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
KIAA0562	9731	broad.mit.edu	37	1	3755638	3755638	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3755638C>T	uc001aky.2	-	8	1140	c.781G>A	c.(781-783)GTG>ATG	p.V261M	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Missense_Mutation_p.V261M	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	261	Potential.					centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		TCCTTCTCCACGGCACAGCGT	0.493													4	117	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27106138	27106138	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27106138A>G	uc001bmv.1	+	20	6122	c.5749A>G	c.(5749-5751)ACT>GCT	p.T1917A	ARID1A_uc001bmu.1_Missense_Mutation_p.T1700A|ARID1A_uc001bmx.1_Missense_Mutation_p.T763A|ARID1A_uc009vsm.1_Missense_Mutation_p.T245A|ARID1A_uc009vsn.1_Missense_Mutation_p.T159A	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1917					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CATGTTGTCTACTCGGTCTAG	0.547			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								3	29	---	---	---	---	PASS
SF3A3	10946	broad.mit.edu	37	1	38455264	38455264	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38455264G>A	uc001cci.2	-	2	224	c.100C>T	c.(100-102)CGG>TGG	p.R34W	SF3A3_uc010oik.1_Missense_Mutation_p.R34W	NM_006802	NP_006793	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3	34					nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ATCTGGTCCCGGAGCTGAAAA	0.567													4	52	---	---	---	---	PASS
ZCCHC11	23318	broad.mit.edu	37	1	52937624	52937624	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52937624C>T	uc001ctx.2	-	14	3112	c.2878G>A	c.(2878-2880)GAT>AAT	p.D960N	ZCCHC11_uc001cty.2_Missense_Mutation_p.D960N|ZCCHC11_uc001ctz.2_Missense_Mutation_p.D960N|ZCCHC11_uc009vze.1_Missense_Mutation_p.D960N|ZCCHC11_uc009vzf.1_Missense_Mutation_p.D719N|ZCCHC11_uc001cub.2_Missense_Mutation_p.D960N	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	960					miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						AAAGACTTACCAAAACATCTT	0.299													5	249	---	---	---	---	PASS
CSDE1	7812	broad.mit.edu	37	1	115282361	115282361	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115282361A>G	uc001efk.2	-	3	617	c.151T>C	c.(151-153)TTC>CTC	p.F51L	CSDE1_uc001efi.2_Missense_Mutation_p.F97L|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_Missense_Mutation_p.F51L|CSDE1_uc001efm.2_Missense_Mutation_p.F97L|CSDE1_uc009wgv.2_Missense_Mutation_p.F51L|CSDE1_uc001efn.2_Missense_Mutation_p.F51L	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	51	CSD 1.				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAACAGTGGAAGAAAAGTCTA	0.378													7	240	---	---	---	---	PASS
GDAP2	54834	broad.mit.edu	37	1	118461355	118461355	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118461355T>C	uc001ehf.2	-	3	479	c.180A>G	c.(178-180)AAA>AAG	p.K60K	GDAP2_uc001ehg.2_Silent_p.K60K	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	60	Macro.									ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		CCACATCTCCTTTCCTGAAGA	0.348													6	217	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152059140	152059140	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152059140C>T	uc001ezo.1	-	3	1083	c.1018G>A	c.(1018-1020)GCT>ACT	p.A340T		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	340							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			GTCTGGTCAGCATCCTTTCCT	0.453													6	373	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186281887	186281887	+	3'UTR	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186281887C>A	uc001grv.2	-	51					PRG4_uc001gru.3_Intron|PRG4_uc001grt.3_Intron|PRG4_uc009wyl.2_Intron|PRG4_uc009wym.2_Intron|PRG4_uc010poo.1_Intron	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTTATTAAACATGCCACTTA	0.378			T	NTRK1	papillary thyroid								51	286	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226564967	226564967	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226564967C>A	uc001hqd.3	-	13	1954	c.1783G>T	c.(1783-1785)GTG>TTG	p.V595L		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1	595					cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CTACCGATCACCGTACCCACA	0.512								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					5	136	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50724564	50724564	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50724564A>G	uc010fbq.2	-	14	4383	c.2906T>C	c.(2905-2907)CTT>CCT	p.L969P	NRXN1_uc002rxb.3_Missense_Mutation_p.L601P|NRXN1_uc002rxe.3_Missense_Mutation_p.L929P|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTGGAAAAAAAGATGCATAGA	0.393													6	260	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102460601	102460601	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102460601G>A	uc002tbg.2	+	12	1116	c.1061G>A	c.(1060-1062)CGA>CAA	p.R354Q	MAP4K4_uc002tbc.2_Missense_Mutation_p.R354Q|MAP4K4_uc002tbd.2_Missense_Mutation_p.R354Q|MAP4K4_uc002tbe.2_Missense_Mutation_p.R354Q|MAP4K4_uc002tbf.2_Missense_Mutation_p.R354Q|MAP4K4_uc010yvy.1_Missense_Mutation_p.R354Q|MAP4K4_uc002tbh.2_Missense_Mutation_p.R354Q|MAP4K4_uc002tbi.2_Missense_Mutation_p.R207Q|MAP4K4_uc010yvz.1_Missense_Mutation_p.R334Q|MAP4K4_uc002tbk.2_5'UTR|MAP4K4_uc002tbj.1_Missense_Mutation_p.R250Q	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	354					intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						ACTCTTCGCCGAGATTTCCTG	0.512													42	87	---	---	---	---	PASS
TMEM37	140738	broad.mit.edu	37	2	120194742	120194742	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120194742T>C	uc002tly.2	+	2	333	c.299T>C	c.(298-300)GTG>GCG	p.V100A		NM_183240	NP_899063	Q8WXS4	CCGL_HUMAN	transmembrane protein 37	100	Helical; (Potential).					integral to membrane	calcium channel activity|voltage-gated ion channel activity			breast(1)	1						TTGGCCGTGGTGGCCGCCATT	0.632													4	19	---	---	---	---	PASS
ZRANB3	84083	broad.mit.edu	37	2	135966529	135966529	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135966529C>G	uc002tum.2	-	18	2632	c.2515G>C	c.(2515-2517)GTT>CTT	p.V839L	ZRANB3_uc002tuk.2_Missense_Mutation_p.V382L|ZRANB3_uc002tul.2_Missense_Mutation_p.V837L	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	839						intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		GCTACGGCAACATCTTCTTTG	0.393													52	162	---	---	---	---	PASS
LY75	4065	broad.mit.edu	37	2	160636594	160636594	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160636594G>T	uc002ubb.3	-	37	5383	c.5314C>A	c.(5314-5316)CTG>ATG	p.L1772M	LY75_uc010fos.2_Missense_Mutation_p.L1716M|CD302_uc002uba.2_Missense_Mutation_p.L131M|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor	1638	Extracellular (Potential).|C-type lectin 10.				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TTGATGTGCAGAAAAGCACAG	0.383													20	339	---	---	---	---	PASS
METTL5	29081	broad.mit.edu	37	2	170668934	170668934	+	Intron	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170668934C>T	uc002ufn.2	-						METTL5_uc002ufo.2_Intron|METTL5_uc002ufp.2_Intron|METTL5_uc002ufq.1_Silent_p.S208S	NM_014168	NP_054887	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity|nucleic acid binding			central_nervous_system(1)	1						TTTTCAATACCGAATGTAGAC	0.229													6	298	---	---	---	---	PASS
ACADL	33	broad.mit.edu	37	2	211070458	211070458	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211070458T>C	uc002vdz.3	-	6	894	c.666A>G	c.(664-666)GAA>GAG	p.E222E		NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor	222					carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		GGGAGGGAGCTTCATGATTTG	0.408													8	366	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238277320	238277320	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238277320C>T	uc002vwl.2	-	10	5071	c.4786G>A	c.(4786-4788)GTG>ATG	p.V1596M	COL6A3_uc002vwo.2_Missense_Mutation_p.V1390M|COL6A3_uc010znj.1_Missense_Mutation_p.V989M	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1596	VWFA 8.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AACTCTCGCACTGTGAAGACC	0.552													27	73	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191572	10191572	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191572G>T	uc003bvc.2	+	3	778	c.565G>T	c.(565-567)GAA>TAA	p.E189*	VHL_uc003bvd.2_Nonsense_Mutation_p.E148*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	189					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.E189K(3)|p.E189fs*12(2)|p.D187_N193del(1)|p.E189fs*27(1)|p.E189fs*25(1)|p.Y185fs*11(1)|p.E189fs*13(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)		CGAAGATCTGGAAGACCACCC	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				16	42	---	---	---	---	PASS
IP6K1	9807	broad.mit.edu	37	3	49775709	49775709	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49775709G>A	uc003cxm.1	-	3	685	c.370C>T	c.(370-372)CGG>TGG	p.R124W	IP6K1_uc003cxn.1_5'UTR|IP6K1_uc011bcv.1_5'UTR|IP6K1_uc003cxo.2_Missense_Mutation_p.R124W	NM_153273	NP_695005	Q92551	IP6K1_HUMAN	inositol hexakisphosphate kinase 1 isoform 1	124					phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0						CTGCCTGACCGGTGCAGGCTC	0.557													5	33	---	---	---	---	PASS
CHMP2B	25978	broad.mit.edu	37	3	87302584	87302584	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87302584G>A	uc003dqp.3	+	5	715	c.455G>A	c.(454-456)GGT>GAT	p.G152D	CHMP2B_uc011bgn.1_Missense_Mutation_p.G111D	NM_014043	NP_054762	Q9UQN3	CHM2B_HUMAN	chromatin modifying protein 2B	152					cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane|mitochondrion|nucleus	protein domain specific binding			skin(2)|ovary(1)	3	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		ATCTTTGACGGTTCTGATGAC	0.358													131	167	---	---	---	---	PASS
FAM194A	131831	broad.mit.edu	37	3	150384662	150384662	+	Missense_Mutation	SNP	C	A	A	rs150155678		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150384662C>A	uc003eyg.2	-	13	1697	c.1640G>T	c.(1639-1641)GGA>GTA	p.G547V	FAM194A_uc003eyh.2_Missense_Mutation_p.G401V	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	547										skin(2)|ovary(1)	3						GATGCGGACTCCAATATAACG	0.413													132	319	---	---	---	---	PASS
RARRES1	5918	broad.mit.edu	37	3	158415529	158415529	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158415529C>G	uc003fci.2	-	6	894	c.823G>C	c.(823-825)GAA>CAA	p.E275Q		NM_206963	NP_996846	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene	275	Extracellular (Potential).				negative regulation of cell proliferation	integral to membrane					0			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	GAGGCTTCTTCTGGTGTCTGT	0.413													131	354	---	---	---	---	PASS
MUC20	200958	broad.mit.edu	37	3	195447805	195447805	+	5'UTR	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195447805T>C	uc010hzo.2	+	1						NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CCCTCCTCCCTGGTTTGAGGA	0.627													6	32	---	---	---	---	PASS
UBA6	55236	broad.mit.edu	37	4	68501215	68501215	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68501215T>C	uc003hdg.3	-	20	1850	c.1798A>G	c.(1798-1800)ACT>GCT	p.T600A	UBA6_uc003hdh.1_Missense_Mutation_p.T126A	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2	600					protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						ATAACTTCAGTGTGTCCCTTA	0.328													6	309	---	---	---	---	PASS
NHEDC2	133308	broad.mit.edu	37	4	103988700	103988700	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103988700T>C	uc003hwx.3	-	2	880	c.8A>G	c.(7-9)GAT>GGT	p.D3G	NHEDC2_uc003hwy.2_Missense_Mutation_p.D3G|NHEDC2_uc011cew.1_Missense_Mutation_p.D3G|NHEDC2_uc011cex.1_Missense_Mutation_p.D3G|NHEDC2_uc011cey.1_Missense_Mutation_p.D3G	NM_178833	NP_849155	Q86UD5	NHDC2_HUMAN	Na+/H+ exchanger domain containing 2	3					sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)		TTTATCTTCATCCCCCATTAT	0.358													150	361	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175896768	175896768	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175896768C>T	uc003iuc.2	+	5	762	c.92C>T	c.(91-93)CCG>CTG	p.P31L	ADAM29_uc003iud.2_Missense_Mutation_p.P31L|ADAM29_uc010irr.2_Missense_Mutation_p.P31L|ADAM29_uc011cki.1_Missense_Mutation_p.P31L	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	31			P -> L (in a colorectal cancer sample; somatic mutation).		proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding	p.P31L(1)		skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CACAGCCCTCCGGATGTGGTG	0.517													17	61	---	---	---	---	PASS
FASTKD3	79072	broad.mit.edu	37	5	7867988	7867988	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7867988C>T	uc003jeb.2	-	2	346	c.209G>A	c.(208-210)GGA>GAA	p.G70E	FASTKD3_uc011cmp.1_Intron|FASTKD3_uc003jec.2_Intron|MTRR_uc010itn.1_5'Flank|MTRR_uc003jee.3_5'Flank|MTRR_uc003jed.2_5'Flank|MTRR_uc003jef.3_5'Flank|MTRR_uc003jeg.3_5'Flank|MTRR_uc010ito.2_5'Flank	NM_024091	NP_076996	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	70					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4						AAGGTCATTTCCATTTTTCGA	0.443													22	102	---	---	---	---	PASS
CTNND2	1501	broad.mit.edu	37	5	10973694	10973694	+	Silent	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10973694G>A	uc003jfa.1	-	22	3694	c.3549C>T	c.(3547-3549)AGC>AGT	p.S1183S	CTNND2_uc010itt.2_Silent_p.S1092S|CTNND2_uc011cmy.1_Silent_p.S846S|CTNND2_uc011cmz.1_Silent_p.S750S|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Silent_p.S775S	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1183					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						TGGTGTACTCGCTGGCGGGAG	0.522													5	105	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32088407	32088407	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32088407C>A	uc003jhl.2	+	20	5241	c.4853C>A	c.(4852-4854)CCC>CAC	p.P1618H	PDZD2_uc003jhm.2_Missense_Mutation_p.P1618H	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1618					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GCTCATCTTCCCACCCAGGCT	0.552													16	42	---	---	---	---	PASS
UGT3A1	133688	broad.mit.edu	37	5	35988568	35988568	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35988568T>C	uc003jjv.1	-	2	337	c.180A>G	c.(178-180)GGA>GGG	p.G60G	UGT3A1_uc003jjw.1_RNA|UGT3A1_uc011coq.1_Silent_p.G60G|UGT3A1_uc011cor.1_Intron|UGT3A1_uc003jjy.1_Silent_p.G6G	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	60	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCAAAAACTTTCCACTCTGAT	0.338													6	248	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45262590	45262590	+	Silent	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262590C>T	uc003jok.2	-	8	2131	c.2106G>A	c.(2104-2106)GCG>GCA	p.A702A		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	702	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						GGCTGCAGACCGCGGTGGTGT	0.587													17	36	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127664442	127664442	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127664442G>A	uc003kuu.2	-	34	4856	c.4417C>T	c.(4417-4419)CGC>TGC	p.R1473C	FBN2_uc003kuv.2_Missense_Mutation_p.R1440C	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1473	EGF-like 24; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CACTCGCAGCGATATGCACCC	0.478													106	100	---	---	---	---	PASS
PCDHB6	56130	broad.mit.edu	37	5	140530050	140530050	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140530050G>C	uc003lir.2	+	1	212	c.212G>C	c.(211-213)AGA>ACA	p.R71T	PCDHB6_uc011dah.1_Intron	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	71	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAAGGGAACAGACAACATTTG	0.537													31	135	---	---	---	---	PASS
PCDHB7	56129	broad.mit.edu	37	5	140553198	140553198	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140553198T>C	uc003lit.2	+	1	956	c.782T>C	c.(781-783)GTT>GCT	p.V261A		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	261	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTTCCATGGTTGTCTCCGTG	0.473													7	98	---	---	---	---	PASS
DPYSL3	1809	broad.mit.edu	37	5	146798117	146798117	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146798117C>A	uc003lon.1	-	3	316	c.206G>T	c.(205-207)GGC>GTC	p.G69V	DPYSL3_uc003loo.2_Missense_Mutation_p.G183V	NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	69					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)			GACATCGATGCCTCCAGGGAT	0.473													52	192	---	---	---	---	PASS
HTR4	3360	broad.mit.edu	37	5	147928374	147928374	+	Silent	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147928374C>A	uc003lpn.2	-	4	374	c.210G>T	c.(208-210)TCG>TCT	p.S70S	HTR4_uc010jgu.1_RNA|HTR4_uc003lpi.1_Silent_p.S70S|HTR4_uc003lpj.1_Silent_p.S70S|HTR4_uc003lpk.2_Silent_p.S70S|HTR4_uc011dby.1_Silent_p.S70S|HTR4_uc003lpl.2_Silent_p.S70S|HTR4_uc003lpm.2_Silent_p.S70S|HTR4_uc010jgv.2_RNA|HTR4_uc003lpo.1_Silent_p.S70S	NM_000870	NP_000861	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform b	70	Helical; Name=2; (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)	TCACCAGCACCGAAACCAGCA	0.383													6	314	---	---	---	---	PASS
C5orf47	133491	broad.mit.edu	37	5	173426710	173426710	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173426710T>G	uc003mcw.3	+	3	524	c.419T>G	c.(418-420)GTA>GGA	p.V140G	C5orf47_uc003mcv.2_Intron	NM_001144954	NP_001138426	Q569G3	CE047_HUMAN	hypothetical protein LOC133491	140											0						AAGGTTTTAGTATGGAATAGA	0.338													138	519	---	---	---	---	PASS
KIF13A	63971	broad.mit.edu	37	6	17987359	17987359	+	Silent	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17987359G>A	uc003ncg.3	-	2	177	c.72C>T	c.(70-72)ACC>ACT	p.T24T	KIF13A_uc003ncf.2_Silent_p.T24T|KIF13A_uc003nch.3_Silent_p.T24T|KIF13A_uc003nci.3_Silent_p.T24T|KIF13A_uc003nck.2_RNA	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	24	Kinesin-motor.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CCACGCACTTGGTGTTCAGTT	0.612													5	157	---	---	---	---	PASS
PTK7	5754	broad.mit.edu	37	6	43107148	43107148	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43107148G>C	uc003oub.1	+	10	1701	c.1503G>C	c.(1501-1503)AAG>AAC	p.K501N	PTK7_uc003ouc.1_Missense_Mutation_p.K501N|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Missense_Mutation_p.K509N|PTK7_uc010jyj.1_Intron	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	501	Extracellular (Potential).				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AAACAGAAAAGCTCAAGTTCA	0.597													18	32	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90573378	90573378	+	Silent	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90573378A>G	uc003pnr.2	+	7	2146	c.1950A>G	c.(1948-1950)GAA>GAG	p.E650E	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Silent_p.E650E|CASP8AP2_uc011dzz.1_Silent_p.E650E	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	650					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTATCTCAGAAACCAACAAGG	0.443													5	83	---	---	---	---	PASS
GRIK2	2898	broad.mit.edu	37	6	102266328	102266328	+	Silent	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102266328C>T	uc003pqp.3	+	9	1536	c.1287C>T	c.(1285-1287)TCC>TCT	p.S429S	GRIK2_uc003pqn.2_Silent_p.S429S|GRIK2_uc003pqo.3_Silent_p.S429S|GRIK2_uc010kcw.2_Silent_p.S429S	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	429	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)	ATTCCTTATCCAATCGTTCTT	0.373													5	319	---	---	---	---	PASS
PMS2	5395	broad.mit.edu	37	7	6026491	6026491	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6026491T>C	uc003spl.2	-	11	1992	c.1905A>G	c.(1903-1905)GAA>GAG	p.E635E	PMS2_uc003spj.2_Silent_p.E529E|PMS2_uc003spk.2_Silent_p.E500E|PMS2_uc011jwl.1_Silent_p.E500E|PMS2_uc010ktg.2_Silent_p.E324E|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Intron	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	635					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TTTGCTGTGCTTCATGATGTA	0.388			Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				10	435	---	---	---	---	PASS
PDE1C	5137	broad.mit.edu	37	7	31855612	31855612	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31855612C>T	uc003tcm.1	-	15	2208	c.1739G>A	c.(1738-1740)CGG>CAG	p.R580Q	PDE1C_uc003tcn.1_Missense_Mutation_p.R580Q|PDE1C_uc003tco.1_Missense_Mutation_p.R640Q|PDE1C_uc003tcr.2_Missense_Mutation_p.R580Q|PDE1C_uc003tcs.2_Missense_Mutation_p.R580Q	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	580					activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			TTTGTTTGCCCGTGTTCCATT	0.468													6	518	---	---	---	---	PASS
STEAP1	26872	broad.mit.edu	37	7	89791288	89791288	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89791288G>T	uc003ujx.2	+	4	858	c.658G>T	c.(658-660)GTG>TTG	p.V220L	STEAP1_uc010lem.2_Missense_Mutation_p.V220L	NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	220	Ferric oxidoreductase.|Helical; (Potential).				electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)					GGAGATTTATGTGTCTCTGGG	0.393													100	564	---	---	---	---	PASS
ZCWPW1	55063	broad.mit.edu	37	7	100014766	100014766	+	Silent	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100014766G>A	uc003uut.2	-	6	650	c.402C>T	c.(400-402)GCC>GCT	p.A134A	ZCWPW1_uc011kjq.1_Silent_p.A13A|ZCWPW1_uc003uur.2_Silent_p.A13A|ZCWPW1_uc003uus.2_Silent_p.A13A|ZCWPW1_uc011kjr.1_Silent_p.A133A|ZCWPW1_uc003uuu.1_Silent_p.A133A|ZCWPW1_uc011kjs.1_Silent_p.A13A	NM_017984	NP_060454	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	134							zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTACGGGCTGGGCACAAGAAG	0.418													5	238	---	---	---	---	PASS
NAPEPLD	222236	broad.mit.edu	37	7	102782275	102782275	+	Intron	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102782275G>A	uc003vbc.2	-						NAPEPLD_uc003vbd.2_Intron|NAPEPLD_uc011klj.1_Intron|NAPEPLD_uc003vbe.2_Intron|NAPEPLD_uc003vbf.2_Intron|RPL19P12_uc011klk.1_RNA	NM_198990	NP_945341	Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D						phospholipid catabolic process	membrane	metal ion binding			skin(1)	1						ATCTGCTGACGGGAGTTGGCA	0.532													4	28	---	---	---	---	PASS
MDFIC	29969	broad.mit.edu	37	7	114563692	114563692	+	Intron	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114563692T>C	uc003vhf.2	+						MDFIC_uc003vhg.2_RNA	NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein						activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1						TTGAAATAAATAAACAAGGTT	0.363													5	93	---	---	---	---	PASS
ZNF467	168544	broad.mit.edu	37	7	149468119	149468119	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149468119C>G	uc003wgd.2	-	2	144	c.3G>C	c.(1-3)ATG>ATC	p.M1I	ZNF467_uc003wgc.2_Missense_Mutation_p.M1I	NM_207336	NP_997219	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	1					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGGTCTCTCTCATGGTAACCC	0.547													43	94	---	---	---	---	PASS
GALNTL5	168391	broad.mit.edu	37	7	151684265	151684265	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151684265A>C	uc003wkp.2	+	5	780	c.557A>C	c.(556-558)GAC>GCC	p.D186A	GALNTL5_uc003wkq.2_Intron|GALNTL5_uc003wkr.2_RNA|GALNTL5_uc003wks.2_RNA|GALNTL5_uc010lqf.2_Missense_Mutation_p.D75A	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	186	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GAAAAACTAGACTATCACCTG	0.353													25	178	---	---	---	---	PASS
MAK16	84549	broad.mit.edu	37	8	33354168	33354168	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33354168T>C	uc003xjj.2	+	8	588	c.548T>C	c.(547-549)ATT>ACT	p.I183T	C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898	Q9BXY0	MAK16_HUMAN	MAK16 homolog	183						nucleolus				ovary(1)	1						AACTTCCCCATTCATGCCTTC	0.373													136	297	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72984017	72984017	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72984017A>G	uc003xza.2	-	2	372	c.197T>C	c.(196-198)TTC>TCC	p.F66S		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	66	Cytoplasmic (Potential).|ANK 1.					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	ATAATGCAAGAAGAAGGTGTC	0.353													10	512	---	---	---	---	PASS
NIPAL2	79815	broad.mit.edu	37	8	99234790	99234790	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99234790T>C	uc003yil.1	-	5	731	c.475A>G	c.(475-477)AAC>GAC	p.N159D	NIPAL2_uc011lgw.1_5'UTR|NIPAL2_uc003yim.1_Missense_Mutation_p.N159D	NM_024759	NP_079035	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	159	Helical; (Potential).					integral to membrane					0						GGAGCAAAGTTCACCAGTAAA	0.363													8	583	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139153542	139153542	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139153542C>T	uc003yuy.2	-	17	3860	c.3689G>A	c.(3688-3690)CGG>CAG	p.R1230Q	FAM135B_uc003yux.2_Missense_Mutation_p.R1131Q|FAM135B_uc003yuz.2_RNA	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1230										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GAACCGGGGCCGTGTGAGGAC	0.537										HNSCC(54;0.14)			5	279	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139845296	139845296	+	Silent	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139845296C>T	uc003yvd.2	-	5	1278	c.831G>A	c.(829-831)GTG>GTA	p.V277V		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	277	TSP N-terminal.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TACTTTGCACCACAGGGAAGG	0.512										HNSCC(7;0.00092)			45	112	---	---	---	---	PASS
GALT	2592	broad.mit.edu	37	9	34648884	34648884	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34648884G>T	uc003zve.2	+	8	880	c.813G>T	c.(811-813)GAG>GAT	p.E271D	GALT_uc003zvf.2_Missense_Mutation_p.E162D|GALT_uc003zvg.2_Missense_Mutation_p.E143D|GALT_uc003zvh.2_Missense_Mutation_p.E223D|GALT_uc011lop.1_Missense_Mutation_p.E223D|IL11RA_uc003zvi.2_5'Flank	NM_000155	NP_000146	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase	271					galactose catabolic process	cytosol	UDP-glucose:hexose-1-phosphate uridylyltransferase activity|zinc ion binding				0	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		CCCCTGCTGAGCGTGATGGTC	0.617									Galactosemia				4	14	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413553	68413553	+	RNA	SNP	T	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413553T>G	uc004aex.2	+	1		c.108T>G								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TCCACGTCCTTCAGCTCCCCC	0.498													3	14	---	---	---	---	PASS
COL15A1	1306	broad.mit.edu	37	9	101818627	101818627	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101818627G>T	uc004azb.1	+	35	3484	c.3278G>T	c.(3277-3279)GGT>GTT	p.G1093V		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	1093	Triple-helical region 8 (COL8).				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				GGAAGACCTGGTGATCCTGGG	0.637													5	14	---	---	---	---	PASS
FAM149B1	317662	broad.mit.edu	37	10	74994648	74994648	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74994648G>T	uc009xqz.2	+	11	1647	c.1426G>T	c.(1426-1428)GGC>TGC	p.G476C	FAM149B1_uc010qkf.1_Missense_Mutation_p.G454C|FAM149B1_uc001jtq.2_Missense_Mutation_p.G362C|FAM149B1_uc009xra.2_Missense_Mutation_p.G266C	NM_173348	NP_775483	Q96BN6	F149B_HUMAN	hypothetical protein LOC317662	476											0						ACCACCTATTGGCACAGCTGA	0.512													5	141	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105938823	105938823	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105938823T>C	uc001kxw.2	-	19	2540	c.2424A>G	c.(2422-2424)AAA>AAG	p.K808K	C10orf79_uc009xxq.2_Silent_p.K116K|C10orf79_uc001kxx.3_Silent_p.K809K	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	808											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		GTTTTATCTCTTTCCTTTTCT	0.289													7	387	---	---	---	---	PASS
LGR4	55366	broad.mit.edu	37	11	27389995	27389995	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27389995A>G	uc001mrj.3	-	18	2760	c.2275T>C	c.(2275-2277)TTT>CTT	p.F759L	LGR4_uc001mrk.3_Missense_Mutation_p.F735L	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	759	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1						GGGCAGAAAAAGATGCAATTG	0.388													6	252	---	---	---	---	PASS
API5	8539	broad.mit.edu	37	11	43356873	43356873	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43356873T>C	uc010rfh.1	+	12	1497	c.1324T>C	c.(1324-1326)TCC>CCC	p.S442P	API5_uc010rfg.1_Missense_Mutation_p.S431P|API5_uc001mxf.2_Missense_Mutation_p.S442P|API5_uc010rfi.1_Missense_Mutation_p.S388P|API5_uc001mxg.2_Missense_Mutation_p.S316P	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	442					anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3						AGTAACACTATCCTGGAAACC	0.353													7	386	---	---	---	---	PASS
OR7E5P	219445	broad.mit.edu	37	11	55746807	55746807	+	3'UTR	SNP	A	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55746807A>T	uc010riu.1	-	4						NR_027688				SubName: Full=HCG2036849; SubName: Full=Seven transmembrane helix receptor;												0						TCCATAAAATAAGCAAACAAC	0.488													4	24	---	---	---	---	PASS
OR5M8	219484	broad.mit.edu	37	11	56258051	56258051	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56258051A>C	uc001nix.1	-	1	796	c.796T>G	c.(796-798)TCT>GCT	p.S266A		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)					TGTTCAACAGATTCCTTTGAG	0.383													44	82	---	---	---	---	PASS
GLYATL2	219970	broad.mit.edu	37	11	58607026	58607026	+	Silent	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58607026G>A	uc001nnd.3	-	2	191	c.60C>T	c.(58-60)AGC>AGT	p.S20S	GLYATL2_uc009ymq.2_Silent_p.S20S	NM_145016	NP_659453	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	20						mitochondrion	glycine N-acyltransferase activity			ovary(1)|skin(1)	2		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	ATTCAGGGATGCTCTTTTCTA	0.428													7	365	---	---	---	---	PASS
EED	8726	broad.mit.edu	37	11	85979540	85979540	+	Silent	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85979540C>T	uc001pbp.2	+	9	1360	c.903C>T	c.(901-903)ACC>ACT	p.T301T	EED_uc010rtm.1_Silent_p.T301T|EED_uc001pbq.2_Silent_p.T301T|EED_uc001pbr.2_Silent_p.T301T|EED_uc001pbs.2_Intron|EED_uc010rtn.1_Intron	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a	301	Interaction with EZH2 (By similarity).|Required for interaction with the matrix protein MA of HIV-1.|Required for interaction with the matrix protein MA of HIV-1.			ST->AA: Impairs interaction with the matrix protein MA of HIV-1.	negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				ATTTTTCTACCAGAGACATAC	0.323													7	706	---	---	---	---	PASS
CCDC81	60494	broad.mit.edu	37	11	86097128	86097128	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86097128G>A	uc001pbx.1	+	2	543	c.115G>A	c.(115-117)GTG>ATG	p.V39M	CCDC81_uc001pbw.1_Missense_Mutation_p.V39M	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	39										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				ATCAGAATTTGTGAGACGGCA	0.294													102	191	---	---	---	---	PASS
CEP164	22897	broad.mit.edu	37	11	117280564	117280564	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117280564G>A	uc001prc.2	+	30	4126	c.3979G>A	c.(3979-3981)GCT>ACT	p.A1327T	CEP164_uc001prb.2_Missense_Mutation_p.A1322T|CEP164_uc001prf.2_RNA|CEP164_uc009yzp.1_RNA|CEP164_uc001prg.1_Missense_Mutation_p.A752T	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1327					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CTTATCATCTGCTACACCCAC	0.642													3	16	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123909221	123909221	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909221A>T	uc001pzq.1	-	1	488	c.488T>A	c.(487-489)TTC>TAC	p.F163Y		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	163	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GGGCAAATGGAAAGTCAATAT	0.572													21	107	---	---	---	---	PASS
C11orf45	219833	broad.mit.edu	37	11	128772493	128772493	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128772493G>T	uc001qeu.2	-	4	591	c.397C>A	c.(397-399)CCC>ACC	p.P133T	KCNJ5_uc001qet.2_Intron|KCNJ5_uc009zck.2_Intron|C11orf45_uc009zcl.2_Missense_Mutation_p.P133T|C11orf45_uc001qev.2_Missense_Mutation_p.P133T	NM_145013	NP_659450	Q8TAV5	CK045_HUMAN	hypothetical protein LOC219833 precursor	133						extracellular region					0	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)		GCACTGAGGGGGTAGCCCAGG	0.622													10	38	---	---	---	---	PASS
USP5	8078	broad.mit.edu	37	12	6969582	6969582	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6969582G>A	uc001qri.3	+	11	1330	c.1271G>A	c.(1270-1272)GGC>GAC	p.G424D	USP5_uc001qrh.3_Missense_Mutation_p.G424D	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	424					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4						ATCGGCAAGGGCCACCCTGAA	0.587													8	31	---	---	---	---	PASS
PDE3A	5139	broad.mit.edu	37	12	20792854	20792854	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20792854T>A	uc001reh.1	+	10	2236	c.2214T>A	c.(2212-2214)TAT>TAA	p.Y738*		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	738	Catalytic (By similarity).				lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	TTATGAATTATTTTCATGCTT	0.274													178	419	---	---	---	---	PASS
PDE1B	5153	broad.mit.edu	37	12	54970410	54970410	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54970410G>A	uc001sgd.1	+	14	1598	c.1432G>A	c.(1432-1434)GTG>ATG	p.V478M	PDE1B_uc010soz.1_Missense_Mutation_p.V341M|PDE1B_uc010spa.1_Missense_Mutation_p.V437M|PDE1B_uc001sgf.2_Missense_Mutation_p.V341M|PDE1B_uc001sge.2_Missense_Mutation_p.V458M|PDE1B_uc009znq.2_Missense_Mutation_p.V274M	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	478	Catalytic (By similarity).				activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding	p.V478M(1)		upper_aerodigestive_tract(1)|ovary(1)	2						CAACCCTGATGTGGTCAGCTT	0.582													28	64	---	---	---	---	PASS
TIMELESS	8914	broad.mit.edu	37	12	56816773	56816773	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56816773G>C	uc001slf.2	-	19	2464	c.2296C>G	c.(2296-2298)CTA>GTA	p.L766V		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	766					cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8						AAAGTCACTAGCTCCTGTAGG	0.493													35	100	---	---	---	---	PASS
PPP1R12A	4659	broad.mit.edu	37	12	80214706	80214706	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80214706T>C	uc001syz.2	-	8	1229	c.962A>G	c.(961-963)GAG>GGG	p.E321G	PPP1R12A_uc010suc.1_Missense_Mutation_p.E234G|PPP1R12A_uc001sza.2_Missense_Mutation_p.E321G|PPP1R12A_uc010sud.1_Missense_Mutation_p.E321G|PPP1R12A_uc001szb.2_Missense_Mutation_p.E321G|PPP1R12A_uc001szc.2_Missense_Mutation_p.E321G	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	321						contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7						AATCAACGTCTCTTTGCTGTT	0.363													8	491	---	---	---	---	PASS
PPP1R12A	4659	broad.mit.edu	37	12	80226222	80226222	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80226222T>C	uc001syz.2	-	4	804	c.537A>G	c.(535-537)AGA>AGG	p.R179R	PPP1R12A_uc010suc.1_Silent_p.R92R|PPP1R12A_uc001sza.2_Silent_p.R179R|PPP1R12A_uc010sud.1_Silent_p.R179R|PPP1R12A_uc001szb.2_Silent_p.R179R|PPP1R12A_uc001szc.2_Silent_p.R179R	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	179						contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7						GCCTGGCATCTCTAAGCATGA	0.398													6	266	---	---	---	---	PASS
CCDC41	51134	broad.mit.edu	37	12	94702622	94702622	+	Silent	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94702622T>C	uc001tdd.2	-	17	2659	c.2073A>G	c.(2071-2073)AAA>AAG	p.K691K	CCDC41_uc001tde.2_Silent_p.K691K	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	683	Potential.										0						CCTCTAGTTGTTTTCTTTGTG	0.388													9	741	---	---	---	---	PASS
GNPTAB	79158	broad.mit.edu	37	12	102183823	102183823	+	Silent	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102183823G>A	uc001tit.2	-	3	395	c.216C>T	c.(214-216)CCC>CCT	p.P72P	GNPTAB_uc001tiu.1_Silent_p.P72P	NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase	72					cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						CAATCGGCATGGGCAGACAAA	0.433													5	294	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133359043	133359043	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133359043G>A	uc001ukz.1	-	17	3863	c.3304C>T	c.(3304-3306)CGC>TGC	p.R1102C	GOLGA3_uc001ula.1_Missense_Mutation_p.R1102C	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1102	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TCCTCAAGGCGTTTTATCTTC	0.473													27	179	---	---	---	---	PASS
IFT88	8100	broad.mit.edu	37	13	21205163	21205163	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21205163G>T	uc001unh.2	+	18	1731	c.1335G>T	c.(1333-1335)GAG>GAT	p.E445D	IFT88_uc001uni.2_Missense_Mutation_p.E436D|IFT88_uc001unj.2_Missense_Mutation_p.E435D|IFT88_uc010tcq.1_Missense_Mutation_p.E416D|IFT88_uc001unk.2_Missense_Mutation_p.E191D|IFT88_uc001unl.1_Missense_Mutation_p.E63D	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1	445	TPR 5.				cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		AGGCTGTAGAGATCTTAAAAG	0.383													41	359	---	---	---	---	PASS
LRCH1	23143	broad.mit.edu	37	13	47303069	47303069	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47303069C>T	uc001vbj.2	+	17	2088	c.1852C>T	c.(1852-1854)CAC>TAC	p.H618Y	LRCH1_uc001vbk.2_Missense_Mutation_p.H653Y|LRCH1_uc001vbl.3_Missense_Mutation_p.H618Y	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)	618	CH.									ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TCTGGTCAACCACATCCGCCC	0.517													47	93	---	---	---	---	PASS
NEK5	341676	broad.mit.edu	37	13	52667190	52667190	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52667190C>T	uc001vge.2	-	13	1348	c.1208G>A	c.(1207-1209)TGG>TAG	p.W403*	NEK5_uc001vgf.2_Nonsense_Mutation_p.W403*	NM_199289	NP_954983	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	403							ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		ACAATATTACCATTGACTTGG	0.358													5	334	---	---	---	---	PASS
LOC647288	647288	broad.mit.edu	37	13	75814325	75814325	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75814325C>A	uc010ths.1	-	1	193	c.152G>T	c.(151-153)GGA>GTA	p.G51V		NR_027466				Homo sapiens mRNA; cDNA DKFZp434F0327 (from clone DKFZp434F0327).												0						AACAAAAAATCCAACAACAGC	0.443													10	543	---	---	---	---	PASS
LOC643677	643677	broad.mit.edu	37	13	103400138	103400138	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103400138T>C	uc001vpm.2	-	4	3049	c.2909A>G	c.(2908-2910)GAG>GGG	p.E970G		NM_001146197	NP_001139669			hypothetical protein LOC643677												0						TGGACTATTCTCCAAAATAGT	0.418													9	578	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106054693	106054693	+	RNA	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106054693C>A	uc010tyt.1	-	3650		c.62793G>T			uc001yrs.2_RNA|uc001yrt.2_Missense_Mutation_p.D20Y					Parts of antibodies, mostly variable regions.												0						GGGGTGCTGTCGAGGCTCAGC	0.607													4	12	---	---	---	---	PASS
ARHGAP11A	9824	broad.mit.edu	37	15	32916525	32916525	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32916525A>G	uc001zgy.1	+	4	1171	c.449A>G	c.(448-450)GAG>GGG	p.E150G	ARHGAP11A_uc010ubw.1_5'UTR|ARHGAP11A_uc001zgw.2_Missense_Mutation_p.E150G|ARHGAP11A_uc001zgx.2_Missense_Mutation_p.E150G|ARHGAP11A_uc010ubx.1_5'UTR	NM_014783	NP_055598	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A isoform 1	150	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		TTAGGCACAGAGGAAAAGAAT	0.418													7	418	---	---	---	---	PASS
ODF3L1	161753	broad.mit.edu	37	15	76016536	76016536	+	5'UTR	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76016536C>A	uc002bax.1	+	1						NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1												0						TGCCCAGCCCCAGCCATGAAA	0.607													6	21	---	---	---	---	PASS
RPL3L	6123	broad.mit.edu	37	16	1997038	1997038	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1997038C>A	uc002cnh.2	-	6	797	c.750G>T	c.(748-750)AAG>AAT	p.K250N		NM_005061	NP_005052	Q92901	RL3L_HUMAN	ribosomal protein L3-like	250					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0						TGCAGGCCACCTTGCGCAGGC	0.667													3	8	---	---	---	---	PASS
ARHGAP17	55114	broad.mit.edu	37	16	24971030	24971030	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24971030A>G	uc002dnb.2	-	9	779	c.686T>C	c.(685-687)GTC>GCC	p.V229A	ARHGAP17_uc002dna.2_5'Flank|ARHGAP17_uc002dnc.2_Missense_Mutation_p.V229A|ARHGAP17_uc010vcf.1_Missense_Mutation_p.V50A|ARHGAP17_uc002dnf.2_Missense_Mutation_p.V137A|ARHGAP17_uc002dng.1_Intron	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	229	BAR.				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)		CTTTTCTAAGACTGCTAATGC	0.478													8	383	---	---	---	---	PASS
ZNF629	23361	broad.mit.edu	37	16	30794999	30794999	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30794999C>T	uc002dzs.1	-	3	858	c.650G>A	c.(649-651)TGG>TAG	p.W217*		NM_001080417	NP_001073886	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	217	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)			GTTGGAGCTCCAGCTGAAGCA	0.632													4	65	---	---	---	---	PASS
HSF4	3299	broad.mit.edu	37	16	67200251	67200251	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67200251G>T	uc002erl.1	+	7	1479	c.514G>T	c.(514-516)GTG>TTG	p.V172L	HSF4_uc002erm.1_Missense_Mutation_p.V172L|HSF4_uc002ern.1_RNA|HSF4_uc010cec.1_RNA	NM_001040667	NP_001035757	Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4 isoform b	172	Hydrophobic repeat HR-A/B.				response to stress	nucleus	sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		GCGGGAGGTGGTGACACTTCG	0.627													3	15	---	---	---	---	PASS
CLEC18C	283971	broad.mit.edu	37	16	70030117	70030117	+	Intron	SNP	C	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70030117C>G	uc002exy.2	+						PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_RNA	NM_182619	NP_872425	Q8NCF0	CL18C_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						AGGGGCTCATCATGAGTGCCA	0.423													4	67	---	---	---	---	PASS
ZNF624	57547	broad.mit.edu	37	17	16526924	16526924	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16526924T>C	uc010cpi.1	-	6	1359	c.1276A>G	c.(1276-1278)AGG>GGG	p.R426G		NM_020787	NP_065838	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	426	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GACTTGTTCCTAAAGGCTTTC	0.388													6	317	---	---	---	---	PASS
PIGW	284098	broad.mit.edu	37	17	34893245	34893245	+	Silent	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34893245C>A	uc002hmy.1	+	2	338	c.295C>A	c.(295-297)CGA>AGA	p.R99R	MYO19_uc002hmw.2_5'Flank|MYO19_uc010cuu.2_5'Flank|MYO19_uc010wcy.1_5'Flank|MYO19_uc010wcz.1_5'Flank|MYO19_uc010wda.1_5'Flank|MYO19_uc002hmx.2_5'Flank|PIGW_uc002hmz.1_Silent_p.R99R	NM_178517	NP_848612	Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan, class W	99					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	O-acyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCAAATATACCGAAGGAGGAC	0.428													5	242	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	40001990	40001990	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40001990G>T	uc010cxr.2	+	3	1439	c.1297G>T	c.(1297-1299)GGG>TGG	p.G433W	KLHL10_uc010wfv.1_Missense_Mutation_p.G427W|KLHL10_uc010wfw.1_Missense_Mutation_p.G345W	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	433	Kelch 3.					cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				AACACTTTATGGGAAGGTAAA	0.502													5	15	---	---	---	---	PASS
SRP68	6730	broad.mit.edu	37	17	74053545	74053545	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74053545T>C	uc002jqk.1	-	8	952	c.917A>G	c.(916-918)AAG>AGG	p.K306R	SRP68_uc010wsu.1_Missense_Mutation_p.K205R|SRP68_uc002jql.1_Missense_Mutation_p.K268R	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	306					response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						TTTGTCAATCTTCACTGGAAC	0.448													7	388	---	---	---	---	PASS
ARHGAP28	79822	broad.mit.edu	37	18	6859884	6859884	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6859884G>T	uc010wzi.1	+	4	421	c.183G>T	c.(181-183)AGG>AGT	p.R61S	ARHGAP28_uc002knc.2_Missense_Mutation_p.R186S|ARHGAP28_uc002knd.2_Missense_Mutation_p.R79S|ARHGAP28_uc002kne.2_Missense_Mutation_p.R79S|ARHGAP28_uc002knf.2_Missense_Mutation_p.R70S			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;	61					signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				CGGTTCCCAGGAGTGACTCTG	0.438													104	244	---	---	---	---	PASS
PEPD	5184	broad.mit.edu	37	19	33878351	33878351	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33878351C>T	uc002nur.3	-	15	1516	c.1381G>A	c.(1381-1383)GGC>AGC	p.G461S	PEPD_uc010xrr.1_Missense_Mutation_p.G420S|PEPD_uc010xrs.1_Missense_Mutation_p.G397S|PEPD_uc002nuq.3_Missense_Mutation_p.G140S	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1	461					cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)					AGCTCTATGCCGCTGTCAGTC	0.592													3	30	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232117	35232117	+	Silent	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35232117C>T	uc002nvu.3	+	4	1294	c.831C>T	c.(829-831)GGC>GGT	p.G277G	ZNF181_uc010xsa.1_Silent_p.G276G|ZNF181_uc010xsb.1_Silent_p.G276G|ZNF181_uc010xsc.1_Silent_p.G212G	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	277	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTAGCCATGGCTCATCCCTTA	0.443													6	140	---	---	---	---	PASS
ETFB	2109	broad.mit.edu	37	19	51857732	51857732	+	Intron	SNP	G	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51857732G>C	uc002pwh.2	-						ETFB_uc002pwg.2_Missense_Mutation_p.P54R	NM_001985	NP_001976	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		agagtttgtaggcagGGGCAG	0.264													7	17	---	---	---	---	PASS
TGM6	343641	broad.mit.edu	37	20	2398051	2398051	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2398051C>T	uc002wfy.1	+	10	1571	c.1510C>T	c.(1510-1512)CCT>TCT	p.P504S	TGM6_uc010gal.1_Missense_Mutation_p.P504S	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	504					cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)	GGTGCTAGAGCCTCCCATGCT	0.657													4	6	---	---	---	---	PASS
C20orf118	140711	broad.mit.edu	37	20	35507457	35507457	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35507457T>G	uc002xgg.1	+	3	211	c.203T>G	c.(202-204)TTC>TGC	p.F68C		NM_080628	NP_542195	A0PJX2	CT118_HUMAN	hypothetical protein LOC140711	68											0		Myeloproliferative disorder(115;0.00874)				AGCTTTCACTTCCCACCAAGA	0.617													6	15	---	---	---	---	PASS
NDUFV3	4731	broad.mit.edu	37	21	44323941	44323941	+	Intron	SNP	A	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44323941A>G	uc002zcn.2	+						NDUFV3_uc002zcm.2_Silent_p.R273R	NM_001001503	NP_001001503	P56181	NDUV3_HUMAN	NADH-ubiquinone oxidoreductase flavoprotein 3						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I|nucleus	NADH dehydrogenase (ubiquinone) activity			ovary(2)	2				STAD - Stomach adenocarcinoma(101;0.0606)	NADH(DB00157)	AAACATTTAGATTAAATGAAA	0.398													40	62	---	---	---	---	PASS
ARSD	414	broad.mit.edu	37	X	2838604	2838604	+	Intron	SNP	C	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2838604C>A	uc004cqy.2	-						ARSD_uc004cqz.1_Intron|ARSD_uc004cra.1_Intron|ARSD_uc004crb.3_Missense_Mutation_p.L159F	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGAATATTCCCAACCACCGTA	0.299													17	9	---	---	---	---	PASS
TBX22	50945	broad.mit.edu	37	X	79286353	79286353	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79286353G>A	uc010nmg.1	+	9	1440	c.1306G>A	c.(1306-1308)GCA>ACA	p.A436T	TBX22_uc004edi.1_Missense_Mutation_p.A316T|TBX22_uc004edj.1_Missense_Mutation_p.A436T	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	436					multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1)	15						GTATCTACAAGCACCTAATTC	0.423													7	160	---	---	---	---	PASS
ATP1B4	23439	broad.mit.edu	37	X	119500536	119500536	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119500536C>T	uc004esr.2	+	2	304	c.220C>T	c.(220-222)CAA>TAA	p.Q74*	ATP1B4_uc004esq.2_Nonsense_Mutation_p.Q74*|ATP1B4_uc011mtx.1_Nonsense_Mutation_p.Q74*|ATP1B4_uc011mty.1_Nonsense_Mutation_p.Q74*	NM_001142447	NP_001135919	Q9UN42	AT1B4_HUMAN	ATPase, (Na+)/K+ transporting, beta 4	74	Nuclear (Potential).				ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2						ggaagaggGTCAAGGTCAGCC	0.363													35	20	---	---	---	---	PASS
SLC2A5	6518	broad.mit.edu	37	1	9102469	9102470	+	Intron	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9102469_9102470delTG	uc001apo.2	-						SLC2A5_uc010nzy.1_Intron|SLC2A5_uc010nzz.1_Intron|SLC2A5_uc010oaa.1_Intron|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_Intron|SLC2A5_uc001app.3_Intron	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		aatatgtatatgtgtgtgtgtg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9442879	9442880	+	IGR	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9442879_9442880delTT								SPSB1 (13291 upstream) : SLC25A33 (156648 downstream)																							CCTCCTCCTCTTGCGTTGCTCA	0.564													4	2	---	---	---	---	
TNFRSF8	943	broad.mit.edu	37	1	12189760	12189761	+	Intron	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12189760_12189761delTT	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-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;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)		tgctggcctcttctctctcagg	0.000													4	2	---	---	---	---	
HNRNPCL1	343069	broad.mit.edu	37	1	12908384	12908385	+	Intron	INS	-	A	A	rs143606605		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12908384_12908385insA	uc010obf.1	-						LOC649330_uc009vno.2_5'Flank	NM_001013631	NP_001013653	O60812	HNRCL_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleotide binding				0						ATTGCATTTAGAAAAAAAATCA	0.356													6	3	---	---	---	---	
PRAMEF5	343068	broad.mit.edu	37	1	13109617	13109617	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13109617delC	uc001aur.2	-						PRAMEF5_uc001aus.1_Intron	NM_001013407	NP_001013425	Q5TYX0	PRAM5_HUMAN	PRAME family member 5												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		cacctgtaatcccagcacttt	0.159													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15358049	15358050	+	Intron	INS	-	TGTGT	TGTGT	rs139569205	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15358049_15358050insTGTGT	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						GCTACTCAGGGtgtgttgtgtt	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18951093	18951093	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18951093delA								KLHDC7A (138554 upstream) : PAX7 (6407 downstream)																							AGATAAATACAAAAAAAAAAA	0.448													2	4	---	---	---	---	
ECE1	1889	broad.mit.edu	37	1	21548667	21548668	+	Intron	INS	-	CA	CA	rs151259864	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21548667_21548668insCA	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		gtgtgtgcatgcacacacacac	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25051530	25051530	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25051530delA								SRRM1 (51759 upstream) : CLIC4 (20230 downstream)																							CTCCAGCCGGAAAAGCCTGAG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25510154	25510154	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25510154delA								RUNX3 (218542 upstream) : SYF2 (38613 downstream)																							CCTCACATGCAAAGGCCTTCC	0.373													4	2	---	---	---	---	
MAN1C1	57134	broad.mit.edu	37	1	26033101	26033101	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26033101delG	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		AGAGTGTTCTGGGAAAAGAAG	0.547													4	2	---	---	---	---	
PDIK1L	149420	broad.mit.edu	37	1	26449196	26449196	+	3'UTR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26449196delT	uc010oew.1	+	3					PDIK1L_uc001blj.3_3'UTR|PDIK1L_uc009vsb.2_3'UTR	NM_152835	NP_690048	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like							nucleus	ATP binding|protein serine/threonine kinase activity				0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TTTTGTGGGATTTTTTTTTTC	0.303													4	2	---	---	---	---	
CLSPN	63967	broad.mit.edu	37	1	36215601	36215602	+	Intron	INS	-	T	T	rs141897285		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36215601_36215602insT	uc001bzi.2	-						CLSPN_uc009vux.2_Intron	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin						activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACTTTTTTCTATTTTTTTTTTT	0.312													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37610926	37610926	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37610926delC								GRIK3 (111082 upstream) : ZC3H12A (329193 downstream)																							GGACTCAACACCCTGAGGCTT	0.498													4	2	---	---	---	---	
MTF1	4520	broad.mit.edu	37	1	38312685	38312685	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38312685delC	uc001cce.1	-						MTF1_uc009vvj.1_Intron	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CGACTCCATTCCCCACACCGG	0.468													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38516246	38516246	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38516246delC								POU3F1 (3796 upstream) : RRAGC (788769 downstream)																							CATAGGCATACCATCATACTC	0.522													4	2	---	---	---	---	
RIMKLA	284716	broad.mit.edu	37	1	42875426	42875427	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42875426_42875427delAA	uc001chi.2	+							NM_173642	NP_775913	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						AAGTCATTTCAAAAAGAGTGAT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	44654346	44654346	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44654346delT								KLF17 (53539 upstream) : DMAP1 (24779 downstream)																							ttttcttctcttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55718030	55718030	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55718030delT								USP24 (37268 upstream) : None (None downstream)																							CTATTTCTCCTTAAAGTCTGG	0.259													4	2	---	---	---	---	
MIER1	57708	broad.mit.edu	37	1	67394273	67394274	+	Intron	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67394273_67394274delCA	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'Flank|MIER1_uc001ddi.2_5'Flank	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TCTTTGCCTTCAGCTCTTTTCA	0.366													4	2	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70562395	70562396	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70562395_70562396insA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TTCCTAGACTGAAAAAAAAAGA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91050435	91050436	+	IGR	DEL	CC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91050435_91050436delCC								ZNF326 (556341 upstream) : BARHL2 (127144 downstream)																							ACCTCTGTCTCCCAGGTGGGTT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	92927204	92927204	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92927204delC								RPAP2 (73472 upstream) : GFI1 (13115 downstream)																							tttcagttttctcatgcataa	0.154													4	2	---	---	---	---	
SLC30A7	148867	broad.mit.edu	37	1	101436606	101436606	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101436606delC	uc001dtn.2	+						SLC30A7_uc001dto.2_Intron	NM_001144884	NP_001138356	Q8NEW0	ZNT7_HUMAN	zinc transporter like 2						zinc ion transport	Golgi apparatus|integral to membrane	cation transmembrane transporter activity|protein binding				0		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		AAGTCCTAAGCCCCCAACTTC	0.393													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145041680	145041681	+	Intron	DEL	AA	-	-	rs10544872		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145041680_145041681delAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'Flank|PDE4DIP_uc001eln.3_5'Flank|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_5'Flank|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AAAAATACAGAAAGTTATATAG	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152072738	152072739	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152072738_152072739insT								TCHHL1 (11198 upstream) : TCHH (6054 downstream)																							tttttagttagttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152302117	152302118	+	Intron	DEL	CT	-	-	rs61816762		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152302117_152302118delCT	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																		ctctctctccctctctctctct	0.262													4	2	---	---	---	---	
INTS3	65123	broad.mit.edu	37	1	153723143	153723143	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153723143delA	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_5'Flank|INTS3_uc001fcw.2_5'Flank	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ccactgACTTAGGGACACTTA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	154895243	154895243	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154895243delA								KCNN3 (52489 upstream) : PMVK (1966 downstream)																							GACATGCTGGAATCAAGCAGG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158242991	158242992	+	IGR	DEL	GG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158242991_158242992delGG								CD1A (14935 upstream) : CD1C (16571 downstream)																							agtcacctcagggtatgggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159059223	159059223	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159059223delT								AIM2 (12576 upstream) : CADM3 (82154 downstream)																							ACCAAAAGGATAAAAACCAAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165350585	165350586	+	IGR	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165350585_165350586delAC								LMX1A (25110 upstream) : RXRG (19765 downstream)																							acatacacatacacacacacac	0.188													4	2	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179588010	179588010	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179588010delA	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						AAAACTATTTAGTAAATAAGT	0.294													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185003253	185003253	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185003253delT								FAM129A (59571 upstream) : RNF2 (11298 downstream)																							CCTATAGTCCTTTTTACCCAA	0.358													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210817050	210817050	+	Intron	DEL	T	-	-	rs72235524		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210817050delT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		AGTAGATTCATTTTTTTTTTT	0.348													4	3	---	---	---	---	
RPS6KC1	26750	broad.mit.edu	37	1	213303467	213303467	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213303467delA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		AACAGGATTTAAAAAAAAGTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226599286	226599287	+	IGR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226599286_226599287insA								PARP1 (3485 upstream) : C1orf95 (137214 downstream)																							ATAGACAAGAGAAAAAAAAAAA	0.218													4	2	---	---	---	---	
SNAP47	116841	broad.mit.edu	37	1	227936590	227936591	+	Intron	INS	-	TT	TT			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227936590_227936591insTT	uc001hrf.2	+						SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_Intron|SNAP47_uc001hre.2_Intron|SNAP47_uc001hrg.1_Intron	NM_053052	NP_444280	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa							endomembrane system|membrane|perinuclear region of cytoplasm				ovary(1)	1						TCTTCAGTTTGTTTAAGAATGC	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228933205	228933206	+	IGR	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228933205_228933206delTT								RHOU (50796 upstream) : RAB4A (473673 downstream)																							TTAAGGTCTCTTTTTGTTATAA	0.347													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230239927	230239927	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230239927delG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGTAGGTTCTGGGGTGGTGGG	0.547													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231837648	231837648	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231837648delT	uc001huz.2	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc010pwm.1_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				CACAAAAATGTTTGCTTGAAT	0.264													177	80	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231886509	231886509	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231886509delT	uc001huz.2	+						TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				TTGTGTTCCCTTTCTCCCTAG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238101298	238101298	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238101298delT								LOC100130331 (9681 upstream) : LOC339535 (542388 downstream)																							gttcctgtcctttttagtgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238933027	238933028	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238933027_238933028insT								LOC339535 (283710 upstream) : CHRM3 (616837 downstream)																							AACATCACTGATTAAAAAAAAA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238933030	238933032	+	IGR	DEL	AAA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238933030_238933032delAAA								LOC339535 (283713 upstream) : CHRM3 (616833 downstream)																							ATCACTGATTAAAAAAAAAAAAA	0.325													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	313137	313137	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:313137delT								FAM150B (24829 upstream) : TMEM18 (354838 downstream)																							TTGAGTTTCATTTCTAAGTAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2978009	2978009	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2978009delC	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		tcacccccagccccaacactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8992866	8992866	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8992866delA								KIDINS220 (15111 upstream) : MBOAT2 (3835 downstream)																							CACAAATTAGAAAAAAAAAAC	0.318													4	4	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	20928577	20928577	+	Intron	DEL	A	-	-	rs113580844		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20928577delA	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTTATGGGGAAAAAAAAAAA	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	24995018	24995018	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24995018delG								NCOA1 (1450 upstream) : C2orf79 (18120 downstream)																							TAACAAGATTGAAGGAACACA	0.259													4	2	---	---	---	---	
LCLAT1	253558	broad.mit.edu	37	2	30861945	30861945	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30861945delA	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2						tccaccATGTAAAATGCTTCT	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37759422	37759422	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37759422delG								QPCT (158958 upstream) : CDC42EP3 (111321 downstream)																							ACAATAGACTGGGCAGTCTAC	0.348													4	2	---	---	---	---	
SLC3A1	6519	broad.mit.edu	37	2	44539068	44539068	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44539068delT	uc002ruc.3	+						SLC3A1_uc002rtz.2_Intron|SLC3A1_uc002rua.2_Intron|SLC3A1_uc002rub.2_Intron|SLC3A1_uc002rud.3_Intron|SLC3A1_uc002rue.3_Intron	NM_000341	NP_000332	Q07837	SLC31_HUMAN	solute carrier family 3, member 1						carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	gtgaaagtactttttaaaaag	0.139													4	2	---	---	---	---	
SIX2	10736	broad.mit.edu	37	2	45233731	45233732	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45233731_45233732insA	uc002ruo.2	-						SIX2_uc002rup.2_Intron	NM_016932	NP_058628	Q9NPC8	SIX2_HUMAN	SIX homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			pancreas(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GACAGATCCCGGGCTTGTGGCC	0.594													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	51192059	51192059	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51192059delT	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxd.1_Intron	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TACTCTGGAATTTTTGTTGAG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51283634	51283634	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51283634delT								NRXN1 (23960 upstream) : None (None downstream)																							ttccttttagttggaagtgtt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59507258	59507258	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59507258delG								None (None upstream) : None (None downstream)																							CTTGAGGAGTGGGGCTGTGTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66243055	66243055	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66243055delA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		AAACAGCTTGAAAAAAAATGG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67518112	67518112	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67518112delT								MEIS1 (718222 upstream) : ETAA1 (106330 downstream)																							AGTGTACATGTTAGAGATTAG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96518290	96518292	+	IGR	DEL	ACA	-	-	rs71786585		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96518290_96518292delACA								TRIM43 (252823 upstream) : LOC729234 (158007 downstream)																							GGACTAAAACACAACATTCTTCT	0.177													5	3	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101680343	101680343	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101680343delA	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						ggtcatggccaaaaaaaaaac	0.284													4	2	---	---	---	---	
LIMS1	3987	broad.mit.edu	37	2	109274195	109274195	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109274195delT	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_Intron	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						CCTTCCTTCCTTTTTTTTGTG	0.393													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119615653	119615653	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119615653delT								EN1 (9894 upstream) : MARCO (84092 downstream)																							ATGTTTCCAATTTACCAAGgg	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119651802	119651802	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119651802delG								EN1 (46043 upstream) : MARCO (47943 downstream)																							CCTTCTGTCTGCAGTTGGACA	0.413													4	2	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128308242	128308242	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128308242delA	uc002top.2	+							NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GGAAGGCATGAAAGGTGAGAA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146191405	146191405	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146191405delA								ZEB2 (913474 upstream) : None (None downstream)																							AAATAGCCTCAACCTACTGCT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	153882729	153882730	+	IGR	INS	-	A	A	rs148291740	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153882729_153882730insA								ARL6IP6 (264962 upstream) : RPRM (451122 downstream)																							tagaatcgatgaaccaacactg	0.000													3	5	---	---	---	---	
ACVR1	90	broad.mit.edu	37	2	158643545	158643545	+	Intron	DEL	A	-	-	rs74898722		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158643545delA	uc002tzm.3	-						ACVR1_uc002tzn.3_Intron|ACVR1_uc010fog.2_Intron	NM_001111067	NP_001104537	Q04771	ACVR1_HUMAN	activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	TGAAGCTGAGAAAAAAAAAAA	0.433													4	3	---	---	---	---	
BAZ2B	29994	broad.mit.edu	37	2	160492119	160492119	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160492119delT	uc002uau.1	-									Q9UIF8	BAZ2B_HUMAN	SubName: Full=Putative uncharacterized protein DKFZp686H10114;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						AATTTGTTTCTTTTTTTTTTT	0.313													2	4	---	---	---	---	
RBMS1	5937	broad.mit.edu	37	2	161129852	161129852	+	3'UTR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161129852delA	uc002ubo.2	-	14					ITGB6_uc010fow.1_5'Flank|RBMS1_uc002ubj.2_3'UTR|RBMS1_uc002ubk.2_3'UTR|RBMS1_uc002ubl.2_3'UTR|RBMS1_uc002ubn.2_3'UTR|RBMS1_uc002ubi.3_3'UTR|RBMS1_uc002ubm.2_3'UTR|RBMS1_uc002ubp.2_3'UTR	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						GCAAAGGTACAAAAAAGGCAC	0.393													4	2	---	---	---	---	
STK39	27347	broad.mit.edu	37	2	169038780	169038780	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169038780delA	uc002uea.2	-							NM_013233	NP_037365	Q9UEW8	STK39_HUMAN	serine threonine kinase 39 (STE20/SPS1 homolog,						response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2						TCTGGAGGAGAAAAAAAAAAC	0.343													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	171011770	171011770	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171011770delC								UBR3 (71133 upstream) : MYO3B (22885 downstream)																							CTCCTGGGAACCAGAGCCAGC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174470084	174470085	+	IGR	DEL	GA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174470084_174470085delGA								CDCA7 (236366 upstream) : SP3 (303174 downstream)																							TCTGTTTCTTGAATTAACCCCT	0.396													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178678686	178678688	+	Intron	DEL	AGG	-	-	rs10534752		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178678686_178678688delAGG	uc002ulq.2	-						PDE11A_uc002ulp.2_Intron|PDE11A_uc002ulr.2_Intron|PDE11A_uc002uls.1_Intron|PDE11A_uc002ult.1_Intron|PDE11A_uc002ulu.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			AGACAACACAAGGAGAAGAGGAA	0.458									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				3	4	---	---	---	---	
SESTD1	91404	broad.mit.edu	37	2	180049584	180049585	+	Intron	INS	-	A	A	rs143602763	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180049584_180049585insA	uc002uni.3	-							NM_178123	NP_835224	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			ttcagggctatatttaaatcca	0.094													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181569883	181569883	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181569883delA								CWC22 (698043 upstream) : UBE2E3 (275229 downstream)																							AAAGTAAAGTAAAAATGGAGA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	182301779	182301780	+	IGR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182301779_182301780insA								UBE2E3 (373629 upstream) : ITGA4 (19839 downstream)																							TCCCACACAGCTCAGCATATCC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	185445559	185445559	+	IGR	DEL	T	-	-	rs79626627		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185445559delT								None (None upstream) : ZNF804A (17534 downstream)																							CTACTCCTGCTTTTTTTTATT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	188739357	188739357	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188739357delG								TFPI (320138 upstream) : GULP1 (417247 downstream)																							gtagatcagtgggaatcaata	0.045													4	2	---	---	---	---	
CASP10	843	broad.mit.edu	37	2	202052152	202052153	+	Intron	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202052152_202052153delTT	uc002uxl.1	+						CASP10_uc002uxi.1_Intron|CASP10_uc010zhn.1_Intron|CASP10_uc002uxj.1_Intron|CASP10_uc002uxk.1_Intron|CASP10_uc010fta.1_Intron|CASP10_uc002uxm.1_Intron|CASP10_uc010ftb.1_Intron	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						GTTTTATGCCTTTTTTTTTTTA	0.257													4	3	---	---	---	---	
TUBA4B	80086	broad.mit.edu	37	2	220127161	220127162	+	Intron	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220127161_220127162delCA	uc002vkv.1	+						TUBA4B_uc002vku.2_Intron	NR_003063				RecName: Full=Putative tubulin-like protein alpha-4B; AltName: Full=Alpha-tubulin 4B;												0						ttgttttcttcacatgcttatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236194188	236194188	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236194188delG								SH3BP4 (229832 upstream) : AGAP1 (208548 downstream)																							TATCCTGCTTGTACTAGGTCC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	237064247	237064247	+	IGR	DEL	G	-	-	rs115420642	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237064247delG								AGAP1 (30133 upstream) : GBX2 (10060 downstream)																							TGCTCTGGAAGGGAAAGGAAG	0.388													4	2	---	---	---	---	
RBM44	375316	broad.mit.edu	37	2	238732446	238732447	+	Intron	INS	-	GTG	GTG			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238732446_238732447insGTG	uc002vxi.3	+							NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44								nucleotide binding|RNA binding			ovary(4)	4		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AGTATGAAAATTCTCTCTTGTA	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239482709	239482709	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239482709delC								ASB1 (121819 upstream) : TWIST2 (273964 downstream)																							ACGTCACCCTCATCTTTCCAG	0.622													4	2	---	---	---	---	
SNED1	25992	broad.mit.edu	37	2	242021008	242021009	+	Intron	INS	-	GG	GG	rs3085964		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242021008_242021009insGG	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron	NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCATCAGGTCATCAAGGAAGGG	0.594													4	4	---	---	---	---	
SNED1	25992	broad.mit.edu	37	2	242021011	242021012	+	Intron	INS	-	TCG	TCG	rs73010045	byFrequency	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242021011_242021012insTCG	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron	NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TCAGGTCATCAAGGAAGGGACA	0.599													5	4	---	---	---	---	
UBE2E1	7324	broad.mit.edu	37	3	23899200	23899200	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23899200delC	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0						GTGGGCAACTCCAAGAGCTGT	0.507													4	2	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27331839	27331843	+	Intron	DEL	GAAAA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27331839_27331843delGAAAA	uc003cdt.1	-						NEK10_uc003cds.1_Intron	NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						TGCTCACAATGAAAAGAAAAGGATT	0.312													1	6	---	---	---	---	
DCLK3	85443	broad.mit.edu	37	3	36777296	36777296	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36777296delC	uc003cgi.2	-							NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	9						CTTGCTGTTTCCCAGGCAGCA	0.259													4	2	---	---	---	---	
DLEC1	9940	broad.mit.edu	37	3	38103043	38103043	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38103043delA	uc003cho.1	+						DLEC1_uc003chp.1_Intron|DLEC1_uc010hgv.1_Intron|DLEC1_uc010hgw.1_5'Flank|DLEC1_uc003chq.1_5'Flank	NM_007335	NP_031361	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform						negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|skin(2)|breast(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AGCTCTTCAGAAAGCATGCTC	0.358													4	2	---	---	---	---	
WDR48	57599	broad.mit.edu	37	3	39132867	39132867	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39132867delA	uc003cit.2	+						WDR48_uc011ayt.1_Intron|WDR48_uc011ayu.1_Intron|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_Intron	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GTTTCCCTTTAATACCTTGTA	0.303													5	4	---	---	---	---	
CCBP2	1238	broad.mit.edu	37	3	42872183	42872183	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42872183delT	uc003cme.2	+						CCBP2_uc003cmc.1_Intron|CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmf.2_Intron|CCBP2_uc003cmg.2_Intron	NM_001296	NP_001287	O00590	CCBP2_HUMAN	chemokine binding protein 2						chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity			lung(4)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.241)		TTTTCTTTTCTTTTTTTTTTT	0.443													2	4	---	---	---	---	
SETD2	29072	broad.mit.edu	37	3	47164342	47164343	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47164342_47164343delGA	uc003cqs.2	-	3	1836_1837	c.1783_1784delTC	c.(1783-1785)TCAfs	p.S595fs	SETD2_uc003cqv.2_Frame_Shift_Del_p.S584fs	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	595					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)		ACTACCTTTTGAACAAGGTGTC	0.307			N|F|S|Mis		clear cell renal carcinoma								43	23	---	---	---	---	
DOCK3	1795	broad.mit.edu	37	3	51379784	51379784	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51379784delC	uc011bds.1	+							NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TGTAACCTAGCCCAGAAAGGA	0.478													4	2	---	---	---	---	
OR5H1	26341	broad.mit.edu	37	3	97850353	97850354	+	5'Flank	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97850353_97850354delTT	uc011bgt.1	+							NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGGCAGTATGTTACCTCTGACA	0.233													4	2	---	---	---	---	
FILIP1L	11259	broad.mit.edu	37	3	99651329	99651329	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99651329delT	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron|uc003dtq.2_5'Flank	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						tttttgaatatttttttttca	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105332555	105332555	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105332555delA								ALCAM (36812 upstream) : CBLB (44555 downstream)																							TCTAGCAATTAAAAAAAAAGG	0.378													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110566097	110566098	+	IGR	INS	-	TA	TA	rs142057352	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110566097_110566098insTA								None (None upstream) : PVRL3 (224767 downstream)																							cttttgatgtcgtgtgtgtgag	0.079													3	3	---	---	---	---	
SLC9A10	285335	broad.mit.edu	37	3	111949987	111949988	+	Intron	INS	-	C	C	rs9288944		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111949987_111949988insC	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						ctctctctttttctccctttct	0.129													7	4	---	---	---	---	
C3orf15	89876	broad.mit.edu	37	3	119450519	119450519	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119450519delC	uc003ede.3	+						C3orf15_uc010hqy.1_Intron|C3orf15_uc010hqz.2_Intron|C3orf15_uc011bjd.1_Intron|C3orf15_uc011bje.1_Intron|C3orf15_uc010hra.1_Intron	NM_033364	NP_203528	Q7Z4T9	AAT1_HUMAN	AAT1-alpha							mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)		AAGATTTTTACCCCCATTGAA	0.269													4	2	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119748921	119748921	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119748921delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATCTAGTTGGAAAAAAAAAAT	0.259													7	4	---	---	---	---	
FSTL1	11167	broad.mit.edu	37	3	120127673	120127674	+	Intron	INS	-	TA	TA	rs34150101		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120127673_120127674insTA	uc003eds.2	-						FSTL1_uc011bjh.1_Intron	NM_007085	NP_009016	Q12841	FSTL1_HUMAN	follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)		ctgtgtgtgtgtctgtTCTTGT	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127550450	127550451	+	IGR	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127550450_127550451delTC								MGLL (8399 upstream) : KBTBD12 (83867 downstream)																							tcctagcttttctcaaagagca	0.243													4	2	---	---	---	---	
COL6A6	131873	broad.mit.edu	37	3	130329247	130329247	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130329247delT	uc010htl.2	+						COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						CCATTCAGTATTTTTTTCCAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133412816	133412816	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133412816delC								TOPBP1 (32079 upstream) : TF (6395 downstream)																							GGTTCCATCACCCCATCAGTG	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133794083	133794083	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133794083delG								SLCO2A1 (45163 upstream) : RYK (81895 downstream)																							ccaagactttgggttttcttc	0.100													4	2	---	---	---	---	
SLC25A36	55186	broad.mit.edu	37	3	140689553	140689553	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140689553delA	uc003etr.2	+						SLC25A36_uc003ets.2_Intron|SLC25A36_uc003etq.2_Intron|SLC25A36_uc011bmz.1_Intron	NM_001104647	NP_001098117	Q96CQ1	S2536_HUMAN	solute carrier family 25, member 36 isoform a						response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						TTTTGCTTTTAAAAGAATCTG	0.303													4	2	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141044865	141044865	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141044865delA	uc003etw.2	+							NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TTCTTTAATTAAAAAAAAAGT	0.313													5	3	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149272438	149272438	+	Intron	DEL	A	-	-	rs142486325		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149272438delA	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron	NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			AAGTCTAGGGAAAAAAAAAAA	0.338													2	4	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	156149098	156149098	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156149098delC	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GATTATTTTTCTAAACTCTGT	0.313													4	2	---	---	---	---	
SI	6476	broad.mit.edu	37	3	164757421	164757421	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164757421delT	uc003fei.2	-							NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	GATAATACAGTTTTTTTTTTC	0.244										HNSCC(35;0.089)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175924780	175924780	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175924780delT								NAALADL2 (401354 upstream) : TBL1XR1 (813763 downstream)																							tctctgctaatttttttttct	0.010													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	186005915	186005915	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186005915delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TAAAACCTACTTTAGTAGCAC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	415851	415851	+	IGR	DEL	T	-	-	rs146931675		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:415851delT								ZNF141 (38092 upstream) : ABCA11P (3373 downstream)																							CACACCCTACttttttttttt	0.109													5	3	---	---	---	---	
PIGG	54872	broad.mit.edu	37	4	515273	515274	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:515273_515274insA	uc003gak.3	+						PIGG_uc003gaj.3_Intron|PIGG_uc011bux.1_Intron|PIGG_uc010ibf.2_Intron|PIGG_uc003gal.3_Intron|PIGG_uc003gai.2_Intron|PIGG_uc011buw.1_Intron|PIGG_uc003gam.2_Intron|PIGG_uc003gan.2_Intron	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4						CTGCAGGTGATAAAAAAAAATC	0.406													4	2	---	---	---	---	
POLN	353497	broad.mit.edu	37	4	2178409	2178409	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2178409delT	uc003ger.2	-						POLN_uc010ich.1_Intron|POLN_uc011bvi.1_Intron	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			agacctggcctctctggagtc	0.164								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					3	3	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2363006	2363006	+	Intron	DEL	A	-	-	rs10706213		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2363006delA	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gey.3_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						CTCTCGGTTCAAAAAATACAA	0.443													4	3	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7713214	7713214	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7713214delA	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						GGCCTCTGGTAATATGGCCGG	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9273621	9273622	+	IGR	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9273621_9273622delAC								LOC650293 (321495 upstream) : USP17 (86487 downstream)																							CCCAGcacaaacacacacacac	0.233													4	2	---	---	---	---	
LCORL	254251	broad.mit.edu	37	4	17964379	17964379	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17964379delA	uc003gpq.2	-						LCORL_uc011bxk.1_Intron	NM_153686	NP_710153	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						ATAAATAAGTAAAAAAAAAGA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	20101310	20101310	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20101310delA								None (None upstream) : SLIT2 (153925 downstream)																							GTGTGCATTTAAAAAAAAAAA	0.199													4	2	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40438204	40438204	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40438204delC	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						aaaaaaaaaacaaacaaacaa	0.164													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	41343361	41343361	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41343361delT								UCHL1 (72916 upstream) : LIMCH1 (19443 downstream)																							ccttgaattgtcctcttccaa	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49534603	49534604	+	IGR	INS	-	T	T	rs143333563		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49534603_49534604insT								CWH43 (470510 upstream) : None (None downstream)																							ATACTAAGTAATTAAAAAAAAA	0.129													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58998315	58998315	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58998315delC								None (None upstream) : None (None downstream)																							TGAAGCATGGCCTCTTTGCAT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	74501093	74501093	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74501093delG								RASSF6 (14753 upstream) : IL8 (105182 downstream)																							aaaaacttctgggatacagca	0.000													4	2	---	---	---	---	
MTHFD2L	441024	broad.mit.edu	37	4	75025262	75025263	+	Intron	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75025262_75025263delTC	uc003hhn.1	+						MTHFD2L_uc011cbj.1_Intron|MTHFD2L_uc011cbk.1_Intron|MTHFD2L_uc003hho.2_Intron|uc003hhq.1_5'Flank|MTHFD2L_uc003hhr.3_Intron|MTHFD2L_uc003hhs.2_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)			AATTTCCCTGTCAGCTTGCTGT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78117801	78117802	+	IGR	INS	-	T	T	rs148699591	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78117801_78117802insT								CCNG2 (26591 upstream) : CXCL13 (315105 downstream)																							GATGAGAGAAGTTACAGGTGGT	0.421													3	3	---	---	---	---	
ANXA3	306	broad.mit.edu	37	4	79500531	79500532	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79500531_79500532delAA	uc003hld.2	+						ANXA3_uc003hle.2_Intron|ANXA3_uc010ijk.2_Intron	NM_005139	NP_005130	P12429	ANXA3_HUMAN	annexin A3						defense response to bacterium|neutrophil degranulation|phagocytosis|positive regulation of angiogenesis|positive regulation of endothelial cell migration|positive regulation of sequence-specific DNA binding transcription factor activity	phagocytic vesicle membrane|plasma membrane|specific granule	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity				0						agtgggttctaaaccagaagtg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82545937	82545938	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82545937_82545938insT								RASGEF1B (152876 upstream) : HNRNPD (728529 downstream)																							TATTGGTTCTATTTTTTTCCAC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90258360	90258360	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90258360delC								GPRIN3 (29199 upstream) : SNCA (386891 downstream)																							CAATTTAGCTCCTCAAGCCAG	0.423													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	92252685	92252686	+	Intron	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92252685_92252686delAC	uc003hsv.3	+							NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						atttgaccttaccctctttacc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97490929	97490929	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97490929delT								PDHA2 (728305 upstream) : C4orf37 (989105 downstream)																							GGCTTTTCCCTTATCCTAATG	0.413													4	2	---	---	---	---	
SLC39A8	64116	broad.mit.edu	37	4	103217489	103217489	+	Intron	DEL	T	-	-	rs35003556		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103217489delT	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AGAAGTCATCTTTTTAAGTGA	0.308													3	3	---	---	---	---	
NFKB1	4790	broad.mit.edu	37	4	103484409	103484410	+	Intron	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103484409_103484410delTC	uc011ceq.1	+						NFKB1_uc011cep.1_Intron	NM_003998	NP_003989	P19838	NFKB1_HUMAN	nuclear factor kappa-B, subunit 1 isoform 1						anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|breast(2)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)	TGGAAGAAAATCTTAAGTTTCA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104734272	104734272	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104734272delC								TACR3 (93299 upstream) : CXXC4 (659073 downstream)																							atataaaattcttggttgttt	0.000													4	2	---	---	---	---	
NPNT	255743	broad.mit.edu	37	4	106848318	106848319	+	Intron	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106848318_106848319delTG	uc003hya.2	+						NPNT_uc011cfc.1_Intron|NPNT_uc011cfd.1_Intron|NPNT_uc011cfe.1_Intron|NPNT_uc010ilt.1_Intron|NPNT_uc011cff.1_Intron|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor						cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		ACATAACACATGTGTGTGTGTG	0.282													4	3	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	142956098	142956099	+	Intron	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142956098_142956099delAC	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					ATCACCTGGAACACACACACAC	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144906215	144906216	+	IGR	DEL	CC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144906215_144906216delCC								GYPE (79499 upstream) : GYPA (11041 downstream)																							CCACCTCTCTCCCCCGCTACTG	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	168508112	168508112	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168508112delT								SPOCK3 (352371 upstream) : ANXA10 (505595 downstream)																							ctttttaccatttttttatct	0.109													4	2	---	---	---	---	
SH3RF1	57630	broad.mit.edu	37	4	170018010	170018010	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170018010delA	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)		ACTTAGTACTAACAAAGACTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180936561	180936562	+	IGR	INS	-	T	T	rs147359670	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180936561_180936562insT								None (None upstream) : None (None downstream)																							GCTGTTTTGTGGTTGATGTGTG	0.361													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184340606	184340606	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184340606delC								WWC2 (98679 upstream) : CDKN2AIP (25183 downstream)																							AACTGATTCTCCAGGGACCAG	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	186460789	186460790	+	IGR	DEL	GA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186460789_186460790delGA								PDLIM3 (4077 upstream) : SORBS2 (45809 downstream)																							ttcaaagagtgaaggcaaatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190568016	190568017	+	IGR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190568016_190568017insA								None (None upstream) : FRG1 (293957 downstream)																							aaaagcaaatgaaaaaaaaTTA	0.252													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2445626	2445626	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2445626delG								IRX4 (562746 upstream) : IRX2 (300655 downstream)																							AGTGGTTTTAGGAAACTTTGA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5798969	5798969	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5798969delG								KIAA0947 (308632 upstream) : FLJ33360 (511585 downstream)																							tgatgtgtgtggcttaaacag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10620951	10620952	+	IGR	INS	-	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10620951_10620952insC								ROPN1L (155814 upstream) : DAP (58391 downstream)																							ggcagatatttcccctctgtaa	0.000													4	2	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14481080	14481080	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14481080delA	uc003jff.2	+						TRIO_uc003jfg.2_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)					ttgtctatttaaaaaaaaaaa	0.154													10	6	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15510117	15510117	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15510117delC	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						TCAGCATTTTCCCCGTTCCGT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30180751	30180751	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30180751delA								None (None upstream) : None (None downstream)																							AAGAGTAACTAAAAAAAAAGA	0.323													6	3	---	---	---	---	
GOLPH3	64083	broad.mit.edu	37	5	32135385	32135386	+	Intron	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32135385_32135386delAC	uc003jhp.1	-							NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						ggggtttgttaccaccacagct	0.119													10	5	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	37016506	37016506	+	Intron	DEL	T	-	-	rs75032300		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37016506delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GCTTTAACAATTTTTTTTTTT	0.269													3	3	---	---	---	---	
HEATR7B2	133558	broad.mit.edu	37	5	41010468	41010468	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41010468delG	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8						TACCCTTTTTGCAAAATGAGT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42236296	42236296	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42236296delT								FBXO4 (294633 upstream) : GHR (187730 downstream)																							CACTGATCTCTTTCTGTCACC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	44777208	44777208	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44777208delA								FGF10 (388424 upstream) : MRPS30 (31819 downstream)																							TCACTGCTGGAAAAAAAATTA	0.338													4	2	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53313659	53313659	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53313659delA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				AGCAATAGACAAAAGACACTC	0.433													4	2	---	---	---	---	
PPAP2A	8611	broad.mit.edu	37	5	54787189	54787189	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54787189delT	uc003jqa.2	-						PPAP2A_uc003jpz.2_Intron|PPAP2A_uc003jqb.2_Intron	NM_003711	NP_003702	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|androgen receptor signaling pathway|germ cell migration|negative regulation of cell proliferation|phospholipid dephosphorylation|regulation of lipid metabolic process|sphingolipid metabolic process	integral to plasma membrane|membrane fraction	phosphatidate phosphatase activity|sphingosine-1-phosphate phosphatase activity			ovary(2)	2		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				AAATAAACAATAAAAGAGACT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55611752	55611753	+	IGR	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55611752_55611753delTG								ANKRD55 (82566 upstream) : MAP3K1 (499147 downstream)																							tacagggtgctgtgtgaagtgg	0.000													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	58271964	58271964	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58271964delT	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jrt.2_Intron|PDE4D_uc003jru.2_Intron|PDE4D_uc003jrv.2_Intron|PDE4D_uc003jrw.2_Intron|PDE4D_uc003jrs.2_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	TGTTTGTTAGTTTTTTTAATT	0.353													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59705727	59705727	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59705727delC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	CAGGGAAGAACAAAGCAGTCA	0.468													4	2	---	---	---	---	
CWC27	10283	broad.mit.edu	37	5	64096894	64096895	+	Intron	DEL	CC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64096894_64096895delCC	uc003jtn.1	+						CWC27_uc003jtl.2_Intron|CWC27_uc003jtm.2_Intron|CWC27_uc010iwt.1_Intron	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						TTGCTTTTTTCCTTTCAAATTC	0.297													8	4	---	---	---	---	
CWC27	10283	broad.mit.edu	37	5	64259773	64259774	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64259773_64259774insA	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						TGACTTTCTGGAAAAAAAATTG	0.347													4	2	---	---	---	---	
TMEM171	134285	broad.mit.edu	37	5	72424584	72424587	+	Intron	DEL	ATCT	-	-	rs139783612		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72424584_72424587delATCT	uc003kcm.2	+						TMEM171_uc003kcn.3_Intron	NM_173490	NP_775761	Q8WVE6	TM171_HUMAN	transmembrane protein 171 isoform 1							integral to membrane					0		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		TACTCCAGGCATCTATCTTTATGT	0.230													2	4	---	---	---	---	
PDE8B	8622	broad.mit.edu	37	5	76528951	76528952	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76528951_76528952delAA	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)		GCTTATAAGTAAAGAGGAAGGC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88829334	88829335	+	IGR	INS	-	TCT	TCT			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88829334_88829335insTCT								MEF2C (629465 upstream) : CETN3 (860196 downstream)																							tcatgaatagatcttctgtcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	100020403	100020403	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100020403delC								FAM174A (97963 upstream) : ST8SIA4 (122237 downstream)																							ttacctttttcccacaagaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102085895	102085898	+	IGR	DEL	CTAA	-	-	rs143162211		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102085895_102085898delCTAA								SLCO6A1 (251175 upstream) : PAM (115629 downstream)																							TCAACTTGGTCTAACTACCTCTTA	0.348													4	2	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108133721	108133721	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108133721delT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		ttcagtTGTGTTTTTTTTTTT	0.114													4	2	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111246045	111246045	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111246045delT	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947	Q16612	NP311_HUMAN	neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		TTAAATCATCTTTTTTTTCCA	0.378													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	113109568	113109568	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113109568delT								YTHDC2 (178589 upstream) : KCNN2 (588448 downstream)																							atccccttggttcctttatta	0.000													4	2	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115562357	115562357	+	Intron	DEL	A	-	-	rs66601712		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115562357delA	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		AACACAAGGGAAAAAAAAAAT	0.363													2	4	---	---	---	---	
SNCAIP	9627	broad.mit.edu	37	5	121787400	121787400	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121787400delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		AATCCCCAGGAAAAAAAAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122613207	122613207	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122613207delT								PRDM6 (89463 upstream) : CEP120 (67373 downstream)																							CTTCCTGCAATTTTTTGCCCT	0.418													4	2	---	---	---	---	
ADAMTS19	171019	broad.mit.edu	37	5	129000902	129000902	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129000902delT	uc003kvb.1	+						ADAMTS19_uc010jdh.1_Intron	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)		TTCCACTGGGTTTTTTTTTTT	0.373													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129202346	129202346	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129202346delC								ADAMTS19 (127970 upstream) : CHSY3 (38177 downstream)																							GGACTCTGATCAAGCTGGAGT	0.214													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130825550	130825550	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130825550delT	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		tactataaacTTTTTTTTTTT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131389692	131389692	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131389692delC								ACSL6 (41822 upstream) : IL3 (6655 downstream)																							TCTACAGGGGCCAAGTGTGTG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133121818	133121818	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133121818delC								FSTL4 (173595 upstream) : C5orf15 (169381 downstream)																							CGTGATTCTTCCCCACCCAAG	0.542													4	2	---	---	---	---	
CDKN2AIPNL	91368	broad.mit.edu	37	5	133738314	133738314	+	3'UTR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133738314delA	uc011cxs.1	-	3						NM_080656	NP_542387	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like												0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			tgtcgataagaaaaaaaaaaa	0.129													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133856358	133856358	+	IGR	DEL	T	-	-	rs10712727		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133856358delT								CDKN2AIPNL (108769 upstream) : PHF15 (3708 downstream)																							ctttgaatgcttttttttttc	0.000													3	4	---	---	---	---	
CDC23	8697	broad.mit.edu	37	5	137524389	137524389	+	3'UTR	DEL	A	-	-	rs79925684		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137524389delA	uc003lcl.2	-	16						NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTTGGGGGCCAAAAAAAAAAA	0.423													5	3	---	---	---	---	
IK	3550	broad.mit.edu	37	5	140038070	140038070	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140038070delT	uc003lgq.2	+							NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein						cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			acccggctaatttttttgtac	0.000													4	2	---	---	---	---	
PCDHAC2	56134	broad.mit.edu	37	5	140365195	140365195	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140365195delG	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.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_Intron	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTTTCCGTGAACCAGCTGT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145131614	145131614	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145131614delC								None (None upstream) : PRELID2 (6968 downstream)																							gactgcagatccctaagagaa	0.164													4	2	---	---	---	---	
JAKMIP2	9832	broad.mit.edu	37	5	147134514	147134514	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147134514delG	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGAGCTTTGGGGGTAGGTG	0.433													4	2	---	---	---	---	
AFAP1L1	134265	broad.mit.edu	37	5	148648888	148648888	+	5'Flank	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148648888delT	uc003lqh.2	+						AFAP1L1_uc003lqg.3_5'Flank|AFAP1L1_uc010jgy.2_5'Flank	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1								protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCTTAGCCTTTTTTACTTT	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152159491	152159491	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152159491delA	uc003lux.1	-											Homo sapiens cDNA FLJ35529 fis, clone SPLEN2001912.																		ggcacactctaaacatccctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154066271	154066271	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154066271delT								MIR1303 (850 upstream) : LARP1 (26191 downstream)																							cctttctggcTTTGGAGATGG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159939724	159939725	+	IGR	DEL	CT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159939724_159939725delCT								MIR146A (27267 upstream) : ATP10B (50402 downstream)																							acctgaatacctctctgtctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162685345	162685345	+	IGR	DEL	A	-	-	rs151080570		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162685345delA								None (None upstream) : CCNG1 (179232 downstream)																							CAGAAACAGtaaaaaaaaaaa	0.358													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166969791	166969791	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166969791delA	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)		AAGATTTTATAAAACCAATAA	0.294													4	2	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167876251	167876251	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167876251delT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron|WWC1_uc010jjf.1_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GGGTTTGTGGTTTTTTTTTCT	0.124													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168541520	168541520	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168541520delC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTTGAACAACCCCCAGACTC	0.373													4	2	---	---	---	---	
C5orf41	153222	broad.mit.edu	37	5	172507522	172507522	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172507522delT	uc003mch.2	+						C5orf41_uc003mcg.2_Intron|C5orf41_uc003mcf.2_Intron|C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835	Q8IUR6	CE041_HUMAN	luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AAAAGTCAACTTTTTTTTTGA	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174261463	174261463	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174261463delC								MSX2 (103562 upstream) : DRD1 (606213 downstream)																							CCCCAAGTGTCCTGACACTCC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175116842	175116842	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175116842delC								HRH2 (3599 upstream) : CPLX2 (106768 downstream)																							ATCCGGAGTTCCCAACAACCT	0.552													4	2	---	---	---	---	
UIMC1	51720	broad.mit.edu	37	5	176396898	176396898	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176396898delA	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mfh.1_Intron|UIMC1_uc010jkj.1_Intron|UIMC1_uc003mff.1_5'Flank	NM_016290	NP_057374	Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCACTATACTAAACCCTTTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	364622	364623	+	IGR	DEL	GA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:364622_364623delGA								DUSP22 (13269 upstream) : IRF4 (27129 downstream)																							GACAGGTCATGAACCCCCTGAA	0.450													4	2	---	---	---	---	
KIFC1	3833	broad.mit.edu	37	6	33374868	33374868	+	Intron	DEL	A	-	-	rs35560427		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33374868delA	uc003oef.3	+						KIFC1_uc011drf.1_Intron	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1						blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						AAAGCTGATTAAAAAAAAAAG	0.209													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	36400719	36400720	+	IGR	DEL	AG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36400719_36400720delAG								PXT1 (32408 upstream) : KCTD20 (9824 downstream)																							AAAAAAAAAAAGGTACTTCTTA	0.267													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38819696	38819696	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38819696delC	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						ttcctaatttccccatccctc	0.119													4	2	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42234653	42234653	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42234653delA	uc003osd.2	-						TRERF1_uc011duq.1_Intron|TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			accactgcctaatgtctcata	0.164													4	2	---	---	---	---	
GTPBP2	54676	broad.mit.edu	37	6	43591274	43591274	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43591274delA	uc003ovs.2	-						GTPBP2_uc010jyv.2_Intron|GTPBP2_uc003ovt.1_Intron	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2								GTP binding|GTPase activity			liver(1)|skin(1)	2	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			ATTCCCCAATAGGCAGCAATA	0.453													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56426662	56426663	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56426662_56426663insA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAAATAACGTTATCCCAAGTGA	0.277													2	4	---	---	---	---	
DST	667	broad.mit.edu	37	6	56426666	56426668	+	Intron	DEL	CCA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56426666_56426668delCCA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TAACGTTATCCCAAGTGACAAAA	0.281													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57323077	57323077	+	Intron	DEL	G	-	-	rs67240761		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57323077delG	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)		aagcattgcaggaaaaaaaca	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99465262	99465263	+	IGR	INS	-	A	A	rs926862	byFrequency	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99465262_99465263insA								FBXL4 (69413 upstream) : C6orf168 (255531 downstream)																							aaagacagaggaaaaaaaaata	0.069													4	2	---	---	---	---	
SEC63	11231	broad.mit.edu	37	6	108245767	108245767	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108245767delA	uc003psc.3	-						SEC63_uc003psb.3_5'Flank	NM_007214	NP_009145	Q9UGP8	SEC63_HUMAN	SEC63-like protein						protein folding|protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|receptor activity|unfolded protein binding			ovary(1)|skin(1)	2		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		gagactctgtaaaaaaaaaTG	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115736048	115736048	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115736048delT								None (None upstream) : FRK (526645 downstream)																							ACGATGGATCTTCAACTACAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	116207677	116207677	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116207677delA								None (None upstream) : FRK (55016 downstream)																							CTTCTCCCTCAAAAAAAAATT	0.363													4	2	---	---	---	---	
HEY2	23493	broad.mit.edu	37	6	126079979	126079979	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126079979delT	uc003qad.2	+						HEY2_uc011ebr.1_Intron	NM_012259	NP_036391	Q9UBP5	HEY2_HUMAN	hairy/enhancer-of-split related with YRPW motif						negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription initiation from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|Notch signaling pathway|smooth muscle cell differentiation|transcription, DNA-dependent	transcriptional repressor complex	histone deacetylase binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		ATGTTCTTAATTTTTTTCCCC	0.388													4	3	---	---	---	---	
C6orf217	100131814	broad.mit.edu	37	6	135855060	135855060	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135855060delT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron|C6orf217_uc003qgm.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0						GTGCCATCTCTTTTTTTTGCT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	140842458	140842458	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140842458delT								None (None upstream) : None (None downstream)																							GCAGTGTTTCTTTGGCAATGG	0.358													4	2	---	---	---	---	
LOC153910	153910	broad.mit.edu	37	6	142890908	142890908	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142890908delA	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0						AGGAAGAGGGAAAGGGTGGAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	143018427	143018427	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143018427delT								LOC153910 (59401 upstream) : HIVEP2 (54178 downstream)																							AGCATGCTGATTAGGTCATAT	0.383													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149387544	149387545	+	Intron	DEL	GC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149387544_149387545delGC	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)		agttttgatggcaaggagccag	0.134													4	2	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	716300	716300	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:716300delC	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CGGGAAGCCACCCCTGCGTGG	0.607													4	2	---	---	---	---	
SP4	6671	broad.mit.edu	37	7	21468148	21468148	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21468148delC	uc003sva.2	+						SP4_uc003svb.2_Intron	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						ccctccttctcccccaccccc	0.403													4	3	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26386733	26386744	+	Intron	DEL	GTGCACACACAC	-	-	rs71731608		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26386733_26386744delGTGCACACACAC	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0						TCTAGGGAGTGTGcacacacacgtgcacacac	0.401													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	27443646	27443647	+	IGR	INS	-	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27443646_27443647insG								EVX1 (157454 upstream) : HIBADH (121416 downstream)																							TGCAGTGATCAGGGAAAAAGGG	0.436													4	2	---	---	---	---	
HIBADH	11112	broad.mit.edu	37	7	27672554	27672554	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27672554delA	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	ATTTTCAAGCAAAAAAAAAAG	0.388													4	2	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29351107	29351107	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29351107delC	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						aggatcatagccccacttcac	0.070													4	2	---	---	---	---	
PLEKHA8	84725	broad.mit.edu	37	7	30101797	30101797	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30101797delT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						TACCACCTTATTTTTTTTTTG	0.308											OREG0017934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
NPSR1	387129	broad.mit.edu	37	7	34871460	34871461	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34871460_34871461insA	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|AAA1_uc010kwy.2_Intron|AAA1_uc003tek.3_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)	CCGACAATTGCAAAAAAAAAAA	0.312													2	4	---	---	---	---	
URGCP	55665	broad.mit.edu	37	7	43946623	43946623	+	5'Flank	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43946623delG	uc003tiw.2	-						URGCP_uc003tiv.2_5'Flank|URGCP_uc003tix.2_5'Flank|URGCP_uc003tiy.2_5'Flank|URGCP_uc003tiz.2_Intron|URGCP_uc011kbj.1_Intron	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3						cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4						gcagtgctgtgttggacgagt	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	50508306	50508306	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50508306delA								IKZF1 (35510 upstream) : FIGNL1 (3528 downstream)																							CTTCTGGGGGAAAAAAAATGC	0.363													4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76627136	76627137	+	Intron	DEL	GT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76627136_76627137delGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						tggacgtgtggtgtgtgtgtgg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	86723920	86723920	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86723920delA								KIAA1324L (34906 upstream) : DMTF1 (57757 downstream)																							cagtcagcacaaaaaaattat	0.124													4	2	---	---	---	---	
SLC25A40	55972	broad.mit.edu	37	7	87479520	87479520	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87479520delA	uc003uje.2	-							NM_018843	NP_061331	Q8TBP6	S2540_HUMAN	mitochondrial carrier family protein						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			haematopoietic_and_lymphoid_tissue(1)	1	Esophageal squamous(14;0.00202)					AAGAGCTTAGAAAAAAAGCTT	0.274													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90486129	90486129	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90486129delA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TGTGGGCTTGAAAAAAAAGTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	92178017	92178017	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92178017delC								MGC16142 (8940 upstream) : FAM133B (12057 downstream)																							TGTAATTTTTCATTCTTACCA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96560945	96560945	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96560945delA								SHFM1 (221742 upstream) : DLX6AS (36883 downstream)																							TAGCCTTGAGAAAAAAAAAGT	0.413													4	2	---	---	---	---	
ZKSCAN1	7586	broad.mit.edu	37	7	99621024	99621024	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99621024delT	uc003usk.1	+						ZKSCAN1_uc003usj.2_Intron|ZKSCAN1_uc003usl.1_Intron|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36						viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TACTAATGACTTTTTTTTTAT	0.393													4	2	---	---	---	---	
PMS2L1	5379	broad.mit.edu	37	7	99928385	99928385	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99928385delT	uc003uuh.2	-						PMS2L1_uc003uui.2_Intron|PMS2L1_uc010lgv.1_Intron|PMS2L1_uc003uuj.1_Intron	NR_003613				Homo sapiens PMS2L13 mRNA, partial cds.												0						TTCTTTCCTCTTTTTTTTTTT	0.144													5	3	---	---	---	---	
DNAJC2	27000	broad.mit.edu	37	7	102963381	102963381	+	Intron	DEL	T	-	-	rs75138416		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									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													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114694618	114694619	+	IGR	INS	-	TT	TT	rs147212842	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114694618_114694619insTT								MDFIC (35355 upstream) : TFEC (880583 downstream)																							ctaataggttgtttgctgcacc	0.153													1	5	---	---	---	---	
ASZ1	136991	broad.mit.edu	37	7	117044478	117044479	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117044478_117044479insA	uc003vjb.2	-						ASZ1_uc011kno.1_Intron|ASZ1_uc011knp.1_Intron	NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			ttccttttttttttttttgact	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118453148	118453148	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118453148delG								ANKRD7 (570366 upstream) : None (None downstream)																							TCTAATCTCTGGGGGTTAATA	0.318													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122074395	122074395	+	Intron	DEL	A	-	-	rs79849585	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122074395delA	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						AAGGTAGGGGAAAAAAAAAAG	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142604272	142604272	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142604272delG								TRPV6 (20795 upstream) : TRPV5 (1376 downstream)																							AAAGGGAGATGGGAATGGAGG	0.522													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142654701	142654701	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142654701delT	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					CCAGGCCTACTTCTGTCTTCC	0.299													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148241800	148241800	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148241800delC								CNTNAP2 (123714 upstream) : C7orf33 (45857 downstream)																							TGGGAAGACACCACGGGAAGG	0.438													4	2	---	---	---	---	
UBE3C	9690	broad.mit.edu	37	7	156991227	156991227	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156991227delT	uc010lqs.2	+						UBE3C_uc003wng.2_Intron	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TGTAtttgtcttttttttttt	0.308													4	3	---	---	---	---	
ESYT2	57488	broad.mit.edu	37	7	158619973	158619973	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158619973delA	uc003wob.1	-						ESYT2_uc003wod.1_Intron	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3						CACTTCCTGCAAATTTCAGCA	0.294													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1873966	1873966	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1873966delC	uc003wpr.2	+						ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpv.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CCGCTCTTTGCCTTGGCAGAC	0.527													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4349235	4349235	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4349235delA	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)		ccagaatggcaacacaaccaa	0.000													4	2	---	---	---	---	
ERI1	90459	broad.mit.edu	37	8	8870434	8870435	+	Intron	DEL	TT	-	-	rs35319524		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8870434_8870435delTT	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163	Q8IV48	ERI1_HUMAN	three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)	ttcaataaagtttaagctgtgt	0.000													2	4	---	---	---	---	
PSD3	23362	broad.mit.edu	37	8	18392906	18392906	+	3'UTR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18392906delA	uc003wza.2	-	16					PSD3_uc003wyx.3_3'UTR|PSD3_uc003wyy.2_3'UTR|PSD3_uc003wyz.2_3'UTR	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CTTTAACCTTAAAAAAAAGTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19159170	19159170	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19159170delA								PSD3 (287974 upstream) : SH2D4A (12037 downstream)																							AATTTAACATAAAAAAAGACA	0.244													4	2	---	---	---	---	
DOK2	9046	broad.mit.edu	37	8	21771309	21771309	+	5'Flank	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21771309delC	uc003wzy.1	-						DOK2_uc003wzx.1_5'Flank|DOK2_uc003wzz.1_5'Flank|DOK2_uc010lth.1_5'Flank	NM_003974	NP_003965	O60496	DOK2_HUMAN	docking protein 2						blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		tcttttttttctttttttttt	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23630679	23630680	+	IGR	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23630679_23630680delTC								NKX2-6 (66757 upstream) : STC1 (68754 downstream)																							TTCTACTTTGTCAAGAAAAATG	0.401													4	2	---	---	---	---	
ADRA1A	148	broad.mit.edu	37	8	26724687	26724687	+	5'Flank	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26724687delA	uc003xfh.1	-						ADRA1A_uc003xfc.1_5'Flank|ADRA1A_uc010lul.1_5'Flank|ADRA1A_uc003xfd.1_5'Flank|ADRA1A_uc003xfe.1_5'Flank|ADRA1A_uc010lum.1_5'Flank|ADRA1A_uc003xff.1_5'Flank|ADRA1A_uc003xfg.1_5'Flank|uc010lun.1_RNA	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1						activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)	ATAAGAAAAGAAAAAAAAATG	0.423													4	2	---	---	---	---	
TRIM35	23087	broad.mit.edu	37	8	27162288	27162288	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27162288delG	uc003xfl.1	-						TRIM35_uc010lup.1_Intron|TRIM35_uc003xfm.1_RNA	NM_171982	NP_741983	Q9UPQ4	TRI35_HUMAN	tripartite motif-containing 35 isoform 2						apoptosis|induction of apoptosis|negative regulation of mitotic cell cycle	cytoplasm|nucleus	zinc ion binding				0		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)		CTTGCCTCCTggactgaaggt	0.090													4	2	---	---	---	---	
UNC5D	137970	broad.mit.edu	37	8	35343552	35343552	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35343552delT	uc003xjr.1	+							NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GTCACACTGCTTTTTTTTCTA	0.408													4	2	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48640092	48640092	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48640092delC	uc003xqd.2	+						KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron|KIAA0146_uc003xqg.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				TGGGTTTTGTCCCCACCTCCT	0.438													4	2	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56340897	56340897	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56340897delA	uc003xsf.2	+							NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			gcaacctggtaatcccatcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61858160	61858160	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61858160delG								CHD7 (78697 upstream) : CLVS1 (342365 downstream)																							cactgtgcctggcctctgtgc	0.000													4	2	---	---	---	---	
MTFR1	9650	broad.mit.edu	37	8	66605637	66605637	+	Intron	DEL	A	-	-	rs75044467		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66605637delA	uc003xvm.2	+						MTFR1_uc011lep.1_Intron|MTFR1_uc003xvn.2_Intron|MTFR1_uc003xvo.1_Intron	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1							mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			actttgtctcaaaaaaaaaaa	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87247548	87247548	+	IGR	DEL	A	-	-	rs35314286		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87247548delA								SLC7A13 (4939 upstream) : WWP1 (107446 downstream)																							ctttattgctaaaaaaatatg	0.000													6	4	---	---	---	---	
RBM12B	389677	broad.mit.edu	37	8	94745437	94745438	+	3'UTR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745437_94745438insA	uc003yfz.2	-	3						NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTTTAAATTTGAAAAAAAAAAA	0.282													5	3	---	---	---	---	
SDC2	6383	broad.mit.edu	37	8	97613888	97613888	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97613888delG	uc003yhv.1	+						SDC2_uc011lgu.1_Intron	NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	aaaaaaaaaagaaacaaaaCA	0.204													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101922630	101922631	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101922630_101922631delAA								PABPC1 (188315 upstream) : YWHAZ (8173 downstream)																							CACTGGGTCTAAACTCTGTCTC	0.485													4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107333781	107333781	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107333781delT	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)			CTGAATGGTGTTAAGACTATT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112690984	112690984	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112690984delT								None (None upstream) : CSMD3 (544177 downstream)																							GGGACTTCCCTTTTCAGCCTG	0.408													4	2	---	---	---	---	
SLC30A8	169026	broad.mit.edu	37	8	118103311	118103311	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118103311delT	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TGAAAACATCTTTTTTTTTTT	0.323													2	5	---	---	---	---	
ENPP2	5168	broad.mit.edu	37	8	120650439	120650439	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120650439delA	uc003yot.1	-						ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATTTGAGTACAAAAATGGAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126542382	126542383	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126542382_126542383delAA								TRIB1 (91740 upstream) : None (None downstream)																							atgactttttaagagtcttccc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128043865	128043865	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128043865delT								FAM84B (473399 upstream) : LOC727677 (258197 downstream)																							TCTTTATCTCTTTTACAGGAG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137326244	137326244	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137326244delT								KHDRBS3 (666398 upstream) : None (None downstream)																							agaagggtgattttttttaca	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139947414	139947414	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139947414delC								COL22A1 (21178 upstream) : KCNK9 (665668 downstream)																							GCCATTCTCTCCAAATCTCCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143164707	143164708	+	IGR	INS	-	AC	AC			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143164707_143164708insAC								MIR1302-7 (297033 upstream) : NCRNA00051 (115009 downstream)																							acacaccacagacacacacatc	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2325305	2325307	+	IGR	DEL	TAC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2325305_2325307delTAC								SMARCA2 (131684 upstream) : FLJ35024 (97395 downstream)																							TGAATAATAATACtaatagccat	0.015													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	10172628	10172629	+	Intron	DEL	CT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10172628_10172629delCT	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)		CTTCTTCAACCTCATTTAATGC	0.426										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11903377	11903377	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11903377delT								None (None upstream) : TYRP1 (790009 downstream)																							ttgttttcactttttttttgt	0.000													4	2	---	---	---	---	
TTC39B	158219	broad.mit.edu	37	9	15264244	15264244	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15264244delA	uc003zlr.1	-						TTC39B_uc010mie.1_Intron|TTC39B_uc011lmq.1_Intron|TTC39B_uc011lmr.1_Intron|TTC39B_uc010mif.1_Intron|TTC39B_uc010mig.1_Intron|TTC39B_uc011lms.1_Intron	NM_152574	NP_689787	Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B								binding			ovary(1)	1						tgaacaagctaaaaaatctaa	0.164													4	2	---	---	---	---	
BNC2	54796	broad.mit.edu	37	9	16512483	16512484	+	Intron	DEL	CA	-	-	rs113858472		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16512483_16512484delCA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc011lmv.1_Intron|BNC2_uc003zmo.1_Intron	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		Aacacacgcgcacacacacaca	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	23850916	23850916	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23850916delA								ELAVL2 (24853 upstream) : None (None downstream)																							GTCAGCGTTCAAAAAAAGTAC	0.403													4	2	---	---	---	---	
DDX58	23586	broad.mit.edu	37	9	32467097	32467097	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32467097delA	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mjk.1_Intron|DDX58_uc011lnr.1_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		gggaagaggtaaaatgaagag	0.159													4	2	---	---	---	---	
CD72	971	broad.mit.edu	37	9	35633401	35633401	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35633401delT	uc010mkw.1	-									P21854	CD72_HUMAN	Homo sapiens mRNA for CD72 antigen variant protein.						axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity				0			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			gcttgctatctttttgacagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66459932	66459933	+	5'Flank	DEL	AA	-	-	rs112939877	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459932_66459933delAA	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		accatatgagaagtttaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68489056	68489057	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68489056_68489057delAA								FAM27B (694867 upstream) : MIR1299 (513182 downstream)																							AAAAACAAACAAAAAAAACCCC	0.312													4	3	---	---	---	---	
RMI1	80010	broad.mit.edu	37	9	86617962	86617962	+	3'UTR	DEL	T	-	-	rs11296264		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86617962delT	uc004anq.3	+	3					RMI1_uc004anr.3_3'UTR|RMI1_uc004anp.3_3'UTR|RMI1_uc004ans.3_3'UTR	NM_024945	NP_079221	Q9H9A7	RMI1_HUMAN	RMI1, RecQ mediated genome instability 1,						DNA replication	nucleus					0						TAAGTTAATCttttttttttt	0.114													4	2	---	---	---	---	
SLC35D2	11046	broad.mit.edu	37	9	99113698	99113698	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99113698delG	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron|SLC35D2_uc004awe.2_3'UTR	NM_007001	NP_008932	Q76EJ3	S35D2_HUMAN	solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)				GAGAGATACTGGGACAAAATA	0.333													4	2	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101193726	101193727	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101193726_101193727insA	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	agtaagttctcaaaaattattc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101566225	101566225	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101566225delC								ANKS6 (7431 upstream) : GALNT12 (3756 downstream)																							agtgaaaggaccacagaatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121205231	121205231	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121205231delT								TLR4 (725467 upstream) : DBC1 (723677 downstream)																							gctggtttcctttttgttacc	0.000													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123903270	123903270	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123903270delT	uc004bkx.1	+						CEP110_uc004bky.1_Intron|CEP110_uc004bkz.1_Intron|CEP110_uc004bla.1_Intron|CEP110_uc010mvo.1_5'Flank	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						ATTTTGGATCTTTTTTTTGGT	0.264													4	2	---	---	---	---	
DAB2IP	153090	broad.mit.edu	37	9	124328565	124328565	+	5'Flank	DEL	G	-	-	rs80030483		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124328565delG	uc004bln.2	+							NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2						gaacttattcgggggggcact	0.109													3	3	---	---	---	---	
ENG	2022	broad.mit.edu	37	9	130593072	130593072	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130593072delC	uc004bsj.3	-						ENG_uc011mam.1_Intron|ENG_uc004bsk.3_Intron	NM_001114753	NP_001108225	P17813	EGLN_HUMAN	endoglin isoform 1 precursor						artery morphogenesis|BMP signaling pathway|cell adhesion|cell chemotaxis|central nervous system vasculogenesis|chronological cell aging|detection of hypoxia|extracellular matrix disassembly|heart looping|negative regulation of endothelial cell proliferation|negative regulation of nitric-oxide synthase activity|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of protein autophosphorylation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|patterning of blood vessels|positive regulation of BMP signaling pathway|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of systemic arterial blood pressure|positive regulation of transcription from RNA polymerase II promoter|regulation of cell adhesion|regulation of cell proliferation|regulation of transcription, DNA-dependent|regulation of transforming growth factor beta receptor signaling pathway|smooth muscle tissue development|transforming growth factor beta receptor signaling pathway|venous blood vessel morphogenesis|wound healing	cell surface|external side of plasma membrane|extracellular space|membrane fraction	activin binding|galactose binding|glycosaminoglycan binding|protein homodimerization activity|transforming growth factor beta binding|transforming growth factor beta receptor activity|transforming growth factor beta receptor, cytoplasmic mediator activity|transmembrane receptor activity|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding				0						GTCCCCACCACCTTTCCTGCA	0.428									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				4	2	---	---	---	---	
GOLGA2	2801	broad.mit.edu	37	9	131024603	131024607	+	Intron	DEL	AAAAC	-	-	rs111944122		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131024603_131024607delAAAAC	uc011maw.1	-						GOLGA2_uc010mxw.2_Intron|GOLGA2_uc004buh.2_5'Flank|GOLGA2_uc004bul.1_Intron|uc004bun.2_5'Flank	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2							Golgi cisterna membrane	protein binding			ovary(1)	1						ATGATGCTTTaaaacaaaacaaaac	0.332													4	2	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131324315	131324315	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131324315delG	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						AGAGGTGGGTGGTCAGGGAGT	0.378													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1527844	1527845	+	Intron	DEL	GC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1527844_1527845delGC	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTTGTTCATTGCTGTCCTGTCA	0.525													4	2	---	---	---	---	
PITRM1	10531	broad.mit.edu	37	10	3198910	3198910	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3198910delA	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|PITRM1_uc001igw.1_Intron			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						TTCACACACTAAAAATGCACA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4385358	4385359	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4385358_4385359delAA								KLF6 (557885 upstream) : LOC100216001 (236085 downstream)																							acgtcatgctaagtaaacaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11682651	11682652	+	IGR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11682651_11682652insA								USP6NL (28972 upstream) : ECHDC3 (101704 downstream)																							GTGGCCAAGGCAAAAAACAGTC	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	15505715	15505715	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15505715delT								FAM171A1 (92657 upstream) : ITGA8 (53373 downstream)																							ttgacagccctttttttttcc	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29027897	29027897	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29027897delG								BAMBI (56029 upstream) : LYZL1 (550093 downstream)																							cacaagaagaggggcagcaga	0.000													4	2	---	---	---	---	
LYZL2	119180	broad.mit.edu	37	10	30901429	30901429	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30901429delT	uc001ivk.2	-							NM_183058	NP_898881	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2						cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0		Prostate(175;0.151)				AAACTCAAGCTTTTTTTTCCC	0.383													4	3	---	---	---	---	
ZEB1	6935	broad.mit.edu	37	10	31609541	31609541	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31609541delA	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_RNA|ZEB1_uc009xlm.1_5'Flank|ZEB1_uc009xln.1_5'Flank|ZEB1_uc009xlo.1_5'Flank|ZEB1_uc009xlp.2_5'Flank|LOC220930_uc010qed.1_5'Flank	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				CGTGAGAGTTAAAAAAAAAGA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42704179	42704179	+	IGR	DEL	G	-	-	rs9630137		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42704179delG								None (None upstream) : LOC441666 (123136 downstream)																							TCTGGATCATGGGTGACAGAC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44303754	44303754	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44303754delT								HNRNPA3P1 (17889 upstream) : CXCL12 (561853 downstream)																							CAGTGTAGTATTTTTAGGCAA	0.398													4	2	---	---	---	---	
TSPAN15	23555	broad.mit.edu	37	10	71246106	71246106	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71246106delC	uc001jpo.1	+							NM_012339	NP_036471	O95858	TSN15_HUMAN	transmembrane 4 superfamily member 15							integral to plasma membrane|membrane fraction					0						CCCCTCCCTACCCCAGACAGC	0.507													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73447608	73447608	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73447608delG	uc001jrx.3	+						CDH23_uc001jry.2_Intron|CDH23_uc001jrz.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						CCCCGGCCAAGCTCCTTGACA	0.418													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	79201595	79201595	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79201595delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	GCCTGAGATCTTTTTTTTTTC	0.453													4	2	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91486458	91486458	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91486458delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						ACTAAAAATATTTTTTGACTT	0.254													4	2	---	---	---	---	
PCGF5	84333	broad.mit.edu	37	10	92959009	92959009	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92959009delC	uc001khh.2	+						PCGF5_uc001khg.2_Intron	NM_032373	NP_115749	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1						gaagctgactcccaggtgtag	0.114													4	2	---	---	---	---	
NT5C2	22978	broad.mit.edu	37	10	104849890	104849890	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104849890delG	uc001kwo.2	-						NT5C2_uc010qqp.1_Intron|NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	GCTGGAAATTGGAAAAGATGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125014092	125014093	+	IGR	INS	-	CAC	CAC			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125014092_125014093insCAC								BUB3 (89206 upstream) : GPR26 (411778 downstream)																							catcatcatcacaccaccacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125231550	125231550	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125231550delG	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																		tcatttgcctgggcaagaggc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126881944	126881944	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126881944delA								CTBP2 (32320 upstream) : LOC100169752 (380996 downstream)																							aaaacaaaacaaaaccccagt	0.025													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583269	127583269	+	Intron	DEL	C	-	-	rs10709545		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583269delC	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AATACTAATGCTAATCCTTTA	0.303													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130213673	130213674	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130213673_130213674delAA								MKI67 (289205 upstream) : None (None downstream)																							gcctcatcttaacttgatcatc	0.020													4	2	---	---	---	---	
INPP5A	3632	broad.mit.edu	37	10	134430112	134430112	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134430112delG	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		atgtggtTTTGGGGTTGCAGT	0.289													4	2	---	---	---	---	
OR51B5	282763	broad.mit.edu	37	11	5376762	5376763	+	Intron	INS	-	A	A	rs145155018	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5376762_5376763insA	uc001maq.1	-						HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_001005567	NP_001005567	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAACACTAGCACCTGCTTCTC	0.475													2	4	---	---	---	---	
TRIM22	10346	broad.mit.edu	37	11	5748653	5748653	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5748653delT	uc009yet.1	+						TRIM5_uc001mbq.1_Intron|OR56B1_uc001mbs.1_Intron|OR56B1_uc009yev.1_Intron	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22						immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TGTCAGGGTGTTTCAAAGTGG	0.403													4	2	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14825453	14825453	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14825453delT	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						ACTTTTCCTGTTTTTAAAAAT	0.343													322	140	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15928695	15928696	+	IGR	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15928695_15928696delCA								INSC (659943 upstream) : SOX6 (59300 downstream)																							cctggccctccacacacacaca	0.099													6	3	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21092112	21092112	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21092112delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						cctaatttgcaaaaaaataca	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	23037715	23037715	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23037715delA								SVIP (186333 upstream) : None (None downstream)																							catttaccctaaagttgctaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	23188058	23188059	+	IGR	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23188058_23188059delTG								SVIP (336676 upstream) : None (None downstream)																							agcatggcaatgtgagaatatg	0.020													4	2	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33639896	33639896	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33639896delA	uc001mup.3	+							NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758							integral to membrane				ovary(2)	2						CAGCATCTGGAAAAAAAAAAA	0.338													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42639081	42639081	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42639081delT								None (None upstream) : API5 (694424 downstream)																							acagcagacattttTTCATAT	0.189													4	2	---	---	---	---	
ALX4	60529	broad.mit.edu	37	11	44312149	44312149	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44312149delG	uc001myb.2	-							NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4						hair follicle development						0						cagcaatgttgttggagaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48486667	48486668	+	IGR	INS	-	T	T	rs138127835	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48486667_48486668insT								OR4C45 (112668 upstream) : OR4A47 (23677 downstream)																							TGATATGATGATTTTTTCTGAG	0.297													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60117597	60117597	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60117597delT								MS4A6E (9157 upstream) : MS4A7 (28361 downstream)																							ATATTCTTACTGAAAGAGCCT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69808848	69808848	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69808848delG								FGF3 (174656 upstream) : ANO1 (115560 downstream)																							TACTCCTGGTGGGGAAGGAGA	0.617													4	2	---	---	---	---	
FOLH1B	219595	broad.mit.edu	37	11	89409583	89409584	+	Intron	INS	-	T	T	rs112834075		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89409583_89409584insT	uc001pda.2	+							NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B						proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|skin(2)|central_nervous_system(1)	6						tcttttcttacttttttttttt	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	97808686	97808686	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97808686delA								None (None upstream) : None (None downstream)																							ataaggagccaggagtcagga	0.000													4	2	---	---	---	---	
ARHGAP42	143872	broad.mit.edu	37	11	100849437	100849437	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100849437delT	uc001pge.2	+						ARHGAP42_uc001pgd.2_Intron	NM_152432	NP_689645	A6NI28	RHG42_HUMAN	Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0						AAAATGTTCCTTTTACTGCTC	0.433													4	2	---	---	---	---	
CASP5	838	broad.mit.edu	37	11	104871386	104871386	+	Intron	DEL	T	-	-	rs45440097		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104871386delT	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor						apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		TTTTGTTTTGTTTTTTTTTTC	0.363													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109231232	109231232	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109231232delT								DDX10 (419586 upstream) : C11orf87 (61643 downstream)																							AATTCAACTCTTACCCAGGTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109353936	109353936	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109353936delA								C11orf87 (54098 upstream) : ZC3H12C (609990 downstream)																							aaaaagtctcaaaaaactgag	0.000													4	2	---	---	---	---	
ARHGAP20	57569	broad.mit.edu	37	11	110479423	110479423	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110479423delA	uc001pkz.1	-						ARHGAP20_uc001pky.1_Intron|ARHGAP20_uc009yyb.1_Intron|ARHGAP20_uc001pla.1_Intron	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TCTTTCTTAGAAAAAAATTTA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112436331	112436332	+	IGR	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112436331_112436332delTC								PTS (295654 upstream) : NCAM1 (395663 downstream)																							CTGCATTTTTTCTCCTGACTCC	0.441													4	2	---	---	---	---	
NCAM1	4684	broad.mit.edu	37	11	113146345	113146346	+	3'UTR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113146345_113146346insA	uc001pns.2	+	6					uc010rwu.1_5'Flank|NCAM1_uc001pnt.2_3'UTR			P13591	NCAM1_HUMAN	SubName: Full=cDNA FLJ52974, highly similar to Neural cell adhesion molecule 1, 140 kDa isoform;						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		TCACTTGTAAGAAAATGAGACA	0.366													4	2	---	---	---	---	
ZW10	9183	broad.mit.edu	37	11	113618699	113618700	+	Intron	DEL	TA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113618699_113618700delTA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		AAGGAAACACTAAAAAGAAGCA	0.248													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	117927900	117927900	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117927900delA	uc001prx.1	-						uc001pry.1_Intron|uc001prz.1_Intron|uc009yzs.1_Intron|uc001psa.1_Intron					Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit26-03-15-R.																		GTGCTCTCTTAAGAAGGAGGA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127378242	127378242	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127378242delT								KIRREL3 (504887 upstream) : ETS1 (950414 downstream)																							actttgtctatttttttttgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129611447	129611447	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129611447delT								BARX2 (289274 upstream) : TMEM45B (74294 downstream)																							gcaccttgacttttttttcat	0.035													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131837604	131837605	+	Intron	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131837604_131837605insT	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						TCTTCTCTCTCTTTTTTGCTGC	0.401													4	2	---	---	---	---	
GLB1L2	89944	broad.mit.edu	37	11	134213971	134213971	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134213971delT	uc001qhp.2	+						GLB1L2_uc009zdg.1_5'Flank	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor						carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		CTTGTAGCTGTTTTTTTGATA	0.463													4	2	---	---	---	---	
SLC6A13	6540	broad.mit.edu	37	12	369475	369475	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:369475delA	uc001qic.1	-						SLC6A13_uc009zdj.1_5'Flank|SLC6A13_uc010sdl.1_Intron|SLC6A13_uc001qid.1_Intron	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			TGCTTCCACTATAAGGCCCTC	0.493													4	2	---	---	---	---	
KCNA6	3742	broad.mit.edu	37	12	4924263	4924263	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4924263delT	uc001qng.2	+							NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3						ctttctccagttttctttctt	0.090										HNSCC(72;0.22)			4	2	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6180747	6180748	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6180747_6180748insA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	AAAGAAGAAAGAAAAAAAAACT	0.421													4	2	---	---	---	---	
SCNN1A	6337	broad.mit.edu	37	12	6456271	6456272	+	3'UTR	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6456271_6456272delCA	uc001qnx.2	-	13					SCNN1A_uc001qnv.2_3'UTR|SCNN1A_uc001qnw.2_3'UTR|SCNN1A_uc010sfb.1_3'UTR	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform						excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)	cagaagcgttcacaaaagtaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	7694670	7694670	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7694670delA								CD163 (38256 upstream) : APOBEC1 (107327 downstream)																							ccccatagccaaaaaaaagaa	0.060													4	2	---	---	---	---	
LOC642846	642846	broad.mit.edu	37	12	9457510	9457511	+	Intron	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9457510_9457511insT	uc010sgp.1	+						LOC642846_uc001qvp.2_Intron	NR_024374				Homo sapiens cDNA FLJ60280 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX11 (EC 3.6.1.-).												0						tcgtgcctgcctttttTTTCTT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16204482	16204482	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16204482delT								DERA (14168 upstream) : MGST1 (295594 downstream)																							actagttggattttttttttA	0.015													3	3	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18527326	18527326	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18527326delA	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				AATCATAACCAAAAAAAAACT	0.269													3	3	---	---	---	---	
PLCZ1	89869	broad.mit.edu	37	12	18878222	18878222	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18878222delG	uc010sid.1	-						PLCZ1_uc001rdv.3_Intron|PLCZ1_uc001rdw.3_Intron	NM_033123	NP_149114	Q86YW0	PLCZ1_HUMAN	phospholipase C, zeta 1						intracellular signal transduction|lipid catabolic process|multicellular organismal development	nucleus|perinuclear region of cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CAAGGGAAGCGGGGAGAAGAA	0.438													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26877951	26877952	+	Intron	INS	-	CA	CA			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877951_26877952insCA	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.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)					TAAATGATTATAATATAGTGTG	0.366													9	5	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29822054	29822054	+	Intron	DEL	A	-	-	rs5797330		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29822054delA	uc001rjb.2	-						TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TCCAAGTGACAAATGTAGCTG	0.483													1	7	---	---	---	---	
RND1	27289	broad.mit.edu	37	12	49258906	49258907	+	Intron	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49258906_49258907delAC	uc001rsn.2	-							NM_014470	NP_055285	Q92730	RND1_HUMAN	GTP-binding protein RHO6 precursor						actin filament organization|axon guidance|negative regulation of cell adhesion|neuron remodeling|small GTPase mediated signal transduction	adherens junction|cytoskeleton|cytosol	GTP binding|GTPase activity|receptor binding			ovary(1)	1						GCGATCAGGGACACACACACAC	0.545													4	2	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49863671	49863671	+	Intron	DEL	A	-	-	rs112020645		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49863671delA	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						attctgtctcaaaaaaaaaag	0.129													4	2	---	---	---	---	
DIP2B	57609	broad.mit.edu	37	12	51080676	51080676	+	Intron	DEL	A	-	-	rs62672860		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51080676delA	uc001rwv.2	+						DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						GAATGACGGCAAAAAAAAAAG	0.343													4	2	---	---	---	---	
TFCP2	7024	broad.mit.edu	37	12	51493732	51493732	+	Intron	DEL	T	-	-	rs55976164		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51493732delT	uc001rxw.2	-						TFCP2_uc001rxv.1_Intron|TFCP2_uc009zlx.1_Intron|TFCP2_uc001rxx.2_Intron|TFCP2_uc009zly.1_Intron	NM_005653	NP_005644	Q12800	TFCP2_HUMAN	transcription factor CP2						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGTAGTAGGGTTTTTTTTTTC	0.234													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	64220076	64220077	+	IGR	DEL	TA	-	-	rs10570694		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64220076_64220077delTA								TMEM5 (17189 upstream) : SRGAP1 (18464 downstream)																							AAGAAGAGTTTATCAGCTGTTG	0.446													2	4	---	---	---	---	
E2F7	144455	broad.mit.edu	37	12	77458037	77458040	+	Intron	DEL	ACTG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77458037_77458040delACTG	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						ACCCTTGACAACTGTATTATAAAC	0.377													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82319500	82319500	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82319500delT								PPFIA2 (166391 upstream) : CCDC59 (426590 downstream)																							gggctcgttcttTTTTTTTTC	0.010													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92808241	92808241	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92808241delA								BTG1 (268568 upstream) : CLLU1OS (5629 downstream)																							aagagatgggaaaaaaagaaa	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108389484	108389484	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108389484delT								ASCL4 (219064 upstream) : WSCD2 (134027 downstream)																							tttggttttcttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108438162	108438162	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108438162delG								ASCL4 (267742 upstream) : WSCD2 (85349 downstream)																							GAGCCACTAAGGACAGTAAAA	0.493													4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109626138	109626138	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109626138delA	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	cttcccttccattgccttcct	0.000													4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109626141	109626141	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109626141delG	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	cccttccattgccttcctgcc	0.000													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	118020769	118020769	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118020769delT	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)					CTGACTCCAATTTTTTTTTGT	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119701415	119701416	+	IGR	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119701415_119701416insA								HSPB8 (68865 upstream) : LOC144742 (20214 downstream)																							AGAGAGGGAACAAAAAAAACCC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127465803	127465803	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127465803delT	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																		AGTGCAAGCGTTTTTTTTTTC	0.443													3	5	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129800830	129800830	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129800830delT	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		gcgtttagggttacaaacact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131814739	131814742	+	IGR	DEL	TCCA	-	-	rs72419588		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131814739_131814742delTCCA								LOC116437 (117264 upstream) : SFRS8 (380893 downstream)																							ttctctctcttccatccatccatc	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132006465	132006468	+	IGR	DEL	TAGG	-	-	rs111764591		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132006465_132006468delTAGG								LOC116437 (308990 upstream) : SFRS8 (189167 downstream)																							ggctcctgactaggtaggtcagca	0.069													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20879521	20879521	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20879521delA								GJB6 (72987 upstream) : CRYL1 (98288 downstream)																							TTTTGTATGGAGAGAGGTAAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21677941	21677941	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21677941delT								LATS2 (42219 upstream) : SAP18 (36712 downstream)																							tattttttaattttttttgag	0.184													6	3	---	---	---	---	
EFHA1	221154	broad.mit.edu	37	13	22145237	22145237	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22145237delT	uc001uof.2	-							NM_152726	NP_689939	Q8IYU8	EFHA1_HUMAN	EF-hand domain family, member A1								calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)		TTCAGGTTGCTTTTTTTTTGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23173650	23173650	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23173650delT								FGF9 (895010 upstream) : SGCG (581410 downstream)																							ATTATTTTTGTTTTTTAACAC	0.318													4	2	---	---	---	---	
SGCG	6445	broad.mit.edu	37	13	23861544	23861547	+	Intron	DEL	TGAA	-	-	rs145628381		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23861544_23861547delTGAA	uc001uom.2	+						SGCG_uc009zzv.2_Intron|SGCG_uc009zzw.2_Intron	NM_000231	NP_000222	Q13326	SGCG_HUMAN	gamma sarcoglycan						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		cacaaagaactgaatgaattctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	28289702	28289703	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28289702_28289703insT								POLR1D (48155 upstream) : GSX1 (77077 downstream)																							gggaagtatgatttagcaggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29579666	29579666	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29579666delG								SLC46A3 (286516 upstream) : MTUS2 (19082 downstream)																							AAAGCAGGGTGGAGAGGAGTC	0.493													4	2	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33270686	33270686	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33270686delA	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TTTCAGCTCTAAAAAAAAAAA	0.393													6	8	---	---	---	---	
KL	9365	broad.mit.edu	37	13	33602866	33602867	+	Intron	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33602866_33602867delTG	uc001uus.2	+						KL_uc001uur.1_Intron	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor						aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		aatgcaattatgaacttcaaag	0.000													4	2	---	---	---	---	
RFC3	5983	broad.mit.edu	37	13	34414228	34414229	+	Intron	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34414228_34414229delTG	uc001uva.2	+							NM_181558	NP_853536	P40938	RFC3_HUMAN	replication factor C 3 isoform 2						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|response to organophosphorus|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				0		Hepatocellular(188;0.0191)|Lung SC(185;0.0548)		all cancers(112;5.09e-06)|Epithelial(112;6.52e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00107)|OV - Ovarian serous cystadenocarcinoma(117;0.0285)|GBM - Glioblastoma multiforme(144;0.123)		tggtgcgatttgtgtgtgtgtt	0.000													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36367957	36367957	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36367957delA	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		AGATGACCAGAAAAAAAATTC	0.323													4	2	---	---	---	---	
SOHLH2	54937	broad.mit.edu	37	13	36853240	36853241	+	Intron	DEL	AA	-	-	rs67303077		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36853240_36853241delAA	uc010tei.1	-						C13orf38_uc010tej.1_Intron|C13orf38_uc010tek.1_Intron|C13orf38_uc010tel.1_Intron|C13orf38_uc010tem.1_Intron|C13orf38_uc010abm.2_Intron|C13orf38_uc010abn.2_Intron|C13orf38_uc010abo.2_Intron	NM_017826	NP_060296	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic						cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		tgcccaagctaaaaaaaaaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	38108535	38108536	+	5'Flank	INS	-	T	T	rs147097172	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38108535_38108536insT	uc001uwn.1	+											Homo sapiens cDNA FLJ34747 fis, clone MESAN2009418.																		TTCATTTCTCATTATGTCTGAG	0.421													2	5	---	---	---	---	
LRCH1	23143	broad.mit.edu	37	13	47137129	47137130	+	Intron	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47137129_47137130delCA	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TCCCTAGAGTCACACTTTATTT	0.411													4	2	---	---	---	---	
UCHL3	7347	broad.mit.edu	37	13	76141688	76141688	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76141688delT	uc001vjq.2	+						UCHL3_uc001vjr.2_Intron	NM_006002	NP_005993	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3						ubiquitin-dependent protein catabolic process	cytoplasm	cysteine-type peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity				0				GBM - Glioblastoma multiforme(99;0.0125)		GATTTACAAAttttttttttt	0.149													6	3	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	96821338	96821338	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96821338delT	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TGATTATTTCTGGCCTGCTGT	0.368													4	2	---	---	---	---	
PCCA	5095	broad.mit.edu	37	13	100863315	100863316	+	Intron	INS	-	TCA	TCA			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100863315_100863316insTCA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	taaaattctcctcatcttttag	0.119													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102542693	102542693	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102542693delA	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTCTTACCTGAAAAAAAAAAC	0.418													6	3	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110896684	110896684	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110896684delA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			ACAACAGTCCAAAAAAACTCC	0.353													4	2	---	---	---	---	
ARHGEF7	8874	broad.mit.edu	37	13	111870356	111870356	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111870356delT	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CAGTTTTTTGTTAGATGTAAT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	113279412	113279412	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113279412delC								TUBGCP3 (36931 upstream) : C13orf35 (21946 downstream)																							ACCCCCGAGTCCCACCTCGTG	0.453													4	2	---	---	---	---	
CHD8	57680	broad.mit.edu	37	14	21876281	21876281	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21876281delA	uc001was.1	-						CHD8_uc001war.1_Intron|CHD8_uc001wav.1_Intron	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8						ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TCTACTAGGTAAAAAAAATAG	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23694291	23694291	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23694291delA								SLC7A8 (41442 upstream) : HOMEZ (48553 downstream)																							caccccacacaaaaaaaaaac	0.000													4	2	---	---	---	---	
TGM1	7051	broad.mit.edu	37	14	24723228	24723228	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24723228delC	uc001wod.2	-						TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1						cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	TGCTAGCTGGCCCCAACCTGC	0.597													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34066132	34066132	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34066132delG	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GCAGTGGACAGGGGCCAGATC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34749191	34749191	+	IGR	DEL	T	-	-	rs2183315	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34749191delT								EGLN3 (328904 upstream) : C14orf147 (152954 downstream)																							aactgcaggcttcctcacaag	0.000													4	2	---	---	---	---	
SOS2	6655	broad.mit.edu	37	14	50628516	50628517	+	Intron	INS	-	C	C	rs112699778		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50628516_50628517insC	uc001wxs.3	-						SOS2_uc010tql.1_Intron|SOS2_uc010tqm.1_5'Flank|SOS2_uc001wxt.2_Intron	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2						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	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					TCttttttttttttttttttga	0.119													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66368076	66368076	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66368076delA								FUT8 (158115 upstream) : C14orf53 (585033 downstream)																							CATCGCAGTCAAAGTAGTAAG	0.458													4	2	---	---	---	---	
DCAF5	8816	broad.mit.edu	37	14	69585167	69585167	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69585167delA	uc001xkp.2	-						DCAF5_uc001xkq.2_Intron|DCAF5_uc001xkr.3_Intron|DCAF5_uc001xks.2_3'UTR	NM_003861	NP_003852	Q96JK2	DCAF5_HUMAN	WD repeat domain 22							CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)	2						CTTTCAGGTTAAAAAAAAGGT	0.303													6	3	---	---	---	---	
KIAA0247	9766	broad.mit.edu	37	14	70125610	70125610	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70125610delG	uc001xlk.2	+						KIAA0247_uc010aqz.2_Intron	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor							integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		TGAGTCACCTGGAGGAGGGGC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70764698	70764702	+	IGR	DEL	CGTAT	-	-	rs56128986		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70764698_70764702delCGTAT								ADAM21P1 (50180 upstream) : COX16 (27097 downstream)																							gagggggatacgtatcctgatatcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	71180851	71180852	+	IGR	DEL	CT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71180851_71180852delCT								TTC9 (38774 upstream) : MAP3K9 (14004 downstream)																							CATATTTTCCCTCTCTCTCTCC	0.396											OREG0022777	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	73015955	73015955	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73015955delT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc001xmz.1_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		CTGTTTTTTGTTTTTTTTTTT	0.483													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	73079138	73079139	+	RNA	INS	-	T	T	rs78960232		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73079138_73079139insT	uc010arh.1	-	1		c.665_666insA								Homo sapiens cDNA FLJ14079 fis, clone HEMBB1002134, weakly similar to ZINC-FINGER PROTEIN NEURO-D4.																		TGTTTCTGTCCTTTTTTTTTTT	0.436													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79075635	79075635	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79075635delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		AACCTCCATGAAAAAAAAAAG	0.388													4	2	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	81001958	81001959	+	Intron	DEL	CT	-	-	rs145417514	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81001958_81001959delCT	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		catgcacacactcacacacaca	0.297													4	2	---	---	---	---	
TTC7B	145567	broad.mit.edu	37	14	91090787	91090787	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91090787delC	uc001xyp.2	-						TTC7B_uc001xyo.2_Intron|TTC7B_uc010ats.2_Intron	NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)				TCATGCCATTCCCCAGGAAGA	0.562													4	2	---	---	---	---	
C14orf159	80017	broad.mit.edu	37	14	91642580	91642580	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91642580delT	uc001xzb.2	+						C14orf159_uc010atv.1_Intron|C14orf159_uc001xyy.2_Intron|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)		tatttatttatttttttttga	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101818484	101818484	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101818484delC								MIR656 (285346 upstream) : DIO3OS (200076 downstream)																							gaagaggtggccacacaggtg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	103686136	103686136	+	IGR	DEL	T	-	-	rs2403143	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103686136delT								TNFAIP2 (82360 upstream) : EIF5 (114357 downstream)																							ATGAGCCGGATGGGCCTTTCC	0.577													4	2	---	---	---	---	
INF2	64423	broad.mit.edu	37	14	105153817	105153818	+	5'Flank	DEL	AC	-	-	rs145012401		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105153817_105153818delAC	uc001ypb.2	+						INF2_uc001ypc.2_5'Flank|INF2_uc001yoy.3_5'Flank	NM_022489	NP_071934	Q27J81	INF2_HUMAN	inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		acacacacatacacacacacac	0.450													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106483668	106483668	+	Intron	DEL	C	-	-	rs111362207		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106483668delC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GCTCATGTGTCCCCCGCACTG	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20472844	20472844	+	IGR	DEL	G	-	-	rs71399656		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20472844delG								None (None upstream) : GOLGA6L6 (264250 downstream)																							CCAGACACGTGGATTGTTTTG	0.318													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21366464	21366466	+	IGR	DEL	ATG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21366464_21366466delATG								NF1P1 (231839 upstream) : LOC646214 (566048 downstream)																							GATGTGGAATATGATGAAGGAGA	0.369													6	3	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29639105	29639105	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29639105delA	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						AGCTCTGATCAAATCTAGTCC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36052570	36052570	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36052570delT	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																		CACCTATGACTTTTTTTTGTG	0.438													3	3	---	---	---	---	
LTK	4058	broad.mit.edu	37	15	41801500	41801502	+	Intron	DEL	CCT	-	-	rs1663365		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41801500_41801502delCCT	uc001zoa.3	-						LTK_uc001zob.3_Intron|LTK_uc010ucx.1_Intron|LTK_uc010bcg.2_Intron	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1						apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TCAGCTGGAGCCTGAAGGCCTCG	0.562										TSP Lung(18;0.14)			4	2	---	---	---	---	
TMEM62	80021	broad.mit.edu	37	15	43442507	43442507	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43442507delT	uc001zqr.2	+						TMEM62_uc010bda.2_Intron	NM_024956	NP_079232	Q0P6H9	TMM62_HUMAN	transmembrane protein 62							integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TATGATTGCCTTTTGTGAGAT	0.383													4	2	---	---	---	---	
SLC28A2	9153	broad.mit.edu	37	15	45561372	45561372	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45561372delA	uc001zva.2	+							NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		taataataataaaaaaaAAAC	0.234													6	3	---	---	---	---	
SCG3	29106	broad.mit.edu	37	15	51974474	51974474	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51974474delA	uc002abh.2	+						SCG3_uc010ufz.1_Intron	NM_013243	NP_037375	Q8WXD2	SCG3_HUMAN	secretogranin III isoform 1 precursor						platelet activation|platelet degranulation	extracellular region|stored secretory granule				ovary(1)	1				all cancers(107;0.00488)		TTCTGGTCAGAAAAAAAAAAA	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53403556	53403556	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53403556delG								ONECUT1 (321347 upstream) : WDR72 (402382 downstream)																							GGCACATAAAGGGCCACAATG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56046667	56046667	+	IGR	DEL	A	-	-	rs28707040		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56046667delA								PRTG (11490 upstream) : NEDD4 (72464 downstream)																							aacaaaaaacaaaaaagaaaG	0.254													4	2	---	---	---	---	
TEX9	374618	broad.mit.edu	37	15	56680976	56680976	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56680976delT	uc002adp.2	+						TEX9_uc002ado.1_Intron|TEX9_uc010ugl.1_Intron|TEX9_uc002adq.1_Intron	NM_198524	NP_940926	Q8N6V9	TEX9_HUMAN	testis expressed 9												0				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		CTGAGGCTTATTTTTTTTTCC	0.294													4	2	---	---	---	---	
SLTM	79811	broad.mit.edu	37	15	59207909	59207910	+	Intron	DEL	TG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59207909_59207910delTG	uc002afp.2	-						SLTM_uc002afo.2_Intron|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron|SLTM_uc002afr.1_Intron	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						GGGTTGTGTCTGTGTGTGTGTG	0.455													4	2	---	---	---	---	
DPP8	54878	broad.mit.edu	37	15	65755881	65755882	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65755881_65755882delAA	uc002aov.2	-						DPP8_uc002aow.2_Intron|DPP8_uc010uiv.1_Intron|DPP8_uc002aox.2_Intron|DPP8_uc002aoy.2_Intron|DPP8_uc002aoz.2_Intron|DPP8_uc010bhj.2_Intron|DPP8_uc002apa.2_Intron|DPP8_uc010bhi.2_Intron|DPP8_uc010bhk.1_Intron	NM_130434	NP_569118	Q6V1X1	DPP8_HUMAN	dipeptidyl peptidase 8 isoform 1						immune response|proteolysis	cytoplasm|membrane|nucleus	aminopeptidase activity|dipeptidyl-peptidase activity|serine-type peptidase activity			ovary(1)	1						actccatctcaaaaaaaaaaaa	0.158													4	2	---	---	---	---	
ZWILCH	55055	broad.mit.edu	37	15	66808185	66808186	+	Intron	DEL	TC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66808185_66808186delTC	uc002aqb.2	+						RPL4_uc002apx.2_Intron|ZWILCH_uc010bhu.1_Intron|ZWILCH_uc002aqa.2_Intron|ZWILCH_uc010bhv.2_Intron	NM_017975	NP_060445	Q9H900	ZWILC_HUMAN	Zwilch						cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1						gcacttatcttccctttctcta	0.015													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	66985420	66985420	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66985420delA								LCTL (127103 upstream) : SMAD6 (9254 downstream)																							TACACACAGGAAACTAAAAGC	0.423													4	2	---	---	---	---	
AAGAB	79719	broad.mit.edu	37	15	67514684	67514684	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67514684delG	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0						gtcccttaatgctgcctggca	0.000													4	2	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	68923656	68923656	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68923656delC	uc002arj.3	+						CORO2B_uc010bic.2_5'Flank	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						ggcagtgttgcccccattttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70180849	70180849	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70180849delA								C15orf50 (45544 upstream) : TLE3 (159694 downstream)																							aatgaccctcaaagcatttga	0.000													4	2	---	---	---	---	
C15orf27	123591	broad.mit.edu	37	15	76478973	76478974	+	Intron	INS	-	TC	TC			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76478973_76478974insTC	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron|C15orf27_uc002bbr.2_Intron	NM_152335	NP_689548	Q2M3C6	CO027_HUMAN	hypothetical protein LOC123591							integral to membrane					0						ccctcctcttatctctctctcc	0.059													4	2	---	---	---	---	
WDR61	80349	broad.mit.edu	37	15	78582622	78582623	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78582622_78582623delAA	uc002bdn.2	-						WDR61_uc002bdo.2_Intron	NM_025234	NP_079510	Q9GZS3	WDR61_HUMAN	WD repeat domain 61								protein binding			ovary(1)|skin(1)	2						AGGGTTTCTTAAATTTTTaatt	0.139													4	2	---	---	---	---	
ANKRD34C	390616	broad.mit.edu	37	15	79580205	79580205	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79580205delC	uc002bet.2	+							NM_001146341	NP_001139813			ankyrin repeat domain 34C												0						GAACGCAGCTCTTACATCCAG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89000980	89000981	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89000980_89000981delAA								NTRK3 (201319 upstream) : MRPL46 (1727 downstream)																							CTATAATGCTaaaaatcttgca	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93883603	93883603	+	Intron	DEL	C	-	-	rs34509376		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93883603delC	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		TTCTTCTGTGCCATGACAAAA	0.358													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	100508837	100508837	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100508837delG								C15orf51 (161705 upstream) : ADAMTS17 (2806 downstream)																							gaatagaacaggaaggctgac	0.000													4	2	---	---	---	---	
LINS1	55180	broad.mit.edu	37	15	101114929	101114929	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101114929delC	uc002bwe.2	-						LINS1_uc002bwd.2_5'Flank|LINS1_uc002bwf.2_Intron|LINS1_uc002bwg.2_Intron|LINS1_uc002bwh.2_Intron|LINS1_uc010usa.1_Intron|LINS1_uc002bwi.2_Intron	NM_001040614	NP_001035704	Q8NG48	LINES_HUMAN	lines homolog 1												0	Lung NSC(78;0.0018)|all_lung(78;0.00223)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00095)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			taaaacaaaacaaaacaaaaA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101386343	101386343	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101386343delG								ASB7 (194441 upstream) : ALDH1A3 (33666 downstream)																							TCATGTGTCTGGGTGAAGGGA	0.507													4	2	---	---	---	---	
LMF1	64788	broad.mit.edu	37	16	931768	931768	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:931768delG	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				CAGCAGGCTTGGCCAGGTGTT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	6019808	6019808	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6019808delT								FAM86A (872019 upstream) : A2BP1 (49324 downstream)																							CTTTGTTTCATTTTTTTTTCT	0.413													5	3	---	---	---	---	
ZC3H7A	29066	broad.mit.edu	37	16	11849855	11849856	+	Intron	DEL	CT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11849855_11849856delCT	uc002dbk.2	-						ZC3H7A_uc002dbh.2_5'Flank|ZC3H7A_uc002dbi.2_Intron|ZC3H7A_uc002dbj.2_Intron|ZC3H7A_uc002dbl.2_Intron	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A							nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						tccatctctactaaaaatacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16974592	16974593	+	IGR	INS	-	C	C	rs149766378	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16974592_16974593insC								LOC339047 (530155 upstream) : XYLT1 (221590 downstream)																							CCTGTCTTTGTCTTTTTTCATC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32152597	32152597	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32152597delA								ZNF267 (223971 upstream) : HERC2P4 (10013 downstream)																							TAAGGCACATAATGAGCAATT	0.318													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33543022	33543023	+	IGR	INS	-	ATT	ATT	rs138472598	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33543022_33543023insATT								SLC6A10P (646559 upstream) : MIR1826 (422485 downstream)																							ACACAATGACAATTACACTTTA	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33862986	33862987	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33862986_33862987delAA								SLC6A10P (966523 upstream) : MIR1826 (102521 downstream)																							agtgtcttacaaaagtctagag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34180389	34180389	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34180389delT								MIR1826 (214797 upstream) : UBE2MP1 (223413 downstream)																							ccctttgtcattttgaaatgt	0.070													8	4	---	---	---	---	
CHD9	80205	broad.mit.edu	37	16	53277091	53277091	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53277091delA	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002eha.1_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc002ehd.2_Intron|CHD9_uc002ehe.1_Intron	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				AATTTGTAAGAAAAAAAATTC	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62599431	62599432	+	IGR	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62599431_62599432delAC								CDH8 (529395 upstream) : None (None downstream)																							acacacacatacacacacacac	0.332													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63956132	63956132	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63956132delT								None (None upstream) : None (None downstream)																							CTCTTCTGCCTTTTTTTTTTT	0.368													3	3	---	---	---	---	
ESRP2	80004	broad.mit.edu	37	16	68266112	68266112	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68266112delA	uc010cfa.1	-						ESRP2_uc002evp.1_Intron|ESRP2_uc002evq.1_Intron	NM_024939	NP_079215	Q9H6T0	ESRP2_HUMAN	RNA binding motif protein 35B						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding|nucleotide binding			ovary(1)	1						ATGGATCAAGAACCAGGGGAG	0.552													107	51	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	79168487	79168488	+	Intron	DEL	TA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79168487_79168488delTA	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)		GTAGATTTTTTATAAATGCAGa	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	905541	905541	+	IGR	DEL	G	-	-	rs74343380	byFrequency	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:905541delG								TIMM22 (153 upstream) : ABR (1219 downstream)																							ACACAGTGCTGGGCACCTTCA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6168983	6168983	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6168983delC								WSCD1 (141238 upstream) : AIPL1 (158077 downstream)																							taccacgactcccGGCTTCCT	0.055													4	2	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9183033	9183035	+	Intron	DEL	CAA	-	-	rs72255121		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9183033_9183035delCAA	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						CTCATGCTGCCAACAACAACCCT	0.468													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14920914	14920914	+	IGR	DEL	T	-	-	rs9892792	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14920914delT								HS3ST3B1 (671422 upstream) : PMP22 (212183 downstream)																							TTTTCTGTCATTTTTTTACAC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21224692	21224692	+	IGR	DEL	A	-	-	rs68177356		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21224692delA								MAP2K3 (6143 upstream) : KCNJ12 (55007 downstream)																							GCATCCATCCAGCCGAGAGAG	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21224694	21224695	+	IGR	INS	-	T	T	rs78649602		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21224694_21224695insT								MAP2K3 (6145 upstream) : KCNJ12 (55004 downstream)																							ATCCATCCAGCCGAGAGAGGAG	0.391													4	3	---	---	---	---	
KIAA0100	9703	broad.mit.edu	37	17	26961251	26961251	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26961251delA	uc002hbu.2	-							NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					CAGCAAGCTGAAAAATGACAG	0.433													4	2	---	---	---	---	
TMEM98	26022	broad.mit.edu	37	17	31255784	31255786	+	Intron	DEL	ACT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31255784_31255786delACT	uc002hhq.2	+						TMEM98_uc002hhr.2_Intron	NM_015544	NP_056359	Q9Y2Y6	TMM98_HUMAN	transmembrane protein 98							endoplasmic reticulum|integral to membrane					0		Ovarian(249;0.182)|Breast(31;0.244)	BRCA - Breast invasive adenocarcinoma(9;0.0769)			ACACAAGCACACTAAGAAACATT	0.276													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32181894	32181894	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32181894delA	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)	ATTAGTGTTTAAAAAAACACG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32806858	32806858	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32806858delT								CCL1 (116606 upstream) : C17orf102 (94284 downstream)																							GAACCCAACATTCAGCCTGGG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35436352	35436353	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35436352_35436353insT								AATF (22182 upstream) : ACACA (5575 downstream)																							ttcctttaagatttttctttgt	0.000													4	2	---	---	---	---	
SRCIN1	80725	broad.mit.edu	37	17	36692984	36692984	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36692984delG	uc002hqd.2	-							NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein						exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0						agcccagagtgggggatgtgg	0.085													4	2	---	---	---	---	
RARA	5914	broad.mit.edu	37	17	38505623	38505624	+	Intron	DEL	CG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38505623_38505624delCG	uc002huk.1	+						RARA_uc002hul.3_Intron|RARA_uc010wfe.1_Intron|RARA_uc002hun.1_Intron	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1						apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CTGGCCAGCCCGTGTATCTGCC	0.559			T	PML|ZNF145|TIF1|NUMA1|NPM1	APL								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38864000	38864000	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38864000delT								KRT24 (3998 upstream) : KRT25 (40274 downstream)																							GGGTTAGTGATTCTCAGTGTG	0.448													4	2	---	---	---	---	
SLC35B1	10237	broad.mit.edu	37	17	47781253	47781254	+	Intron	INS	-	CT	CT			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47781253_47781254insCT	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron	NM_005827	NP_005818	P78383	S35B1_HUMAN	solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0						CTGACACACGACTCTCCTTCAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58476668	58476668	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58476668delA								USP32 (7082 upstream) : C17orf64 (23197 downstream)																							tgttctacagaaaaaaaatgc	0.000													4	2	---	---	---	---	
TEX2	55852	broad.mit.edu	37	17	62226463	62226464	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62226463_62226464insA	uc002jec.2	-						TEX2_uc002jed.2_Intron|TEX2_uc002jee.2_Intron	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2						signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TGTAGGAAGATATTAAAGAACA	0.391													43	31	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2091647	2091647	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2091647delA								C18orf2 (684466 upstream) : METTL4 (445878 downstream)																							TACATGCAAGAAAAAAAAAAG	0.383													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5672381	5672382	+	IGR	INS	-	A	A	rs11390127		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5672381_5672382insA								EPB41L3 (41739 upstream) : TMEM200C (217802 downstream)																							AAGTCATATCCCACCATGATGC	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12118721	12118721	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12118721delT	uc002kqs.2	+											RecName: Full=UPF0634 protein E;																		ttgtcatatctttttagcatg	0.015													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13299844	13299845	+	Intron	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13299844_13299845delAA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		cctgtctcttaaaaaaaaaaGG	0.223													4	2	---	---	---	---	
POTEC	388468	broad.mit.edu	37	18	14535288	14535288	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14535288delT	uc010dln.2	-						POTEC_uc010xaj.1_Intron	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2											skin(3)	3						Ttttggatgattttttttttc	0.184													6	3	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	18961783	18961783	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18961783delC	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						accaaggtttctaaaaagaag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	33442950	33442950	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33442950delA								GALNT1 (151153 upstream) : MIR187 (41831 downstream)																							GAATAGGGGCAAATATGAGGT	0.433													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48129841	48129842	+	Intron	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48129841_48129842delAC	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)		TCCTATGTCTACACACACACAT	0.500													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55756769	55756770	+	Intron	INS	-	AGGG	AGGG			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55756769_55756770insAGGG	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lha.1_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						GGTTGATAGGCACTGAATGGGA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61679824	61679825	+	IGR	INS	-	GC	GC	rs141866778	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61679824_61679825insGC								SERPINB8 (23217 upstream) : C18orf20 (67418 downstream)																							tgtgtgtgtgtgcgtgtgtgtg	0.243													4	3	---	---	---	---	
NETO1	81832	broad.mit.edu	37	18	70434951	70434951	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70434951delA	uc002lkw.2	-						NETO1_uc002lkx.1_Intron|NETO1_uc002lky.1_Intron	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3						memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		CAAAAGCTTTAAAAAAAACag	0.199													4	2	---	---	---	---	
PQLC1	80148	broad.mit.edu	37	18	77680275	77680275	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77680275delA	uc002lnl.2	-						PQLC1_uc010dre.2_Intron|PQLC1_uc002lnk.2_Intron|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1 isoform 1							integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)		gaggagagacaggaaccgagg	0.055													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5583331	5583331	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5583331delT								PLAC2 (15326 upstream) : SAFB2 (3680 downstream)																							ggttgttgggtttttttggaa	0.065													5	3	---	---	---	---	
TNPO2	30000	broad.mit.edu	37	19	12821704	12821704	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12821704delT	uc002muo.2	-						TNPO2_uc002mup.2_Intron|TNPO2_uc002muq.2_Intron|TNPO2_uc002mur.2_Intron	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)						intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						GATCAGCttctttttttttgt	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	12895597	12895598	+	IGR	DEL	AC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12895597_12895598delAC								HOOK2 (9163 upstream) : JUNB (6688 downstream)																							AGAGAAGGCAACACACACACAC	0.510													4	2	---	---	---	---	
CRTC1	23373	broad.mit.edu	37	19	18858139	18858139	+	Intron	DEL	A	-	-	rs76215850	byFrequency	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18858139delA	uc002nkb.3	+						CRTC1_uc010ebv.2_Intron|CRTC1_uc010ebw.2_Intron|CRTC1_uc002nkc.3_Intron	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform						interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519						CACTTATGACAAAAAAAAAGA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29043647	29043648	+	Intron	INS	-	A	A			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29043647_29043648insA	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																		CGAAAGAAAGGAAAAAAAAAAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29568351	29568351	+	IGR	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29568351delG								LOC148145 (108296 upstream) : UQCRFS1 (129816 downstream)																							TTGCAGAAAAGGGGGAGACAC	0.388													4	2	---	---	---	---	
UBA2	10054	broad.mit.edu	37	19	34922498	34922499	+	Intron	INS	-	TT	TT	rs113731177		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34922498_34922499insTT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			ACTTCATGTTGTATTTTTGCTG	0.287													6	3	---	---	---	---	
WDR62	284403	broad.mit.edu	37	19	36587620	36587621	+	Intron	INS	-	A	A	rs10853946	by1000genomes	TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36587620_36587621insA	uc002odc.2	+						WDR62_uc002odd.2_Intron	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ctcaaaaaaagaaaaaaaaaga	0.000													4	2	---	---	---	---	
RYR1	6261	broad.mit.edu	37	19	38976694	38976695	+	Frame_Shift_Ins	INS	-	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38976694_38976695insG	uc002oit.2	+	34	5529_5530	c.5399_5400insG	c.(5398-5400)CCTfs	p.P1800fs	RYR1_uc002oiu.2_Frame_Shift_Ins_p.P1800fs	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1800	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	CGCCTCAGCCCTGCCATCCCGC	0.733													4	2	---	---	---	---	
CBLC	23624	broad.mit.edu	37	19	45286206	45286206	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45286206delA	uc002ozs.2	+						CBLC_uc010ejt.2_Intron	NM_012116	NP_036248	Q9ULV8	CBLC_HUMAN	Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				AAGAGAAGAGAAGGTCAGGTT	0.428			M		AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50223451	50223452	+	IGR	DEL	TT	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50223451_50223452delTT								CPT1C (6463 upstream) : TSKS (19560 downstream)																							ttcttttttctttttttttttt	0.149													4	2	---	---	---	---	
SIGLEC16	400709	broad.mit.edu	37	19	50475704	50475704	+	Intron	DEL	G	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50475704delG	uc002prf.2	+						uc010ybk.1_Intron	NR_002825				Homo sapiens cDNA FLJ50062 complete cds, highly similar to Sialic acid-binding Ig-like lectin 11 precursor.												0						TCTGATTCCTGGCGGACAGTC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53707098	53707099	+	IGR	INS	-	AC	AC			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53707098_53707099insAC								ZNF665 (10479 upstream) : ZNF677 (31539 downstream)																							TCTCCCCCATGTGCTTGGTAAA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57250776	57250776	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57250776delA	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																		AGGAAGAGATAAAGGGGTCAG	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18241243	18241243	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18241243delT								CSRP2BP (72228 upstream) : ZNF133 (27878 downstream)																							tcaatggtacttttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24117488	24117488	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24117488delA								GGTLC1 (148072 upstream) : TMEM90B (332347 downstream)																							TGATCAAAGGAGGGAAGGTGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25043269	25043270	+	IGR	DEL	CA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25043269_25043270delCA								ACSS1 (3653 upstream) : VSX1 (8862 downstream)																							TCTGTGACCCCACACACACACA	0.351													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26129265	26129266	+	IGR	DEL	GA	-	-	rs139001833		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26129265_26129266delGA								C20orf191 (34588 upstream) : MIR663 (59556 downstream)																							TTTTAATATTGAGTTAGGTTTT	0.262													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26206435	26206435	+	IGR	DEL	T	-	-	rs143738104		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26206435delT								MIR663 (17521 upstream) : None (None downstream)																							GCATTTATAATTTTAAGATGC	0.279													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29590215	29590216	+	IGR	INS	-	T	T	rs142088020		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29590215_29590216insT								None (None upstream) : FRG1B (21663 downstream)																							tgtcttcttagtttggttattt	0.015													15	7	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29626725	29626725	+	Intron	DEL	C	-	-	rs113929874		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29626725delC	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						ATAAGCTCAGCCTTTGAGTAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31175767	31175767	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31175767delA	uc002wxy.2	+						uc002wxx.2_5'Flank					RecName: Full=Putative uncharacterized protein MGC163334;																		gagcaagggcaaaagccccaa	0.000													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47334125	47334125	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47334125delA	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)			CCAGCATTGCAAAAAAAAACC	0.338													4	2	---	---	---	---	
SPO11	23626	broad.mit.edu	37	20	55911150	55911150	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55911150delT	uc002xye.2	+						SPO11_uc002xyf.2_Intron	NM_012444	NP_036576	Q9Y5K1	SPO11_HUMAN	meiotic recombination protein SPO11 isoform a						female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)			CCTCAAGttctttttttttta	0.199								Editing_and_processing_nucleases					5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57156000	57156000	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57156000delA	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																		accaggtattatcgacattga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10709830	10709831	+	IGR	INS	-	C	C	rs148302105		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10709830_10709831insC								None (None upstream) : TPTE (196912 downstream)																							ttatggtgaaaaaaagtgtctt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10717006	10717007	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10717006_10717007delAA								None (None upstream) : TPTE (189736 downstream)																							cagattctacaaaaagagtgtc	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10756265	10756270	+	IGR	DEL	ATCTTC	-	-	rs139653617		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10756265_10756270delATCTTC								None (None upstream) : TPTE (150473 downstream)																							aaaatgaaatatcttcacataaaaat	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11063807	11063807	+	Intron	DEL	A	-	-	rs113289634		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11063807delA	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)		tattcagaggaaaaaaatata	0.070													3	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11068910	11068911	+	Intron	DEL	AT	-	-	rs147061174		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11068910_11068911delAT	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)		ttctcttatcatatgtgtaatt	0.000													3	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14493164	14493165	+	IGR	INS	-	T	T			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14493164_14493165insT								C21orf99 (2595 upstream) : POTED (489333 downstream)																							TACATAGTAGAACTATATCTGA	0.376													3	6	---	---	---	---	
DNAJC28	54943	broad.mit.edu	37	21	34860328	34860328	+	3'UTR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34860328delA	uc002yrv.2	-	2					DNAJC28_uc002yrw.2_3'UTR	NM_017833	NP_060303	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28								heat shock protein binding				0						acgccgtctcaaaaaaaaaGG	0.169													6	3	---	---	---	---	
SLC5A3	6526	broad.mit.edu	37	21	35475730	35475732	+	3'UTR	DEL	ATA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35475730_35475732delATA	uc002yto.2	+	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						TGTTTCTTTTATATCCATTAAAA	0.330													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38172456	38172457	+	Intron	INS	-	C	C			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38172456_38172457insC	uc010gnb.2	-						HLCS_uc002yvs.2_Intron	NM_000411	NP_000402	P50747	BPL1_HUMAN	holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GGCCAGCTTGACCCCACCACTC	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	41215385	41215385	+	IGR	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41215385delC								IGSF5 (41364 upstream) : PCP4 (23962 downstream)																							CGTACATGGTCGTGTGTGTGT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17375815	17375816	+	IGR	INS	-	A	A	rs145883088		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17375815_17375816insA								HSFYL1 (65590 upstream) : GAB4 (67013 downstream)																							acgcagaagctaaaaaaaaagt	0.000													1	5	---	---	---	---	
HIRA	7290	broad.mit.edu	37	22	19424345	19424345	+	Intron	DEL	A	-	-	rs68015924		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19424345delA	uc010gro.1	-						HIRA_uc010grp.2_Intron	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					TCAAATGGGGAAAAAAAAATG	0.438													9	4	---	---	---	---	
CABIN1	23523	broad.mit.edu	37	22	24428139	24428140	+	Intron	DEL	GC	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24428139_24428140delGC	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron|CABIN1_uc010guk.1_Intron|CABIN1_uc002zzk.1_Intron	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						CAGTGGGTGAGCAGCAGAGAGT	0.540													4	2	---	---	---	---	
ADRBK2	157	broad.mit.edu	37	22	26030411	26030411	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26030411delT	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	GCTTAGGGTGTTTTACTCAAA	0.343													4	2	---	---	---	---	
NF2	4771	broad.mit.edu	37	22	30051931	30051932	+	Intron	DEL	TT	-	-	rs113985281		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30051931_30051932delTT	uc003age.3	+						NF2_uc003afy.3_Intron|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						AAGTTTAAGAtttttttttttt	0.173			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				3	5	---	---	---	---	
LOC646851	646851	broad.mit.edu	37	22	39023979	39023979	+	Intron	DEL	T	-	-	rs147411497		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39023979delT	uc011anx.1	-						LOC646851_uc011anw.1_Intron			B7Z7C6	B7Z7C6_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000348086;												0						tttttccaggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41585697	41585697	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41585697delT	uc003azm.2	-											Homo sapiens, clone IMAGE:5580334, mRNA.																		ctgcTGGCCATTTTTTTTTTC	0.219													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48178219	48178219	+	Intron	DEL	C	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48178219delC	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		CTGTGGGCTTCGGTGACAGCT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1221851	1221851	+	IGR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1221851delT								SHOX (601706 upstream) : CRLF2 (93036 downstream)																							ATCTTCCCAATTCTCATCAAC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1370025	1370026	+	IGR	INS	-	TATC	TATC			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1370025_1370026insTATC								CRLF2 (38495 upstream) : CSF2RA (17667 downstream)																							atgataggtgatatctaggtag	0.069													4	4	---	---	---	---	
CSF2RA	1438	broad.mit.edu	37	X	1420247	1420248	+	Intron	DEL	AG	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1420247_1420248delAG	uc010nct.2	+						CSF2RA_uc011mhb.1_Intron|CSF2RA_uc004cpq.2_Intron|CSF2RA_uc004cpn.2_Intron|CSF2RA_uc004cpo.2_Intron|CSF2RA_uc010ncu.2_Intron|CSF2RA_uc011mhc.1_Intron|CSF2RA_uc004cpp.2_Intron|CSF2RA_uc010ncv.2_Intron|CSF2RA_uc004cpr.2_Intron	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain							extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	aaaaaaaaaaagaaaaaGTAGA	0.218													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	8375105	8375106	+	IGR	INS	-	G	G			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8375105_8375106insG								VCX2 (235797 upstream) : VCX3B (57765 downstream)																							aggttactcttggggaaaactg	0.005													4	2	---	---	---	---	
NHS	4810	broad.mit.edu	37	X	17743338	17743338	+	Intron	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17743338delT	uc004cxx.2	+						NHS_uc011mix.1_Intron|NHS_uc004cxy.2_Intron|NHS_uc004cxz.2_Intron|NHS_uc004cya.2_Intron	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					TATATATTGATTTTTTTTCTG	0.333													4	2	---	---	---	---	
SMS	6611	broad.mit.edu	37	X	22012650	22012650	+	3'UTR	DEL	T	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22012650delT	uc004dag.2	+	11					SMS_uc010nfs.2_RNA|SMS_uc010nft.2_3'UTR	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	GCTTAGGGTGTTTTTTTTTTG	0.318													4	2	---	---	---	---	
FUNDC1	139341	broad.mit.edu	37	X	44401935	44401935	+	Intron	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44401935delA	uc004dgc.2	-							NM_173794	NP_776155	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1												0						GGGCTGCCTTAAAAAAAAAAT	0.592													4	2	---	---	---	---	
EDA	1896	broad.mit.edu	37	X	69180707	69180707	+	Intron	DEL	A	-	-	rs66880741		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69180707delA	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3						ccaaaaatacaaaaaaaaaaa	0.075													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9960320	9960321	+	IGR	INS	-	A	A	rs148334492		TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9960320_9960321insA								TTTY22 (309466 upstream) : None (None downstream)																							CACCAAGCCTGAAAAATGTATA	0.342													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	14389587	14389587	+	IGR	DEL	A	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14389587delA								None (None upstream) : TTTY15 (384711 downstream)																							GATTAAAAAGAAAAAAAAAAT	0.358													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	22722113	22722114	+	IGR	DEL	AA	-	-			TCGA-B0-5402-01A-01D-1501-10	TCGA-B0-5402-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:22722113_22722114delAA								TTTY10 (40999 upstream) : EIF1AY (15497 downstream)																							acaaaaagagaaaaaaaaaatg	0.000													4	2	---	---	---	---	
