457	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140635457delA	uc003yvf.1	-						KCNK9_uc003yvg.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)			AATGAGGTACAAATCTAATAC	0.438													4	2	---	---	---	---	
FLJ43860	389690	broad.mit.edu	37	8	142477469	142477471	+	Intron	DEL	CCC	-	-	rs79462875	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142477469_142477471delCCC	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			cccttcctggcccttcctggccc	0.591													8	6	---	---	---	---	
FLJ43860	389690	broad.mit.edu	37	8	142477473	142477479	+	Intron	DEL	TCCTGGC	-	-	rs73713678	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142477473_142477479delTCCTGGC	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			tcctggcccttcctggcccAGCCCCAG	0.594													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143209117	143209118	+	IGR	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143209117_143209118delAG								MIR1302-7 (341443 upstream) : NCRNA00051 (70599 downstream)																							ggagggacacagagagagagag	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1965980	1965981	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1965980_1965981delAC								DMRT2 (908427 upstream) : SMARCA2 (49361 downstream)																							TTGTTCTTGAACACACACACAT	0.431													4	2	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	4141219	4141220	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4141219_4141220delGA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron|GLIS3_uc003zib.1_Intron|GLIS3_uc010mhg.1_Intron	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		gagacagaaggagagagagagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	4306634	4306634	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4306634delG								GLIS3 (6599 upstream) : SLC1A1 (183810 downstream)																							AGATTTTCCTGGAATGGCATT	0.398													4	2	---	---	---	---	
MLANA	2315	broad.mit.edu	37	9	5903864	5903864	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5903864delT	uc003zjo.1	+							NM_005511	NP_005502	Q16655	MAR1_HUMAN	melan-A							endoplasmic reticulum membrane|integral to plasma membrane|melanosome|trans-Golgi network	protein binding				0		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		atgcacttacttttttttttt	0.000													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	8730941	8730942	+	Intron	INS	-	C	C	rs144682589	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8730941_8730942insC	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GCCATTCAAGACACCGGAATGA	0.406										TSP Lung(15;0.13)			2	5	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9040580	9040580	+	Intron	DEL	T	-	-	rs150140078		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9040580delT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TCCCGAAGAATTTTTTTTTTC	0.323										TSP Lung(15;0.13)			4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9879357	9879358	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9879357_9879358insA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		cttgtgatgagaaaaaaatgcc	0.050										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	13716745	13716745	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13716745delT								MPDZ (437182 upstream) : NFIB (365103 downstream)																							TGCAAGGTTGTAAATGAATCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19231542	19231542	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19231542delT								PLIN2 (103969 upstream) : DENND4C (59160 downstream)																							CTGTCACGTCTTTTTTTTTTT	0.378													3	4	---	---	---	---	
ELAVL2	1993	broad.mit.edu	37	9	23797262	23797262	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23797262delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		AGGCGTTTTCAAAAAAATACA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26540529	26540529	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26540529delA								TUSC1 (861673 upstream) : C9orf82 (300155 downstream)																							ctctagtgagaaaaaaggcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26662155	26662155	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26662155delT								TUSC1 (983299 upstream) : C9orf82 (178529 downstream)																							ctgctcagcattttacaaaag	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29811130	29811130	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29811130delT								MIR873 (922177 upstream) : None (None downstream)																							tatagcccccttttttggcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	42958559	42958559	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:42958559delA								AQP7P3 (65424 upstream) : LOC642929 (181980 downstream)																							TTATAATTTTAGAATTCCCAC	0.338													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44799721	44799722	+	IGR	INS	-	C	C	rs141633865	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44799721_44799722insC								None (None upstream) : FAM27C (190514 downstream)																							agtaaaatgctcaacaccaagg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66316516	66316517	+	IGR	INS	-	CA	CA			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66316516_66316517insCA								FAM74A4 (822130 upstream) : LOC442421 (179953 downstream)																							aaaggaacacccacacacacac	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66473147	66473148	+	IGR	INS	-	A	A	rs75438927	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66473147_66473148insA								FAM74A4 (978761 upstream) : LOC442421 (23322 downstream)																							tatagaattttaaaaatagcct	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68398095	68398095	+	IGR	DEL	C	-	-	rs74487823		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68398095delC								FAM27B (603906 upstream) : MIR1299 (604144 downstream)																							CCATGCTTAGCTTGGGTTTCT	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68723864	68723864	+	5'Flank	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68723864delG	uc004aez.1	+						uc004afa.1_5'Flank|uc010mnp.1_5'Flank					Homo sapiens cDNA, FLJ18209.																		CTCAAATCTTGTCCAAAGCCA	0.338													4	2	---	---	---	---	
SMC5	23137	broad.mit.edu	37	9	72963129	72963130	+	Intron	INS	-	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72963129_72963130insG	uc004ahr.2	+						SMC5_uc011lry.1_Intron	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						TCACTTTTTTTGGGGGGGGTTA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81456036	81456036	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81456036delT								PSAT1 (511029 upstream) : TLE4 (730842 downstream)																							CACAAAGCCATTACAGCAACC	0.423													4	2	---	---	---	---	
FRMD3	257019	broad.mit.edu	37	9	86087022	86087023	+	Intron	INS	-	T	T	rs145301236	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86087022_86087023insT	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2						GAAAAACTCCATTCCCAGCCCT	0.262													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	89178761	89178761	+	IGR	DEL	A	-	-	rs113671099		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89178761delA								ZCCHC6 (209383 upstream) : GAS1 (380518 downstream)																							AAACCTTTAGAATCTGTGCCC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92523697	92523697	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92523697delT								LOC100129066 (189023 upstream) : DIRAS2 (848417 downstream)																							ccccaaatccttttttttttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92738821	92738821	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92738821delA								LOC100129066 (404147 upstream) : DIRAS2 (633293 downstream)																							gctacatctgaaaaaaaagca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	100651833	100651833	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100651833delC								FOXE1 (32847 upstream) : C9orf156 (14939 downstream)																							GGGTGCATTTCCAGGTTAGtg	0.269													4	2	---	---	---	---	
HEMGN	55363	broad.mit.edu	37	9	100699981	100699981	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100699981delA	uc004axy.2	-						HEMGN_uc004axz.2_Intron	NM_197978	NP_932095	Q9BXL5	HEMGN_HUMAN	hemogen						cell differentiation|multicellular organismal development					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				aaaaaaatttaaaacAATGTC	0.085													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104814712	104814712	+	IGR	DEL	T	-	-	rs79662696		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104814712delT								GRIN3A (313850 upstream) : CYLC2 (942881 downstream)																							CCAGCGGCCCTTTTTCCCTAG	0.289													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105146364	105146364	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105146364delT								GRIN3A (645502 upstream) : CYLC2 (611229 downstream)																							TACTTTCTTGTTTTTTTTTCT	0.299													5	3	---	---	---	---	
SLC44A1	23446	broad.mit.edu	37	9	108079819	108079819	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108079819delT	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron	NM_080546	NP_536856	Q8WWI5	CTL1_HUMAN	CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)	GACTAGATGGTTATGAGGGTT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109520131	109520131	+	IGR	DEL	G	-	-	rs716875	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109520131delG								TMEM38B (982687 upstream) : ZNF462 (105247 downstream)																							CACTCCCAATGGGGGAGTTCT	0.498													4	2	---	---	---	---	
TNC	3371	broad.mit.edu	37	9	117841507	117841507	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117841507delT	uc004bjj.3	-						TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor						cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						CTTCTTCTCCTTTTTTTTTTT	0.333													4	2	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	118984002	118984002	+	Intron	DEL	C	-	-	rs398293	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118984002delC	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						CCCCGCAAGGCAAAAAAAAAG	0.333													3	3	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119621317	119621317	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119621317delC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						ctttgcttttccagcttctaa	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120629649	120629649	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120629649delA								TLR4 (149885 upstream) : None (None downstream)																							GGGAAAAAGGAAAAAAAGGTG	0.383													4	2	---	---	---	---	
TTLL11	158135	broad.mit.edu	37	9	124704219	124704219	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124704219delT	uc011lyl.1	-						TTLL11_uc004blr.2_Intron|uc004bls.1_Intron	NM_001139442	NP_001132914	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0						CCTCTTTCTCTTTCCCCACTG	0.527													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126470422	126470422	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126470422delA	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						TAGCAAAAACAAAAAAAAAGA	0.234													4	3	---	---	---	---	
PSMB7	5695	broad.mit.edu	37	9	127124760	127124760	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127124760delT	uc004boj.2	-						PSMB7_uc010mwm.2_Intron	NM_002799	NP_002790	Q99436	PSB7_HUMAN	proteasome beta 7 subunit proprotein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0						CTTTCATCCATTTCCCTGTGT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	129559338	129559338	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129559338delA								LMX1B (96027 upstream) : ZBTB43 (7947 downstream)																							cccctttgacatcatcacgag	0.020													4	2	---	---	---	---	
GLE1	2733	broad.mit.edu	37	9	131277677	131277678	+	Intron	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131277677_131277678delTT	uc004bvj.2	+						GLE1_uc004bvi.2_Intron|GLE1_uc010myd.2_Intron	NM_001003722	NP_001003722	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator homolog isoform 1						poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0						CTGACCTAAATTTTTTTTTTGC	0.292													4	2	---	---	---	---	
LAMC3	10319	broad.mit.edu	37	9	133901946	133901947	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133901946_133901947delCT	uc004caa.1	+	2	746_747	c.648_649delCT	c.(646-651)GCCTACfs	p.A216fs		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	216_217	Laminin N-terminal.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GGCCCAGCGCCTACAACTTCGA	0.668													4	2	---	---	---	---	
ABO	28	broad.mit.edu	37	9	136131057	136131057	+	Frame_Shift_Del	DEL	G	-	-	rs56392308		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136131057delG	uc004cda.1	-	8	1086	c.1061delC	c.(1060-1062)CCGfs	p.P354fs	ABO_uc010naf.1_Frame_Shift_Del_p.P213fs|ABO_uc011mcz.1_Frame_Shift_Del_p.P213fs|ABO_uc010nag.1_Frame_Shift_Del_p.P213fs	NM_020469	NP_065202	P16442	BGAT_HUMAN	ABO blood group (alpha	354	Lumenal (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	fucosylgalactoside 3-alpha-galactosyltransferase activity|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		AGCCGCTCACGGGTTCCGGAC	0.662													6	4	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136716787	136716790	+	Intron	DEL	TGGA	-	-	rs35486728		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136716787_136716790delTGGA	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GACAGAAgggtggatggatggatg	0.206													4	2	---	---	---	---	
PNPLA7	375775	broad.mit.edu	37	9	140438634	140438634	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140438634delG	uc004cnf.2	-						PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TGTCCCCACCGACCTTCCCCC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103753	103754	+	IGR	DEL	CT	-	-	rs113012935		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103753_103754delCT								TUBB8 (8249 upstream) : ZMYND11 (76670 downstream)																							tcaacacttgctttttttttaa	0.000													3	3	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	581226	581226	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:581226delG	uc001ifp.2	-							NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GGCCAGGGGTGGGGAGAGGAG	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4240716	4240717	+	IGR	INS	-	ATT	ATT	rs141698512	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4240716_4240717insATT								KLF6 (413243 upstream) : LOC100216001 (380727 downstream)																							AATTCTCTACCATTTATTTAAG	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8816452	8816452	+	IGR	DEL	T	-	-	rs35565859		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8816452delT								GATA3 (699290 upstream) : None (None downstream)																							AGGTCTTGGCTATAAAAACAT	0.323													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10602648	10602648	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10602648delA								None (None upstream) : SFTA1P (223754 downstream)																							cccagaggggaaaaaaaaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10666350	10666350	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10666350delT								None (None upstream) : SFTA1P (160052 downstream)																							TTCGATGGCATTACCTGAGTC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11454310	11454310	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11454310delG								CELF2 (75640 upstream) : USP6NL (48199 downstream)																							ggccccacctggtgaccccta	0.000													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12598141	12598141	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12598141delT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		CCGCACTGACTTTTTTTTTTG	0.433													3	4	---	---	---	---	
CCDC3	83643	broad.mit.edu	37	10	12943015	12943016	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12943015_12943016insC	uc001ilq.1	-						CCDC3_uc009xjb.1_Intron|CCDC3_uc001ilr.2_Intron|CCDC3_uc009xjc.1_Intron	NM_031455	NP_113643	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3 precursor							endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			ccaaggtcacgcccccttcttt	0.000													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14475710	14475710	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14475710delA	uc001imv.2	-						FRMD4A_uc001imw.1_Intron|MIR1265_hsa-mir-1265|MI0006401_5'Flank			Q9P2Q2	FRM4A_HUMAN	Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						GGCCTTTCACAAAAAAAACAT	0.388													4	2	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14606675	14606675	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14606675delA	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						TCTGCAGGGCAAATGGCACCA	0.398													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17457505	17457505	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17457505delA	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						catcttccctaaaactcattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	17682991	17682991	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17682991delT								PTPLA (23618 upstream) : STAM (3133 downstream)																							tttttgtttgttttttttgtt	0.119													4	2	---	---	---	---	
PIP4K2A	5305	broad.mit.edu	37	10	22918646	22918646	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22918646delT	uc001irl.3	-							NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						TAGTTTTCTCTTACCCTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31427295	31427295	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31427295delG								ZNF438 (106429 upstream) : LOC220930 (178163 downstream)																							tcatgccactgggctgcacac	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	32383363	32383364	+	IGR	INS	-	GA	GA			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32383363_32383364insGA								KIF5B (37992 upstream) : EPC1 (174495 downstream)																							gagaaagcaatgagagagagag	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33748968	33748969	+	IGR	INS	-	A	A	rs72792409		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33748968_33748969insA								NRP1 (124962 upstream) : PARD3 (651129 downstream)																							agaagaaaaagaaaaaaaaaaa	0.074													4	5	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34643058	34643058	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34643058delC	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				TGTCTTTCTTCAAAAAAAAAA	0.274													4	3	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	35026878	35026878	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35026878delG	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				CCACAGCAAAGGGCCCATTAG	0.547													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	35071206	35071206	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35071206delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				GGAAAGACTGAAGTTCTAAGA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45067524	45067525	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45067524_45067525delGA								CXCL12 (186982 upstream) : TMEM72 (339239 downstream)																							agacacacacgagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45156716	45156716	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45156716delA								CXCL12 (276174 upstream) : TMEM72 (250048 downstream)																							ATCTGCCACCAAAGCCCTTTG	0.478													4	2	---	---	---	---	
OR13A1	79290	broad.mit.edu	37	10	45806080	45806081	+	Intron	INS	-	A	A	rs150534006	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45806080_45806081insA	uc001jcc.1	-							NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						tggatttttggaaaaaaactaa	0.129													3	4	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	47001294	47001294	+	3'UTR	DEL	G	-	-	rs66882320		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47001294delG	uc010qfq.1	+	1						NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						GTGAGGCTGTGGGGGCTCGCT	0.627													4	3	---	---	---	---	
PPYR1	5540	broad.mit.edu	37	10	47084228	47084228	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47084228delG	uc001jee.2	+						ANXA8_uc001jed.3_Intron|PPYR1_uc009xna.2_Intron	NM_005972	NP_005963	P50391	NPY4R_HUMAN	pancreatic polypeptide receptor 1						blood circulation|digestion|feeding behavior	integral to plasma membrane				ovary(1)|skin(1)	2						TGACCTTGCTggtctggccca	0.244													4	2	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50151644	50151644	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-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													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	55450806	55450806	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55450806delA								MBL2 (919346 upstream) : PCDH15 (111729 downstream)																							ccactctgccAAAAAAAACTC	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60200421	60200422	+	IGR	DEL	TG	-	-	rs66977406		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60200421_60200422delTG								TFAM (44525 upstream) : BICC1 (72482 downstream)																							ccgatctttttgtcactataga	0.064													5	3	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61043791	61043792	+	Intron	INS	-	TG	TG	rs142909630	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61043791_61043792insTG	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						ATGCTGGGgtatgtgtgtgtgt	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	62832083	62832083	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62832083delT								RHOBTB1 (70885 upstream) : TMEM26 (334318 downstream)																							ttactgtaactttttttttta	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64568469	64568469	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64568469delT								ADO (231 upstream) : EGR2 (3291 downstream)																							TTTTCTGAGCTTTTAACACCA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66336876	66336877	+	IGR	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66336876_66336877delCA								REEP3 (954905 upstream) : ANXA2P3 (248408 downstream)																							cagccagattcacagagacatt	0.000													4	2	---	---	---	---	
AIFM2	84883	broad.mit.edu	37	10	71868601	71868602	+	Intron	INS	-	G	G	rs144672202	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71868601_71868602insG	uc010qjg.1	-						H2AFY2_uc001jqm.2_Intron|H2AFY2_uc001jqn.2_Intron	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like						apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1						TTGTGCTAACTGTGCAAAGCAA	0.500													8	4	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73360796	73360796	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73360796delT	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						AAATCTGTAGTTTTTTTCCTT	0.408													4	2	---	---	---	---	
DLG5	9231	broad.mit.edu	37	10	79651332	79651337	+	Intron	DEL	ACACAC	-	-	rs143485340		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79651332_79651337delACACAC	uc001jzk.2	-						DLG5_uc009xru.1_5'Flank	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	discs large homolog 5						cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			CCCCCAacagacacacacacacacac	0.398													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80123751	80123751	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80123751delT	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		ACAGGGATTATTTTTTTTGGA	0.393													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81575451	81575452	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81575451_81575452insC	uc001kat.2	-											full-length cDNA clone CS0DC003YI17 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																		aatgttgacaacccccccccat	0.000													4	2	---	---	---	---	
ANXA11	311	broad.mit.edu	37	10	81961291	81961291	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81961291delC	uc001kbq.1	-						ANXA11_uc001kbr.1_Intron|ANXA11_uc001kbs.1_Intron|ANXA11_uc001kbt.1_Intron|ANXA11_uc010qly.1_Intron|ANXA11_uc009xsq.1_Intron|ANXA11_uc001kbu.1_Intron	NM_145869	NP_665876	P50995	ANX11_HUMAN	annexin A11						cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			tcttcatcctccaaacctggt	0.194													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	83816091	83816091	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83816091delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		agtgtatttgaaaaaaaaaat	0.000													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	83851427	83851428	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83851427_83851428insC	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		gtgtgtatatgccaaaaaattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91309889	91309889	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91309889delT								SLC16A12 (14576 upstream) : PANK1 (32860 downstream)																							tcttgccatctcctctctccc	0.000													4	2	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94314082	94314082	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94314082delG	uc001kia.2	-							NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	aggctggggtgggaggatggc	0.000													4	2	---	---	---	---	
PDE6C	5146	broad.mit.edu	37	10	95377567	95377567	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95377567delC	uc001kiu.3	+							NM_006204	NP_006195	P51160	PDE6C_HUMAN	phosphodiesterase 6C						visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)				GCTAACTTCACCCCATGGTGC	0.274													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97160610	97160610	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97160610delG	uc001kkp.2	-						SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGTCTCAAAAGAAAAAAAAAA	0.453													2	4	---	---	---	---	
EXOSC1	51013	broad.mit.edu	37	10	99197683	99197683	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99197683delT	uc001kni.2	-						EXOSC1_uc009xvp.1_Intron	NM_016046	NP_057130	Q9Y3B2	EXOS1_HUMAN	exosomal core protein CSL4						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	protein binding|RNA binding				0		Renal(717;0.000147)|Colorectal(252;0.00205)|Ovarian(717;0.00965)		all cancers(201;8.29e-42)|Epithelial(162;5.7e-33)|BRCA - Breast invasive adenocarcinoma(275;0.000315)|Kidney(138;0.000832)|KIRC - Kidney renal clear cell carcinoma(50;0.00269)|STAD - Stomach adenocarcinoma(243;0.202)		CAAATGAAAAttttttttttt	0.159													9	6	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100991972	100991975	+	Intron	DEL	ACAC	-	-	rs12572567	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100991972_100991975delACAC	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)		GCGCGCGcatacacacacacacac	0.353													6	8	---	---	---	---	
PDZD7	79955	broad.mit.edu	37	10	102777649	102777649	+	Intron	DEL	A	-	-	rs66819144		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102777649delA	uc001kso.1	-						PDZD7_uc001ksn.2_Intron	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7							cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		agaaagaaagaaaagaaagaa	0.005													4	4	---	---	---	---	
ACTR1A	10121	broad.mit.edu	37	10	104242538	104242538	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104242538delA	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		ctgctgagctaaaaaaaaaaa	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	110879547	110879547	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110879547delC								None (None upstream) : XPNPEP1 (744977 downstream)																							CAGAGGCCATCCCAACATCAA	0.443													4	2	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115399642	115399642	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115399642delT	uc001laj.2	-						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)		ATAACAAACCTTTTTTTAAAG	0.343													4	2	---	---	---	---	
TRUB1	142940	broad.mit.edu	37	10	116697492	116697492	+	5'Flank	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116697492delG	uc001lcd.2	+						TRUB1_uc010qsl.1_5'Flank	NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		TGGGGTCAGTGGGGGTTTGGG	0.383													4	2	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121182972	121182973	+	Intron	INS	-	GC	GC	rs145491614	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121182972_121182973insGC	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		AGAAAACATCTGCTGCAAAGGG	0.460													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121235388	121235389	+	IGR	INS	-	T	T	rs141821551	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121235388_121235389insT								GRK5 (20258 upstream) : RGS10 (23951 downstream)																							taaggattgtcttttttttcac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121473769	121473770	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121473769_121473770delTG								BAG3 (36442 upstream) : INPP5F (11839 downstream)																							AAtgtgtgtatgtgtgtgtgtg	0.361													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121839222	121839222	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121839222delT								SEC23IP (137977 upstream) : PPAPDC1A (377244 downstream)																							ATTTAACCCCTTTATGGACAG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125023763	125023763	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125023763delA								BUB3 (98877 upstream) : GPR26 (402108 downstream)																							CTTCAATTTCAAGAGTGACCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125078908	125078908	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125078908delG								BUB3 (154022 upstream) : GPR26 (346963 downstream)																							caggtagtctggggcctgttc	0.139													4	2	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126712661	126712662	+	Intron	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126712661_126712662delCA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron|CTBP2_uc001lie.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CATTATCCTCCACACACACACC	0.540													4	2	---	---	---	---	
C10orf90	118611	broad.mit.edu	37	10	128189944	128189944	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128189944delA	uc001ljq.2	-						C10orf90_uc001ljp.2_Intron|C10orf90_uc010qum.1_Intron|C10orf90_uc009yao.2_Intron	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TTTCTGAGTGAGGGAGCACAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132389029	132389029	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132389029delT								GLRX3 (406245 upstream) : TCERG1L (501627 downstream)																							aagtcaatgatttttagtaag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133143913	133143913	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133143913delA								TCERG1L (33929 upstream) : PPP2R2D (604047 downstream)																							aaagaaaaggaaaaAGGAGGA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133657110	133657114	+	IGR	DEL	CGAGT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133657110_133657114delCGAGT								TCERG1L (547126 upstream) : PPP2R2D (90846 downstream)																							Gtgttttagccgagtcctcttcacg	0.302													4	3	---	---	---	---	
DPYSL4	10570	broad.mit.edu	37	10	134012500	134012501	+	Intron	DEL	TG	-	-	rs148943316	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134012500_134012501delTG	uc009ybb.2	+							NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4						axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CCGCCTCTGATGCCGAGGGGCC	0.688													8	5	---	---	---	---	
DPYSL4	10570	broad.mit.edu	37	10	134012503	134012508	+	Intron	DEL	CGAGGG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134012503_134012508delCGAGGG	uc009ybb.2	+							NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4						axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CCTCTGATGCCGAGGGGCCATGGTCT	0.689													7	5	---	---	---	---	
LSP1	4046	broad.mit.edu	37	11	1874152	1874152	+	5'Flank	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1874152delT	uc001lui.2	+							NM_002339	NP_002330	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 1						cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GTGGTTTGGGTTTTTTTTTTT	0.537											OREG0003781	type=REGULATORY REGION|Gene=LSP1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	3	3	---	---	---	---	
ART1	417	broad.mit.edu	37	11	3680214	3680215	+	Intron	INS	-	C	C	rs140021907	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3680214_3680215insC	uc001lye.1	+						ART1_uc009yeb.1_Intron	NM_004314	NP_004305	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1 precursor						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane|sarcoplasmic reticulum membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)	Becaplermin(DB00102)	ATCCTACAAGACCTGTTCACGT	0.495													6	7	---	---	---	---	
HBG1	3047	broad.mit.edu	37	11	5269986	5269987	+	Intron	DEL	AC	-	-	rs72362527		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5269986_5269987delAC	uc001mah.1	-						HBG2_uc001mai.1_Intron	NM_000559	NP_000550	P69891	HBG1_HUMAN	A-gamma globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity|protein binding				0		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)		acacacgctgacacacacacac	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6161691	6161691	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6161691delA								OR56B4 (31725 upstream) : OR52B2 (28895 downstream)																							aagaatttagaaggtttgagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6782982	6782982	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6782982delA								GVIN1 (15312 upstream) : OR2AG2 (6256 downstream)																							TTCATACCCTAAAAAAGTTGA	0.433													4	2	---	---	---	---	
SWAP70	23075	broad.mit.edu	37	11	9770250	9770251	+	Intron	INS	-	G	G	rs139533719	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9770250_9770251insG	uc001mhw.2	+						SWAP70_uc001mhx.2_Intron	NM_015055	NP_055870	Q9UH65	SWP70_HUMAN	SWAP-70 protein							cytoplasm|lamellipodium|nucleus|plasma membrane	calcium ion binding|DNA binding			ovary(2)|central_nervous_system(1)	3				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		ccagctagtgaggagaattatt	0.119													0	9	---	---	---	---	
MICAL2	9645	broad.mit.edu	37	11	12188440	12188440	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12188440delG	uc001mjz.2	+						MICAL2_uc010rch.1_Intron|MICAL2_uc001mjy.2_Intron|MICAL2_uc001mka.2_Intron|MICAL2_uc010rci.1_Intron|MICAL2_uc001mkb.2_Intron|MICAL2_uc001mkc.2_Intron	NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		AACAGCTAAAGGGAGTGCATA	0.517													4	4	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14873052	14873053	+	Intron	INS	-	GG	GG	rs145444420	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14873052_14873053insGG	uc001mln.2	+						PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						ATGGGTATAATGGGgtgtgtgt	0.327													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16247697	16247697	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16247697delT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						GTTTAGTCAATTTTTTTTTCT	0.289													4	2	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	18022306	18022308	+	Intron	DEL	CAC	-	-	rs35804255		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18022306_18022308delCAC	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron|SERGEF_uc001mno.1_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						AATACCATATCACAATACCATAT	0.197													3	9	---	---	---	---	
UEVLD	55293	broad.mit.edu	37	11	18561574	18561574	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18561574delC	uc001mot.2	-						UEVLD_uc001mou.2_Intron|UEVLD_uc010rde.1_Intron|UEVLD_uc010rdf.1_Intron|UEVLD_uc010rdg.1_Intron|UEVLD_uc001mov.2_Intron	NM_001040697	NP_001035787	Q8IX04	UEVLD_HUMAN	ubiquitin-conjugating enzyme E2-like isoform a						cellular carbohydrate metabolic process|protein modification process|protein transport		binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor				0						CTATTCATCACCATCTTGCCA	0.194													4	2	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19164280	19164280	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19164280delT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						TAGGATACACtttttttttct	0.124													3	3	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21420105	21420105	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21420105delC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						GTAGACTCTTCCCAGGCAAAA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25380397	25380397	+	IGR	DEL	T	-	-	rs76818806		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25380397delT								LUZP2 (276215 upstream) : ANO3 (830432 downstream)																							tagaagcagcttagggttcct	0.010													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29972195	29972195	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29972195delG								None (None upstream) : KCNA4 (59571 downstream)																							aatgcccacagggagacaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	32213693	32213693	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32213693delA								RCN1 (86422 upstream) : WT1 (195632 downstream)																							ttacagaggtaatcaagttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35108506	35108506	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35108506delT								PDHX (90832 upstream) : CD44 (51911 downstream)																							ttgctggagattttttacatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43636458	43636459	+	IGR	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43636458_43636459delAA								MIR129-2 (33425 upstream) : HSD17B12 (65684 downstream)																							taaagtccttaaatactaattc	0.000													4	2	---	---	---	---	
TP53I11	9537	broad.mit.edu	37	11	44955672	44955672	+	3'UTR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44955672delA	uc001myi.2	-	10					TP53I11_uc001myf.1_Intron|TP53I11_uc001myj.2_3'UTR|TP53I11_uc001myk.2_3'UTR|TP53I11_uc001myl.2_3'UTR|TP53I11_uc001mym.2_3'UTR	NM_006034	NP_006025	O14683	P5I11_HUMAN	p53-induced protein						negative regulation of cell proliferation|response to stress	integral to membrane				ovary(1)	1						TTGTCAGGCCAGGAGAGTGGG	0.592													4	2	---	---	---	---	
MTCH2	23788	broad.mit.edu	37	11	47647567	47647567	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47647567delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0						acccaactacttttttttttt	0.109													4	2	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48165046	48165047	+	Intron	DEL	TC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48165046_48165047delTC	uc001ngp.3	+							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						ACCAACTCTGTCTCTCTCTCTC	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49435979	49435979	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49435979delG								FOLH1 (205757 upstream) : LOC440040 (144101 downstream)																							gcactgctgtgggattttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56580778	56580778	+	Intron	DEL	A	-	-	rs67308709		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56580778delA	uc001njg.1	-						uc001njh.1_Intron					Homo sapiens mRNA for hypothetical protein, complete cds, clone:Hsa11-digit22-05-16-R.																		TTATTTCCATAAGCAAGTATT	0.423													5	7	---	---	---	---	
TNKS1BP1	85456	broad.mit.edu	37	11	57088165	57088165	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57088165delG	uc001njr.2	-	2	428	c.116delC	c.(115-117)CCTfs	p.P39fs	TNKS1BP1_uc001njs.2_Frame_Shift_Del_p.P39fs|TNKS1BP1_uc009ymd.1_5'UTR	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	39	Arg/Glu/Lys/Pro-rich (charged).				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				GGGCTTGACAGGGGGTTTGGC	0.627													4	2	---	---	---	---	
GLYATL2	219970	broad.mit.edu	37	11	58607344	58607344	+	Intron	DEL	A	-	-	rs77495706		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58607344delA	uc001nnd.3	-						GLYATL2_uc009ymq.2_Intron	NM_145016	NP_659453	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2							mitochondrion	glycine N-acyltransferase activity			ovary(1)|skin(1)	2		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	AATTCCACTTAAAAAGTACAT	0.279													4	5	---	---	---	---	
DAK	26007	broad.mit.edu	37	11	61114010	61114028	+	3'UTR	DEL	TCACTGCTGTGCTGAGGTG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61114010_61114028delTCACTGCTGTGCTGAGGTG	uc001nre.2	+	18						NM_015533	NP_056348	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2						glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding				0						TCAGCTCCTCTCACTGCTGTGCTGAGGTGGCCTTTGTCA	0.626													13	6	---	---	---	---	
SLC22A12	116085	broad.mit.edu	37	11	64363561	64363562	+	Intron	INS	-	ATGG	ATGG	rs146602952		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64363561_64363562insATGG	uc001oam.1	+						SLC22A12_uc009ypr.1_Intron|SLC22A12_uc001oal.1_Intron|SLC22A12_uc009yps.1_Intron|SLC22A12_uc001oan.1_Intron|SLC22A12_uc009ypt.2_Intron	NM_144585	NP_653186	Q96S37	S22AC_HUMAN	urate anion exchanger 1 isoform a						cellular homeostasis|response to drug|urate metabolic process	apical plasma membrane|brush border membrane|integral to membrane	PDZ domain binding|urate transmembrane transporter activity			ovary(1)	1						ttgatggttgaatggatggatg	0.000													4	2	---	---	---	---	
PPFIA1	8500	broad.mit.edu	37	11	70226194	70226195	+	Intron	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70226194_70226195delTT	uc001opo.2	+						PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opr.2_Intron|PPFIA1_uc001ops.2_Intron|uc001opt.1_Intron	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b						cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			AACAGGAATATTAAGAATGAGA	0.248													4	2	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72288803	72288809	+	Intron	DEL	AGTCAGG	-	-	rs147098484		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72288803_72288809delAGTCAGG	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	gatcacctgaagtcaggagttcaagac	0.063													4	2	---	---	---	---	
PAK1	5058	broad.mit.edu	37	11	77143347	77143348	+	Intron	INS	-	A	A	rs144929956	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77143347_77143348insA	uc001oyh.3	-						PAK1_uc001oyg.3_Intron	NM_002576	NP_002567	Q13153	PAK1_HUMAN	p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)					cttaatctgataaaggcatcta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79245236	79245236	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79245236delC								ODZ4 (93541 upstream) : None (None downstream)																							GTGGGTTCTTCACCTGGTGAC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79317055	79317055	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79317055delT								ODZ4 (165360 upstream) : None (None downstream)																							ATGTGACTTATTTATATCATG	0.338													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83487759	83487760	+	Intron	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83487759_83487760delCT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ctgcaccatcctctctccttca	0.000													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84918876	84918876	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84918876delT	uc001pak.2	-							NM_001142699	NP_001136171	Q15700	DLG2_HUMAN	chapsyn-110 isoform 1							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TCCAGCCtcctttttacccct	0.189													4	2	---	---	---	---	
NAALAD2	10003	broad.mit.edu	37	11	89881892	89881892	+	Intron	DEL	A	-	-	rs113106506		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89881892delA	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron|NAALAD2_uc001pdd.2_Intron|NAALAD2_uc001pde.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				aggcatagtcaaaaaaaagag	0.104													4	4	---	---	---	---	
NAALAD2	10003	broad.mit.edu	37	11	89906700	89906700	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89906700delT	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TTTGTAAAGATTTTAAGTTCT	0.284													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92199062	92199062	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92199062delA	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGAAACAGGGAAAAAAAAAGA	0.199										TCGA Ovarian(4;0.039)			4	2	---	---	---	---	
PIWIL4	143689	broad.mit.edu	37	11	94290005	94290005	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94290005delT	uc010rue.1	+						PIWIL4_uc009ywk.1_Intron			Q7Z3Z4	PIWL4_HUMAN	Homo sapiens PIWIL1 mRNA, complete cds.						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding			skin(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				agtaccatgctttttttggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	95441272	95441272	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95441272delA								SESN3 (475567 upstream) : FAM76B (60834 downstream)																							ATTCAGAGAGAAAAAAAAAAG	0.174													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	98354559	98354559	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98354559delT								None (None upstream) : CNTN5 (537312 downstream)																							tttttgtgacttttttttttc	0.030													2	4	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103175643	103175643	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103175643delT	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)		TATAAAAATCTTTTTTTAAAG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109316670	109316670	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109316670delA								C11orf87 (16832 upstream) : ZC3H12C (647256 downstream)																							TGAAGGTACCAAAATACATCG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112288815	112288815	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112288815delT								PTS (148138 upstream) : NCAM1 (543180 downstream)																							GGGCATCTGCTTTTTAGCTCT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116595035	116595035	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116595035delT								None (None upstream) : BUD13 (23853 downstream)																							TTTTTAGTGATTTTTTTTTCC	0.393													4	2	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116964710	116964710	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116964710delT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						CGTCATGCTATTAGGGCACCA	0.174													4	2	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125271639	125271640	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125271639_125271640delGA	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)		GAGCCTGTATGAGAGAGAGAAA	0.465													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128166505	128166506	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128166505_128166506insA								None (None upstream) : ETS1 (162150 downstream)																							ttttaaatgttaaaaaaaaaaa	0.005													4	3	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131788643	131788643	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131788643delC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						AATCCCCTCTCCTGAAGCATG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133436225	133436225	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133436225delT								OPCML (33822 upstream) : SPATA19 (274292 downstream)																							catagagcaattttttttttc	0.000													4	2	---	---	---	---	
LOC283174	283174	broad.mit.edu	37	11	133771745	133771746	+	5'Flank	DEL	CG	-	-	rs4937851	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133771745_133771746delCG	uc001qgw.2	-							NR_024344				Homo sapiens full length insert cDNA clone YY74A12.												0						acaccacacacgcaccacacac	0.084													4	2	---	---	---	---	
JAM3	83700	broad.mit.edu	37	11	134016901	134016902	+	Intron	INS	-	TG	TG			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134016901_134016902insTG	uc001qhb.1	+						JAM3_uc009zcz.1_Intron	NM_032801	NP_116190	Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3 precursor						angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		tatgctagaaatgtctgtgtgt	0.208													4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1481446	1481446	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1481446delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			ATGAAAAGGCTTTTTTTTTTA	0.328													4	2	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	9022043	9022044	+	Intron	DEL	AC	-	-	rs144859122		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9022043_9022044delAC	uc001quz.3	+						A2ML1_uc001qva.1_Intron|A2ML1_uc010sgm.1_Intron|A2ML1_uc001qvb.1_Intron	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						tttctggtagacacatttaaaa	0.099													7	4	---	---	---	---	
PZP	5858	broad.mit.edu	37	12	9316049	9316049	+	Intron	DEL	A	-	-	rs71453676		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9316049delA	uc001qvl.2	-						PZP_uc009zgl.2_Intron|PZP_uc010sgo.1_Intron|PZP_uc009zgm.1_Intron	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						actccgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10347189	10347190	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10347189_10347190delGA								C12orf59 (2787 upstream) : GABARAPL1 (18299 downstream)																							ggaataaagggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10839296	10839296	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10839296delT								STYK1 (12405 upstream) : CSDA (12382 downstream)																							aacagcatccttatctgccac	0.000													4	2	---	---	---	---	
LRP6	4040	broad.mit.edu	37	12	12395488	12395488	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12395488delT	uc001rah.3	-						LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				CCTCTGAGCCTTACAAACTCT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13342449	13342449	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13342449delG								GSG1 (85830 upstream) : EMP1 (7153 downstream)																							AATGATGCCAGGAGTCTGAAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13436153	13436153	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13436153delT								EMP1 (66446 upstream) : C12orf36 (87870 downstream)																							agattttgagtttttttttgg	0.070													4	2	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	14035354	14035355	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14035354_14035355insT	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	ACAAATAAAAATTTTTTTTTCA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15009586	15009586	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15009586delG								ART4 (13173 upstream) : MGP (25241 downstream)																							aactatacctggcaagaggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17074216	17074217	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17074216_17074217delTG								LMO3 (311458 upstream) : None (None downstream)																							tgtgtatgtatgtgtgtgtgtg	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19870940	19870941	+	IGR	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19870940_19870941delTG								AEBP2 (195767 upstream) : PDE3A (651256 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.356													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24251759	24251759	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24251759delA	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						CACCAGAAGGAAAGCTCTGAA	0.498													4	2	---	---	---	---	
BCAT1	586	broad.mit.edu	37	12	25005932	25005932	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25005932delT	uc001rgd.3	-						BCAT1_uc001rgc.2_Intron|BCAT1_uc010six.1_Intron|BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)	GGAAGAGAGCTTTATGATTGG	0.343													4	2	---	---	---	---	
BCAT1	586	broad.mit.edu	37	12	25075098	25075098	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25075098delT	uc001rgd.3	-						BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)	AGATTGTTCCttttttttgag	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25812547	25812547	+	IGR	DEL	T	-	-	rs35340178		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25812547delT								IFLTD1 (11059 upstream) : RASSF8 (299422 downstream)																							TCTAATTCACTTTCTTAACAT	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	26031794	26031795	+	IGR	INS	-	CCT	CCT	rs150755718	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26031794_26031795insCCT								IFLTD1 (230306 upstream) : RASSF8 (80174 downstream)																							ttgcaaagctgcctctattttt	0.025													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	26095369	26095369	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26095369delT								IFLTD1 (293881 upstream) : RASSF8 (16600 downstream)																							TGTAGCTGTGTTTTTTTTTTC	0.433													5	4	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26587893	26587893	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26587893delG	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					TTTACTTCCTGGTGTATTTGC	0.368													4	2	---	---	---	---	
C12orf70	341346	broad.mit.edu	37	12	27645184	27645184	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27645184delT	uc010sjq.1	+							NM_001145010	NP_001138482	A6NFE2	CL070_HUMAN	hypothetical protein LOC341346							integral to membrane					0						gtCGTTTTACTTTTTTTTCAC	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29255749	29255750	+	IGR	INS	-	A	A	rs142606862	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29255749_29255750insA								CCDC91 (552651 upstream) : FAR2 (46482 downstream)																							CTAAATACGTTAAAAATAGGTT	0.248													1	5	---	---	---	---	
DNM1L	10059	broad.mit.edu	37	12	32860889	32860889	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32860889delA	uc001rld.2	+						DNM1L_uc010skf.1_Intron|DNM1L_uc010skg.1_Intron|DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192	O00429	DNM1L_HUMAN	dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					tctctcaaagaaaaaaaaaaa	0.080													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33600609	33600611	+	IGR	DEL	ACA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33600609_33600611delACA								SYT10 (7855 upstream) : ALG10 (574605 downstream)																							aaaaacccccacaacaacaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34311363	34311364	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34311363_34311364insA								ALG10 (130129 upstream) : None (None downstream)																							gattgcctaagaaaaaaaaaga	0.000													4	2	---	---	---	---	
PRICKLE1	144165	broad.mit.edu	37	12	42981750	42981750	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42981750delT	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571	Q96MT3	PRIC1_HUMAN	prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TTTTTTTTTGTTTTTTTTTTC	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46003104	46003105	+	IGR	INS	-	T	T	rs146379386	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46003104_46003105insT								ANO6 (168917 upstream) : LOC400027 (116705 downstream)																							GAATTCTTTCCTTTTTTTTTCT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55252643	55252643	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55252643delA								MUCL1 (471 upstream) : KIAA0748 (91222 downstream)																							gtgactgatgaattgagagta	0.000													4	2	---	---	---	---	
KIAA0748	9840	broad.mit.edu	37	12	55371793	55371793	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55371793delT	uc001sgn.3	-						KIAA0748_uc010spd.1_Intron|KIAA0748_uc001sgo.3_Intron	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840											ovary(1)|central_nervous_system(1)	2						CAAGAAACCGTTTTTTTTTTG	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55706581	55706581	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55706581delG								OR6C6 (17565 upstream) : OR6C1 (7803 downstream)																							TCATCGTAAAGATTCAATAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56027517	56027517	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56027517delT								OR6C4 (81579 upstream) : OR10P1 (3159 downstream)																							agctattgaaTTTTTTTTAAG	0.169													4	2	---	---	---	---	
GNS	2799	broad.mit.edu	37	12	65138323	65138323	+	Intron	DEL	C	-	-	rs3830374		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65138323delC	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		ACAAAGTAATCTCTGTAGTCG	0.413													5	4	---	---	---	---	
IRAK3	11213	broad.mit.edu	37	12	66648277	66648277	+	3'UTR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66648277delT	uc001sth.2	+	12					IRAK3_uc010ssy.1_3'UTR	NM_007199	NP_009130	Q9Y616	IRAK3_HUMAN	interleukin-1 receptor-associated kinase 3						interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|negative regulation of innate immune response|negative regulation of interleukin-12 production|negative regulation of interleukin-6 production|negative regulation of macrophage cytokine production|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein catabolic process|negative regulation of protein complex disassembly|negative regulation of toll-like receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of macrophage tolerance induction|positive regulation of NF-kappaB transcription factor activity|response to exogenous dsRNA|response to lipopolysaccharide|response to peptidoglycan	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein heterodimerization activity|protein homodimerization activity|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(2)|central_nervous_system(1)	8				GBM - Glioblastoma multiforme(28;0.0203)		atgttaaggatttttttttct	0.104													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66857115	66857115	+	Intron	DEL	A	-	-	rs63157261		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66857115delA	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stj.2_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)		GTCTTTCTTTAAAAAAAAAAT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68139246	68139246	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68139246delT								DYRK2 (82803 upstream) : IFNG (409304 downstream)																							TTTGTTCACATTTTTTTTTGC	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70330959	70330960	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70330959_70330960insA	uc001svu.1	+						uc010stn.1_Intron					RecName: Full=Uncharacterized protein C12orf28; Flags: Precursor;																		ATTTTCATGGTAAAAAAAAGTA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76581686	76581686	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76581686delA								NAP1L1 (102948 upstream) : BBS10 (156580 downstream)																							gagaagattgaaaaaaaaagt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	81154121	81154121	+	5'Flank	DEL	C	-	-	rs55974163	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81154121delC	uc001szh.2	+											Homo sapiens cDNA clone IMAGE:4838041.																		aaaaaaaaaacccttttcttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90393405	90393406	+	IGR	INS	-	TTC	TTC	rs148815598	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90393405_90393406insTTC								LOC338758 (287677 upstream) : C12orf12 (952587 downstream)																							TTATGACAGAATTCTTTGTCAG	0.401													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96040484	96040485	+	IGR	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96040484_96040485delCA								USP44 (95221 upstream) : NTN4 (11099 downstream)																							ATCTCTGGGTCACAGATGATTG	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96844349	96844350	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96844349_96844350delGA								CDK17 (50126 upstream) : C12orf63 (197403 downstream)																							agaaaaaaaggagagagagaga	0.000													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100086037	100086038	+	Intron	INS	-	A	A	rs143789952	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100086037_100086038insA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		tacaataatccggtgagaattg	0.000													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100340741	100340741	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100340741delG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GCAAGTTTGTGGTGGTTTGTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102391714	102391715	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102391714_102391715insT								DRAM1 (74315 upstream) : CCDC53 (15003 downstream)																							TGGtttttctcttttttttgag	0.064													4	2	---	---	---	---	
IGF1	3479	broad.mit.edu	37	12	102858748	102858748	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102858748delT	uc001tjp.3	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						GAACAAAGTCTTTAAGCAAGC	0.408													4	2	---	---	---	---	
PAH	5053	broad.mit.edu	37	12	103274163	103274163	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103274163delT	uc001tjq.1	-						PAH_uc010swc.1_Intron	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase						catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	CTCCAGGACATTGCCACCAAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	103582023	103582023	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103582023delT								ASCL1 (227736 upstream) : C12orf42 (49347 downstream)																							TTCCTTTTTATTTTTTTGGCA	0.229													4	2	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103659577	103659578	+	Intron	INS	-	TGTTTTGTTT	TGTTTTGTTT	rs139900787	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103659577_103659578insTGTTTTGTTT	uc001tjs.2	-									Q96LP6	CL042_HUMAN	Homo sapiens cDNA FLJ25323 fis, clone TST00323.											ovary(1)|central_nervous_system(1)	2						ATTTCTTAGGCtgttttgtttt	0.361													4	2	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103873561	103873561	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103873561delA	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923	Q96LP6	CL042_HUMAN	hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2						ttcatgagataaaaaacaacg	0.000													4	2	---	---	---	---	
CHST11	50515	broad.mit.edu	37	12	104873313	104873313	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104873313delA	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883	Q9NPF2	CHSTB_HUMAN	carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0						GTTTGAGAGTAAGGTTGGGAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105682696	105682696	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105682696delG								APPL2 (52688 upstream) : C12orf75 (41718 downstream)																							ATGAATCCATGGGGGAACCCC	0.383													4	2	---	---	---	---	
SLC24A6	80024	broad.mit.edu	37	12	113740859	113740860	+	Intron	DEL	AC	-	-	rs138136092		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113740859_113740860delAC	uc001tvc.2	-						SLC24A6_uc001tuz.2_Intron|SLC24A6_uc001tva.2_Intron|SLC24A6_uc001tvb.2_Intron	NM_024959	NP_079235	Q6J4K2	NCKX6_HUMAN	solute carrier family 24 member 6 precursor						response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1						AAGGTGGTAGacacacacacac	0.183													4	2	---	---	---	---	
TBX5	6910	broad.mit.edu	37	12	114799120	114799120	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114799120delT	uc001tvo.2	-						TBX5_uc001tvp.2_Intron|TBX5_uc001tvq.2_Intron	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1						cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		TGCAAAGCCCTTTTCCATATC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115641633	115641633	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115641633delG								TBX3 (519664 upstream) : MED13L (754750 downstream)																							CTGTGGTTTTGGGAGGATTTA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115999741	115999741	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115999741delA								TBX3 (877772 upstream) : MED13L (396642 downstream)																							gtgccaggctagagtccagac	0.174													4	2	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116709010	116709011	+	Intron	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116709010_116709011delGT	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		AAACAAATACgtgtgtgtgtgt	0.282													4	2	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117290182	117290183	+	3'UTR	INS	-	TTCCCC	TTCCCC	rs140709252	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-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													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117872510	117872510	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117872510delC								NOS1 (72928 upstream) : KSR2 (18307 downstream)																							acatacacaaccctcacacac	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117872526	117872527	+	IGR	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117872526_117872527insC								NOS1 (72944 upstream) : KSR2 (18290 downstream)																							cacacacaccttcacacatgca	0.297													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	118199451	118199451	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118199451delT	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					catgtgcatgttacactatat	0.139													4	2	---	---	---	---	
BCL7A	605	broad.mit.edu	37	12	122481642	122481642	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122481642delA	uc001ubp.2	+						BCL7A_uc001ubo.2_Intron	NM_001024808	NP_001019979	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		gatccgtctcaaaaaaaaaaa	0.289			T	MYC	BNHL								10	5	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124916419	124916420	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124916419_124916420delAC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		acacagagagacacacacacac	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127522373	127522374	+	Intron	INS	-	TG	TG	rs142349417	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127522373_127522374insTG	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																		aaatacatatatgtgtgtgtgt	0.188													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128181586	128181587	+	IGR	INS	-	GTG	GTG			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128181586_128181587insGTG								None (None upstream) : TMEM132C (717704 downstream)																							tgatgatggtagtgatactgga	0.000													6	3	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	131196041	131196042	+	Intron	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131196041_131196042delTT	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)		tattctgggcttttaaaatgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132157534	132157534	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132157534delG								LOC116437 (460059 upstream) : SFRS8 (38101 downstream)																							GGTCACTTGTGGGGAAAGACT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132167748	132167748	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132167748delT								LOC116437 (470273 upstream) : SFRS8 (27887 downstream)																							tgttttggggttttcatggtg	0.045													4	3	---	---	---	---	
EP400	57634	broad.mit.edu	37	12	132540970	132540971	+	Intron	INS	-	CACA	CACA	rs144547692	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132540970_132540971insCACA	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		cacaacacacgcacacacacac	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21484220	21484220	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21484220delT								XPO4 (7307 upstream) : LATS2 (62958 downstream)																							tatttttttgttttttttttt	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24930507	24930508	+	IGR	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24930507_24930508delCA								C1QTNF9 (33842 upstream) : PARP4 (64567 downstream)																							acacactcatcacacacacacc	0.069													4	2	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25541679	25541679	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25541679delT	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						TTGAtttttcttttttttgag	0.174													4	2	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26184768	26184768	+	Intron	DEL	T	-	-	rs148367176	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26184768delT	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)		attttaggacttttttttcta	0.000													4	2	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26228071	26228072	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26228071_26228072delGA	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)		GGATGCTGGCGAGAGAGAGAGA	0.500													4	2	---	---	---	---	
POLR1D	51082	broad.mit.edu	37	13	28201419	28201419	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28201419delT	uc001urp.2	+						POLR1D_uc010aam.2_Intron|POLR1D_uc001urq.2_Intron	NM_152705	NP_689918	Q9Y2S0	RPAC2_HUMAN	polymerase (RNA) I polypeptide D isoform 2						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)		GTGGGTCTGGTTTTTTTTTTT	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	32307021	32307021	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32307021delA								B3GALTL (400612 upstream) : RXFP2 (6658 downstream)																							CCCAAGAATTAAAAAAAAAAA	0.343													5	4	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33680675	33680675	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33680675delA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		CATAAAACAGAAAATAAAGAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	34802113	34802113	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34802113delT								RFC3 (261419 upstream) : NBEA (714343 downstream)																							taggacattattttttttcct	0.000													4	2	---	---	---	---	
C13orf36	400120	broad.mit.edu	37	13	37258432	37258432	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37258432delA	uc001uvt.3	+							NM_203451	NP_982276	A2A2V5	CM036_HUMAN	hypothetical protein LOC400120							integral to membrane				skin(1)	1						agactctgtcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40798157	40798160	+	IGR	DEL	ACAT	-	-	rs56282723		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40798157_40798160delACAT								COG6 (432355 upstream) : LOC646982 (123113 downstream)																							acacacacacacatacacacacat	0.275													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	42936843	42936843	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42936843delC								AKAP11 (39441 upstream) : TNFSF11 (200029 downstream)																							AACTTGATATCCAAACCTTTA	0.274													4	2	---	---	---	---	
TSC22D1	8848	broad.mit.edu	37	13	45072459	45072460	+	Intron	DEL	AC	-	-	rs138021403		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45072459_45072460delAC	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		aacaaacaaaaCCAAAAACAAA	0.178													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48954160	48954160	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48954160delT	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AAACAACTTCTTTTTTTTTTT	0.129		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			19	9	---	---	---	---	
GUCY1B2	2974	broad.mit.edu	37	13	51570337	51570338	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51570337_51570338delAC	uc001vfc.3	-							NR_003923				Homo sapiens soluble guanylyl cyclase subunit beta 2 (GUCY1B2) mRNA, complete cds.												0						acacacacatacacacacacac	0.267													5	3	---	---	---	---	
TPTE2P3	220115	broad.mit.edu	37	13	53108619	53108620	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53108619_53108620insA	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						actaataatacaaaaaaaactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55149891	55149892	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55149891_55149892insA								MIR1297 (263708 upstream) : None (None downstream)																							CCATTTGTGATAAAAAGTTTTG	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	56185728	56185729	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56185728_56185729delAC								None (None upstream) : None (None downstream)																							ACACACATATACACACACACAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61225256	61225256	+	IGR	DEL	T	-	-	rs113556715		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61225256delT								TDRD3 (77244 upstream) : PCDH20 (758565 downstream)																							caccagcatctttaaagagct	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61483796	61483796	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61483796delT								TDRD3 (335784 upstream) : PCDH20 (500025 downstream)																							GAAGGAGACATTTTTTACTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63633384	63633385	+	IGR	DEL	TT	-	-	rs72302550		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63633384_63633385delTT								None (None upstream) : OR7E156P (678183 downstream)																							TGCTGAACTCTTTGTGCATAAA	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66271187	66271187	+	IGR	DEL	A	-	-	rs67856146		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66271187delA								None (None upstream) : PCDH9 (605780 downstream)																							ATGGGAAGTGAAAAAAAAAAA	0.333													4	2	---	---	---	---	
PCDH9	5101	broad.mit.edu	37	13	67167961	67167961	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67167961delA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTACTTTGTTAATAATTTTCT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68337533	68337533	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68337533delA								PCDH9 (533065 upstream) : None (None downstream)																							tcagaaagtcaaaaaaaaatt	0.090													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70962597	70962597	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70962597delT								ATXN8OS (248712 upstream) : None (None downstream)																							gcacaatttcttatggaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	76904079	76904082	+	IGR	DEL	ACAC	-	-	rs71773316		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76904079_76904082delACAC								LMO7 (470075 upstream) : KCTD12 (550222 downstream)																							acatgcactaacacacacacacac	0.284													5	3	---	---	---	---	
SLAIN1	122060	broad.mit.edu	37	13	78273650	78273650	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78273650delC	uc010thy.1	+						SLAIN1_uc001vkk.1_Intron	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B											ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		TTCTGTTTTTCCAAGCTGTGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82790489	82790490	+	IGR	INS	-	TTCT	TTCT	rs143119594	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82790489_82790490insTTCT								None (None upstream) : None (None downstream)																							attctggaaaattctatctggc	0.000													4	4	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	93253169	93253169	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93253169delT	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				tgaactcctctacaagcaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	101348767	101348767	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101348767delG								TMTC4 (21664 upstream) : NALCN (357363 downstream)																							gttgatgcgaggggaccagtg	0.000													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102574901	102574901	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102574901delC	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						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)					TGACAATATGccctttttcaa	0.179													4	2	---	---	---	---	
C13orf27	93081	broad.mit.edu	37	13	103418479	103418479	+	3'UTR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103418479delA	uc001vpo.2	-	6					C13orf27_uc001vpn.2_3'UTR|C13orf27_uc001vpp.2_3'UTR	NM_138779	NP_620134	Q5JUR7	CM027_HUMAN	hypothetical protein LOC93081												0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAAAATTCAGATGTTTAATTT	0.279													4	2	---	---	---	---	
C13orf27	93081	broad.mit.edu	37	13	103418482	103418483	+	3'UTR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103418482_103418483insA	uc001vpo.2	-	6					C13orf27_uc001vpn.2_3'UTR|C13orf27_uc001vpp.2_3'UTR	NM_138779	NP_620134	Q5JUR7	CM027_HUMAN	hypothetical protein LOC93081												0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					AATTCAGATGTTTAATTTTTTT	0.282													4	2	---	---	---	---	
ERCC5	2073	broad.mit.edu	37	13	103504185	103504186	+	Intron	INS	-	T	T	rs145456994	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103504185_103504186insT	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Intron|ERCC5_uc010tjc.1_5'Flank|ERCC5_uc010tjd.1_5'Flank	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GCAATCACTTATTTTTTTTTAA	0.178			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104620198	104620200	+	IGR	DEL	GAA	-	-	rs138536982		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104620198_104620200delGAA								SLC10A2 (901002 upstream) : None (None downstream)																							gtgttggtgtgaaggtgatcagt	0.000													4	2	---	---	---	---	
TNFSF13B	10673	broad.mit.edu	37	13	108956832	108956832	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108956832delT	uc001vqr.2	+						TNFSF13B_uc010agj.2_Intron	NM_006573	NP_006564	Q9Y275	TN13B_HUMAN	tumor necrosis factor superfamily, member 13b						cell proliferation|immune response|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity|tumor necrosis factor receptor binding				0	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)			TCTTGTAAACTTTAGGTCTGT	0.423													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112260991	112260991	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112260991delA								C13orf16 (264398 upstream) : SOX1 (460922 downstream)																							ATGTAGCTGGAAGCTGAGGGA	0.214													4	2	---	---	---	---	
MCF2L	23263	broad.mit.edu	37	13	113670037	113670037	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113670037delC	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GAAGAGACAGCCAGCAACATG	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19052644	19052644	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19052644delT								None (None upstream) : OR11H12 (324950 downstream)																							tacaaaacgattgtttcaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19396845	19396845	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19396845delA								OR11H12 (18273 upstream) : POTEG (156520 downstream)																							aggaactgacaaaaaaaaaaa	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20032431	20032431	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20032431delA								P704P (12159 upstream) : OR4Q3 (183156 downstream)																							GGAAAAGATTAAAAAAAAATA	0.209													4	2	---	---	---	---	
DHRS2	10202	broad.mit.edu	37	14	24109921	24109921	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24109921delT	uc001wkt.3	+						DHRS2_uc010aku.1_Intron|DHRS2_uc001wku.3_Intron|DHRS2_uc010akv.2_Intron|DHRS2_uc001wkv.3_Intron	NM_182908	NP_878912	Q13268	DHRS2_HUMAN	dehydrogenase/reductase member 2 isoform 1						C21-steroid hormone metabolic process|cellular response to oxidative stress|myeloid dendritic cell differentiation|negative regulation of apoptosis|negative regulation of cell proliferation|response to toxin	mitochondrion|nuclear envelope	binding|carbonyl reductase (NADPH) activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00659)		GCACTCTCACTTGCCAACATC	0.527													4	2	---	---	---	---	
NRL	4901	broad.mit.edu	37	14	24560660	24560660	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24560660delG	uc001wlp.2	-						NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_5'Flank|PCK2_uc001wls.2_5'Flank|PCK2_uc001wlt.2_5'Flank|PCK2_uc010tnw.1_5'Flank|PCK2_uc010ald.2_5'Flank|PCK2_uc010ale.2_5'Flank|PCK2_uc010tnx.1_5'Flank|PCK2_uc001wlu.3_5'Flank	NM_006177	NP_006168	P54845	NRL_HUMAN	neural retina leucine zipper						response to stimulus|transcription from RNA polymerase II promoter|visual perception	nucleus	leucine zipper domain binding|sequence-specific DNA binding				0				GBM - Glioblastoma multiforme(265;0.0181)		TAGGAGAAAAGGAGGCAAGTG	0.383													4	2	---	---	---	---	
SIP1	8487	broad.mit.edu	37	14	39584421	39584422	+	Intron	INS	-	TT	TT	rs142029567	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39584421_39584422insTT	uc001wuq.2	+						SIP1_uc001wur.2_Intron|SIP1_uc001wus.2_Intron|SIP1_uc010amx.2_Intron	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)		TTGTTTGTttgtttatagagag	0.168													5	3	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	48026076	48026076	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48026076delA	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						ATTATTTGCTAAAATTTCtgc	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	48161550	48161550	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48161550delT								MDGA2 (17562 upstream) : None (None downstream)																							CTGTGCTTTCTTTTTTTTCCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53320431	53320432	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53320431_53320432insT								GNPNAT1 (62045 upstream) : FERMT2 (3558 downstream)																							CAGTGTCTCTGTTTTTAGAATT	0.401													4	2	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58724216	58724217	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58724216_58724217delAA	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						accccgtatcaaaaaaaaaaaa	0.109													3	3	---	---	---	---	
ZBTB1	22890	broad.mit.edu	37	14	64978267	64978268	+	Intron	INS	-	CTTA	CTTA	rs140546514	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64978267_64978268insCTTA	uc001xhh.3	+						ZBTB1_uc010aqg.2_Intron|ZBTB1_uc001xhi.2_Intron	NM_001123329	NP_001116801	Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		AAACTTTACATCTTATGAGCAT	0.317													5	3	---	---	---	---	
SPTB	6710	broad.mit.edu	37	14	65303226	65303226	+	Intron	DEL	A	-	-	rs75027904		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65303226delA	uc001xhs.2	-						SPTB_uc001xhu.2_Intron	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a						actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AAGGCAAAACAAAAAAAAGGG	0.458													2	4	---	---	---	---	
LIN52	91750	broad.mit.edu	37	14	74568164	74568165	+	Intron	DEL	TT	-	-	rs80309834		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74568164_74568165delTT	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845	Q52LA3	LIN52_HUMAN	lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)		ATGAtttttctttttttttttt	0.158													4	2	---	---	---	---	
ESRRB	2103	broad.mit.edu	37	14	76952902	76952902	+	Intron	DEL	T	-	-	rs35762017		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76952902delT	uc001xsq.1	+						ESRRB_uc001xsr.2_Intron|ESRRB_uc001xso.2_Intron	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)		AATTACGTGCTTTTTTTTTTT	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77352628	77352628	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77352628delT								C14orf166B (15983 upstream) : C14orf4 (138260 downstream)																							GTGACAGGGATTTTTTTTTTT	0.418													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77741226	77741227	+	IGR	INS	-	A	A	rs139121294	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77741226_77741227insA								NGB (3571 upstream) : POMT2 (72 downstream)																							GCACTCAAAACATTCTTCTCAG	0.470													4	4	---	---	---	---	
GSTZ1	2954	broad.mit.edu	37	14	77793494	77793494	+	Intron	DEL	G	-	-	rs10716979		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77793494delG	uc001xtj.2	+						GSTZ1_uc001xtk.2_Intron|GSTZ1_uc010ass.2_Intron|GSTZ1_uc001xtm.2_Intron	NM_145870	NP_665877	O43708	MAAI_HUMAN	glutathione transferase zeta 1 isoform 1						glutathione metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol|mitochondrion	glutathione peroxidase activity|glutathione transferase activity|maleylacetoacetate isomerase activity|protein homodimerization activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	GACCCTGGGAGGGTGGGTGGC	0.642													2	5	---	---	---	---	
ISM2	145501	broad.mit.edu	37	14	77941865	77941866	+	3'UTR	INS	-	AGGGCCCTACC	AGGGCCCTACC	rs143122984	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77941865_77941866insAGGGCCCTACC	uc001xtz.2	-	7					ISM2_uc001xua.2_3'UTR|ISM2_uc001xty.2_3'UTR|ISM2_uc010tvl.1_3'UTR	NM_199296	NP_954993	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1							extracellular region				skin(1)	1						AGGGGCGGGTGAGGAAAGTTCT	0.624													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80503764	80503764	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80503764delA								NRXN3 (173006 upstream) : DIO2 (160106 downstream)																							acatcaaactaaaaagctttg	0.000													4	2	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	81364128	81364128	+	Intron	DEL	T	-	-	rs149535917		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81364128delT	uc001xux.2	-						C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		ctCAAATCAAtttttttttcc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82447519	82447519	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82447519delA								SEL1L (447314 upstream) : None (None downstream)																							CATTCTTGGTAAGCAATGGCT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84323103	84323103	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84323103delT								None (None upstream) : None (None downstream)																							tggtttcctatttttttccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85467473	85467473	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85467473delA								None (None upstream) : FLRT2 (529015 downstream)																							CTAAAAACAGAAAAAAAAAAT	0.284													4	3	---	---	---	---	
C14orf159	80017	broad.mit.edu	37	14	91676721	91676721	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91676721delA	uc001xzb.2	+						C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836	Q7Z3D6	CN159_HUMAN	hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		caaaaacagcaaaaaattagc	0.000													4	2	---	---	---	---	
OTUB2	78990	broad.mit.edu	37	14	94503996	94503996	+	Intron	DEL	A	-	-	rs35415907		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94503996delA	uc001yci.2	+						OTUB2_uc001ych.2_Intron	NM_023112	NP_075601	Q96DC9	OTUB2_HUMAN	OTU domain, ubiquitin aldehyde binding 2						cellular amino acid metabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination		omega peptidase activity|protein binding|ubiquitin-specific protease activity				0		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		CTTTCATTCCAAAAAAAAAAA	0.239													7	7	---	---	---	---	
SERPINA12	145264	broad.mit.edu	37	14	94986237	94986245	+	5'Flank	DEL	GGTGGTGAC	-	-	rs147168993	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94986237_94986245delGGTGGTGAC	uc001ydj.2	-							NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)		aggtggtgatggtggtgacggaggtggtg	0.072													6	4	---	---	---	---	
SERPINA12	145264	broad.mit.edu	37	14	94986268	94986269	+	5'Flank	INS	-	TGC	TGC			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94986268_94986269insTGC	uc001ydj.2	-							NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)		gatggtggtggtggtgATGGTA	0.074													6	4	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95711323	95711324	+	Intron	INS	-	ACAC	ACAC			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95711323_95711324insACAC	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		CATATATGTGTATacacacaca	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98881537	98881537	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98881537delC								C14orf64 (437076 upstream) : C14orf177 (296413 downstream)																							AAGAGACCCACCACACAAGCC	0.378													4	2	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100133415	100133415	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100133415delG	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				GCCTCTCCGTGGGGAAACCCC	0.577													4	2	---	---	---	---	
EVL	51466	broad.mit.edu	37	14	100580507	100580508	+	Intron	INS	-	G	G	rs140941930	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100580507_100580508insG	uc001ygt.2	+						EVL_uc001ygv.2_Intron|EVL_uc001ygu.2_Intron|EVL_uc010avu.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				GAAGGAGGGCCGGGGGGGAATC	0.515													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106035350	106035350	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106035350delC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						CCAGTCACGTCCcacacactc	0.080													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107099093	107099094	+	Intron	INS	-	G	G	rs140761011	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107099093_107099094insG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GGTACCCTGCAGGAGGTTTGTG	0.540													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20408853	20408853	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20408853delG								None (None upstream) : GOLGA6L6 (328241 downstream)																							ccactgggttgggggtaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20524821	20524822	+	IGR	INS	-	A	A	rs75144308		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20524821_20524822insA								None (None upstream) : GOLGA6L6 (212272 downstream)																							TTTTCTAAAATAAAAAAAAATC	0.282													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20869307	20869308	+	IGR	DEL	CA	-	-	rs113986689		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20869307_20869308delCA								GOLGA8C (88281 upstream) : BCL8 (748 downstream)																							CACTAAGATGCACAGAGTACTC	0.282													2	4	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	27078864	27078864	+	Intron	DEL	T	-	-	rs35241747		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27078864delT	uc001zbb.2	-							NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	tacctgtagatttttttgtag	0.015													4	2	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29713129	29713129	+	Intron	DEL	T	-	-	rs77218545		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29713129delT	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						ctgcagcatctttttaggtga	0.254													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	34010200	34010200	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34010200delA	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						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)		TACTATTTGGAATCACTTAGT	0.463													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	34023258	34023258	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34023258delG	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						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)		GTGAGTCCCTGGTAGGTGAGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36065608	36065610	+	Intron	DEL	TAG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36065608_36065610delTAG	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																		CAATAATCTAtagtagtagtagt	0.399													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38998121	38998122	+	IGR	INS	-	C	C	rs72523382		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38998121_38998122insC								C15orf53 (5882 upstream) : C15orf54 (544763 downstream)																							GAGTTGGGATAGCATCAGTCAG	0.490													2	4	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40230378	40230378	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40230378delA	uc001zkm.1	+						EIF2AK4_uc001zkl.2_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		tgagagctggaaccatatctg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	42944470	42944470	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42944470delA	uc001zqg.2	+						uc001zqh.2_Intron					Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																		TCTATTGCTTAAAAAAAAAAA	0.368													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	44011205	44011206	+	Intron	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44011205_44011206delAG	uc010uec.1	-						uc001zsr.1_5'Flank					Homo sapiens cDNA FLJ16411 fis, clone BRACE2016362.																		CTCATGGAACAGAGAGAGAAAG	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48123068	48123069	+	IGR	INS	-	ACACACAC	ACACACAC	rs144809286	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48123068_48123069insACACACAC								SEMA6D (56649 upstream) : SLC24A5 (290100 downstream)																							TATCTACATAGacacacacaca	0.124													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	49017372	49017373	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49017372_49017373insA								FBN1 (79454 upstream) : CEP152 (12976 downstream)																							AGCGTCACAAGAAAAAAAAAAT	0.213													4	2	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54570051	54570052	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54570051_54570052insA	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)		TAATGTTGTAGAAAAAAATGAT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55368568	55368568	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55368568delC								UNC13C (447763 upstream) : RSL24D1 (104953 downstream)																							TTCCCCATTGCCCAACACAAT	0.378													4	2	---	---	---	---	
CGNL1	84952	broad.mit.edu	37	15	57803211	57803212	+	Intron	INS	-	T	T	rs146821506	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57803211_57803212insT	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		GAGGACGTGGGTTGTTTTCTGA	0.431													4	2	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	62949484	62949485	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62949484_62949485delTG	uc002alb.3	+							NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						AGTTCTTGTCTGTGTGTGTGTG	0.436													4	2	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63619700	63619700	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63619700delT	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	aaatgtagggttttttttttt	0.104													4	4	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63672559	63672559	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63672559delA	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	gagagaagggaGGCAGAGCTG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	66925389	66925389	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66925389delC	uc002aqe.2	+											Homo sapiens cDNA FLJ38816 fis, clone LIVER2007568.																		TTGACTCCTTCCCCAGGCACT	0.597													4	2	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	68886001	68886001	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68886001delT	uc002arj.3	+							NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						TCTGGGTTTGTTTTTTTTTTT	0.453													4	3	---	---	---	---	
ARIH1	25820	broad.mit.edu	37	15	72836895	72836896	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72836895_72836896delAC	uc002aut.3	+							NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding						ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						TTacatacatacacacacacac	0.257													6	3	---	---	---	---	
PML	5371	broad.mit.edu	37	15	74297934	74297935	+	Intron	INS	-	T	T	rs113972054		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74297934_74297935insT	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						CCCCAGCAATCTTTTTTTTTTT	0.421			T	RARA|PAX5	APL|ALL								6	7	---	---	---	---	
C15orf27	123591	broad.mit.edu	37	15	76503251	76503260	+	Intron	DEL	GCATTTTCCA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76503251_76503260delGCATTTTCCA	uc010bkp.2	+									Q2M3C6	CO027_HUMAN	RecName: Full=Transmembrane protein C15orf27;							integral to membrane					0						TCTAGACCTTGCATTTTCCAGAGAAAGCAG	0.357													4	3	---	---	---	---	
RCN2	5955	broad.mit.edu	37	15	77228416	77228416	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77228416delT	uc002bcd.2	+						RCN2_uc002bce.2_Intron|RCN2_uc010bks.2_Intron	NM_002902	NP_002893	Q14257	RCN2_HUMAN	reticulocalbin 2 precursor							endoplasmic reticulum lumen	calcium ion binding				0						CCCATTCCCATTTTTAAACAC	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84082425	84082425	+	IGR	DEL	G	-	-	rs112411833	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84082425delG								BNC1 (128957 upstream) : SH3GL3 (33666 downstream)																							TGAGGGATCTGGGGACTGGGC	0.453													4	2	---	---	---	---	
MESP2	145873	broad.mit.edu	37	15	90320746	90320746	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90320746delG	uc002bon.2	+						MESP2_uc010uqa.1_Intron	NM_001039958	NP_001035047	Q0VG99	MESP2_HUMAN	mesoderm posterior 2 homolog						Notch signaling pathway	nucleus	DNA binding				0	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			CTTTCTCAGAGGGTGGAAAGT	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91936201	91936201	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91936201delA								SV2B (97553 upstream) : SLCO3A1 (460737 downstream)																							gctctgcagtaagcagagaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93895173	93895173	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93895173delG	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		CAATCACCATGGGAGAGAGTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94253838	94253838	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94253838delA								RGMA (621405 upstream) : MCTP2 (520963 downstream)																							gctccaatttaaaggccaaac	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98535967	98535967	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98535967delA								ARRDC4 (18900 upstream) : FAM169B (444424 downstream)																							GGGGATAATTAAAAAAAAAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98742273	98742273	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98742273delC								ARRDC4 (225206 upstream) : FAM169B (238118 downstream)																							TAAGAGTCAACCACCAATGCA	0.383													4	2	---	---	---	---	
DNAJA3	9093	broad.mit.edu	37	16	4480147	4480147	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4480147delA	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4						cctgtctcttaaaaaaaaaaa	0.149													4	2	---	---	---	---	
DNAJA3	9093	broad.mit.edu	37	16	4480158	4480158	+	Intron	DEL	T	-	-	rs8060219	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4480158delT	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4						aaaaaaaaaaTTTTGAAAAGG	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5464178	5464179	+	Intron	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5464178_5464179delGT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																		AAAAACAAGGGTGATCACTTGA	0.431													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6073644	6073644	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6073644delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.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)		TCCTAGCACGTTTGCTCTGAA	0.468													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7718664	7718665	+	Intron	DEL	AC	-	-	rs71394334		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7718664_7718665delAC	uc002cys.2	+						A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.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)		ACAGAACAGAacacacacacac	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8519291	8519291	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8519291delA								A2BP1 (755951 upstream) : TMEM114 (100212 downstream)																							CAGCGTGCATAAGGGAAGAAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9282426	9282426	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9282426delG								C16orf72 (68881 upstream) : GRIN2A (564841 downstream)																							caaagagcaaggggctgttac	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13854559	13854560	+	IGR	DEL	TC	-	-	rs117375310	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13854559_13854560delTC								SHISA9 (520287 upstream) : ERCC4 (159454 downstream)																							CACTGTACGATCTCTCTCTCTC	0.500													4	2	---	---	---	---	
ERCC4	2072	broad.mit.edu	37	16	14032095	14032095	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14032095delG	uc002dce.2	+						ERCC4_uc010uyz.1_Intron	NM_005236	NP_005227	Q92889	XPF_HUMAN	excision repair cross-complementing rodent						double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10						ATATGTCCTTGGGTGGGTGGC	0.373			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17079281	17079281	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17079281delC								LOC339047 (634844 upstream) : XYLT1 (116902 downstream)																							ttcccaaggtccctcaacttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18018598	18018601	+	IGR	DEL	AAAC	-	-	rs113180260		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18018598_18018601delAAAC								XYLT1 (453860 upstream) : NOMO2 (492582 downstream)																							aaaaaaaCAAAAACAAAAAAGTCT	0.108													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18212255	18212255	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18212255delA								XYLT1 (647517 upstream) : NOMO2 (298928 downstream)																							tccttaggagaaaaaaaaatg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20622633	20622636	+	IGR	DEL	CTAA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20622633_20622636delCTAA								ACSM2B (34938 upstream) : ACSM1 (11923 downstream)																							actggctgagctaattagaggctt	0.025													4	2	---	---	---	---	
ARHGAP17	55114	broad.mit.edu	37	16	25007435	25007436	+	Intron	INS	-	GG	GG	rs112297139		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25007435_25007436insGG	uc002dnb.2	-						ARHGAP17_uc002dnc.2_Intron|ARHGAP17_uc010vcf.1_Intron|ARHGAP17_uc002dng.1_Intron	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)		TTTATTTTTTTGGGGGGGGAGG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25051654	25051655	+	IGR	INS	-	TAAG	TAAG			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25051654_25051655insTAAG								ARHGAP17 (24979 upstream) : LCMT1 (71392 downstream)																							atcacaataaataaaTAGGAAA	0.203													4	2	---	---	---	---	
IL21R	50615	broad.mit.edu	37	16	27441475	27441475	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27441475delG	uc002doq.1	+						IL21R_uc002dor.1_Intron|IL21R_uc002dos.1_Intron	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor						natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4						CGGGTGGGGAGGGCCCCCATC	0.647			T	BCL6	NHL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32554319	32554319	+	IGR	DEL	A	-	-	rs142875489		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32554319delA								HERC2P4 (390445 upstream) : TP53TG3B (130522 downstream)																							acaaagggacacttgcaaaca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33398556	33398556	+	IGR	DEL	T	-	-	rs112274831		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33398556delT								SLC6A10P (502093 upstream) : MIR1826 (566952 downstream)																							CTCATCTTTCTGGGGAATCTT	0.378													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33945635	33945635	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33945635delA								None (None upstream) : MIR1826 (19873 downstream)																							tacataaaggaaaaaaaaagg	0.005													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33986874	33986874	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33986874delC								MIR1826 (21282 upstream) : UBE2MP1 (416928 downstream)																							tcctttttcaccataggcctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48391408	48391408	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48391408delC	uc002efk.1	+						SIAH1_uc002efl.2_Intron					Homo sapiens cDNA FLJ31489 fis, clone NT2NE2003308.																		GTTTAACCTACACAAATACCA	0.448													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49207513	49207514	+	IGR	DEL	TA	-	-	rs34876661		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49207513_49207514delTA								N4BP1 (563393 upstream) : CBLN1 (104697 downstream)																							GTGGTGAATTTATGTTTCTTCT	0.406													5	5	---	---	---	---	
NOD2	64127	broad.mit.edu	37	16	50726832	50726833	+	5'Flank	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50726832_50726833delGT	uc010cbk.1	+						NOD2_uc010cbj.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain						activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)				ggaaagcagggtgtgtgtgtgt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51564335	51564335	+	IGR	DEL	A	-	-	rs76081829		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51564335delA								SALL1 (379152 upstream) : TOX3 (907583 downstream)																							caaaagggggaaaaaaatcag	0.045													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51749539	51749539	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51749539delA								SALL1 (564356 upstream) : TOX3 (722379 downstream)																							TCTCCAGTCTAAAGGGACAGG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54578834	54578834	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54578834delT								IRX3 (258456 upstream) : IRX5 (386277 downstream)																							CTTGCAAGGATTTTTTTTTTT	0.463													7	4	---	---	---	---	
CNOT1	23019	broad.mit.edu	37	16	58573529	58573529	+	Intron	DEL	A	-	-	rs66742130		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58573529delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc010vik.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TCTACGTTGGAAAAAAAAAAA	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63479012	63479012	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63479012delA								None (None upstream) : None (None downstream)																							GTAAAAAAAGAAAAAAAAAAC	0.299													4	2	---	---	---	---	
CDH11	1009	broad.mit.edu	37	16	65048632	65048632	+	Intron	DEL	T	-	-	rs34142434		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65048632delT	uc002eoi.2	-						CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		ATGTAGACGGTTTTAGGAACT	0.353			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73638145	73638146	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73638145_73638146insT								HTA (510475 upstream) : PSMD7 (692535 downstream)																							gctttaaatagttttttttccc	0.074													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	79099749	79099751	+	Intron	DEL	TGC	-	-	rs113498257		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79099749_79099751delTGC	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)		gagtcagctatgctgtcatattc	0.103													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79688407	79688408	+	IGR	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79688407_79688408delGA								MAF (53785 upstream) : DYNLRB2 (886446 downstream)																							TTGTGTGAATGAGAGAGAGAGC	0.436													4	2	---	---	---	---	
CENPN	55839	broad.mit.edu	37	16	81058170	81058171	+	Intron	INS	-	CAACTCAGC	CAACTCAGC	rs150158893	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81058170_81058171insCAACTCAGC	uc002ffx.2	+						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						AGTGTCCTGCTCAACTCAGCCA	0.401													22	12	---	---	---	---	
GAN	8139	broad.mit.edu	37	16	81353315	81353315	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81353315delC	uc002fgo.2	+							NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)				TTCCCCCCGACCCCCCCTTAT	0.408													4	2	---	---	---	---	
FBXO31	79791	broad.mit.edu	37	16	87419752	87419752	+	5'Flank	DEL	C	-	-	rs66485329		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87419752delC	uc002fjw.2	-						FBXO31_uc010vot.1_Intron	NM_024735	NP_079011	Q5XUX0	FBX31_HUMAN	F-box protein 31						cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0272)		AGATCAGGGACCTCAGGAGGC	0.512													4	16	---	---	---	---	
ZC3H18	124245	broad.mit.edu	37	16	88690882	88690883	+	Intron	INS	-	AGC	AGC	rs143096278	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88690882_88690883insAGC	uc002fky.2	+						ZC3H18_uc010voz.1_Intron|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_5'Flank	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GTCCAGGCACGAGCGTGCTCAC	0.653													11	8	---	---	---	---	
ZNF276	92822	broad.mit.edu	37	16	89795917	89795918	+	Intron	INS	-	GT	GT	rs140314842	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89795917_89795918insGT	uc002fos.3	+						ZNF276_uc010ciq.2_Intron|ZNF276_uc002fop.2_Intron|ZNF276_uc002foq.3_Intron|ZNF276_uc010cir.2_Intron|ZNF276_uc002for.3_Intron|ZNF276_uc010cis.2_Intron|ZNF276_uc002fot.3_Intron|ZNF276_uc010vpm.1_Intron|ZNF276_uc010cit.1_Intron	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TGAGAAGGTGGGTCCTCCTGGT	0.649													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4568954	4568955	+	IGR	DEL	TA	-	-	rs149684563		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4568954_4568955delTA								ALOX15 (23365 upstream) : PELP1 (5725 downstream)																							agccatagtctataaaccctgt	0.252													1	5	---	---	---	---	
PELP1	27043	broad.mit.edu	37	17	4608883	4608884	+	5'Flank	DEL	TG	-	-	rs10562310		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4608883_4608884delTG	uc002fyi.3	-						PELP1_uc010vsf.1_5'Flank	NM_014389	NP_055204	Q8IZL8	PELP1_HUMAN	proline, glutamic acid and leucine rich protein						transcription, DNA-dependent	cytoplasm|MLL1 complex	protein binding			ovary(1)|central_nervous_system(1)	2						TTTTTTAAACTGTGGTATGAAT	0.361													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5903015	5903015	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5903015delA								NLRP1 (415183 upstream) : WSCD1 (69422 downstream)																							ctcaaaaaagaaaaaaaaaag	0.025													4	5	---	---	---	---	
NTN1	9423	broad.mit.edu	37	17	9130545	9130546	+	Intron	INS	-	CAAA	CAAA	rs145040800		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9130545_9130546insCAAA	uc002glw.3	+							NM_004822	NP_004813	O95631	NET1_HUMAN	netrin 1 precursor						apoptosis|axon guidance		protein binding				0						caccatcacatcacatacacca	0.094													3	3	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9202557	9202557	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9202557delT	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						GTTTTCCACATTTTTTTTGTG	0.448													3	4	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10308044	10308047	+	Intron	DEL	ACAC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10308044_10308047delACAC	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGCAGGCTTTacacacacacacac	0.304									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				9	7	---	---	---	---	
MAP2K4	6416	broad.mit.edu	37	17	12026480	12026481	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12026480_12026481insA	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron|MAP2K4_uc010vvi.1_Intron|MAP2K4_uc010vvj.1_Intron	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		tcacttttttgaaaaaaaaatt	0.000			D|Mis|N		pancreatic|breast|colorectal								4	2	---	---	---	---	
AKAP10	11216	broad.mit.edu	37	17	19856713	19856714	+	Intron	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19856713_19856714insA	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron|AKAP10_uc010vze.1_Intron	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					taatagaaaagaaataataaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21338266	21338266	+	IGR	DEL	C	-	-	rs148232145		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21338266delC								KCNJ12 (15087 upstream) : C17orf51 (93306 downstream)																							GAGACCAGAACCTTTACATAT	0.488													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21351164	21351165	+	IGR	INS	-	TG	TG	rs77745849		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21351164_21351165insTG								KCNJ12 (27985 upstream) : C17orf51 (80407 downstream)																							TCCATCATACATGTGCCCTTGG	0.510													4	5	---	---	---	---	
NLK	51701	broad.mit.edu	37	17	26452496	26452496	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26452496delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		agaaattaaatttttttaatg	0.129													4	2	---	---	---	---	
SUZ12P	440423	broad.mit.edu	37	17	29062327	29062327	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29062327delT	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfp.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0						TGTTATTAGCTTTTTTTTTTT	0.199													9	4	---	---	---	---	
RAB11FIP4	84440	broad.mit.edu	37	17	29727245	29727245	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29727245delT	uc002hgn.1	+							NM_032932	NP_116321	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)						cytokinesis|interspecies interaction between organisms|protein transport	cleavage furrow|endocytic vesicle|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding			skin(1)	1		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				gaaagaaacatTAGTGCCGAA	0.229													4	2	---	---	---	---	
RAB11FIP4	84440	broad.mit.edu	37	17	29854649	29854664	+	Intron	DEL	ATTTTGCTTACAAATA	-	-	rs11275605		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29854649_29854664delATTTTGCTTACAAATA	uc002hgn.1	+						RAB11FIP4_uc002hgo.2_Intron	NM_032932	NP_116321	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)						cytokinesis|interspecies interaction between organisms|protein transport	cleavage furrow|endocytic vesicle|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding			skin(1)	1		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				ATAATTTACTATTTTGCTTACAAATAGTCCTTACTA	0.102													9	4	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31601660	31601661	+	Intron	INS	-	T	T	rs140624581	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31601660_31601661insT	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)	cccatgcttggtttgaccccaa	0.163													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32130841	32130842	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32130841_32130842insT	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)	TGTAACTGGCATTTTTTTTTAT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33704121	33704121	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33704121delA								SLFN11 (3401 upstream) : SLFN12 (33962 downstream)																							AATTGTTCTCAAAAAAAAAAT	0.318													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33715905	33715905	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33715905delT								SLFN11 (15185 upstream) : SLFN12 (22178 downstream)																							ttatctttggtttgactggat	0.000													4	2	---	---	---	---	
AP2B1	163	broad.mit.edu	37	17	33969845	33969845	+	Intron	DEL	A	-	-	rs71366468		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33969845delA	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		ACTACAACTTAAAAAAATGTA	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35058878	35058878	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35058878delT								MRM1 (93472 upstream) : LHX1 (235621 downstream)																							GTAATCCTCCTTTCTTCCATG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36395288	36395289	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36395288_36395289delAA	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																		actccatctcaaaaaaaaaaaa	0.163													3	3	---	---	---	---	
KRT13	3860	broad.mit.edu	37	17	39661067	39661067	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39661067delA	uc002hwu.1	-						KRT13_uc002hwv.1_Intron|KRT13_uc002hww.2_Intron|KRT13_uc010wfr.1_Intron|KRT13_uc010cxo.2_Intron|KRT13_uc002hwx.1_Intron	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a						epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)				GGAAAGCAGTAAAAAAACTGA	0.363													4	2	---	---	---	---	
DHX8	1659	broad.mit.edu	37	17	41591077	41591077	+	Intron	DEL	C	-	-	rs118127166		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41591077delC	uc002idu.1	+						DHX8_uc010wif.1_Intron|DHX8_uc010wig.1_Intron	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8							catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		AGtttttaatctttttttttt	0.144													7	4	---	---	---	---	
LOC100128977	100128977	broad.mit.edu	37	17	43938562	43938563	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43938562_43938563delAC	uc010wjz.1	-							NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0						AGTGATCCTGACACACACACAA	0.564													4	2	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44260472	44260472	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44260472delA	uc002ikc.2	-						KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				tgcttttcagaaaaaagaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	44354570	44354570	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44354570delA								KIAA1267 (51853 upstream) : ARL17B (9293 downstream)																							AAAGCTACATAAAATAACCAG	0.403													6	3	---	---	---	---	
ARL17B	641522	broad.mit.edu	37	17	44368266	44368267	+	Intron	INS	-	A	A	rs111769986		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44368266_44368267insA	uc002ikf.2	-											Homo sapiens full length insert cDNA clone ZD50C03.												0						GTACCTGAAATAAGTTTGCTGT	0.391													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47635153	47635154	+	IGR	DEL	AT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47635153_47635154delAT								NGFR (42788 upstream) : NXPH3 (18144 downstream)																							agatagacagataggtagataa	0.069													4	2	---	---	---	---	
FAM117A	81558	broad.mit.edu	37	17	47827640	47827641	+	Intron	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47827640_47827641delAC	uc002ipk.2	-						FAM117A_uc010wlz.1_Intron	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A											ovary(1)	1						tcacatgcagacacacacacac	0.178													3	3	---	---	---	---	
SPATA20	64847	broad.mit.edu	37	17	48622142	48622143	+	5'Flank	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48622142_48622143insC	uc002irf.2	+						SPATA20_uc002irc.2_Intron|SPATA20_uc002ire.2_5'Flank|SPATA20_uc002ird.2_5'Flank	NM_022827	NP_073738	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20						cell differentiation|mannose metabolic process|multicellular organismal development|spermatogenesis	extracellular region	mannose-6-phosphate isomerase activity|protein binding				0	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			tggacatttttctgtcccagcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52522513	52522514	+	IGR	DEL	TA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52522513_52522514delTA								KIF2B (619940 upstream) : TOM1L1 (455538 downstream)																							AGCTGGAGTCTATagaaaaagt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53425525	53425526	+	IGR	INS	-	TGTT	TGTT	rs139978129	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53425525_53425526insTGTT								HLF (23099 upstream) : MMD (44449 downstream)																							TGGGCTGTTTCTGTTTGTTTGT	0.342													3	3	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55569580	55569580	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55569580delG	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		CATGAAAAACGGGGGAAGGAT	0.408			T	HOXA9	CML								4	2	---	---	---	---	
MAP3K3	4215	broad.mit.edu	37	17	61724224	61724224	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61724224delT	uc002jbg.2	+						MAP3K3_uc002jbe.2_Intron|MAP3K3_uc002jbf.2_Intron|MAP3K3_uc002jbh.2_Intron|MAP3K3_uc010wpo.1_Intron|MAP3K3_uc010wpp.1_Intron	NM_002401	NP_002392	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3						MAPKKK cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autophosphorylation	cytosol	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			lung(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)	6						GTGCGGCACATGTACACATAA	0.418													4	2	---	---	---	---	
KPNA2	3838	broad.mit.edu	37	17	66037018	66037020	+	Intron	DEL	TTT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66037018_66037020delTTT	uc002jgk.2	+						KPNA2_uc002jgl.2_Intron	NM_002266	NP_002257	P52292	IMA2_HUMAN	karyopherin alpha 2						DNA metabolic process|G2 phase of mitotic cell cycle|interspecies interaction between organisms|M phase specific microtubule process|NLS-bearing substrate import into nucleus|regulation of DNA recombination	cytoplasm|nuclear pore|nucleoplasm	histone deacetylase binding|nuclear localization sequence binding|protein transporter activity			central_nervous_system(2)	2	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CCAAATAGTATTTTTTATTTATT	0.207													14	8	---	---	---	---	
CPSF4L	642843	broad.mit.edu	37	17	71254152	71254152	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71254152delT	uc010dfk.1	-							NM_001129885	NP_001123357	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor								RNA binding|zinc ion binding				0						AAGGGAGAGCttttttttttt	0.318													6	3	---	---	---	---	
SAP30BP	29115	broad.mit.edu	37	17	73697167	73697167	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73697167delG	uc002jpe.2	+						SAP30BP_uc002jpc.1_Intron|SAP30BP_uc010wsf.1_Intron|SAP30BP_uc010wsg.1_Intron|SAP30BP_uc002jpf.2_Intron	NM_013260	NP_037392	Q9UHR5	S30BP_HUMAN	transcriptional regulator protein						apoptosis|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACCTCTCTCTGCAGTTCAGCT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74646994	74646995	+	IGR	INS	-	TTTTG	TTTTG	rs139084267	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74646994_74646995insTTTTG								ST6GALNAC1 (7100 upstream) : MXRA7 (24814 downstream)																							GCTGACCCTAACAATATGTGCA	0.149													6	3	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75387399	75387399	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75387399delA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			GGGTTGCTGTAACAGAGTGCC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75512351	75512352	+	IGR	INS	-	G	G	rs56207888	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75512351_75512352insG								SEPT9 (15675 upstream) : FLJ45079 (362757 downstream)																							actcatgtcatggggggttgtc	0.000													4	2	---	---	---	---	
TNRC6C	57690	broad.mit.edu	37	17	76067505	76067505	+	Intron	DEL	T	-	-	rs75702970		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76067505delT	uc002jud.2	+						TNRC6C_uc002juf.2_Intron|TNRC6C_uc002jue.2_Intron	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2						gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TAGAAAATGCttttttttttt	0.199													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76533269	76533270	+	IGR	INS	-	AAAG	AAAG	rs112022113		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76533269_76533270insAAAG								DNAH17 (64413 upstream) : CYTH1 (136861 downstream)																							caaaaaaaaaaaaagaaaaaaa	0.243													14	7	---	---	---	---	
NPLOC4	55666	broad.mit.edu	37	17	79562978	79562980	+	Intron	DEL	GTT	-	-	rs145761561		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-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													4	3	---	---	---	---	
COLEC12	81035	broad.mit.edu	37	18	391303	391304	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:391303_391304delTG	uc002kkm.2	-							NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TGAGTGGTACTGTGTGTGCGCA	0.421													4	2	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2705085	2705085	+	Intron	DEL	T	-	-	rs140647578		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2705085delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_5'Flank	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						TGTGCGTAGGTTAAGTGCAGA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4985709	4985709	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4985709delT								DLGAP1 (530443 upstream) : LOC642597 (157963 downstream)																							CAGTCAGAAATTTTTCACTGA	0.358													4	2	---	---	---	---	
VAPA	9218	broad.mit.edu	37	18	9914368	9914369	+	Intron	DEL	GC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9914368_9914369delGC	uc002kok.2	+						VAPA_uc002koj.2_Intron	NM_194434	NP_919415	Q9P0L0	VAPA_HUMAN	vesicle-associated membrane protein-associated						cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0						GTGGGGTGGGGCGCGCGGACCG	0.738													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12035683	12035683	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12035683delG								IMPA2 (4807 upstream) : CIDEA (218635 downstream)																							GGAGATGTGAGGGGGGTGGGG	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19546374	19546374	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19546374delA								MIB1 (95464 upstream) : GATA6 (203042 downstream)																							atgcttaatgaaaaaaaatga	0.154													4	2	---	---	---	---	
GATA6	2627	broad.mit.edu	37	18	19755105	19755105	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19755105delT	uc002ktt.1	+						GATA6_uc002ktu.1_Intron	NM_005257	NP_005248	Q92908	GATA6_HUMAN	GATA binding protein 6						blood coagulation|cardiac vascular smooth muscle cell differentiation|cellular response to hypoxia|intestinal epithelial cell differentiation|male gonad development|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor-beta1 production|negative regulation of transforming growth factor-beta2 production|outflow tract septum morphogenesis|positive regulation of angiogenesis|positive regulation of cell cycle arrest|positive regulation of transcription from RNA polymerase II promoter|response to drug|response to growth factor stimulus		protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(3)	3	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			AAAGACAGCATTTTTTTTTCC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22091319	22091319	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22091319delG								HRH4 (31399 upstream) : ZNF521 (550569 downstream)																							attgaggTGCGGGTCAAAAGT	0.239													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22934476	22934476	+	5'Flank	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22934476delC	uc002kvk.2	-						ZNF521_uc010xbe.1_5'Flank|ZNF521_uc010dly.2_5'Flank|ZNF521_uc002kvl.2_5'Flank	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					AGGCAAAACTCCCACTGATTT	0.403			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28306962	28306963	+	IGR	INS	-	CT	CT	rs148665611	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28306962_28306963insCT								MIR302F (428036 upstream) : DSC3 (263090 downstream)																							TGAAGAATGAGCTGTCTCATGA	0.371													3	3	---	---	---	---	
B4GALT6	9331	broad.mit.edu	37	18	29264143	29264144	+	Intron	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29264143_29264144delAA	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766	Q9UBX8	B4GT6_HUMAN	beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			CGTCTGAAATAACATTTAAAAC	0.416													38	18	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	31345126	31345126	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31345126delT								ASXL3 (17727 upstream) : NOL4 (85944 downstream)																							AGTACTTACATTTTTTACCCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	33851058	33851058	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33851058delG								MOCOS (2374 upstream) : FHOD3 (26644 downstream)																							ccaaagttctgggattacaag	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35264085	35264085	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35264085delG								CELF4 (118085 upstream) : None (None downstream)																							GGGTCAGCTAGGAGCAAAGCC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	40260678	40260678	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40260678delT	uc002lau.2	+											Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TACATATGGCTTTTTTTTCCA	0.303													4	2	---	---	---	---	
C18orf25	147339	broad.mit.edu	37	18	43790463	43790463	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43790463delA	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492	Q96B23	CR025_HUMAN	ARKadia-like 1 isoform a											central_nervous_system(2)	2						gtacctttccaaaatctaaat	0.000													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48154335	48154335	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48154335delC	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		TCAAGGTGTTCTTTCAAAGCA	0.527													4	2	---	---	---	---	
SMAD4	4089	broad.mit.edu	37	18	48609103	48609103	+	3'UTR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48609103delT	uc010xdp.1	+	12					SMAD4_uc002lfb.3_3'UTR	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		gaatttttagttttttttttt	0.050									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53813828	53813828	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53813828delA								TCF4 (510643 upstream) : TXNL1 (456227 downstream)																							ACAAGCAAGCAAAAAAACTCT	0.373													4	2	---	---	---	---	
WDR7	23335	broad.mit.edu	37	18	54560425	54560425	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54560425delT	uc002lgk.1	+						WDR7_uc002lgl.1_Intron	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		TGCTGGTGACTTTTTTTTTTT	0.328													3	3	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56193769	56193769	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56193769delT	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						ACAGCTGCCCTTTCAAAAGCC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57893482	57893482	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57893482delG								PMAIP1 (321944 upstream) : MC4R (145082 downstream)																							gccagtccttggggcccagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	59666612	59666612	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59666612delA								RNF152 (106308 upstream) : PIGN (44848 downstream)																							TCAGTTGCTGACCAGAGTGAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68057758	68057758	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68057758delA								SOCS6 (60324 upstream) : None (None downstream)																							TTGGACAGCTAAAAATTATCG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68863511	68863511	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68863511delT								SOCS6 (866077 upstream) : None (None downstream)																							CTGAAAATAATTAGTTCTGTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69771034	69771034	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69771034delA								None (None upstream) : CBLN2 (432881 downstream)																							GAAGTGAAAGAAAAAAAAAAa	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70188402	70188402	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70188402delT								None (None upstream) : CBLN2 (15513 downstream)																							agttaaattattagtgtttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73243688	73243688	+	IGR	DEL	G	-	-	rs35907326		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73243688delG								C18orf62 (104099 upstream) : ZNF516 (827931 downstream)																							TGCCTGGTTAGGGGGTTGTGT	0.552													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73290108	73290108	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73290108delC								C18orf62 (150519 upstream) : ZNF516 (781511 downstream)																							ACTGGCATTGCCACGACATTG	0.468													4	2	---	---	---	---	
ADNP2	22850	broad.mit.edu	37	18	77867941	77867942	+	Intron	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77867941_77867942insT	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)		ATCTGCCCAGGTTTTTTTTTCC	0.480													4	2	---	---	---	---	
MADCAM1	8174	broad.mit.edu	37	19	500236	500237	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:500236_500237insC	uc002los.2	+						MADCAM1_uc002lot.2_Intron|MADCAM1_uc010drq.2_Intron	NM_130760	NP_570116	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion						cell adhesion|immune response|regulation of immune response|signal transduction	integral to membrane|membrane fraction|plasma membrane					0		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		ggtgactctcacccctttgaca	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6615274	6615275	+	IGR	INS	-	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6615274_6615275insG								CD70 (24111 upstream) : TNFSF14 (49291 downstream)																							gagagagaggagagagagagag	0.000													4	3	---	---	---	---	
LASS4	79603	broad.mit.edu	37	19	8306911	8306911	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8306911delC	uc002mjg.2	+						LASS4_uc002mjh.2_Intron|LASS4_uc002mji.2_Intron|LASS4_uc010dvz.2_Intron	NM_024552	NP_078828	Q9HA82	CERS4_HUMAN	LAG1 homolog, ceramide synthase 4							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1						CTGGTTATAGCCATGCCtgag	0.274													4	2	---	---	---	---	
ZNF563	147837	broad.mit.edu	37	19	12445109	12445109	+	5'Flank	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12445109delA	uc002mtp.2	-						ZNF563_uc002mtq.2_5'Flank	NM_145276	NP_660319	Q8TA94	ZN563_HUMAN	zinc finger protein 563						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATACAACAGGAAAAAAAAAGC	0.373													3	4	---	---	---	---	
DNASE2	1777	broad.mit.edu	37	19	12991483	12991483	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12991483delA	uc002mvn.1	-						DNASE2_uc010xmr.1_Intron	NM_001375	NP_001366	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal precursor						apoptosis	lysosome	deoxyribonuclease II activity|DNA binding|protein binding				0						aaaaacaaagaaaaaaaaaaG	0.269								Direct_reversal_of_damage					25	11	---	---	---	---	
ZNF493	284443	broad.mit.edu	37	19	21605537	21605537	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21605537delT	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						TCATTTATAATTTTTTCTCAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24065805	24065805	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24065805delT								RPSAP58 (54888 upstream) : ZNF254 (150442 downstream)																							ccattttctgttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27847234	27847235	+	IGR	DEL	AA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27847234_27847235delAA								None (None upstream) : LOC148189 (434167 downstream)																							cagattctacaaaaagagtgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29147113	29147113	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29147113delT	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																		atagctaaacttTTtttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29516152	29516153	+	IGR	DEL	AC	-	-	rs112552400		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29516152_29516153delAC								LOC148145 (56097 upstream) : UQCRFS1 (182014 downstream)																							aaaaaaaaaaacaaaaCACCTT	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30558715	30558716	+	IGR	INS	-	ATCC	ATCC	rs143825259		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30558715_30558716insATCC								C19orf2 (52104 upstream) : ZNF536 (304612 downstream)																							TCTACGTATCTatccatccatc	0.218													4	3	---	---	---	---	
YIF1B	90522	broad.mit.edu	37	19	38803054	38803054	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38803054delA	uc002ohz.2	-						YIF1B_uc002ohw.2_5'Flank|YIF1B_uc002ohx.2_Intron|YIF1B_uc010xtx.1_Intron|YIF1B_uc010xty.1_Intron|YIF1B_uc002oia.2_Intron|YIF1B_uc002ohy.2_Intron|YIF1B_uc002oib.2_Intron	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5							integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ggccctctttaaaaaaaaaag	0.000													4	2	---	---	---	---	
CYP2F1	1572	broad.mit.edu	37	19	42067826	42067827	+	Intron	DEL	GA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42067826_42067827delGA	uc010xvw.1	+						CEACAM21_uc002orc.1_Intron			P24903	CP2F1_HUMAN	SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						gggggtgggggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42289492	42289492	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42289492delC								CEACAM6 (13379 upstream) : CEACAM3 (11042 downstream)																							gaagtgtcttccagttctaaa	0.149											OREG0025488	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ARHGEF1	9138	broad.mit.edu	37	19	42407087	42407087	+	Intron	DEL	T	-	-	rs76291947		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42407087delT	uc002orx.2	+						ARHGEF1_uc002ory.2_Intron|ARHGEF1_uc002orz.2_Intron|ARHGEF1_uc002osa.2_Intron|ARHGEF1_uc002osb.2_Intron|ARHGEF1_uc002osc.2_Intron|ARHGEF1_uc002osd.2_Intron|ARHGEF1_uc002ose.2_Intron	NM_004706	NP_004697	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor 1 isoform						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GGCTCTCCTCTTTTTTTTTTA	0.358													12	6	---	---	---	---	
OPA3	80207	broad.mit.edu	37	19	46071236	46071238	+	Intron	DEL	GAT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46071236_46071238delGAT	uc002pck.3	-						OPA3_uc002pcj.3_Intron|OPA3_uc010xxk.1_Intron	NM_025136	NP_079412	Q9H6K4	OPA3_HUMAN	OPA3 protein isoform b						response to stimulus|visual perception	mitochondrion					0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		GATCCAGTCAGATGATGATGATG	0.251													4	2	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47685386	47685386	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47685386delC	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TCTTCAATTTCCCCTCATTCA	0.254													4	2	---	---	---	---	
NAPSA	9476	broad.mit.edu	37	19	50863358	50863358	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50863358delA	uc002prx.2	-						NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein						proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		TTGGCTGTGGAAGGTAGAGTT	0.468													4	2	---	---	---	---	
ASPDH	554235	broad.mit.edu	37	19	51015274	51015277	+	Intron	DEL	AGAA	-	-	rs35220044		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51015274_51015277delAGAA	uc010enz.2	-						JOSD2_uc002psn.1_5'Flank|JOSD2_uc002pso.1_5'Flank|JOSD2_uc002psp.1_5'Flank|JOSD2_uc002psq.1_5'Flank|ASPDH_uc002psr.3_Intron	NM_001114598	NP_001108070	A6ND91	ASPD_HUMAN	aspartate dehydrogenase isoform 1						NAD biosynthetic process|NADP catabolic process		aspartate dehydrogenase activity|NADP binding				0						AATAAAGGTCAGAAAGAAAGAAAG	0.515													6	6	---	---	---	---	
ZNF766	90321	broad.mit.edu	37	19	52789441	52789442	+	Intron	INS	-	C	C	rs149933354	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52789441_52789442insC	uc002pyr.1	+						ZNF766_uc002pys.1_Intron|ZNF766_uc002pyt.1_Intron	NM_001010851	NP_001010851	Q5HY98	ZN766_HUMAN	zinc finger protein 766						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		AGTGGGCTTTTCCCCcctaatt	0.168													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	58937562	58937562	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58937562delG								ZNF584 (7872 upstream) : ZNF132 (6620 downstream)																							GGCTGGGGCTGGGGGTAGAGG	0.527													4	2	---	---	---	---	
TRIM28	10155	broad.mit.edu	37	19	59061999	59062000	+	3'UTR	INS	-	G	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59061999_59062000insG	uc002qtg.1	+	17					TRIM28_uc010eut.1_3'UTR|TRIM28_uc002qth.1_3'UTR	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein						epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		TGGTGGCCTGACTCCCACTCCC	0.594													4	2	---	---	---	---	
FAM110A	83541	broad.mit.edu	37	20	832704	832705	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:832704_832705delTG	uc010fzz.2	+									Q9BQ89	F110A_HUMAN	Homo sapiens F10 mRNA for hypothetical protein, complete cds.							microtubule organizing center|spindle pole	protein binding				0						GCtgtgtgtatgtgtgtgtgtg	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4096342	4096342	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4096342delT								RNF24 (100126 upstream) : SMOX (33108 downstream)																							cccctcaatatttttttccct	0.000													4	2	---	---	---	---	
PAK7	57144	broad.mit.edu	37	20	9683311	9683311	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9683311delT	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			TTCTCCCCTGTTATCCAAACT	0.264													4	2	---	---	---	---	
C20orf94	128710	broad.mit.edu	37	20	10466993	10466994	+	Intron	INS	-	AG	AG	rs143408998	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10466993_10466994insAG	uc010zre.1	+							NM_001009608	NP_001009608	Q5VYV7	CT094_HUMAN	hypothetical protein LOC128710								protein binding				0						TTACCATGCACAGAGTGGTTAG	0.396													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24122597	24122597	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24122597delT								GGTLC1 (153181 upstream) : TMEM90B (327238 downstream)																							TCTCTCACACTTTTTAAGGTC	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25864547	25864548	+	IGR	INS	-	A	A	rs62214090	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25864547_25864548insA								FAM182B (15761 upstream) : LOC100134868 (125887 downstream)																							CCATGGGCTTCGTTTTTGTATT	0.337													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26122909	26122909	+	IGR	DEL	C	-	-	rs1937058		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26122909delC								C20orf191 (28232 upstream) : MIR663 (65913 downstream)																							tcttttttttcttttgcaaga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29597565	29597566	+	IGR	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29597565_29597566delTT								None (None upstream) : FRG1B (14313 downstream)																							ttttataaacttgttctaaaaa	0.129													4	2	---	---	---	---	
MYLK2	85366	broad.mit.edu	37	20	30414936	30414936	+	Intron	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30414936delG	uc002wwq.2	+						MYLK2_uc002wws.2_Intron	NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase						cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			aagagagagagggggggaaaa	0.114													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31167059	31167060	+	Intron	DEL	CA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31167059_31167060delCA	uc002wxx.2	-											SubName: Full=LOC284804 protein; Flags: Fragment;																		acactccacgcacacacacaca	0.292													4	2	---	---	---	---	
ITCH	83737	broad.mit.edu	37	20	33053846	33053847	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33053846_33053847insC	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron|MIR644_hsa-mir-644|MI0003659_5'Flank	NM_031483	NP_113671	Q96J02	ITCH_HUMAN	itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6						ctgttagatttttatatgtgcc	0.000													6	3	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47353356	47353359	+	Intron	DEL	TGAC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47353356_47353359delTGAC	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGACTTGCAGTGACATAAAAAGCC	0.407													4	2	---	---	---	---	
SNAI1	6615	broad.mit.edu	37	20	48599943	48599943	+	Intron	DEL	G	-	-	rs113706921		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48599943delG	uc002xuz.2	+							NM_005985	NP_005976	O95863	SNAI1_HUMAN	snail 1 homolog						epithelial to mesenchymal transition|mesoderm formation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|zinc ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CTCCGCAAGAGGGGAAGGAGA	0.667													4	2	---	---	---	---	
TMEM189-UBE2V1	387522	broad.mit.edu	37	20	48706677	48706677	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48706677delT	uc002xvf.2	-						UBE2V1_uc002xvb.2_Intron|UBE2V1_uc002xva.2_Intron|UBE2V1_uc002xvc.2_Intron|UBE2V1_uc002xvd.2_Intron|UBE2V1_uc002xve.2_Intron	NM_199203	NP_954673	Q13404	UB2V1_HUMAN	TMEM189-UBE2V1 readthrough transcript						cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein K63-linked ubiquitination|regulation of DNA repair|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-UEV1A complex|ubiquitin ligase complex	acid-amino acid ligase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			ccttctttgattttttagtcc	0.020													4	2	---	---	---	---	
PTPN1	5770	broad.mit.edu	37	20	49130431	49130431	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49130431delA	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)	CACTTCACTTAAAAAAAAAAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53539771	53539771	+	IGR	DEL	T	-	-	rs11476909		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53539771delT								DOK5 (272062 upstream) : None (None downstream)																							ATAtatttcatcaaaattaag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53653538	53653538	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53653538delC								DOK5 (385829 upstream) : CBLN4 (918959 downstream)																							tggaaaatggccagttagctt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55956902	55956903	+	IGR	INS	-	CTGT	CTGT	rs148400568	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55956902_55956903insCTGT								RAE1 (3384 upstream) : RBM38 (9560 downstream)																							ATGGGGCTGTGCTGTCGGTATA	0.406											OREG0026063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56031577	56031578	+	IGR	INS	-	TTTTG	TTTTG	rs138213018	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56031577_56031578insTTTTG								RBM38 (47193 upstream) : CTCFL (32302 downstream)																							acttgactcctttttgttttgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56521611	56521614	+	IGR	DEL	CAAA	-	-	rs112417611		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56521611_56521614delCAAA								PMEPA1 (235070 upstream) : C20orf85 (204369 downstream)																							TTCATCATCCCAAACAGATTTTAG	0.485													2	4	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60464350	60464353	+	Intron	DEL	ATGG	-	-	rs113089640		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60464350_60464353delATGG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TCTTTAAAGCatggatggatggat	0.225													2	4	---	---	---	---	
OSBPL2	9885	broad.mit.edu	37	20	60848040	60848041	+	Intron	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60848040_60848041delGT	uc002yck.1	+						OSBPL2_uc002ycl.1_Intron|OSBPL2_uc011aah.1_Intron	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform						lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			agtgcttggggtgtgtgtgttg	0.208													4	2	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60903684	60903686	+	Intron	DEL	CAT	-	-	rs71884793		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60903684_60903686delCAT	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCAGAATCAACATCATCGTCAGA	0.635													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61715967	61715968	+	RNA	INS	-	C	C	rs139661993	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61715967_61715968insC	uc002yec.1	+	4		c.2952_2953insC								Homo sapiens cDNA FLJ46471 fis, clone THYMU3023394.																		CGGACCACCAGCCCCCCTTCAC	0.574													2	6	---	---	---	---	
SRMS	6725	broad.mit.edu	37	20	62177661	62177663	+	Intron	DEL	GAT	-	-	rs73611618		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62177661_62177663delGAT	uc002yfi.1	-							NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory								ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|lung(1)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CCCCCAGGACGATGTGTGAGTGC	0.675													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10753559	10753559	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10753559delA								None (None upstream) : TPTE (153184 downstream)																							atctagacagaagcaatctga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10793289	10793289	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10793289delA								None (None upstream) : TPTE (113454 downstream)																							aattgagtggaatggaatgga	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11089002	11089002	+	Intron	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11089002delC	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)		ATAAAAAATACTTTAAAATAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11131530	11131530	+	IGR	DEL	T	-	-	rs111915958		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11131530delT								BAGE (32593 upstream) : None (None downstream)																							ACAGGGTCTCTTTGGGATGAT	0.279													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11177870	11177871	+	IGR	INS	-	G	G	rs140577992		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11177870_11177871insG								BAGE (78933 upstream) : None (None downstream)																							ccgaggcaggcggatcacctga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32227690	32227691	+	IGR	INS	-	A	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32227690_32227691insA								KRTAP7-1 (25639 upstream) : KRTAP11-1 (25275 downstream)																							CCTGCAAAGTCAAAATGGCCAG	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34304539	34304539	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34304539delT								C21orf62 (118486 upstream) : OLIG2 (93700 downstream)																							atcccagcactttgggaggcc	0.164													4	2	---	---	---	---	
SLC5A3	6526	broad.mit.edu	37	21	35459751	35459751	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35459751delA	uc002yto.2	+						MRPS6_uc002ytp.2_Intron	NM_006933	NP_008864	P53794	SC5A3_HUMAN	solute carrier family 5 (inositol transporters),							integral to plasma membrane	myo-inositol:sodium symporter activity			ovary(2)	2						aggacacatcagggaacaaca	0.050													4	2	---	---	---	---	
KCNJ6	3763	broad.mit.edu	37	21	39215035	39215035	+	Intron	DEL	C	-	-	rs66659935		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39215035delC	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	GAGCCTCTTACCACAATGCCG	0.537													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39728425	39728426	+	IGR	DEL	AC	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39728425_39728426delAC								KCNJ15 (54681 upstream) : ERG (23526 downstream)																							caccagagatacacacacacac	0.149											OREG0026215	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41538228	41538228	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41538228delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AAGAGACAAGAAAAAAAATCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42370610	42370610	+	IGR	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42370610delT								DSCAM (151571 upstream) : C21orf130 (142817 downstream)																							tagctgtaggttttttttttt	0.000													4	2	---	---	---	---	
TMPRSS2	7113	broad.mit.edu	37	21	42883262	42883262	+	Intron	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42883262delA	uc010gos.1	-							NM_005656	NP_005647	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 2						proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24)	prostate(2523)|central_nervous_system(1)	2524		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				gcatacaaccaaaaaatgcac	0.000			T	ERG|ETV1|ETV4|ETV5	prostate 								4	2	---	---	---	---	
DIP2A	23181	broad.mit.edu	37	21	47905150	47905151	+	Intron	DEL	TG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47905150_47905151delTG	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	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)		caataggttttgtgtgtgtgtg	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16601841	16601844	+	IGR	DEL	GTGA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16601841_16601844delGTGA								OR11H1 (152037 upstream) : CCT8L2 (469804 downstream)																							ctgctgggttgtgagtgtttgtca	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16929133	16929133	+	IGR	DEL	G	-	-	rs113117133		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16929133delG								OR11H1 (479329 upstream) : CCT8L2 (142515 downstream)																							gtaggcttcagaaggttggta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17512710	17512711	+	IGR	DEL	TT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17512710_17512711delTT								GAB4 (23598 upstream) : CECR7 (4749 downstream)																							TTTCTGCTAATTTTTTTTTTTT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20064143	20064144	+	IGR	INS	-	AGGAG	AGGAG	rs143475645	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20064143_20064144insAGGAG								C22orf25 (10696 upstream) : DGCR8 (3690 downstream)																							atcagccagtcagaagacaaag	0.005													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22657416	22657419	+	Intron	DEL	ACTA	-	-	rs138873705		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22657416_22657419delACTA	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0						ATGATGAAATACTAACTGTTTTAC	0.402													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22808841	22808841	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22808841delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						cgtttttcccttaagggaagt	0.000													4	2	---	---	---	---	
PIWIL3	440822	broad.mit.edu	37	22	25144620	25144620	+	Intron	DEL	T	-	-	rs35486129		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25144620delT	uc003abd.1	-						PIWIL3_uc011ajx.1_Intron|PIWIL3_uc011ajy.1_Intron|PIWIL3_uc010gut.1_Intron	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3						cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4						TAAGGATATATTTGAAAAAAT	0.269													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25648761	25648761	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25648761delA								CRYBB2 (20925 upstream) : IGLL3 (65127 downstream)																							tgggaggcagaggtgggcaga	0.000													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33685362	33685363	+	Intron	DEL	CT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33685362_33685363delCT	uc003and.3	-						LARGE_uc011amd.1_Intron|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)				ctgactgctcctctctctcctg	0.045													4	2	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37066324	37066325	+	Intron	INS	-	C	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37066324_37066325insC	uc003aps.1	-							NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						GCCAGTTCATTTTTGAAACCCA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37355016	37355016	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37355016delA								CSF2RB (18539 upstream) : C22orf33 (32145 downstream)																							GCACAGAGTTAGCACTTGAAA	0.353													4	2	---	---	---	---	
APOBEC3G	60489	broad.mit.edu	37	22	39475886	39475886	+	Intron	DEL	A	-	-	rs113088243		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39475886delA	uc003awx.2	+						APOBEC3G_uc003awy.2_5'UTR	NM_021822	NP_068594	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						base conversion or substitution editing|DNA cytosine deamination|innate immune response|interspecies interaction between organisms|negative regulation of retroviral genome replication|negative regulation of transposition|positive regulation of defense response to virus by host|response to virus|viral reproduction	apolipoprotein B mRNA editing enzyme complex|cytosol|mitochondrion	cytidine deaminase activity|dCTP deaminase activity|protein homodimerization activity|RNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2	Melanoma(58;0.04)					ctaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	39707782	39707785	+	IGR	DEL	CAGA	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39707782_39707785delCAGA								PDGFB (66825 upstream) : RPL3 (1103 downstream)																							AACAGAGACTCAGACACACAGTTA	0.588													6	7	---	---	---	---	
RANGAP1	5905	broad.mit.edu	37	22	41666944	41666944	+	Intron	DEL	G	-	-	rs34333301		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41666944delG	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						CTAATGAgctgaacagtcagc	0.279													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44264896	44264896	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44264896delA								SULT4A1 (6518 upstream) : PNPLA5 (10663 downstream)																							tgagatagagaaaaggggaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47964938	47964939	+	IGR	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47964938_47964939delAG								TBC1D22A (395216 upstream) : FAM19A5 (920349 downstream)																							gtatgcacctagtttcaccgtg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48344817	48344817	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48344817delA								TBC1D22A (775095 upstream) : FAM19A5 (540471 downstream)																							accctttgggaaaaggtgaga	0.000													4	2	---	---	---	---	
TUBGCP6	85378	broad.mit.edu	37	22	50683032	50683033	+	5'UTR	INS	-	T	T	rs150242575	by1000genomes	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50683032_50683033insT	uc003bkb.1	-	1					TUBGCP6_uc010har.1_5'UTR|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hau.1_5'UTR	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CAGAACTGGTATTTTTTAAAGG	0.609													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	561597	561598	+	IGR	INS	-	CT	CT			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:561597_561598insCT								PPP2R3B (213970 upstream) : SHOX (23481 downstream)																							GCAGACTGTCACTGGGGAGCCT	0.455													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5661618	5661618	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5661618delC								None (None upstream) : NLGN4X (146466 downstream)																							aatctgttgtcccactccaca	0.124													4	2	---	---	---	---	
SYAP1	94056	broad.mit.edu	37	X	16772851	16772851	+	Intron	DEL	A	-	-	rs34569073		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16772851delA	uc004cxp.2	+						SYAP1_uc004cxo.2_Intron|SYAP1_uc011miv.1_Intron	NM_032796	NP_116185	Q96A49	SYAP1_HUMAN	SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)					actccgtgtcaaaaaaaaaaa	0.189													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	66381310	66381311	+	IGR	DEL	AG	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66381310_66381311delAG								EDA2R (522202 upstream) : AR (382563 downstream)																							ccacacacacagacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	77587447	77587448	+	IGR	DEL	GT	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77587447_77587448delGT								CYSLTR1 (4360 upstream) : ZCCHC5 (324118 downstream)																							GAGTCTGCGGGTGTGTGTGGTC	0.515													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	79732312	79732312	+	IGR	DEL	G	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79732312delG								FAM46D (31502 upstream) : BRWD3 (199371 downstream)																							GAAGATTGCTGGGGGTTTTTA	0.443													4	2	---	---	---	---	
TMEM164	84187	broad.mit.edu	37	X	109350274	109350274	+	Intron	DEL	T	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109350274delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3						CCAAACAGCCTTTTCCACTTT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	133301110	133301110	+	IGR	DEL	A	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133301110delA								GPC3 (181444 upstream) : MIR363 (2298 downstream)																							TGAAATGTTCAAAAAAAAAAA	0.269													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13199593	13199593	+	IGR	DEL	C	-	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13199593delC								None (None upstream) : None (None downstream)																							CATCACCTCTCCCAAAGGACA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13401240	13401241	+	IGR	INS	-	T	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13401240_13401241insT								None (None upstream) : None (None downstream)																							cttttttcatgtttttttaagt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13430917	13430918	+	IGR	INS	-	AA	AA			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13430917_13430918insAA								None (None upstream) : None (None downstream)																							TTTAAACTTGGAAAAAATTGAA	0.361													5	3	---	---	---	---	
