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
ACAP3	116983	broad.mit.edu	37	1	1233244	1233244	+	Silent	SNP	G	A	A	rs144855997		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1233244G>A	uc001aeb.2	-	14	1160	c.1086C>T	c.(1084-1086)ATC>ATT	p.I362I	ACAP3_uc001ady.2_Silent_p.I92I|ACAP3_uc001aea.2_Silent_p.I320I	NM_030649	NP_085152	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH	362	PH.				filopodium assembly|regulation of ARF GTPase activity|signal transduction		ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding				0						AGGCGGAGGCGATGCTGGCCT	0.682													10	5	---	---	---	---	PASS
KDM1A	23028	broad.mit.edu	37	1	23406041	23406041	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23406041G>T	uc001bgi.2	+						KDM1A_uc001bgj.2_Intron	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b						blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2						TCTTTCTTATGGTAGGTGGTG	0.478													4	29	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27100060	27100060	+	Intron	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27100060A>G	uc001bmv.1	+						ARID1A_uc001bmt.1_Intron|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Intron|ARID1A_uc001bmx.1_Intron|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'Flank	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a						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)		TGCCTCTCCAATTTTGTTTAG	0.557			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								14	23	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34052159	34052159	+	Silent	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34052159C>G	uc001bxn.1	-	47	7031	c.7002G>C	c.(7000-7002)CTG>CTC	p.L2334L	CSMD2_uc001bxm.1_Silent_p.L2332L	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2334	Sushi 13.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTTTGCAGGTCAGAATTTCAT	0.493													13	25	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38187350	38187350	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38187350C>A	uc009vvi.2	-	11	2214	c.2128G>T	c.(2128-2130)GAG>TAG	p.E710*	EPHA10_uc001cbt.2_5'Flank|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	710	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity	p.L710M(1)		breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAACGCCCTCCAGCCGCACG	0.652													8	10	---	---	---	---	PASS
ZNF684	127396	broad.mit.edu	37	1	41006273	41006273	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41006273C>A	uc001cft.1	+	3	282	c.31C>A	c.(31-33)CAG>AAG	p.Q11K		NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	11	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			AGTGACATTCCAGGATGTGGC	0.428													5	55	---	---	---	---	PASS
EPS15	2060	broad.mit.edu	37	1	51871588	51871588	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51871588G>T	uc001csq.1	-	16	1758	c.1666C>A	c.(1666-1668)CAG>AAG	p.Q556K	EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Missense_Mutation_p.Q242K	NM_001981	NP_001972	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway	556					cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2						GGAGATTCCTGGTGTATGGGC	0.423			T	MLL	ALL								5	69	---	---	---	---	PASS
PARS2	25973	broad.mit.edu	37	1	55224198	55224198	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55224198C>G	uc001cxy.2	-	2	720	c.637G>C	c.(637-639)GAC>CAC	p.D213H		NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)	213					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)	GGGGAGGAGTCAAAGGTGTAC	0.557													21	28	---	---	---	---	PASS
LEPROT	54741	broad.mit.edu	37	1	65895678	65895678	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65895678G>T	uc001dcf.2	+	3	315	c.226G>T	c.(226-228)GGA>TGA	p.G76*	LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc001dci.2_Intron|LEPR_uc009waq.2_Intron|LEPROT_uc009wap.2_Nonsense_Mutation_p.G85*	NM_017526	NP_059996	O15243	OBRG_HUMAN	leptin receptor gene-related protein	76	Helical; (Potential).					endosome membrane|Golgi membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTTCACTACTGGAATTGTTGT	0.448													6	147	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	97547958	97547958	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97547958C>A	uc001drv.2	-	22	2972	c.2835G>T	c.(2833-2835)GTG>GTT	p.V945V		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	945	4Fe-4S ferredoxin-type 2.				'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	CAATCATAGCCACAACTTGCT	0.393													5	48	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118548056	118548056	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118548056G>T	uc001ehk.2	-	32	4825	c.4757C>A	c.(4756-4758)CCT>CAT	p.P1586H		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1586						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GTTTCCCTCAGGATCCAGAAC	0.438													5	80	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118635898	118635898	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118635898T>A	uc001ehk.2	-	8	1122	c.1054A>T	c.(1054-1056)ATG>TTG	p.M352L		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	352						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ATGTCATACATCAAGCAGGCA	0.373													10	13	---	---	---	---	PASS
PPIAL4G	644591	broad.mit.edu	37	1	143767766	143767766	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143767766T>A	uc001ejt.2	-	1	116	c.83A>T	c.(82-84)AAG>ATG	p.K28M		NM_001123068	NP_001116540	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like	28	PPIase cyclophilin-type.				protein folding	cytoplasm	peptidyl-prolyl cis-trans isomerase activity				0						CTTTGGAATCTTGTCTGCAAA	0.468													29	199	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145532206	145532206	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145532206G>A	uc001eoa.2	+	8	926	c.850G>A	c.(850-852)GAG>AAG	p.E284K	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.E153K|ITGA10_uc009wiw.2_Missense_Mutation_p.E141K|ITGA10_uc010oyw.1_Missense_Mutation_p.E229K	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	284	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGATGGAGAGGAGCTTCCTGC	0.567													12	49	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152281652	152281652	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152281652G>T	uc001ezu.1	-	3	5746	c.5710C>A	c.(5710-5712)CAA>AAA	p.Q1904K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1904	Ser-rich.|Filaggrin 11.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTGATGATTGTCCCTGGCCC	0.587									Ichthyosis				51	174	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156823678	156823678	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156823678A>G	uc010pht.1	-	2	757	c.503T>C	c.(502-504)GTG>GCG	p.V168A	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_Missense_Mutation_p.V168A	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	168					protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTTGTTGCCCACGATGTGGTT	0.642													5	20	---	---	---	---	PASS
C1orf92	149499	broad.mit.edu	37	1	156899076	156899076	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156899076C>T	uc001fqm.2	+	10	1173	c.1001C>T	c.(1000-1002)TCC>TTC	p.S334F	C1orf92_uc001fql.2_Missense_Mutation_p.S119F	NM_144702	NP_653303	Q8N4P6	LRC71_HUMAN	hypothetical protein LOC149499	334											0	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCACAGCCCTCCTCCTCTCGA	0.552													4	19	---	---	---	---	PASS
CD84	8832	broad.mit.edu	37	1	160523928	160523928	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160523928C>A	uc001fwh.3	-	3	421	c.397G>T	c.(397-399)GGG>TGG	p.G133W	CD84_uc001fwf.3_Missense_Mutation_p.G133W|CD84_uc001fwg.3_Missense_Mutation_p.G133W|CD84_uc009wtn.2_Missense_Mutation_p.G133W|CD84_uc001fwi.3_Missense_Mutation_p.G19W|CD84_uc001fwj.2_Missense_Mutation_p.G133W|CD84_uc001fwk.2_Missense_Mutation_p.G133W	NM_003874	NP_003865	Q9UIB8	SLAF5_HUMAN	CD84 molecule	133	Extracellular (Potential).				blood coagulation|defense response|homophilic cell adhesion|leukocyte migration	integral to plasma membrane	receptor activity	p.G133G(1)		ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TTTGGTTTCCCAAGCCGACCT	0.284													4	19	---	---	---	---	PASS
ARHGAP30	257106	broad.mit.edu	37	1	161039355	161039355	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161039355G>A	uc001fxl.2	-	1	406	c.60C>T	c.(58-60)TGC>TGT	p.C20C	ARHGAP30_uc001fxk.2_Silent_p.C20C|ARHGAP30_uc001fxm.2_5'UTR|ARHGAP30_uc009wtx.2_5'UTR|ARHGAP30_uc001fxn.1_5'UTR	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	20	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCTGCAAGTCGCACCCAAAAA	0.637													22	43	---	---	---	---	PASS
NME7	29922	broad.mit.edu	37	1	169293626	169293626	+	Intron	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169293626T>C	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_Intron	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					GAAAGGCTTATTTACCATTTC	0.363													5	14	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177199026	177199026	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177199026G>A	uc001glf.2	+	2	326	c.14G>A	c.(13-15)TGT>TAT	p.C5Y		NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	5						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						AGGTGGCAGTGTGGCACTCGG	0.652													6	17	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179659920	179659920	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179659920G>T	uc001gnf.1	+	17	3038	c.2788G>T	c.(2788-2790)GAC>TAC	p.D930Y	TDRD5_uc010pnp.1_Missense_Mutation_p.D984Y|TDRD5_uc001gnh.1_Missense_Mutation_p.D485Y	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	930					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						AGAATCTGTAGACCAGCTGTC	0.443													8	41	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193121513	193121513	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193121513C>A	uc001gtb.2	+	10	1154	c.911C>A	c.(910-912)ACG>AAG	p.T304K		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	304					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						TTCGTAGAAACGGAAGGCTTC	0.338									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				3	13	---	---	---	---	PASS
PTPRC	5788	broad.mit.edu	37	1	198678943	198678943	+	Silent	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198678943A>C	uc001gur.1	+	11	1335	c.1155A>C	c.(1153-1155)ACA>ACC	p.T385T	PTPRC_uc001gus.1_Silent_p.T337T|PTPRC_uc001gut.1_Silent_p.T224T|PTPRC_uc009wzf.1_Silent_p.T273T|PTPRC_uc010ppg.1_Silent_p.T321T	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	385	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						TTATTAAAACAGATTTTGGGA	0.269													18	39	---	---	---	---	PASS
ZNF281	23528	broad.mit.edu	37	1	200377463	200377463	+	Silent	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200377463T>C	uc001gve.2	-	2	1478	c.1371A>G	c.(1369-1371)GAA>GAG	p.E457E	ZNF281_uc001gvf.1_Silent_p.E457E|ZNF281_uc001gvg.1_Silent_p.E421E	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	457					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2						TCTTCTGCAGTTCATCTATTC	0.373													19	56	---	---	---	---	PASS
KCNH1	3756	broad.mit.edu	37	1	210856671	210856671	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210856671C>A	uc001hib.2	-	11	3092	c.2922G>T	c.(2920-2922)TCG>TCT	p.S974S	KCNH1_uc001hic.2_Silent_p.S947S	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	974	Cytoplasmic (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ACTGTGGCCTCGATATTTCAA	0.438													5	123	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248202064	248202064	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248202064C>A	uc001idw.2	+	1	591	c.495C>A	c.(493-495)ATC>ATA	p.I165I	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CACTCTGTATCCCATATTGCA	0.433													33	65	---	---	---	---	PASS
THUMPD2	80745	broad.mit.edu	37	2	39963957	39963957	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39963957G>T	uc002rru.2	-	10	1467	c.1430C>A	c.(1429-1431)CCA>CAA	p.P477Q	THUMPD2_uc002rrv.2_RNA|THUMPD2_uc010ynt.1_Missense_Mutation_p.P368Q	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	477							methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)				GCATTCCACTGGTACCAAGGA	0.438													5	72	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61441365	61441365	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61441365G>T	uc002sbe.2	-	68	8534	c.8512C>A	c.(8512-8514)CAT>AAT	p.H2838N		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2838					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TGATCATCATGGTCAGCAAGG	0.478													6	69	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79350303	79350303	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79350303G>A	uc002snz.2	+	6	566	c.463G>A	c.(463-465)GAA>AAA	p.E155K	REG1A_uc010ysd.1_Missense_Mutation_p.E155K	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor	155	C-type lectin.				positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TGTGCCTTGTGAAGACAAGTT	0.413													6	51	---	---	---	---	PASS
EPB41L5	57669	broad.mit.edu	37	2	120830802	120830802	+	Intron	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120830802T>C	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron	NM_020909	NP_065960	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1						AAAAAGTAAGTGCAGACAAAA	0.289													3	47	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141291599	141291599	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141291599C>A	uc002tvj.1	-	47	8725	c.7753G>T	c.(7753-7755)GAT>TAT	p.D2585Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2585	Extracellular (Potential).|LDL-receptor class A 12.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCTTTACAATCTAATTCATCA	0.418										TSP Lung(27;0.18)			8	33	---	---	---	---	PASS
RBMS1	5937	broad.mit.edu	37	2	161141535	161141535	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161141535G>T	uc002ubo.2	-	8	1221	c.777C>A	c.(775-777)TAC>TAA	p.Y259*	RBMS1_uc002ubj.2_Nonsense_Mutation_p.Y223*|RBMS1_uc002ubk.2_Nonsense_Mutation_p.Y223*|RBMS1_uc002ubl.2_Nonsense_Mutation_p.Y254*|RBMS1_uc002ubn.2_Nonsense_Mutation_p.Y256*|RBMS1_uc002ubi.3_Nonsense_Mutation_p.Y256*|RBMS1_uc002ubm.2_Nonsense_Mutation_p.Y226*|RBMS1_uc002ubp.2_Nonsense_Mutation_p.Y259*|RBMS1_uc010fox.2_Nonsense_Mutation_p.Y259*	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting	259					DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						TAGTTGGGTCGTAAGTAAGTG	0.318													26	29	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168108054	168108054	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168108054G>T	uc002udx.2	+	8	10170	c.10152G>T	c.(10150-10152)ACG>ACT	p.T3384T	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.T3209T|XIRP2_uc010fpq.2_Silent_p.T3162T|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	3209					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TAGGAAACACGAGTTTTACAG	0.383													21	80	---	---	---	---	PASS
ABCB11	8647	broad.mit.edu	37	2	169780238	169780238	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169780238G>T	uc002ueo.1	-	28	3986	c.3860C>A	c.(3859-3861)GCT>GAT	p.A1287D	ABCB11_uc010zda.1_Missense_Mutation_p.A705D|ABCB11_uc010zdb.1_Missense_Mutation_p.A763D	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1287	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	TGCCATGACAGCAATGATATC	0.532													10	61	---	---	---	---	PASS
CDCA7	83879	broad.mit.edu	37	2	174230295	174230295	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174230295G>A	uc002uid.1	+	6	904	c.773G>A	c.(772-774)CGA>CAA	p.R258Q	CDCA7_uc002uic.1_Missense_Mutation_p.R337Q|CDCA7_uc010zej.1_Missense_Mutation_p.R293Q|CDCA7_uc010zek.1_Missense_Mutation_p.R216Q	NM_145810	NP_665809	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7 isoform 2	258	Mediates transcriptional activity.				regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)			AGCAATTCTCGAGAGAAGATA	0.478													7	33	---	---	---	---	PASS
TTC30A	92104	broad.mit.edu	37	2	178482680	178482680	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178482680C>A	uc002ulo.2	-	1	1015	c.750G>T	c.(748-750)CTG>CTT	p.L250L		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	250					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AGGCTTCCACCAGAGCAGTCT	0.537													5	73	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179411391	179411391	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179411391A>T	uc010zfg.1	-	290	87284	c.87060T>A	c.(87058-87060)AAT>AAA	p.N29020K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.N22715K|TTN_uc010zfi.1_Missense_Mutation_p.N22648K|TTN_uc010zfj.1_Missense_Mutation_p.N22523K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29947							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CGCCTGCTGCATTCTTGGCTA	0.438													11	36	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179457260	179457260	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179457260G>A	uc010zfg.1	-	250	51992	c.51768C>T	c.(51766-51768)GAC>GAT	p.D17256D	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.D10951D|TTN_uc010zfi.1_Silent_p.D10884D|TTN_uc010zfj.1_Silent_p.D10759D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18183							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGCATCTCTGTCTTCTTTTT	0.388													19	130	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197090571	197090571	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197090571A>T	uc002utm.1	-	23	4124	c.3941T>A	c.(3940-3942)CTT>CAT	p.L1314H	HECW2_uc002utl.1_Missense_Mutation_p.L958H	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	1314	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TGCAAGACCAAGGATCCTACC	0.423													5	33	---	---	---	---	PASS
NRP2	8828	broad.mit.edu	37	2	206562429	206562429	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206562429G>T	uc002vaw.2	+	2	1026	c.235G>T	c.(235-237)GAG>TAG	p.E79*	NRP2_uc002vat.2_Nonsense_Mutation_p.E79*|NRP2_uc002vau.2_Nonsense_Mutation_p.E79*|NRP2_uc002vav.2_Nonsense_Mutation_p.E79*|NRP2_uc002vax.2_Nonsense_Mutation_p.E79*|NRP2_uc002vay.2_Nonsense_Mutation_p.E79*|NRP2_uc010fud.2_Nonsense_Mutation_p.E79*	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	79	Extracellular (Potential).|CUB 1.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						CTTTGAAATCGAGAAGCACGA	0.552													9	289	---	---	---	---	PASS
UNC80	285175	broad.mit.edu	37	2	210654270	210654270	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210654270C>A	uc010zjc.1	+	6	819	c.739C>A	c.(739-741)CCT>ACT	p.P247T	UNC80_uc002vdj.1_Missense_Mutation_p.P247T	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	247						integral to membrane					0						GAGAAGTTCTCCTATCAACAG	0.343													20	99	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211452771	211452771	+	Intron	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211452771T>C	uc002vee.3	+						CPS1_uc010fur.2_Intron	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		CTCTGGTTTTTAAAATGGCAG	0.403													21	104	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219869012	219869012	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219869012C>A	uc002vjl.1	-	33	5301	c.5217G>T	c.(5215-5217)GAG>GAT	p.E1739D	uc010fvz.1_5'Flank|MIR375_hsa-mir-375|MI0000783_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1739						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTTCCCATCCTCCCAGCTGC	0.413													19	61	---	---	---	---	PASS
SPEG	10290	broad.mit.edu	37	2	220309423	220309423	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220309423G>A	uc010fwg.2	+	2	437	c.437G>A	c.(436-438)CGC>CAC	p.R146H	SPEG_uc002vlm.2_RNA|SPEG_uc010fwh.1_5'UTR|SPEG_uc002vln.1_5'UTR	NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	146					muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGAACCCAGCGCCTGGAGCTT	0.632													9	37	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227924170	227924170	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227924170C>A	uc010zlt.1	-	28	2988	c.2334G>T	c.(2332-2334)GTG>GTT	p.V778V		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	778	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TTATCCCTGGCACTCCTGAAA	0.577													25	119	---	---	---	---	PASS
ATG16L1	55054	broad.mit.edu	37	2	234202917	234202917	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234202917C>A	uc002vty.2	+	18	2002	c.1745C>A	c.(1744-1746)GCG>GAG	p.A582E	ATG16L1_uc002vtx.1_Missense_Mutation_p.A419E|ATG16L1_uc002vua.2_Missense_Mutation_p.A563E|ATG16L1_uc002vub.2_Missense_Mutation_p.A440E|ATG16L1_uc002vtz.2_Missense_Mutation_p.A403E|ATG16L1_uc002vud.3_Missense_Mutation_p.A498E	NM_030803	NP_110430	Q676U5	A16L1_HUMAN	APG16 autophagy 16-like isoform 1	582	WD 7.				autophagic vacuole assembly|protein homooligomerization|protein transport	autophagic vacuole|pre-autophagosomal structure membrane	protein binding				0		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		TCCATCAATGCGGTGGCGTGG	0.522													10	43	---	---	---	---	PASS
UGT1A9	54600	broad.mit.edu	37	2	234580705	234580705	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234580705G>T	uc002vus.2	+	1	162	c.125G>T	c.(124-126)AGG>ATG	p.R42M	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Missense_Mutation_p.R42M	NM_021027	NP_066307	O60656	UD19_HUMAN	UDP glycosyltransferase 1 family, polypeptide A9	42					drug metabolic process|flavone metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(3)|breast(1)|skin(1)	5		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Entacapone(DB00494)|Etodolac(DB00749)|Indomethacin(DB00328)|Irinotecan(DB00762)|Mycophenolic acid(DB01024)|Oxyphenonium(DB00219)|Propofol(DB00818)|Sorafenib(DB00398)	TTCACCATGAGGTCGGTGGTG	0.552													14	38	---	---	---	---	PASS
HRH1	3269	broad.mit.edu	37	3	11301422	11301422	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11301422C>A	uc010hdr.2	+	2	1041	c.699C>A	c.(697-699)TCC>TCA	p.S233S	HRH1_uc010hds.2_Silent_p.S233S|HRH1_uc010hdt.2_Silent_p.S233S|HRH1_uc003bwb.3_Silent_p.S233S	NM_001098213	NP_001091683	P35367	HRH1_HUMAN	histamine receptor H1	233	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	CCCTCCCTTCCTTCTCAGAAA	0.537													5	74	---	---	---	---	PASS
TIMP4	7079	broad.mit.edu	37	3	12195893	12195893	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12195893C>A	uc003bwo.2	-	4	718	c.411G>T	c.(409-411)TGG>TGT	p.W137C	SYN2_uc003bwl.1_Intron|SYN2_uc003bwm.2_Intron|SYN2_uc003bwn.2_Intron	NM_003256	NP_003247	Q99727	TIMP4_HUMAN	tissue inhibitor of metalloproteinase 4	137	NTR.						metal ion binding|metalloendopeptidase inhibitor activity				0						ACAGGTCCTCCCAGGGCTCGA	0.493													39	46	---	---	---	---	PASS
NEK10	152110	broad.mit.edu	37	3	27332856	27332856	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27332856T>A	uc003cdt.1	-	19	1776	c.1502A>T	c.(1501-1503)GAA>GTA	p.E501V	NEK10_uc003cds.1_5'UTR	NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3	501	Potential.						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						TTCAATATTTTCAGCAATTTG	0.343													18	25	---	---	---	---	PASS
GOLGA4	2803	broad.mit.edu	37	3	37292888	37292888	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37292888G>T	uc003cgv.2	+	2	379	c.75G>T	c.(73-75)GCG>GCT	p.A25A	GOLGA4_uc010hgr.1_Silent_p.A25A|GOLGA4_uc003cgw.2_Silent_p.A25A|GOLGA4_uc010hgs.2_Silent_p.A25A|GOLGA4_uc003cgu.1_Silent_p.A25A	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	25					Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						AAATCTAGGCGTCCTCCAATT	0.388													15	19	---	---	---	---	PASS
SMARCC1	6599	broad.mit.edu	37	3	47734751	47734751	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47734751C>A	uc003crq.2	-	12	1323	c.1205G>T	c.(1204-1206)GGA>GTA	p.G402V	SMARCC1_uc011bbd.1_Missense_Mutation_p.G293V	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	402					chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TACAGTTCCTCCTTTAACAGG	0.333													5	59	---	---	---	---	PASS
RBM5	10181	broad.mit.edu	37	3	50151525	50151525	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50151525A>G	uc003cyg.2	+	19	1908	c.1760A>G	c.(1759-1761)GAG>GGG	p.E587G	RBM5_uc011bdj.1_Missense_Mutation_p.E531G|RBM5_uc011bdk.1_Missense_Mutation_p.E415G|RBM5_uc003cyh.2_Missense_Mutation_p.E44G	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5	587	Required for interaction with U2AF2.				apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCTCTCTTTGAGAAGAAGGTA	0.448													5	52	---	---	---	---	PASS
ITIH1	3697	broad.mit.edu	37	3	52812955	52812955	+	Intron	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52812955C>T	uc003dfs.2	+						ITIH1_uc010hmn.1_Intron	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1						hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		TCCCTCCCTGCAGTACAGCAG	0.547													14	29	---	---	---	---	PASS
WNT5A	7474	broad.mit.edu	37	3	55513523	55513523	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55513523G>T	uc003dhn.2	-	3	528	c.210C>A	c.(208-210)AGC>AGA	p.S70R	WNT5A_uc003dhm.2_Missense_Mutation_p.S55R|WNT5A_uc010hmw.2_Missense_Mutation_p.S55R|WNT5A_uc010hmx.2_Intron	NM_003392	NP_003383	P41221	WNT5A_HUMAN	wingless-type MMTV integration site family,	70					activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		CTGCCAGTTGGCTGCAGAGAG	0.478													17	106	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58127599	58127599	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58127599A>C	uc003djj.2	+	30	5289	c.5124A>C	c.(5122-5124)GAA>GAC	p.E1708D	FLNB_uc010hne.2_Missense_Mutation_p.E1739D|FLNB_uc003djk.2_Missense_Mutation_p.E1708D|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Missense_Mutation_p.E1539D|FLNB_uc003djm.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1708	Hinge 1 (By similarity).				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CAGATGGGGAAGTCACAGCCG	0.507													24	33	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64672280	64672280	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64672280G>T	uc003dmg.2	-	2	512	c.480C>A	c.(478-480)TCC>TCA	p.S160S	ADAMTS9_uc011bfo.1_Silent_p.S160S|ADAMTS9_uc003dmh.1_5'UTR|ADAMTS9_uc003dmk.1_Silent_p.S160S|uc003dml.2_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	160					glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CCGTGTGCTCGGAGTTGGTAT	0.567													3	15	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73433190	73433190	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73433190T>C	uc003dpl.1	-	10	2623	c.2527A>G	c.(2527-2529)AGC>GGC	p.S843G	PDZRN3_uc011bgh.1_Missense_Mutation_p.S500G|PDZRN3_uc010hoe.1_Missense_Mutation_p.S541G|PDZRN3_uc011bgf.1_Missense_Mutation_p.S560G|PDZRN3_uc011bgg.1_Missense_Mutation_p.S563G	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	843							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CTCCCGTCGCTGGCTCTCCGC	0.657													11	20	---	---	---	---	PASS
NSUN3	63899	broad.mit.edu	37	3	93813893	93813893	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93813893C>T	uc003drl.1	+	5	754	c.638C>T	c.(637-639)CCG>CTG	p.P213L		NM_022072	NP_071355	Q9H649	NSUN3_HUMAN	NOL1/NOP2/Sun domain family, member 3	213							methyltransferase activity			skin(1)	1						GTGGATGCTCCGTGTTCAAAT	0.408													12	34	---	---	---	---	PASS
OR5H15	403274	broad.mit.edu	37	3	97887996	97887996	+	Silent	SNP	T	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97887996T>G	uc011bgu.1	+	1	453	c.453T>G	c.(451-453)GCT>GCG	p.A151A		NM_001005515	NP_001005515	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						CATATATAGCTGGTATTCTTC	0.373													23	22	---	---	---	---	PASS
ALCAM	214	broad.mit.edu	37	3	105250889	105250889	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105250889C>A	uc003dvx.2	+	4	978	c.438C>A	c.(436-438)CTC>CTA	p.L146L	ALCAM_uc003dvw.1_Silent_p.L146L|ALCAM_uc003dvy.2_Silent_p.L146L|ALCAM_uc011bhh.1_Silent_p.L95L|ALCAM_uc010hpp.2_5'Flank	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	146	Extracellular (Potential).|Ig-like V-type 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						CACTGTTTCTCGAAACAGAGC	0.348													6	128	---	---	---	---	PASS
LRRC58	116064	broad.mit.edu	37	3	120054684	120054684	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120054684G>T	uc003edr.2	-	2	713	c.617C>A	c.(616-618)CCT>CAT	p.P206H		NM_001099678	NP_001093148	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	206	LRR 7.										0				GBM - Glioblastoma multiforme(114;0.147)		TGAAAGTTGAGGAGGTATGCT	0.343													6	72	---	---	---	---	PASS
SLC15A2	6565	broad.mit.edu	37	3	121649761	121649761	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121649761A>G	uc003eep.2	+	18	1781	c.1628A>G	c.(1627-1629)TAT>TGT	p.Y543C	SLC15A2_uc011bjn.1_Missense_Mutation_p.Y512C	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	543					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	GGTGAAGACTATGGTGTGTCT	0.368													16	41	---	---	---	---	PASS
PARP15	165631	broad.mit.edu	37	3	122353965	122353965	+	Silent	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122353965C>G	uc003efm.2	+	11	1737	c.1671C>G	c.(1669-1671)CTC>CTG	p.L557L	PARP15_uc003efn.2_Silent_p.L362L|PARP15_uc003efo.1_Silent_p.L304L|PARP15_uc003efp.1_Silent_p.L323L|PARP15_uc011bjt.1_Silent_p.L254L	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	535	PARP catalytic.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		AGAGACTCCTCTTCCATGGGA	0.418													24	37	---	---	---	---	PASS
PLXNA1	5361	broad.mit.edu	37	3	126710360	126710360	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126710360G>T	uc003ejg.2	+	2	1263	c.1259G>T	c.(1258-1260)CGG>CTG	p.R420L		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	443	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		TATGACTATCGGGGCCGCACT	0.657													4	19	---	---	---	---	PASS
C3orf58	205428	broad.mit.edu	37	3	143708453	143708453	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143708453A>G	uc003evo.2	+	3	1598	c.1063A>G	c.(1063-1065)ACT>GCT	p.T355A	C3orf58_uc011bnl.1_Missense_Mutation_p.T146A	NM_173552	NP_775823	Q8NDZ4	CC058_HUMAN	hypothetical protein LOC205428 isoform a	355						COPI vesicle coat|extracellular region				ovary(1)	1						TGCTCGTGCCACTGTGGACCA	0.433													11	57	---	---	---	---	PASS
GPR171	29909	broad.mit.edu	37	3	150916412	150916412	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150916412T>C	uc003eyq.3	-	3	1002	c.762A>G	c.(760-762)ATA>ATG	p.I254M	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_013308	NP_037440	O14626	GP171_HUMAN	G protein-coupled receptor 171	254	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCAATCAGTTATGACTTCTG	0.463													16	51	---	---	---	---	PASS
SCHIP1	29970	broad.mit.edu	37	3	159606697	159606697	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159606697A>T	uc003fcs.1	+	6	1349	c.1283A>T	c.(1282-1284)CAA>CTA	p.Q428L	SCHIP1_uc003fcq.1_Missense_Mutation_p.Q504L|SCHIP1_uc003fcr.1_Missense_Mutation_p.Q417L|SCHIP1_uc003fct.1_Missense_Mutation_p.Q415L|SCHIP1_uc010hvz.1_Missense_Mutation_p.Q388L|SCHIP1_uc003fcu.1_Missense_Mutation_p.Q185L|SCHIP1_uc003fcv.1_Missense_Mutation_p.Q201L	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1	428	Potential.					cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GGGCAGCTACAAGTGATAGTC	0.378													6	58	---	---	---	---	PASS
BCHE	590	broad.mit.edu	37	3	165548334	165548334	+	Missense_Mutation	SNP	C	A	A	rs141243848		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165548334C>A	uc003fem.3	-	2	648	c.488G>T	c.(487-489)CGG>CTG	p.R163L	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	163					choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)	TCTTTCAACCCGAGCCAGAAA	0.418													5	24	---	---	---	---	PASS
APOD	347	broad.mit.edu	37	3	195295761	195295761	+	3'UTR	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195295761T>A	uc003fur.2	-	5						NM_001647	NP_001638	P05090	APOD_HUMAN	apolipoprotein D precursor						lipid metabolic process	extracellular space	lipid binding|lipid transporter activity|protein binding			ovary(2)	2	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)		AGCCTCCCTGTAGAACCTGGT	0.483													7	62	---	---	---	---	PASS
BDH1	622	broad.mit.edu	37	3	197238877	197238877	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197238877G>A	uc003fxr.2	-	8	1323	c.921C>T	c.(919-921)ACC>ACT	p.T307T	BDH1_uc003fxs.2_Silent_p.T307T|BDH1_uc003fxt.2_Silent_p.T220T|BDH1_uc003fxu.2_Silent_p.T307T	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	307					cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	GGGTGGTGGCGGTCAGGGCGT	0.562													15	69	---	---	---	---	PASS
TAPT1	202018	broad.mit.edu	37	4	16189952	16189952	+	Silent	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16189952A>G	uc010ied.1	-	5	720	c.639T>C	c.(637-639)TTT>TTC	p.F213F	TAPT1_uc011bxd.1_RNA|TAPT1_uc011bxe.1_Silent_p.F102F	NM_153365	NP_699196	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation	213						integral to membrane	growth hormone-releasing hormone receptor activity				0						TGTCTTGTCCAAAAGATGAAA	0.323													9	17	---	---	---	---	PASS
MED28	80306	broad.mit.edu	37	4	17623209	17623209	+	Splice_Site	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17623209G>T	uc003gpi.1	+	3	239	c.227_splice	c.e3-1	p.G76_splice	MED28_uc003gpj.2_Splice_Site	NM_025205	NP_079481	Q9H204	MED28_HUMAN	mediator complex subunit 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0						TTTTTTTTAAGGTGTTGATCA	0.313													6	17	---	---	---	---	PASS
TBC1D1	23216	broad.mit.edu	37	4	38138765	38138765	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38138765G>T	uc003gtb.2	+	20	3659	c.3316G>T	c.(3316-3318)GGT>TGT	p.G1106C	TBC1D1_uc011byd.1_Missense_Mutation_p.G1097C|TBC1D1_uc010ifd.2_Missense_Mutation_p.G893C|TBC1D1_uc003gtd.2_Missense_Mutation_p.G118C	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,	1106						nucleus	Rab GTPase activator activity			ovary(1)	1						GGTGGCAAATGGTAGGATCCA	0.527													6	181	---	---	---	---	PASS
PHOX2B	8929	broad.mit.edu	37	4	41750460	41750460	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41750460G>T	uc003gwf.3	-	1	528	c.168C>A	c.(166-168)GGC>GGA	p.G56G		NM_003924	NP_003915	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	56					positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1)	12						GGGAAGGGCAGCCGGACGTGG	0.622			Mis|F		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				6	44	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46305516	46305516	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46305516A>G	uc003gxc.3	-	7	1490	c.817T>C	c.(817-819)TGG>CGG	p.W273R	GABRA2_uc010igc.2_Missense_Mutation_p.W273R|GABRA2_uc011bzc.1_Missense_Mutation_p.W218R|GABRA2_uc003gxe.2_Missense_Mutation_p.W273R	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	273	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	CTGTTAAGCCAGAATGAAACT	0.299													30	47	---	---	---	---	PASS
FIP1L1	81608	broad.mit.edu	37	4	54319142	54319142	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54319142C>A	uc003gzy.2	+	16	1527	c.1341C>A	c.(1339-1341)ACC>ACA	p.T447T	PDGFRA_uc003haa.2_Intron|FIP1L1_uc011bzu.1_Silent_p.T441T|FIP1L1_uc003gzz.2_Silent_p.T373T|FIP1L1_uc003hab.2_Silent_p.T412T|FIP1L1_uc003hac.2_Silent_p.T201T|FIP1L1_uc010ign.2_RNA|FIP1L1_uc003had.2_Missense_Mutation_p.P32Q|FIP1L1_uc003hae.2_Missense_Mutation_p.P32Q	NM_030917	NP_112179	Q6UN15	FIP1_HUMAN	FIP1 like 1 isoform 1	447	Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing	nucleus	RNA binding			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TTGTGGACACCAGCAAGCAGT	0.279			T	PDGFRA	idiopathic hypereosinophilic syndrome								5	94	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62453133	62453133	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62453133G>C	uc010ihh.2	+	2	417	c.244G>C	c.(244-246)GAT>CAT	p.D82H	LPHN3_uc003hcq.3_Missense_Mutation_p.D82H|LPHN3_uc010ihg.1_Missense_Mutation_p.D150H	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	82	SUEL-type lectin.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						TTATCTGCCAGATGCCTATAA	0.373													8	11	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62845347	62845347	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62845347G>A	uc010ihh.2	+	15	2841	c.2668G>A	c.(2668-2670)GTT>ATT	p.V890I	LPHN3_uc003hcq.3_Missense_Mutation_p.V890I|LPHN3_uc003hct.2_Missense_Mutation_p.V283I	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	877	Helical; Name=1; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						GCTGTCCCTTGTTTGTCTCCT	0.478													45	147	---	---	---	---	PASS
AGPAT9	84803	broad.mit.edu	37	4	84525931	84525931	+	3'UTR	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84525931G>T	uc003how.2	+	13					AGPAT9_uc003hox.2_3'UTR|AGPAT9_uc003hoy.2_3'UTR	NM_032717	NP_116106	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)				GAGGACGGATGACAGCCTTTA	0.328													6	19	---	---	---	---	PASS
PPM1K	152926	broad.mit.edu	37	4	89189398	89189398	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89189398C>A	uc003hrm.3	-	5	1186	c.796G>T	c.(796-798)GAT>TAT	p.D266Y		NM_152542	NP_689755	Q8N3J5	PPM1K_HUMAN	protein phosphatase 1K (PP2C domain containing)	266	PP2C-like.				protein dephosphorylation	mitochondrial matrix|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000192)		AGGTCCAAATCTCCAATACTT	0.428													16	63	---	---	---	---	PASS
MIR302D	442896	broad.mit.edu	37	4	113569220	113569220	+	RNA	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113569220A>G	hsa-mir-302d|MI0000774	-			c.8A>G			LARP7_uc003iay.2_Intron|LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank																	0						TCCATGTTAAAGTAGAGGGGG	0.358													10	20	---	---	---	---	PASS
QRFPR	84109	broad.mit.edu	37	4	122254088	122254088	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122254088C>A	uc010inj.1	-	4	1064	c.685G>T	c.(685-687)GTG>TTG	p.V229L	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Splice_Site_p.M228_splice	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	229	Helical; Name=5; (Potential).			VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488).		plasma membrane	neuropeptide Y receptor activity				0						ATAAGCATCACCATAAGAGGC	0.428													13	38	---	---	---	---	PASS
FBXW7	55294	broad.mit.edu	37	4	153249410	153249410	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153249410G>T	uc003ims.2	-	9	1517	c.1368C>A	c.(1366-1368)ACC>ACA	p.T456T	FBXW7_uc011cii.1_Silent_p.T456T|FBXW7_uc003imt.2_Silent_p.T456T|FBXW7_uc011cih.1_Silent_p.T280T|FBXW7_uc003imq.2_Silent_p.T376T|FBXW7_uc003imr.2_Silent_p.T338T	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	456	WD 2.				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GCCCATATAAGGTGTGTATAC	0.408			Mis|N|D|F		colorectal|endometrial|T-ALL								5	73	---	---	---	---	PASS
PDGFC	56034	broad.mit.edu	37	4	157693940	157693940	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157693940G>C	uc003iph.1	-	4	1092	c.601C>G	c.(601-603)CGA>GGA	p.R201G	PDGFC_uc003ipi.1_Missense_Mutation_p.R38G|PDGFC_uc011cis.1_Missense_Mutation_p.R38G|PDGFC_uc011cir.1_Missense_Mutation_p.R45G	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor	201					central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		TCAAGATATCGAATAAGGTCT	0.438													4	17	---	---	---	---	PASS
FAM198B	51313	broad.mit.edu	37	4	159092200	159092200	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159092200T>C	uc003ipp.3	-	2	780	c.328A>G	c.(328-330)ACC>GCC	p.T110A	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.T110A|FAM198B_uc003ipr.3_Missense_Mutation_p.T110A|FAM198B_uc003ips.2_Missense_Mutation_p.T110A|uc003ipt.1_RNA	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	110	Extracellular (Potential).					Golgi membrane|integral to membrane					0						GAGCGTAGGGTAATGTACACC	0.622													5	51	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897024	175897024	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175897024C>A	uc003iuc.2	+	5	1018	c.348C>A	c.(346-348)CTC>CTA	p.L116L	ADAM29_uc003iud.2_Silent_p.L116L|ADAM29_uc010irr.2_Silent_p.L116L|ADAM29_uc011cki.1_Silent_p.L116L	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	116					proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGGTTTCCCTCAGTACCTGTT	0.438													6	31	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183676047	183676047	+	Silent	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183676047C>T	uc003ivd.1	+	21	4564	c.4527C>T	c.(4525-4527)AAC>AAT	p.N1509N	ODZ3_uc003ive.1_Silent_p.N922N	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1509	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		ACTCTATGAACTTCTATGAAG	0.413													11	49	---	---	---	---	PASS
MRPL36	64979	broad.mit.edu	37	5	1799040	1799040	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1799040G>A	uc003jcx.3	-	2	73	c.10C>T	c.(10-12)CTT>TTT	p.L4F	NDUFS6_uc003jcy.2_5'Flank	NM_032479	NP_115868	Q9P0J6	RM36_HUMAN	mitochondrial ribosomal protein L36 precursor	4					translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0				GBM - Glioblastoma multiforme(108;0.241)		CTTATAAAAAGATTTGCCATG	0.448													5	91	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7789771	7789771	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7789771G>T	uc003jdz.1	+	20	2553	c.2486G>T	c.(2485-2487)AGG>ATG	p.R829M	ADCY2_uc011cmo.1_Missense_Mutation_p.R649M|ADCY2_uc010itm.1_Missense_Mutation_p.R25M	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	829	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						TATTACTGTAGGTTAGACTTC	0.438													6	137	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24593512	24593512	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24593512G>T	uc003jgr.1	-	2	420	c.88C>A	c.(88-90)CCT>ACT	p.P30T	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	30					adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		TGTGGCACAGGCGTCCTTCTG	0.398										HNSCC(23;0.051)			26	41	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26915806	26915806	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26915806A>C	uc003jgs.1	-	3	624	c.455T>G	c.(454-456)ATC>AGC	p.I152S	CDH9_uc010iug.2_Missense_Mutation_p.I152S	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	152	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						ATTGTCATTGATATCATGTAT	0.378													16	50	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36137453	36137453	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36137453G>C	uc003jkb.1	-	5	874	c.459C>G	c.(457-459)ATC>ATG	p.I153M		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	153	Helical; (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCCATAGTAGATTGCATTCT	0.348													3	29	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37120354	37120354	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120354A>C	uc011cpa.1	-	49	9343	c.9112T>G	c.(9112-9114)TCT>GCT	p.S3038A	C5orf42_uc003jko.1_Missense_Mutation_p.S69A|C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_Missense_Mutation_p.S1556A|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.S2131A	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	3038										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGCCCAAAAGACTTCCTCTTA	0.368													10	46	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41142975	41142975	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41142975A>T	uc003jmk.2	-	18	2967	c.2757T>A	c.(2755-2757)TGT>TGA	p.C919*	C6_uc003jml.1_Nonsense_Mutation_p.C919*	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	919	Complement control factor I module 2.|C5b-binding domain.|Kazal-like 2.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TCCTGTTTGCACATCTTATAG	0.433													20	116	---	---	---	---	PASS
CDC20B	166979	broad.mit.edu	37	5	54442562	54442562	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54442562C>A	uc003jpo.1	-	3	424	c.249G>T	c.(247-249)AGG>AGT	p.R83S	CDC20B_uc003jpn.1_Missense_Mutation_p.R83S|CDC20B_uc010ivu.1_Missense_Mutation_p.R83S|CDC20B_uc010ivv.1_Missense_Mutation_p.R83S|CDC20B_uc003jpp.2_RNA	NM_152623	NP_689836	Q86Y33	CD20B_HUMAN	CDC20 cell division cycle 20 homolog B isoform	83											0		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			AGGACAGAGCCCTAGTTTGAC	0.522											OREG0016610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	37	54	---	---	---	---	PASS
DEPDC1B	55789	broad.mit.edu	37	5	59982955	59982955	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59982955C>A	uc003jsh.2	-	2	221	c.148G>T	c.(148-150)GTG>TTG	p.V50L	DEPDC1B_uc011cqm.1_Missense_Mutation_p.V50L|DEPDC1B_uc011cqn.1_Missense_Mutation_p.V23L	NM_018369	NP_060839	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B isoform 1	50	DEP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)	1		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				AGCCAATCCACAGCTTCGGCC	0.498													18	17	---	---	---	---	PASS
KIF2A	3796	broad.mit.edu	37	5	61643888	61643888	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61643888G>A	uc003jsy.3	+	3	484	c.173G>A	c.(172-174)AGC>AAC	p.S58N	KIF2A_uc003jsz.3_Missense_Mutation_p.S58N|KIF2A_uc010iwp.2_Missense_Mutation_p.S58N|KIF2A_uc003jsx.3_Missense_Mutation_p.S38N|KIF2A_uc010iwq.2_5'UTR	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1	58	Globular (Potential).				blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		GACCTGGAGAGCATCTTTTCA	0.363													45	82	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70798568	70798568	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70798568A>G	uc003kbp.1	+	15	2454	c.2191A>G	c.(2191-2193)ATT>GTT	p.I731V	BDP1_uc003kbn.1_Missense_Mutation_p.I731V|BDP1_uc003kbo.2_Missense_Mutation_p.I731V	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	731					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		ACAGGAAGAAATTGGGGCCAA	0.418													19	31	---	---	---	---	PASS
AGGF1	55109	broad.mit.edu	37	5	76331382	76331382	+	Silent	SNP	G	T	T	rs146897885	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76331382G>T	uc003ket.2	+	3	690	c.330G>T	c.(328-330)ACG>ACT	p.T110T	AGGF1_uc003kes.2_Silent_p.T110T|AGGF1_uc003keu.1_RNA	NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q	110					angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TTTATCAGACGTACTACAATG	0.294													3	15	---	---	---	---	PASS
STARD4	134429	broad.mit.edu	37	5	110843086	110843086	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110843086T>C	uc003kph.1	-	2	130	c.46A>G	c.(46-48)AAC>GAC	p.N16D	STARD4_uc010jbw.1_5'UTR|STARD4_uc010jbx.1_Intron|STARD4_uc003kpi.1_RNA|STARD4_uc003kpj.2_Missense_Mutation_p.N16D	NM_139164	NP_631903	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain	16	START.				lipid transport		lipid binding			ovary(1)	1		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		ATGAGAGTGTTTTTAAGTTTA	0.368													15	22	---	---	---	---	PASS
SNX2	6643	broad.mit.edu	37	5	122152598	122152598	+	Intron	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122152598A>T	uc003kte.2	+						SNX2_uc011cwn.1_Intron	NM_003100	NP_003091	O60749	SNX2_HUMAN	sorting nexin 2						cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		CTTATTTGTCATTCAATTCCA	0.478													4	9	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140802848	140802848	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140802848C>G	uc003lkq.1	+	1	2312	c.2054C>G	c.(2053-2055)TCT>TGT	p.S685C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.S685C|PCDHGA11_uc003lkp.1_Intron	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	685	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCTAACTCTGAAACCTCA	0.637													19	39	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140802857	140802857	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140802857C>G	uc003lkq.1	+	1	2321	c.2063C>G	c.(2062-2064)TCA>TGA	p.S688*	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Nonsense_Mutation_p.S688*|PCDHGA11_uc003lkp.1_Intron|PCDHGB8P_uc011daz.1_5'Flank	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	688	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGAAACCTCAGACCTCTCG	0.632													19	43	---	---	---	---	PASS
GABRG2	2566	broad.mit.edu	37	5	161580278	161580278	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161580278C>G	uc003lyz.3	+	9	1666	c.1308C>G	c.(1306-1308)ATC>ATG	p.I436M	GABRG2_uc010jjc.2_Missense_Mutation_p.I484M|GABRG2_uc003lyy.3_Missense_Mutation_p.I444M|GABRG2_uc011dej.1_Missense_Mutation_p.I341M	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	436	Cytoplasmic (Probable).|Interaction with GABARAP (Potential).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)		GGATACATATCCGCATTGCCA	0.493													36	48	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170380642	170380642	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170380642G>T	uc003mba.2	+	13	1526	c.1510G>T	c.(1510-1512)GGA>TGA	p.G504*	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	504					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GACAGTTGTAGGAGGAAGATT	0.353			T	TRD@	ALL								11	20	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170380643	170380643	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170380643G>T	uc003mba.2	+	13	1527	c.1511G>T	c.(1510-1512)GGA>GTA	p.G504V	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	504					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACAGTTGTAGGAGGAAGATTA	0.353			T	TRD@	ALL								11	20	---	---	---	---	PASS
F12	2161	broad.mit.edu	37	5	176833016	176833016	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176833016G>A	uc003mgo.3	-	3	211	c.162C>T	c.(160-162)CAC>CAT	p.H54H	F12_uc011dfy.1_5'Flank|F12_uc003mgn.3_5'Flank|F12_uc010jkl.2_RNA	NM_000505	NP_000496	P00748	FA12_HUMAN	coagulation factor XII precursor	54	Fibronectin type-II.				Factor XII activation|fibrinolysis|innate immune response|positive regulation of blood coagulation|positive regulation of fibrinolysis|positive regulation of plasminogen activation|protein autoprocessing|response to misfolded protein|zymogen activation	extracellular space|plasma membrane	serine-type endopeptidase activity				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGCTGCCGGTGGTACTGGA	0.602									Hereditary_Angioedema				17	42	---	---	---	---	PASS
TMEM170B	100113407	broad.mit.edu	37	6	11566033	11566033	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11566033G>C	uc010jpa.2	+	2	232	c.232G>C	c.(232-234)GGA>CGA	p.G78R		NM_001100829	NP_001094299	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	78	Helical; (Potential).					integral to membrane					0						AGTCAGCATTGGATTTCTGGC	0.438													19	87	---	---	---	---	PASS
PRL	5617	broad.mit.edu	37	6	22287628	22287628	+	3'UTR	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22287628G>A	uc003ndp.2	-	5					PRL_uc003ndo.2_3'UTR|PRL_uc003ndq.2_3'UTR	NM_000948	NP_000939	P01236	PRL_HUMAN	prolactin precursor						cell proliferation|cell surface receptor linked signaling pathway|female pregnancy|lactation|positive regulation of JAK-STAT cascade|regulation of multicellular organism growth	cytosol|extracellular region	hormone activity|prolactin receptor binding				0	Ovarian(93;0.163)					AATGGATGTGGGCTTAGCAGT	0.413													23	45	---	---	---	---	PASS
HIST1H2AA	221613	broad.mit.edu	37	6	25726578	25726578	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25726578T>C	uc003nfc.2	-	1	213	c.178A>G	c.(178-180)ACA>GCA	p.T60A	HIST1H2BA_uc003nfd.2_5'Flank	NM_170745	NP_734466	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	60					nucleosome assembly	nucleosome|nucleus	DNA binding				0						ATTTCTGCTGTGAGATACTCT	0.537													28	24	---	---	---	---	PASS
OR2J3	442186	broad.mit.edu	37	6	29080440	29080440	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29080440C>A	uc011dll.1	+	1	773	c.773C>A	c.(772-774)GCC>GAC	p.A258D		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	258	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TTCATTCCGGCCATGTGCATG	0.453													26	42	---	---	---	---	PASS
TRIM39	56658	broad.mit.edu	37	6	30310025	30310025	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30310025G>C	uc010jrz.2	+	9	1858	c.1546G>C	c.(1546-1548)GAT>CAT	p.D516H	TRIM39_uc003npz.2_Missense_Mutation_p.D486H|TRIM39_uc003nqb.2_Missense_Mutation_p.D486H|TRIM39_uc003nqc.2_Missense_Mutation_p.D486H|TRIM39_uc010jsa.1_Intron|RPP21_uc003nqd.1_5'Flank|RPP21_uc003nqe.1_5'Flank|RPP21_uc003nqf.1_5'Flank	NM_021253	NP_067076	Q9HCM9	TRI39_HUMAN	tripartite motif-containing 39 isoform 1	516					apoptosis	cytosol|mitochondrion	identical protein binding|zinc ion binding			ovary(3)	3						GCCCCCAACAGATTGGGAGTG	0.562													15	23	---	---	---	---	PASS
ITPR3	3710	broad.mit.edu	37	6	33634988	33634988	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33634988A>G	uc011drk.1	+	15	1853	c.1634A>G	c.(1633-1635)AAG>AGG	p.K545R		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	545	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						TCAGACCAGAAGAACGCCCCC	0.637													9	22	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38851775	38851775	+	Splice_Site	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38851775G>T	uc003ooe.1	+	54	8208	c.7608_splice	c.e54+1	p.Q2536_splice		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						GGGAGATCAGGTATGGCTGAA	0.294													9	28	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38851776	38851776	+	Splice_Site	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38851776T>A	uc003ooe.1	+	54	8208	c.7608_splice	c.e54+2	p.Q2536_splice		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						GGAGATCAGGTATGGCTGAAA	0.294													9	27	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38866030	38866030	+	Intron	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38866030A>G	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						CTCTCCACCCATAGATGCCAT	0.303													21	59	---	---	---	---	PASS
DAAM2	23500	broad.mit.edu	37	6	39869069	39869069	+	Intron	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39869069C>A	uc003oow.2	+						DAAM2_uc003oox.2_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					CTGTTCTGTCCCTTGACAGTT	0.572													8	212	---	---	---	---	PASS
SRF	6722	broad.mit.edu	37	6	43146615	43146615	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43146615C>A	uc003oui.2	+	6	1901	c.1426C>A	c.(1426-1428)CAC>AAC	p.H476N	SRF_uc011dvf.1_Missense_Mutation_p.H272N	NM_003131	NP_003122	P11831	SRF_HUMAN	serum response factor (c-fos serum response	476					angiogenesis involved in wound healing|cell migration involved in sprouting angiogenesis|cellular senescence|heart looping|muscle cell homeostasis|neuron development|positive regulation of cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of smooth muscle cell differentiation|response to cytokine stimulus|response to hormone stimulus|response to toxin|transcription from RNA polymerase II promoter|trophectodermal cell differentiation	endoplasmic reticulum	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription factor binding			ovary(1)|breast(1)|central_nervous_system(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGTTCAGCTCCACCAGGTAGG	0.502													6	191	---	---	---	---	PASS
CDC5L	988	broad.mit.edu	37	6	44390555	44390555	+	Intron	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44390555C>G	uc003oxl.2	+							NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGGTAAATGTCAATTCCCTTT	0.353													8	41	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54805755	54805755	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54805755G>T	uc003pck.2	+	5	2102	c.1986G>T	c.(1984-1986)AGG>AGT	p.R662S		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	662										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TACTTAAAAGGCGAAGTTTCC	0.338													8	62	---	---	---	---	PASS
BEND6	221336	broad.mit.edu	37	6	56879924	56879924	+	Intron	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56879924A>G	uc010kab.2	+						BEND6_uc003pdi.3_Intron	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6												0						TTTTCTTGCCATTTTAGTGTT	0.393													9	15	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64389923	64389923	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64389923G>T	uc003pep.1	+	2	293	c.267G>T	c.(265-267)ATG>ATT	p.M89I	PHF3_uc010kaf.1_Missense_Mutation_p.M89I|PHF3_uc003pem.2_Missense_Mutation_p.M42I|PHF3_uc010kag.1_Missense_Mutation_p.M1I|PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Missense_Mutation_p.M1I|PHF3_uc011dxs.1_5'UTR|PHF3_uc003peo.2_Missense_Mutation_p.M89I	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	89					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			ACGATATTATGGATGAAGGAG	0.318													5	61	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69945025	69945025	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69945025G>C	uc003pev.3	+	19	3157	c.2709G>C	c.(2707-2709)TGG>TGC	p.W903C	BAI3_uc010kak.2_Missense_Mutation_p.W903C|BAI3_uc011dxx.1_Missense_Mutation_p.W109C|BAI3_uc003pex.1_Missense_Mutation_p.W33C	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	903	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				CAGCATTATGGAGGTAAGTAA	0.378													5	20	---	---	---	---	PASS
SENP6	26054	broad.mit.edu	37	6	76333641	76333641	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76333641G>A	uc003pid.3	+	3	791	c.172G>A	c.(172-174)GAA>AAA	p.E58K	SENP6_uc003pie.3_Missense_Mutation_p.E58K|SENP6_uc003pic.2_Missense_Mutation_p.E58K	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1	58					proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				CAGTGTGGATGAAGATGAGGA	0.313													4	29	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79688325	79688325	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79688325G>T	uc003pir.2	-	24	3099	c.2873C>A	c.(2872-2874)CCA>CAA	p.P958Q	PHIP_uc003piq.2_5'UTR|PHIP_uc011dyp.1_Missense_Mutation_p.P957Q	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	958	Mediates interaction with IRS1 (By similarity).				insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		ACCCATCTGTGGCACAAATGG	0.358													4	28	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90442427	90442427	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90442427C>G	uc003pnn.1	-	34	4907	c.4791G>C	c.(4789-4791)AAG>AAC	p.K1597N		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	1597					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGACCACACACTTTCTGCCAA	0.443													15	56	---	---	---	---	PASS
TRAF3IP2	10758	broad.mit.edu	37	6	111887689	111887689	+	Silent	SNP	G	A	A	rs144166946	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111887689G>A	uc011ebc.1	-	8	2049	c.1434C>T	c.(1432-1434)GAC>GAT	p.D478D	TRAF3IP2_uc011ebb.1_Silent_p.D22D|TRAF3IP2_uc003pvd.2_Silent_p.D70D|TRAF3IP2_uc003pvg.2_Silent_p.D477D|TRAF3IP2_uc003pvf.2_Silent_p.D478D	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	487	SEFIR.				intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GCTCATCCTCGTCCAGCTGCG	0.507													19	62	---	---	---	---	PASS
TRDN	10345	broad.mit.edu	37	6	123698878	123698878	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123698878G>C	uc003pzj.1	-	18	1251	c.1229C>G	c.(1228-1230)CCA>CGA	p.P410R	TRDN_uc003pzk.1_Missense_Mutation_p.P411R|TRDN_uc003pzl.1_Missense_Mutation_p.P411R|TRDN_uc010kem.1_5'UTR	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	410	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TTCTTTCTTTGGTGACTTTGC	0.343													10	46	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	132014720	132014720	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132014720C>A	uc003qcu.3	+	16	1715	c.1368C>A	c.(1366-1368)ATC>ATA	p.I456I	ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Silent_p.I456I	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	456	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		ACGTCAGAATCGACAAAGTTC	0.398													4	49	---	---	---	---	PASS
TAAR2	9287	broad.mit.edu	37	6	132939037	132939037	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132939037C>G	uc003qdl.1	-	2	308	c.308G>C	c.(307-309)AGA>ACA	p.R103T	TAAR2_uc010kfr.1_Missense_Mutation_p.R58T	NM_001033080	NP_001028252	Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2 isoform 1	103	Extracellular (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		CTCCACCGATCTGATCATACT	0.413													12	45	---	---	---	---	PASS
EYA4	2070	broad.mit.edu	37	6	133827274	133827274	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133827274C>G	uc003qec.3	+	14	1680	c.1222C>G	c.(1222-1224)CGC>GGC	p.R408G	EYA4_uc011ecq.1_Missense_Mutation_p.R354G|EYA4_uc011ecr.1_Missense_Mutation_p.R360G|EYA4_uc003qed.3_Missense_Mutation_p.R408G|EYA4_uc003qee.3_Missense_Mutation_p.R385G|EYA4_uc011ecs.1_Missense_Mutation_p.R414G|uc003qef.1_RNA|uc003qeg.1_RNA	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	408					anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		CCTTGGACTCCGCATGGAAGA	0.323													6	22	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143094585	143094585	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143094585G>A	uc003qjd.2	-	5	2034	c.1291C>T	c.(1291-1293)CGG>TGG	p.R431W		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	431					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GGACTAAGCCGACAGTATTTT	0.448													21	74	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144808798	144808798	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144808798G>A	uc003qkt.2	+	28	4029	c.3937G>A	c.(3937-3939)GCT>ACT	p.A1313T		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	1313	Spectrin 9.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAAACTGGAGGCTTTCAACAG	0.498													6	48	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146256083	146256083	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146256083G>T	uc003qlf.2	-	13	3349	c.2950C>A	c.(2950-2952)CCA>ACA	p.P984T	SHPRH_uc003qld.2_Missense_Mutation_p.P984T|SHPRH_uc003qle.2_Missense_Mutation_p.P984T|SHPRH_uc003qlg.1_Missense_Mutation_p.P540T|SHPRH_uc003qlj.1_Missense_Mutation_p.P873T|SHPRH_uc003qlh.2_5'Flank	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	984					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ACAGCCTGTGGGTGACAGCAG	0.438													23	40	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157502211	157502211	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157502211G>A	uc003qqn.2	+	12	3342	c.3190G>A	c.(3190-3192)GAG>AAG	p.E1064K	ARID1B_uc003qqo.2_Missense_Mutation_p.E1024K|ARID1B_uc003qqp.2_Missense_Mutation_p.E1011K|ARID1B_uc010kjl.2_Missense_Mutation_p.E209K	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1069	ARID.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTTCATGGAAGAGAGAGGCTC	0.577													6	33	---	---	---	---	PASS
WTAP	9589	broad.mit.edu	37	6	160164807	160164807	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160164807G>A	uc003qsl.2	+	5	478	c.256G>A	c.(256-258)GAG>AAG	p.E86K	WTAP_uc010kjx.2_Missense_Mutation_p.E86K|WTAP_uc003qsk.2_Missense_Mutation_p.E86K|WTAP_uc003qsm.1_RNA|WTAP_uc003qsn.2_Missense_Mutation_p.E86K	NM_004906	NP_004897	Q15007	FL2D_HUMAN	Wilms' tumour 1-associating protein isoform 1	86					cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		CAAGGAACAAGAGATGCAAGA	0.358													6	33	---	---	---	---	PASS
KDELR2	11014	broad.mit.edu	37	7	6505702	6505702	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6505702C>A	uc003sqe.3	-	4	765	c.604G>T	c.(604-606)GTA>TTA	p.V202L	DAGLB_uc003sqd.3_Intron|KDELR2_uc003sqf.3_Intron	NM_006854	NP_006845	P33947	ERD22_HUMAN	KDEL receptor 2 isoform 1	202	Cytoplasmic (Potential).				intracellular protein transport|protein retention in ER lumen|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	KDEL sequence binding|protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CCCAACATACCTTTTGTAATG	0.488													6	150	---	---	---	---	PASS
TMEM195	392636	broad.mit.edu	37	7	15430477	15430477	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15430477C>A	uc003stb.1	-	7	900	c.730G>T	c.(730-732)GAT>TAT	p.D244Y		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	244					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						AAAATTTTATCCCAAATAATA	0.254													4	7	---	---	---	---	PASS
C7orf16	10842	broad.mit.edu	37	7	31746859	31746859	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31746859G>T	uc003tcl.2	+	5	588	c.430G>T	c.(430-432)GAA>TAA	p.E144*	C7orf16_uc011kaf.1_Nonsense_Mutation_p.E93*	NM_006658	NP_006649	O96001	GSUB_HUMAN	G-substrate isoform 1	144					behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction				ovary(2)|central_nervous_system(1)	3			GBM - Glioblastoma multiforme(11;0.216)			AGCAATCGTGGAAGATGACGA	0.428													16	37	---	---	---	---	PASS
TARP	445347	broad.mit.edu	37	7	38299746	38299746	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38299746G>T	uc003tge.1	-	7	1268	c.891C>A	c.(889-891)ATC>ATA	p.I297I	uc003tfx.1_5'Flank|uc003tfz.1_Intron|TARP_uc003tgb.2_Silent_p.I93I|TARP_uc003tgc.1_Silent_p.I93I|TARP_uc003tgd.1_Silent_p.I93I			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.	Error:Variant_position_missing_in_A2JGV3_after_alignment											0						AGCAGGTGATGATGGCAAAAT	0.458													6	58	---	---	---	---	PASS
UPP1	7378	broad.mit.edu	37	7	48147012	48147012	+	Missense_Mutation	SNP	C	T	T	rs138630287		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48147012C>T	uc003toj.2	+	9	1230	c.701C>T	c.(700-702)GCG>GTG	p.A234V	UPP1_uc003tok.2_Missense_Mutation_p.A234V|UPP1_uc003tol.2_Missense_Mutation_p.A234V|UPP1_uc011kch.1_Missense_Mutation_p.A27V|UPP1_uc003ton.2_Missense_Mutation_p.A97V|UPP1_uc003too.2_Missense_Mutation_p.A97V	NM_181597	NP_853628	Q16831	UPP1_HUMAN	uridine phosphorylase 1	234					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage	cytosol	uridine phosphorylase activity				0						GACAAGCAGGCGTATCTGGAG	0.602													8	30	---	---	---	---	PASS
ZNF117	51351	broad.mit.edu	37	7	64452179	64452179	+	5'Flank	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64452179T>C	uc003ttr.2	-						ZNF117_uc011kdr.1_Missense_Mutation_p.N406S	NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				ctgccaggtatttggagcttc	0.000													8	31	---	---	---	---	PASS
WBSCR28	135886	broad.mit.edu	37	7	73279346	73279346	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73279346C>A	uc003tzk.2	+	2	132	c.96C>A	c.(94-96)CTC>CTA	p.L32L	RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_5'UTR	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886	32						integral to membrane				breast(1)	1		Lung NSC(55;0.159)				GAGATCACCTCTATAATTTCC	0.537													8	401	---	---	---	---	PASS
RSBN1L	222194	broad.mit.edu	37	7	77325946	77325946	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77325946C>A	uc010ldt.1	+	1	204	c.160C>A	c.(160-162)CGG>AGG	p.R54R	RSBN1L_uc003ugm.2_5'Flank|uc003ugj.1_RNA	NM_198467	NP_940869	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	54						nucleus				ovary(1)	1						GAAGGCACCGCGGAGAGTGAA	0.652													6	22	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77756572	77756572	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77756572T>C	uc003ugx.2	-	19	3619	c.3365A>G	c.(3364-3366)TAC>TGC	p.Y1122C	MAGI2_uc003ugy.2_Missense_Mutation_p.Y1108C|MAGI2_uc010ldx.1_Missense_Mutation_p.Y715C	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1122						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GTGCTGCCTGTAGTCCAGTAG	0.637													14	55	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	83014748	83014748	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83014748C>A	uc003uhy.1	-	16	2203	c.1737G>T	c.(1735-1737)GGG>GGT	p.G579G		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	579					axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				CCAAAGCATCCCCTACAACAG	0.358													58	39	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91709280	91709280	+	Silent	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91709280A>G	uc003ulg.2	+	31	8058	c.7833A>G	c.(7831-7833)TTA>TTG	p.L2611L	AKAP9_uc003ulf.2_Silent_p.L2603L|AKAP9_uc003uli.2_Silent_p.L2234L|AKAP9_uc003ulj.2_Silent_p.L381L	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2623	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATCAGAATTAGAAAGCCAGG	0.308			T	BRAF	papillary thyroid								5	61	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	92099241	92099241	+	IGR	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92099241G>C								GATAD1 (10499 upstream) : PEX1 (17097 downstream)																							atgtagttttgagagatctag	0.000													16	14	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103214585	103214585	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103214585C>G	uc003vca.2	-	30	4625	c.4465G>C	c.(4465-4467)GGG>CGG	p.G1489R	RELN_uc010liz.2_Missense_Mutation_p.G1489R	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1489					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TCCCTTTTCCCAGGGCCATTG	0.473													16	67	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110763735	110763735	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110763735C>T	uc003vft.3	+	4	1953	c.907C>T	c.(907-909)CTT>TTT	p.L303F	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.L303F|LRRN3_uc003vfs.3_Missense_Mutation_p.L303F	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	303	Extracellular (Potential).|LRR 10.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CATCGATAGTCTTGCTGTGGA	0.373													13	35	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110763895	110763895	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110763895C>G	uc003vft.3	+	4	2113	c.1067C>G	c.(1066-1068)TCT>TGT	p.S356C	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.S356C|LRRN3_uc003vfs.3_Missense_Mutation_p.S356C	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	356	Extracellular (Potential).|LRR 12.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		ACCATTGAGTCTCTGCCAAAC	0.458													6	38	---	---	---	---	PASS
PAX4	5078	broad.mit.edu	37	7	127255120	127255120	+	Silent	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127255120T>C	uc010lld.1	-	2	356	c.150A>G	c.(148-150)CTA>CTG	p.L50L	PAX4_uc003vmf.2_Silent_p.L48L|PAX4_uc003vmg.1_Silent_p.L50L|PAX4_uc003vmh.2_Silent_p.L48L	NM_006193	NP_006184	O43316	PAX4_HUMAN	paired box 4	58	Paired.				cell differentiation|endocrine pancreas development|organ morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGTAACGCCCTAGGATCTTGC	0.582													14	72	---	---	---	---	PASS
OR2A5	393046	broad.mit.edu	37	7	143748242	143748242	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143748242C>A	uc011ktw.1	+	1	748	c.748C>A	c.(748-750)CTC>ATC	p.L250I		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	250	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)					CATGGTGGGACTCTTCTTTGG	0.592													28	87	---	---	---	---	PASS
GIMAP8	155038	broad.mit.edu	37	7	150164145	150164145	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150164145T>G	uc003whj.2	+	2	689	c.359T>G	c.(358-360)GTG>GGG	p.V120G		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	120						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ATCCAACAAGTGTTTGGAGCT	0.483													9	45	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150840947	150840947	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150840947G>T	uc003wjg.1	+	18	2656	c.2653G>T	c.(2653-2655)GGC>TGC	p.G885C	AGAP3_uc003wje.1_Missense_Mutation_p.G554C|AGAP3_uc003wjj.1_Missense_Mutation_p.G384C|AGAP3_uc003wjk.1_Missense_Mutation_p.G303C	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	849					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						GGAGGGCTGTGGCTTAGCGCC	0.647													11	33	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150840948	150840948	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150840948G>T	uc003wjg.1	+	18	2657	c.2654G>T	c.(2653-2655)GGC>GTC	p.G885V	AGAP3_uc003wje.1_Missense_Mutation_p.G554V|AGAP3_uc003wjj.1_Missense_Mutation_p.G384V|AGAP3_uc003wjk.1_Missense_Mutation_p.G303V	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	849					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						GAGGGCTGTGGCTTAGCGCCT	0.647													12	32	---	---	---	---	PASS
GSR	2936	broad.mit.edu	37	8	30539494	30539494	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30539494G>A	uc003xih.1	-	11	1329	c.1238C>T	c.(1237-1239)ACT>ATT	p.T413I		NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor	413					cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)	GAAGACCACAGTTGGGATGTT	0.428													8	33	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39525607	39525607	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39525607C>G	uc003xni.2	+	14	1417	c.1417C>G	c.(1417-1419)CCT>GCT	p.P473A	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Missense_Mutation_p.P449A	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	473	Disintegrin.|Extracellular (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TAATTGTGTTCCTGACACTTA	0.418													29	38	---	---	---	---	PASS
HGSNAT	138050	broad.mit.edu	37	8	43037324	43037324	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43037324A>T	uc003xpx.3	+	11	1097	c.1049A>T	c.(1048-1050)CAG>CTG	p.Q350L		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	378	Helical; (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GGTGTGCTGCAGCGATTGGGA	0.483													110	504	---	---	---	---	PASS
SNTG1	54212	broad.mit.edu	37	8	51664659	51664659	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51664659G>C	uc010lxy.1	+	19	1754	c.1383G>C	c.(1381-1383)CAG>CAC	p.Q461H	SNTG1_uc003xqs.1_Missense_Mutation_p.Q461H|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	461					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ATACTAAACAGATTGAAGCAA	0.373													3	21	---	---	---	---	PASS
CYP7A1	1581	broad.mit.edu	37	8	59404141	59404141	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59404141T>A	uc003xtm.3	-	6	1471	c.1408A>T	c.(1408-1410)ATA>TTA	p.I470L		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	470					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				TGGCCCTCTATAAGCTCCAAT	0.408									Neonatal_Giant_Cell_Hepatitis				11	48	---	---	---	---	PASS
PREX2	80243	broad.mit.edu	37	8	68956719	68956719	+	Intron	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68956719A>C	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						ATTCCATCTTAAGACGGTTGA	0.373													9	47	---	---	---	---	PASS
NCOA2	10499	broad.mit.edu	37	8	71082563	71082563	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71082563C>A	uc003xyn.1	-	6	577	c.415G>T	c.(415-417)GTG>TTG	p.V139L		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	139	PAS.				cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TTCTCTGACACAAACACAACG	0.408			T	RUNXBP2	AML								11	25	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77763640	77763640	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77763640C>A	uc003yav.2	+	10	4735	c.4348C>A	c.(4348-4350)CAC>AAC	p.H1450N	ZFHX4_uc003yau.1_Missense_Mutation_p.H1495N|ZFHX4_uc003yaw.1_Missense_Mutation_p.H1450N	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1450						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGAGGTGGACCACGAAGGGAA	0.507										HNSCC(33;0.089)			5	55	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885863	88885863	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885863G>A	uc003ydz.2	-	1	434	c.337C>T	c.(337-339)CGG>TGG	p.R113W		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	113										ovary(1)	1						GGGTATACCCGGAGCTCAGGG	0.537													28	64	---	---	---	---	PASS
RBM12B	389677	broad.mit.edu	37	8	94746211	94746211	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94746211C>A	uc003yfz.2	-	3	2621	c.2428G>T	c.(2428-2430)GAC>TAC	p.D810Y		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	810							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			CCCCTGAAGTCTTCATCTGGT	0.577													16	85	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100513915	100513915	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100513915G>C	uc003yiv.2	+	26	3982	c.3871G>C	c.(3871-3873)GGA>CGA	p.G1291R	VPS13B_uc003yiw.2_Missense_Mutation_p.G1291R|VPS13B_uc003yiu.1_Missense_Mutation_p.G1291R|VPS13B_uc003yix.1_Missense_Mutation_p.G761R	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1291					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTCATCCCAGGGAGATTCTAT	0.308													6	63	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113668571	113668571	+	Splice_Site	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113668571C>A	uc003ynu.2	-	18	2976	c.2817_splice	c.e18-1	p.R939_splice	CSMD3_uc003yns.2_Splice_Site_p.R211_splice|CSMD3_uc003ynt.2_Splice_Site_p.R899_splice|CSMD3_uc011lhx.1_Splice_Site_p.R835_splice	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						AGTCTGAAATCTAAGATTAAA	0.338										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	15	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	114111088	114111088	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114111088C>A	uc003ynu.2	-	5	973	c.814G>T	c.(814-816)GTA>TTA	p.V272L	CSMD3_uc003ynt.2_Missense_Mutation_p.V232L|CSMD3_uc011lhx.1_Missense_Mutation_p.V272L|CSMD3_uc010mcx.1_Missense_Mutation_p.V272L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	272	Extracellular (Potential).|CUB 2.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GGCTCTGCTACAATGGTCCAA	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			5	13	---	---	---	---	PASS
NOV	4856	broad.mit.edu	37	8	120431549	120431549	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120431549G>T	uc003yoq.2	+	4	962	c.741G>T	c.(739-741)CGG>CGT	p.R247R		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	247	TSP type-1.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GCATGGTGCGGCCCTGTGAAC	0.562													26	110	---	---	---	---	PASS
ANXA13	312	broad.mit.edu	37	8	124705948	124705948	+	Intron	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124705948T>A	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297	P27216	ANX13_HUMAN	annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TCTGCACACATACATCATACA	0.348													19	101	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	124987553	124987553	+	Intron	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124987553C>A	uc003yqw.2	+							NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AAAAGTAAGACAGGTCCATCC	0.438													21	91	---	---	---	---	PASS
KHDRBS3	10656	broad.mit.edu	37	8	136594138	136594138	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136594138C>A	uc003yuv.2	+	6	1023	c.629C>A	c.(628-630)ACA>AAA	p.T210K	KHDRBS3_uc003yuw.2_Missense_Mutation_p.T210K|KHDRBS3_uc010mek.2_RNA	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal	210					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			GGAGGAGTTACAGCCCGGCCA	0.493													24	43	---	---	---	---	PASS
SLC1A1	6505	broad.mit.edu	37	9	4576030	4576030	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4576030C>T	uc003zij.1	+	9	1141	c.905C>T	c.(904-906)CCG>CTG	p.P302L	C9orf68_uc003zik.2_Intron	NM_004170	NP_004161	P43005	EAA3_HUMAN	solute carrier family 1, member 1	302	Helical; (Potential).				D-aspartate import|L-glutamate import|synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)	GTAATTCTCCCGCTGATATAT	0.413													25	31	---	---	---	---	PASS
GLDC	2731	broad.mit.edu	37	9	6550883	6550883	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6550883G>T	uc003zkc.2	-	21	2682	c.2489C>A	c.(2488-2490)ACG>AAG	p.T830K		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	830					glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	CGCAGTTTCCGTGGCTTGTTT	0.423													98	59	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8486189	8486189	+	Silent	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8486189T>C	uc003zkk.2	-	27	3339	c.2628A>G	c.(2626-2628)AAA>AAG	p.K876K	PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Silent_p.K867K|PTPRD_uc003zkm.2_Silent_p.K863K|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	876	Fibronectin type-III 6.|Extracellular (Potential).				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)		AGTGATCTTCTTTTTCAGAGA	0.498										TSP Lung(15;0.13)			158	33	---	---	---	---	PASS
CER1	9350	broad.mit.edu	37	9	14720184	14720184	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14720184C>A	uc003zlj.2	-	2	753	c.708G>T	c.(706-708)GTG>GTT	p.V236V		NM_005454	NP_005445	O95813	CER1_HUMAN	cerberus 1 precursor	236	CTCK.				BMP signaling pathway	extracellular space	cytokine activity				0				GBM - Glioblastoma multiforme(50;3.16e-06)		GGCACTCCTCCACCAGCATCA	0.522													6	97	---	---	---	---	PASS
FANCG	2189	broad.mit.edu	37	9	35079502	35079502	+	Missense_Mutation	SNP	G	A	A	rs35984312	byFrequency	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35079502G>A	uc003zwb.1	-	1	512	c.20C>T	c.(19-21)TCT>TTT	p.S7F	FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_5'UTR|FANCG_uc011lot.1_Missense_Mutation_p.S7F	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	7					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGAGCCCACAGAGGTGGTCTG	0.647			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				8	46	---	---	---	---	PASS
FANCG	2189	broad.mit.edu	37	9	35079503	35079503	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35079503A>T	uc003zwb.1	-	1	511	c.19T>A	c.(19-21)TCT>ACT	p.S7T	FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_5'UTR|FANCG_uc011lot.1_Missense_Mutation_p.S7T	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	7					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GAGCCCACAGAGGTGGTCTGG	0.647			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				8	45	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35720477	35720477	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35720477T>A	uc003zxt.2	-	12	1590	c.1236A>T	c.(1234-1236)GAA>GAT	p.E412D		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	412	Interaction with LAYN (By similarity).				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCTCATCTCCTTCCAGCCCAA	0.488													87	113	---	---	---	---	PASS
ZCCHC7	84186	broad.mit.edu	37	9	37126431	37126431	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37126431A>T	uc003zzq.2	+	2	275	c.102A>T	c.(100-102)CAA>CAT	p.Q34H	ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Missense_Mutation_p.Q33H|ZCCHC7_uc010mlt.2_Missense_Mutation_p.Q33H|ZCCHC7_uc003zzs.1_Missense_Mutation_p.Q33H	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	34							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		TGGAATTTCAACTCTATAGCC	0.398													10	72	---	---	---	---	PASS
VPS13A	23230	broad.mit.edu	37	9	79968365	79968365	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79968365A>G	uc004akr.2	+	54	7720	c.7460A>G	c.(7459-7461)TAT>TGT	p.Y2487C	VPS13A_uc004akp.3_Missense_Mutation_p.Y2487C|VPS13A_uc004akq.3_Missense_Mutation_p.Y2487C|VPS13A_uc004aks.2_Missense_Mutation_p.Y2448C	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2487					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						AAGACAATATATTTAGTTTCA	0.299													4	25	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107645435	107645435	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107645435C>A	uc004bcl.2	-	5	619	c.306G>T	c.(304-306)GTG>GTT	p.V102V	ABCA1_uc004bcm.2_Silent_p.V42V	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	102	Extracellular.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	ACAGGCGAGCCACACTGTAAA	0.493													17	73	---	---	---	---	PASS
TLR4	7099	broad.mit.edu	37	9	120476154	120476154	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120476154G>T	uc004bjz.2	+	3	2039	c.1748G>T	c.(1747-1749)TGT>TTT	p.C583F	TLR4_uc004bka.2_Missense_Mutation_p.C543F|TLR4_uc004bkb.2_Missense_Mutation_p.C383F	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	583	LRRCT.|Extracellular (Potential).				activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity			lung(10)|ovary(4)|breast(1)|skin(1)	16						GACTTTGCTTGTACTTGTGAA	0.408													15	29	---	---	---	---	PASS
NELF	26012	broad.mit.edu	37	9	140347593	140347593	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140347593G>T	uc004cna.2	-	9	1194	c.962C>A	c.(961-963)GCC>GAC	p.A321D	C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_Missense_Mutation_p.A118D|NELF_uc010nci.2_Missense_Mutation_p.A65D|NELF_uc011mey.1_RNA|NELF_uc011mez.1_Missense_Mutation_p.A298D|NELF_uc004cmz.2_Missense_Mutation_p.A319D|NELF_uc004cnc.2_Missense_Mutation_p.A296D|NELF_uc004cnb.2_Missense_Mutation_p.A291D	NM_001130969	NP_001124441	Q6X4W1	NELF_HUMAN	nasal embryonic LHRH factor isoform a	321						nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)		GTCCTCGAAGGCCTCGTCCAG	0.657													4	34	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5789240	5789240	+	Silent	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5789240C>T	uc001iij.2	+	15	4481	c.3856C>T	c.(3856-3858)CTA>TTA	p.L1286L	C10orf18_uc001iik.2_Silent_p.L130L	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1286										ovary(1)|central_nervous_system(1)	2						TGACTTAGCTCTAACAATATC	0.418													26	124	---	---	---	---	PASS
EPC1	80314	broad.mit.edu	37	10	32562218	32562218	+	Intron	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32562218A>G	uc001iwg.1	-						EPC1_uc001iwi.3_Intron|EPC1_uc009xlt.2_Intron|EPC1_uc001iwh.1_Intron	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1						histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex				ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)				TGCTGAACATAAAATAAAGAA	0.368													3	9	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55582261	55582261	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55582261G>A	uc001jju.1	-	33	5620	c.5225C>T	c.(5224-5226)CCT>CTT	p.P1742L	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.P1739L|PCDH15_uc010qhw.1_Missense_Mutation_p.P1702L|PCDH15_uc010qhx.1_Missense_Mutation_p.P1673L|PCDH15_uc010qhy.1_Missense_Mutation_p.P1749L|PCDH15_uc010qhz.1_Missense_Mutation_p.P1744L|PCDH15_uc010qia.1_Missense_Mutation_p.P1722L|PCDH15_uc010qib.1_Missense_Mutation_p.P1719L	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1742	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				aCAGGCAGAAGGAGAGATGTT	0.209										HNSCC(58;0.16)			3	17	---	---	---	---	PASS
TET1	80312	broad.mit.edu	37	10	70451506	70451506	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70451506A>G	uc001jok.3	+	12	6851	c.6346A>G	c.(6346-6348)AAT>GAT	p.N2116D		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	2116					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9						AACCCATGACAATGTTGTCAC	0.453													20	64	---	---	---	---	PASS
COL13A1	1305	broad.mit.edu	37	10	71690217	71690217	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71690217A>G	uc001jpr.1	+	28	2095	c.1559A>G	c.(1558-1560)GAT>GGT	p.D520G	COL13A1_uc001jqj.1_Missense_Mutation_p.D520G|COL13A1_uc001jps.1_Missense_Mutation_p.D491G|COL13A1_uc001jpt.1_Missense_Mutation_p.D479G|COL13A1_uc001jpu.1_Missense_Mutation_p.D501G|COL13A1_uc001jpv.1_Missense_Mutation_p.D520G|COL13A1_uc001jpx.1_Missense_Mutation_p.D498G|COL13A1_uc001jpw.1_Missense_Mutation_p.D467G|COL13A1_uc001jpy.1_Missense_Mutation_p.D458G|COL13A1_uc001jpz.1_Missense_Mutation_p.D463G|COL13A1_uc001jqa.1_Missense_Mutation_p.D460G|COL13A1_uc001jqc.1_Missense_Mutation_p.D520G|COL13A1_uc001jqb.1_Missense_Mutation_p.D469G|COL13A1_uc001jql.2_Missense_Mutation_p.D520G|COL13A1_uc001jqd.1_Missense_Mutation_p.D508G|COL13A1_uc001jqe.1_Missense_Mutation_p.D503G|COL13A1_uc001jqf.1_Missense_Mutation_p.D501G|COL13A1_uc001jqg.1_Missense_Mutation_p.D498G|COL13A1_uc001jqh.1_Missense_Mutation_p.D520G|COL13A1_uc001jqi.1_Missense_Mutation_p.D520G|COL13A1_uc010qjf.1_Missense_Mutation_p.D310G	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1	520	Extracellular (Potential).|Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	CCAGGAAAGGATGGACCTCCA	0.567													5	9	---	---	---	---	PASS
LRRC20	55222	broad.mit.edu	37	10	72100443	72100443	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72100443T>A	uc001jqx.1	-	3	320	c.98A>T	c.(97-99)AAG>ATG	p.K33M	LRRC20_uc001jqy.1_Missense_Mutation_p.K33M|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1	33											0						GGAGACCAGCTTGCACTCGGC	0.547													8	36	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85993948	85993948	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85993948C>A	uc001kcz.1	-	3	798	c.776G>T	c.(775-777)GGA>GTA	p.G259V		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	259	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0						GCTGGCCACTCCTGGATGGAG	0.617													19	62	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97098986	97098986	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97098986C>A	uc001kkp.2	-	27	2814	c.2769G>T	c.(2767-2769)GTG>GTT	p.V923V	SORBS1_uc001kkk.2_Silent_p.V417V|SORBS1_uc001kkl.2_Silent_p.V525V|SORBS1_uc001kkn.2_Silent_p.V688V|SORBS1_uc001kkm.2_Silent_p.V723V|SORBS1_uc001kko.2_Silent_p.V945V|SORBS1_uc001kkq.2_Silent_p.V774V|SORBS1_uc001kkr.2_Silent_p.V629V|SORBS1_uc001kks.2_Silent_p.V573V|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Silent_p.V670V|SORBS1_uc001kkv.2_Silent_p.V705V|SORBS1_uc001kkw.2_Silent_p.V877V|SORBS1_uc010qoe.1_Silent_p.V638V	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	923	SH3 2.				focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGATCACATCCACGTAGGTGA	0.562													5	68	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115365986	115365986	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115365986C>G	uc001laj.2	-	33	3922	c.3758G>C	c.(3757-3759)GGT>GCT	p.G1253A	NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Missense_Mutation_p.G1218A|NRAP_uc001lal.3_Missense_Mutation_p.G1253A	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1253	Nebulin 33.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTCGGGCAGACCCAGGGTCAT	0.438													9	33	---	---	---	---	PASS
CASP7	840	broad.mit.edu	37	10	115486137	115486137	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115486137C>A	uc001lan.2	+	6	800	c.626C>A	c.(625-627)CCT>CAT	p.P209H	CASP7_uc001lam.2_Missense_Mutation_p.L198I|CASP7_uc001lao.2_Missense_Mutation_p.P242H|CASP7_uc001lap.2_Missense_Mutation_p.P209H|CASP7_uc001laq.2_Missense_Mutation_p.P209H|CASP7_uc010qsa.1_Missense_Mutation_p.P294H|CASP7_uc010qsb.1_Missense_Mutation_p.P184H	NM_033339	NP_203125	P55210	CASP7_HUMAN	caspase 7 isoform alpha	209					activation of caspase activity by cytochrome c|cellular component disassembly involved in apoptosis|induction of apoptosis by intracellular signals|proteolysis	cytosol|endoplasmic reticulum membrane|mitochondrial membrane|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		GATGCTAATCCTCGATACAAG	0.498													5	66	---	---	---	---	PASS
KCNK18	338567	broad.mit.edu	37	10	118960727	118960727	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118960727G>T	uc010qsr.1	+	2	281	c.281G>T	c.(280-282)TGG>TTG	p.W94L		NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	94						integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)		AAGCCTCAGTGGTTTAACAGG	0.527													41	105	---	---	---	---	PASS
CUZD1	50624	broad.mit.edu	37	10	124597003	124597003	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124597003C>G	uc001lgq.2	-	4	848	c.516G>C	c.(514-516)AAG>AAC	p.K172N	CUZD1_uc001lgp.2_5'UTR|CUZD1_uc009yad.2_5'UTR|CUZD1_uc009yaf.2_Intron|CUZD1_uc001lgr.2_5'UTR|CUZD1_uc010qty.1_5'UTR|CUZD1_uc009yae.2_5'UTR|CUZD1_uc001lgs.2_Missense_Mutation_p.K172N|CUZD1_uc010qtz.1_Missense_Mutation_p.K172N	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor	172	Extracellular (Potential).|CUB 2.				cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		CAGGATGCGGCTTTGGGTAAT	0.443													24	59	---	---	---	---	PASS
IKZF5	64376	broad.mit.edu	37	10	124758038	124758038	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124758038C>T	uc001lha.2	-	3	403	c.104G>A	c.(103-105)GGG>GAG	p.G35E		NM_022466	NP_071911	Q9H5V7	IKZF5_HUMAN	zinc finger protein, subfamily 1A, 5	35					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		TTCTTTGTCCCCACTAACTGA	0.408													5	45	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093582	1093582	+	Missense_Mutation	SNP	G	C	C	rs55641679		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093582G>C	uc001lsx.1	+	31	12514	c.12487G>C	c.(12487-12489)GCA>CCA	p.A4163P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4163				P -> A (in Ref. 4).		inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tacGGTGACCGCAACCCCAAC	0.338													4	22	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1271174	1271174	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1271174C>G	uc009ycr.1	+	51	14609	c.14483C>G	c.(14482-14484)TCC>TGC	p.S4828C	MUC5B_uc001ltb.2_Missense_Mutation_p.S4358C	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4355	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACCCCTCCTCCACTCCGGAG	0.657													26	51	---	---	---	---	PASS
TRIM21	6737	broad.mit.edu	37	11	4408217	4408217	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4408217C>A	uc001lyy.1	-	5	852	c.739G>T	c.(739-741)GTG>TTG	p.V247L		NM_003141	NP_003132	P19474	RO52_HUMAN	tripartite motif protein 21	247					cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein deubiquitination|positive regulation of cell cycle|protein autoubiquitination|protein destabilization|protein monoubiquitination|protein polyubiquitination|protein trimerization	cytoplasmic mRNA processing body|nucleus	DNA binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		ACAATTATCACCTCCTGAGGA	0.458													4	8	---	---	---	---	PASS
OR52B2	255725	broad.mit.edu	37	11	6190909	6190909	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6190909G>T	uc010qzy.1	-	1	648	c.648C>A	c.(646-648)ATC>ATA	p.I216I		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	216	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAGACACAGCGATGAGGATAA	0.512													20	37	---	---	---	---	PASS
CTR9	9646	broad.mit.edu	37	11	10776627	10776627	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10776627G>T	uc001mja.2	+	3	416	c.267G>T	c.(265-267)TTG>TTT	p.L89F		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	89					histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGGATACATTGGCAGCGTATT	0.378													7	153	---	---	---	---	PASS
HPS5	11234	broad.mit.edu	37	11	18303747	18303747	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18303747C>A	uc001mod.1	-	22	3357	c.3079G>T	c.(3079-3081)GAG>TAG	p.E1027*	HPS5_uc001moe.1_Nonsense_Mutation_p.E913*|HPS5_uc001mof.1_Nonsense_Mutation_p.E913*	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	1027						cytosol				ovary(1)|pancreas(1)|skin(1)	3						TTCCATTCCTCCACGGTCTCT	0.517									Hermansky-Pudlak_syndrome				5	53	---	---	---	---	PASS
COMMD9	29099	broad.mit.edu	37	11	36296266	36296266	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36296266C>A	uc001mwn.3	-	6	550	c.513G>T	c.(511-513)GTG>GTT	p.V171V	COMMD9_uc009ykj.2_Silent_p.V129V|COMMD9_uc009yki.1_5'Flank	NM_014186	NP_054905	Q9P000	COMD9_HUMAN	COMM domain containing 9 isoform 1	171	COMM.									ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				TGCTCAGCTCCACGGTGACAG	0.542													5	97	---	---	---	---	PASS
LRP4	4038	broad.mit.edu	37	11	46900684	46900684	+	Silent	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46900684C>T	uc001ndn.3	-	21	3143	c.2997G>A	c.(2995-2997)CGG>CGA	p.R999R		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	999	Extracellular (Potential).				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		CACCTGGGGGCCGGCGGCGGT	0.607													28	95	---	---	---	---	PASS
OR4C13	283092	broad.mit.edu	37	11	49974260	49974260	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49974260A>T	uc010rhz.1	+	1	286	c.286A>T	c.(286-288)ATG>TTG	p.M96L		NM_001001955	NP_001001955	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4						CAATGGATGTATGACTCAAGT	0.413													25	49	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55135552	55135552	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55135552G>A	uc010rif.1	+	1	193	c.193G>A	c.(193-195)GTG>ATG	p.V65M		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	65	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AATCTACATGGTGACGATAAT	0.418													8	36	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136373	55136373	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136373G>A	uc010rif.1	+	1	1014	c.1014G>A	c.(1012-1014)GGG>GGA	p.G338G		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	338	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GCTTAGCTGGGAAATGGCTGT	0.368													10	45	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587161	55587161	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587161C>A	uc010rin.1	+	1	56	c.56C>A	c.(55-57)TCA>TAA	p.S19*		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	19	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				TTGGGCTTCTCAGATTACCCA	0.428													21	27	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890170	55890170	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55890170G>T	uc001nii.1	+	1	322	c.322G>T	c.(322-324)GGT>TGT	p.G108C		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					TGTCTTCTTGGGTACTGCTGA	0.453													9	238	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890505	55890505	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55890505G>A	uc001nii.1	+	1	657	c.657G>A	c.(655-657)GTG>GTA	p.V219V		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					CATCCTATGTGTCCATTCTCT	0.438													13	68	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944289	55944289	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944289C>G	uc010rjb.1	+	1	196	c.196C>G	c.(196-198)CTT>GTT	p.L66V		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	66	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					ACTCAGCTGTCTTTCATTTGT	0.443													23	87	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043645	56043645	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56043645C>A	uc001nio.1	+	1	531	c.531C>A	c.(529-531)AGC>AGA	p.S177R		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					CTACATTTAGCCTGTCCTTCT	0.418													8	116	---	---	---	---	PASS
OR4D6	219983	broad.mit.edu	37	11	59224488	59224488	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59224488C>A	uc010rku.1	+	1	55	c.55C>A	c.(55-57)CGT>AGT	p.R19S		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	19	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GGAACTTACACGTTCCCGAGA	0.443													34	93	---	---	---	---	PASS
TM7SF2	7108	broad.mit.edu	37	11	64880868	64880868	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64880868G>C	uc001oct.2	+	4	628	c.481G>C	c.(481-483)GCA>CCA	p.A161P	TM7SF2_uc010rny.1_Missense_Mutation_p.A45P|TM7SF2_uc001ocu.2_Missense_Mutation_p.A161P|TM7SF2_uc001ocv.2_Missense_Mutation_p.A182P	NM_003273	NP_003264	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	161					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane	delta14-sterol reductase activity			ovary(1)	1						TTCGGCCCTGGCACCTGGGGG	0.587											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	81	---	---	---	---	PASS
DPP3	10072	broad.mit.edu	37	11	66254031	66254031	+	Silent	SNP	C	T	T	rs76983925	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66254031C>T	uc001oig.1	+	4	443	c.381C>T	c.(379-381)ATC>ATT	p.I127I	DPP3_uc001oif.1_Silent_p.I127I|DPP3_uc010rpe.1_Silent_p.I116I	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	127					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2						AACGGGTGATCCTAGGGAGTG	0.602													21	114	---	---	---	---	PASS
RBM4	5936	broad.mit.edu	37	11	66411414	66411414	+	Silent	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66411414A>T	uc009yrj.2	+	3	1394	c.906A>T	c.(904-906)TCA>TCT	p.S302S	RBM4_uc009yrk.2_Silent_p.S277S|RBM4_uc001oiw.1_Silent_p.S302S|RBM4_uc001oix.1_Intron|RBM4_uc010rpj.1_Intron|RBM4_uc001oiy.1_Silent_p.S302S|RBM4_uc001oiz.1_Silent_p.S302S	NM_002896	NP_002887	Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	302	Interaction with TNPO3.				circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|negative regulation of translation in response to stress|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|positive regulation of muscle cell differentiation|regulation of alternative nuclear mRNA splicing, via spliceosome|regulation of nucleocytoplasmic transport|RNA splicing|stress-activated MAPK cascade	nuclear speck|nucleolus|stress granule	miRNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|zinc ion binding			ovary(1)	1				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		ctTCCACTTCATATTACGGGC	0.438													8	28	---	---	---	---	PASS
AIP	9049	broad.mit.edu	37	11	67258318	67258318	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67258318G>C	uc001olv.2	+	6	972	c.847G>C	c.(847-849)GAG>CAG	p.E283Q		NM_003977	NP_003968	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	283	TPR 2.				protein maturation by protein folding|protein targeting to mitochondrion	nucleus	signal transducer activity|transcription coactivator activity|transcription factor binding|unfolded protein binding				0						GAATGCCCAGGAGGCCCAGGC	0.667									Familial_Isolated_Pituitary_Adenoma_				4	25	---	---	---	---	PASS
GAL	51083	broad.mit.edu	37	11	68453099	68453099	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68453099G>T	uc001oob.2	+	3	337	c.119G>T	c.(118-120)GGC>GTC	p.G40V		NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein	40					growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		AACAGCGCGGGCTACCTGCTG	0.632													6	60	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68574951	68574951	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68574951G>A	uc001oog.3	-	4	607	c.437C>T	c.(436-438)GCC>GTC	p.A146V	CPT1A_uc001oof.3_Missense_Mutation_p.A146V|CPT1A_uc009ysj.2_Missense_Mutation_p.A146V	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	146	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	GATCTTGGTGGCACGACTCAT	0.597													5	93	---	---	---	---	PASS
ANO1	55107	broad.mit.edu	37	11	70007429	70007429	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70007429G>A	uc001opj.2	+	17	2046	c.1741G>A	c.(1741-1743)GAG>AAG	p.E581K	ANO1_uc001opk.1_Missense_Mutation_p.E523K|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.E290K	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	581	Helical; (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CCTCCTGGACGAGGTGTATGG	0.463													19	245	---	---	---	---	PASS
CTTN	2017	broad.mit.edu	37	11	70255985	70255985	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70255985G>T	uc001opv.3	+	5	416	c.210G>T	c.(208-210)AAG>AAT	p.K70N	CTTN_uc001opu.2_Missense_Mutation_p.K70N|CTTN_uc001opw.3_Missense_Mutation_p.K70N	NM_005231	NP_005222	Q14247	SRC8_HUMAN	cortactin isoform a	70						cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		AGACCCTTAAGGAGAAGGAAC	0.463													12	925	---	---	---	---	PASS
ARRB1	408	broad.mit.edu	37	11	74994459	74994459	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74994459G>A	uc001owe.1	-	5	448	c.226C>T	c.(226-228)CGC>TGC	p.R76C	ARRB1_uc001owf.1_Missense_Mutation_p.R76C	NM_004041	NP_004032	P49407	ARRB1_HUMAN	arrestin beta 1 isoform A	76	Interaction with CHRM2 (By similarity).|Interaction with SRC (By similarity).				G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2						AGGTCCTTGCGAAAGGTCAGG	0.642													39	32	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108224510	108224510	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108224510G>A	uc001pkb.1	+	60	9074	c.8689G>A	c.(8689-8691)GGC>AGC	p.G2897S	ATM_uc009yxr.1_Missense_Mutation_p.G2897S|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.G1549S	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2897	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TTTTGAACAGGGCAAAATCCT	0.408			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			29	52	---	---	---	---	PASS
CBL	867	broad.mit.edu	37	11	119155953	119155953	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119155953C>A	uc001pwe.2	+	11	1756	c.1618C>A	c.(1618-1620)CGA>AGA	p.R540R		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	540	Pro-rich.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCCCACACTTCGAGATCTTCC	0.532									CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome		OREG0021401	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	68	---	---	---	---	PASS
BARX2	8538	broad.mit.edu	37	11	129306955	129306955	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129306955G>T	uc001qfc.3	+							NM_003658	NP_003649	Q9UMQ3	BARX2_HUMAN	BarH-like homeobox 2												0	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		AGGTGAGGACGCAGGGAAGGG	0.602													8	12	---	---	---	---	PASS
IGSF9B	22997	broad.mit.edu	37	11	133805642	133805642	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133805642C>G	uc001qgx.3	-	7	1068	c.837G>C	c.(835-837)AGG>AGC	p.R279S	IGSF9B_uc001qgy.1_Missense_Mutation_p.R121S	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	279	Extracellular (Potential).|Ig-like 3.					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGATGCGCACCCTCAGCTTCA	0.632													5	7	---	---	---	---	PASS
GLB1L2	89944	broad.mit.edu	37	11	134228991	134228991	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134228991C>A	uc001qhp.2	+	7	877	c.689C>A	c.(688-690)ACT>AAT	p.T230N	GLB1L2_uc009zdg.1_RNA	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor	230					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)		CTGCTCCTGACTTCAGACAAC	0.612													4	78	---	---	---	---	PASS
C12orf5	57103	broad.mit.edu	37	12	4461510	4461510	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4461510G>T	uc001qmp.2	+	6	545	c.466G>T	c.(466-468)GGA>TGA	p.G156*		NM_020375	NP_065108	Q9NQ88	TIGAR_HUMAN	TP53-induced glycolysis and apoptosis regulator	156						intracellular	fructose-2,6-bisphosphate 2-phosphatase activity			skin(1)	1			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			GTTTTCCCAAGGATCTCCAAG	0.363													10	33	---	---	---	---	PASS
GUCY2C	2984	broad.mit.edu	37	12	14832636	14832636	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14832636C>A	uc001rcd.2	-	6	922	c.785G>T	c.(784-786)CGA>CTA	p.R262L	GUCY2C_uc009zhz.2_Missense_Mutation_p.R262L	NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor	262	Extracellular (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						AGCCACTGCTCGGTCACCCTT	0.418													4	63	---	---	---	---	PASS
WBP11	51729	broad.mit.edu	37	12	14947584	14947584	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14947584G>T	uc001rci.2	-	7	769	c.608C>A	c.(607-609)CCC>CAC	p.P203H		NM_016312	NP_057396	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	203	Pro-rich.				mRNA processing|RNA splicing|rRNA processing	cytoplasm	single-stranded DNA binding|WW domain binding			ovary(1)|lung(1)	2						TGGACCAGGGGGAGGGCCAGG	0.512													7	162	---	---	---	---	PASS
STK38L	23012	broad.mit.edu	37	12	27450705	27450705	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27450705C>T	uc001rhr.2	+	2	251	c.52C>T	c.(52-54)CGG>TGG	p.R18W	STK38L_uc001rhs.2_RNA|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815	Q9Y2H1	ST38L_HUMAN	serine/threonine kinase 38 like	18					intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)					CAACCATACCCGGGAAAGAGT	0.403													11	53	---	---	---	---	PASS
NELL2	4753	broad.mit.edu	37	12	45173639	45173639	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45173639A>T	uc001rog.2	-	4	1097	c.502T>A	c.(502-504)TGC>AGC	p.C168S	NELL2_uc001rof.3_Missense_Mutation_p.C167S|NELL2_uc001roh.2_Missense_Mutation_p.C168S|NELL2_uc009zkd.2_Missense_Mutation_p.C167S|NELL2_uc010skz.1_Missense_Mutation_p.C218S|NELL2_uc010sla.1_Missense_Mutation_p.C191S|NELL2_uc001roi.1_Missense_Mutation_p.C168S|NELL2_uc010slb.1_Missense_Mutation_p.C167S|NELL2_uc001roj.2_Missense_Mutation_p.C168S	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	168	TSP N-terminal.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		TACTTATTGCAGTCAATGTGT	0.398													13	61	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49443771	49443771	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49443771G>C	uc001rta.3	-	11	3600	c.3600C>G	c.(3598-3600)ATC>ATG	p.I1200M		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1200					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						TGTCGGATTTGATGAGAGTGG	0.592			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			16	41	---	---	---	---	PASS
BIN2	51411	broad.mit.edu	37	12	51685860	51685860	+	Missense_Mutation	SNP	C	A	A	rs150210505		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51685860C>A	uc001ryg.2	-	10	1082	c.1030G>T	c.(1030-1032)GCC>TCC	p.A344S	BIN2_uc009zlz.2_Missense_Mutation_p.A312S|BIN2_uc001ryh.2_Missense_Mutation_p.A220S|BIN2_uc010sng.1_Missense_Mutation_p.A318S	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2	344						cytoplasm	protein binding			ovary(1)	1						TGGGCCTGGGCGGGGCCATTG	0.577													3	22	---	---	---	---	PASS
MIR616	693201	broad.mit.edu	37	12	57913018	57913018	+	RNA	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57913018G>C	hsa-mir-616|MI0003629	-			c.25G>C			DDIT3_uc001soi.2_Intron|DDIT3_uc009zps.2_Intron|DDIT3_uc009zpt.2_Intron																	0						gtcactgaagggttttgagtg	0.000													4	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	66501963	66501963	+	IGR	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66501963C>T								HMGA2 (141895 upstream) : LLPH (14887 downstream)																							GGGGCTCACACAGCCGGCCAG	0.468											OREG0021973	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	53	---	---	---	---	PASS
FRS2	10818	broad.mit.edu	37	12	69968637	69968637	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69968637G>T	uc001suy.2	+	10	1939	c.1429G>T	c.(1429-1431)GAG>TAG	p.E477*	FRS2_uc001suz.2_Nonsense_Mutation_p.E477*|FRS2_uc009zrj.2_Nonsense_Mutation_p.E477*|FRS2_uc009zrk.2_Nonsense_Mutation_p.E477*	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	477					activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GATAGACATCGAGAGAACTGC	0.493													5	113	---	---	---	---	PASS
LIN7A	8825	broad.mit.edu	37	12	81283074	81283074	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81283074G>T	uc001szj.1	-	2	350	c.157C>A	c.(157-159)CTC>ATC	p.L53I	LIN7A_uc001szk.1_RNA	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A	53	L27.				exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2						ACTTTTTTGAGGGATTGTAGC	0.343													4	20	---	---	---	---	PASS
SLC41A2	84102	broad.mit.edu	37	12	105282956	105282956	+	Splice_Site	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105282956C>A	uc001tla.2	-	4	903	c.736_splice	c.e4-1	p.V246_splice		NM_032148	NP_115524	Q96JW4	S41A2_HUMAN	solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2						TTGCCTGAACCTAAAATTTTT	0.299													6	14	---	---	---	---	PASS
IFT81	28981	broad.mit.edu	37	12	110656005	110656005	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110656005G>T	uc001tqi.2	+	19	2135	c.2005G>T	c.(2005-2007)GGT>TGT	p.G669C	IFT81_uc001tqh.2_Missense_Mutation_p.G669C|IFT81_uc001tqj.2_RNA	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	669					cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1						AATTCAGGAGGGTGGGGAGGA	0.388													18	56	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117672370	117672370	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117672370C>A	uc001twm.1	-	21	3921	c.3235G>T	c.(3235-3237)GGT>TGT	p.G1079C		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1079	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	GGAATGTTACCTAAAGCCGTG	0.592													5	29	---	---	---	---	PASS
MPHOSPH8	54737	broad.mit.edu	37	13	20240600	20240600	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20240600C>A	uc001umh.2	+	10	2064	c.2055C>A	c.(2053-2055)CTC>CTA	p.L685L	MPHOSPH8_uc001umg.2_Silent_p.L685L	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	685	ANK 3.				cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TCGTACGACTCGTAATTGAAT	0.443													6	259	---	---	---	---	PASS
SOHLH2	54937	broad.mit.edu	37	13	36747888	36747888	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36747888G>A	uc001uvj.2	-	9	1030	c.941C>T	c.(940-942)ACG>ATG	p.T314M	SOHLH2_uc010tei.1_Missense_Mutation_p.T391M	NM_017826	NP_060296	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic	314					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)		ATTCCAGCACGTATTAGTCAG	0.483													7	72	---	---	---	---	PASS
COG3	83548	broad.mit.edu	37	13	46077414	46077414	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46077414G>T	uc001vak.2	+	14	1625	c.1524G>T	c.(1522-1524)AAG>AAT	p.K508N	COG3_uc001vaj.1_Missense_Mutation_p.K508N|COG3_uc010tfv.1_Missense_Mutation_p.K345N|COG3_uc010aci.2_Missense_Mutation_p.K284N	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3	508					ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AACAGAAGAAGGTACCTTCAG	0.378													5	50	---	---	---	---	PASS
SLAIN1	122060	broad.mit.edu	37	13	78335084	78335084	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78335084G>T	uc010thy.1	+	6	1087	c.1044G>T	c.(1042-1044)ATG>ATT	p.M348I	SLAIN1_uc001vkk.1_Missense_Mutation_p.M271I|SLAIN1_uc001vkl.1_Missense_Mutation_p.M227I|SLAIN1_uc010thz.1_Missense_Mutation_p.M226I|SLAIN1_uc010aex.1_Missense_Mutation_p.M113I|SLAIN1_uc010aey.1_Missense_Mutation_p.M113I|SLAIN1_uc001vkm.2_Missense_Mutation_p.M227I	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B	490										ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		GCAGTAACATGCCTTTATCAA	0.522													16	43	---	---	---	---	PASS
LIG4	3981	broad.mit.edu	37	13	108863508	108863508	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108863508T>A	uc001vqn.2	-	2	382	c.109A>T	c.(109-111)AGA>TGA	p.R37*	LIG4_uc001vqo.2_Nonsense_Mutation_p.R37*|LIG4_uc010agg.1_5'UTR|LIG4_uc010agf.2_Nonsense_Mutation_p.R37*|LIG4_uc001vqp.2_Nonsense_Mutation_p.R37*	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	37					cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					CTGAAGTGTCTGATTTTTTCT	0.363								NHEJ					10	17	---	---	---	---	PASS
OR4M1	441670	broad.mit.edu	37	14	20248579	20248579	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20248579C>A	uc010tku.1	+	1	98	c.98C>A	c.(97-99)TCC>TAC	p.S33Y		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATATTTCTATCCTTCTATTTG	0.413													61	81	---	---	---	---	PASS
RNASE12	493901	broad.mit.edu	37	14	21058511	21058511	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21058511G>T	uc001vxt.2	-	1	472	c.372C>A	c.(370-372)TCC>TCA	p.S124S	RNASE11_uc010ahv.2_5'Flank|RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'Flank|uc001vxu.1_5'Flank	NM_001024822	NP_001019993	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	124						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		CCTCTGTGGGGGAATAGTGGT	0.458													7	98	---	---	---	---	PASS
RPGRIP1	57096	broad.mit.edu	37	14	21793547	21793547	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21793547G>T	uc001wag.2	+						RPGRIP1_uc001wah.2_Intron|RPGRIP1_uc001wai.2_Intron|RPGRIP1_uc001wak.2_Intron|RPGRIP1_uc010aim.2_Intron|RPGRIP1_uc001wal.2_Intron|RPGRIP1_uc001wam.2_Intron	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator						response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GAGGAGGTGAGAAAAAAGATG	0.498													10	5	---	---	---	---	PASS
CDH24	64403	broad.mit.edu	37	14	23519129	23519129	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23519129C>T	uc001wil.2	-	10	1761	c.1501G>A	c.(1501-1503)GTG>ATG	p.V501M	CDH24_uc001wik.3_RNA|CDH24_uc010akf.2_Missense_Mutation_p.V463M	NM_022478	NP_071923	Q86UP0	CAD24_HUMAN	cadherin-like 24 isoform 1	501	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		GCCACTTGCACGCGCGAGGCC	0.542													41	38	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30068938	30068938	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30068938C>G	uc001wqh.2	-	14	2172	c.1991G>C	c.(1990-1992)GGA>GCA	p.G664A		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	664	Protein kinase.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CAGCATGTCTCCATGGAGTTT	0.378													9	39	---	---	---	---	PASS
COCH	1690	broad.mit.edu	37	14	31354195	31354195	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31354195G>T	uc001wqr.2	+						COCH_uc001wqp.2_Intron|COCH_uc001wqq.3_Intron|uc001wqs.2_Intron|COCH_uc001wqt.1_Silent_p.V78V	NM_004086	NP_004077	O43405	COCH_HUMAN	cochlin precursor						sensory perception of sound	proteinaceous extracellular matrix				pancreas(1)|central_nervous_system(1)|skin(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		ATGCAGATGTGGCAGAAAGAA	0.383													5	101	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42357069	42357069	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42357069C>A	uc001wvm.2	+	3	2439	c.1241C>A	c.(1240-1242)ACT>AAT	p.T414N	LRFN5_uc010ana.2_Missense_Mutation_p.T414N	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	414	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		AATGGTGATACTAAATTGAGT	0.353										HNSCC(30;0.082)			9	16	---	---	---	---	PASS
SLC8A3	6547	broad.mit.edu	37	14	70530577	70530577	+	Intron	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70530577C>T	uc001xly.2	-						SLC8A3_uc001xlu.2_Intron|SLC8A3_uc001xlv.2_Intron|SLC8A3_uc001xlw.2_Intron|SLC8A3_uc001xlx.2_Missense_Mutation_p.M618I|SLC8A3_uc001xlz.2_Intron|SLC8A3_uc010ara.2_Intron|SLC8A3_uc001xma.2_Intron	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GGGGGCCCATCATCTCAATGA	0.333													8	71	---	---	---	---	PASS
GPR132	29933	broad.mit.edu	37	14	105518036	105518036	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105518036G>T	uc001yqd.2	-	4	1337	c.438C>A	c.(436-438)TAC>TAA	p.Y146*	GPR132_uc001yqc.2_5'UTR|GPR132_uc001yqe.2_Nonsense_Mutation_p.Y137*	NM_013345	NP_037477	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	146	Cytoplasmic (Potential).				response to stress	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		TCTCCAGCGCGTACACCACGG	0.622													19	28	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106967470	106967470	+	RNA	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106967470C>T	uc010tyt.1	-	201		c.8971G>A								Parts of antibodies, mostly variable regions.												0						AGAAGACCCTCCAGGTCCAGT	0.498													36	51	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20170351	20170351	+	IGR	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20170351C>T								None (None upstream) : GOLGA6L6 (566743 downstream)																							CAAGTCCAGCCCATGGTGAGG	0.527													28	71	---	---	---	---	PASS
SNRPN	6638	broad.mit.edu	37	15	25230274	25230274	+	Intron	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25230274G>C	uc001ywz.1	+						PAR-SN_uc001yxa.1_Intron|PAR-SN_uc001yxc.2_Intron|PAR5_uc001yxd.2_RNA			P63162	RSMN_HUMAN	Homo sapiens SNRPN upstream reading frame protein (SNURF) mRNA, complete cds.						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		TGTTTACTGAGCATGATGAAG	0.378									Prader-Willi_syndrome				15	59	---	---	---	---	PASS
SNORD116-4	100033416	broad.mit.edu	37	15	25310173	25310173	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25310173G>T	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-2_uc001yxp.2_RNA|SNORD116-5_uc001yxq.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						GAATGTGGTTGGATCGATGAT	0.473													5	94	---	---	---	---	PASS
ITPKA	3706	broad.mit.edu	37	15	41794710	41794710	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41794710G>T	uc001znz.2	+							NM_002220	NP_002211	P23677	IP3KA_HUMAN	1D-myo-inositol-trisphosphate 3-kinase A						signal transduction		ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0		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;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TGGTGAGAGCGGGATCCCAAA	0.617													4	17	---	---	---	---	PASS
PYGO1	26108	broad.mit.edu	37	15	55838299	55838299	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55838299G>T	uc010bfl.1	-	3	1238	c.1182C>A	c.(1180-1182)ACC>ACA	p.T394T	PYGO1_uc002adf.1_Silent_p.T394T	NM_015617	NP_056432	Q9Y3Y4	PYGO1_HUMAN	pygopus homolog 1	394	PHD-type.				Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		CAGCCATACAGGTATCACAGC	0.443													13	51	---	---	---	---	PASS
ALDH1A2	8854	broad.mit.edu	37	15	58256106	58256106	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58256106G>T	uc002aex.2	-	9	1121	c.1063C>A	c.(1063-1065)CCC>ACC	p.P355T	ALDH1A2_uc002aey.2_Missense_Mutation_p.P317T|ALDH1A2_uc010ugv.1_Missense_Mutation_p.P334T|ALDH1A2_uc010ugw.1_Missense_Mutation_p.P326T|ALDH1A2_uc002aew.2_Missense_Mutation_p.P259T	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	355					negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	TCAGTGGTGGGGTCAAAGGGA	0.527													21	32	---	---	---	---	PASS
CILP	8483	broad.mit.edu	37	15	65489533	65489533	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65489533C>A	uc002aon.2	-	9	3272	c.3091G>T	c.(3091-3093)GGC>TGC	p.G1031C		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	1031					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7						CGGCAGCTGCCCTGGGGGATG	0.577													13	32	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70347520	70347520	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70347520G>A	uc002asm.2	-	15	2574	c.1455C>T	c.(1453-1455)CAC>CAT	p.H485H	TLE3_uc002ask.2_Silent_p.H412H|TLE3_uc002asl.2_Silent_p.H485H|TLE3_uc010ukd.1_Silent_p.H475H|TLE3_uc010bik.1_Silent_p.H66H|TLE3_uc010bil.1_Silent_p.H482H|TLE3_uc002asn.2_Silent_p.H473H|TLE3_uc002asp.2_Silent_p.H477H|TLE3_uc002aso.2_Silent_p.H480H	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a	485	WD 1.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						CCACCTCCCCGTGGCTGAGTG	0.662													16	37	---	---	---	---	PASS
FLYWCH2	114984	broad.mit.edu	37	16	2946558	2946558	+	Silent	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2946558C>T	uc002csa.2	+	3	479	c.108C>T	c.(106-108)CCC>CCT	p.P36P	FLYWCH2_uc010uwj.1_Silent_p.P36P|FLYWCH2_uc010uwk.1_Silent_p.P36P	NM_138439	NP_612448	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	36											0						CCAGGAAGCCCAGAAAGTTCT	0.642													15	75	---	---	---	---	PASS
CIITA	4261	broad.mit.edu	37	16	10996609	10996609	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10996609G>A	uc002dai.3	+	8	856	c.723G>A	c.(721-723)TGG>TGA	p.W241*	CIITA_uc002daj.3_Nonsense_Mutation_p.W242*|CIITA_uc002dak.3_Nonsense_Mutation_p.W192*|CIITA_uc002dag.2_Nonsense_Mutation_p.W241*|CIITA_uc002dah.2_Nonsense_Mutation_p.W193*|CIITA_uc010bup.1_Nonsense_Mutation_p.W241*	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	241					interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1						ATGGGCTCTGGCAAATCTCTG	0.582			T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								10	51	---	---	---	---	PASS
RRN3	54700	broad.mit.edu	37	16	15180227	15180227	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15180227T>C	uc002dde.2	-	4	405	c.337A>G	c.(337-339)ATA>GTA	p.I113V	PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Missense_Mutation_p.I14V|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Missense_Mutation_p.I113V	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor	113					regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						CTTACTAATATAATACTGATA	0.299													12	40	---	---	---	---	PASS
ANKS4B	257629	broad.mit.edu	37	16	21245162	21245162	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21245162C>A	uc010bwp.1	+	1	147	c.104C>A	c.(103-105)CCT>CAT	p.P35H		NM_145865	NP_665872	Q8N8V4	ANS4B_HUMAN	harmonin-interacting ankyrin-repeat containing	35	ANK 1.									ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0565)		GGCATGACTCCTACTCTCTTG	0.463													7	168	---	---	---	---	PASS
PLK1	5347	broad.mit.edu	37	16	23695281	23695281	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23695281G>T	uc002dlz.1	+	5	960	c.907G>T	c.(907-909)GAG>TAG	p.E303*		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	303	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)		GCTTAATGACGAGTTCTTTAC	0.567													6	280	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30745064	30745064	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30745064C>A	uc002dze.1	+	29	6824	c.6439C>A	c.(6439-6441)CAG>AAG	p.Q2147K	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.Q1942K	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	2147	Helicase C-terminal.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CATGGATGCTCAGGCCCAGGA	0.527													15	50	---	---	---	---	PASS
FAM192A	80011	broad.mit.edu	37	16	57207687	57207687	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57207687C>A	uc010vhk.1	-	2	339	c.80G>T	c.(79-81)AGG>ATG	p.R27M	FAM192A_uc002ekz.3_Missense_Mutation_p.R27M|FAM192A_uc002ekv.3_Translation_Start_Site|FAM192A_uc002ekw.3_Missense_Mutation_p.R27M|FAM192A_uc002ekx.3_Missense_Mutation_p.R27M|FAM192A_uc002eky.3_Missense_Mutation_p.R27M|FAM192A_uc010ccx.2_Missense_Mutation_p.R27M	NM_024946	NP_079222	Q9GZU8	F192A_HUMAN	NEFA-interacting nuclear protein NIP30	27						nucleus					0						TTCTTGCCTCCTTTTGCGCCG	0.363													7	80	---	---	---	---	PASS
JPH3	57338	broad.mit.edu	37	16	87723839	87723839	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87723839C>T	uc002fkd.2	+	4	2127	c.1873C>T	c.(1873-1875)CCC>TCC	p.P625S	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	625	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GGAGACGCATCCCCAGAAAAG	0.657													4	8	---	---	---	---	PASS
NLRP1	22861	broad.mit.edu	37	17	5421068	5421068	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5421068G>T	uc002gci.2	-	15	4610	c.4055C>A	c.(4054-4056)CCA>CAA	p.P1352Q	NLRP1_uc002gcg.1_Missense_Mutation_p.P1356Q|NLRP1_uc002gck.2_Missense_Mutation_p.P1308Q|NLRP1_uc002gcj.2_Missense_Mutation_p.P1322Q|NLRP1_uc002gcl.2_Missense_Mutation_p.P1278Q|NLRP1_uc002gch.3_Missense_Mutation_p.P1308Q	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	1352					defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				GGATTTACCTGGTTTCACCAA	0.398													5	69	---	---	---	---	PASS
NEURL4	84461	broad.mit.edu	37	17	7224163	7224163	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7224163C>A	uc002gga.1	-	21	3447	c.3440G>T	c.(3439-3441)GGG>GTG	p.G1147V	NEURL4_uc002gfy.1_5'Flank|GPS2_uc002gfz.1_5'Flank|NEURL4_uc002ggb.1_Missense_Mutation_p.G1145V	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	1147	NHR 6.						protein binding			upper_aerodigestive_tract(1)|ovary(1)	2						CGTACGGTTCCCATTAGACAA	0.562													7	150	---	---	---	---	PASS
EIF4A1	1973	broad.mit.edu	37	17	7480801	7480801	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7480801G>T	uc002gho.1	+	15	2089	c.764G>T	c.(763-765)CGA>CTA	p.R255L	EIF4A1_uc002ghr.1_Missense_Mutation_p.R255L|EIF4A1_uc002ghq.1_Missense_Mutation_p.R255L|EIF4A1_uc002ghp.1_Missense_Mutation_p.R255L|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	255	Helicase C-terminal.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1						AACGTGGAACGAGAGGTGGGG	0.557													4	39	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578407	7578407	+	Missense_Mutation	SNP	G	C	C	rs138729528		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578407G>C	uc002gim.2	-	5	717	c.523C>G	c.(523-525)CGC>GGC	p.R175G	TP53_uc002gig.1_Missense_Mutation_p.R175G|TP53_uc002gih.2_Missense_Mutation_p.R175G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R43G|TP53_uc010cng.1_Missense_Mutation_p.R43G|TP53_uc002gii.1_Missense_Mutation_p.R43G|TP53_uc010cnh.1_Missense_Mutation_p.R175G|TP53_uc010cni.1_Missense_Mutation_p.R175G|TP53_uc002gij.2_Missense_Mutation_p.R175G|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R82G|TP53_uc002gio.2_Missense_Mutation_p.R43G|TP53_uc010vug.1_Missense_Mutation_p.R136G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	175	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R175H(721)|p.R175L(19)|p.R175C(12)|p.R175G(11)|p.0?(7)|p.R175P(5)|p.R175S(5)|p.R175R(4)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.R175fs*5(2)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*6(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R175fs*72(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.S149fs*72(1)|p.R174_E180>K(1)|p.R174fs*3(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TGGGGGCAGCGCCTCACAACC	0.657		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			10	25	---	---	---	---	PASS
SCO1	6341	broad.mit.edu	37	17	10596167	10596167	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10596167C>A	uc002gmr.3	-	3	537	c.476G>T	c.(475-477)TGG>TTG	p.W159L	SCO1_uc002gms.3_Intron	NM_004589	NP_004580	O75880	SCO1_HUMAN	cytochrome oxidase deficient homolog 1	159					cellular copper ion homeostasis|copper ion transport|generation of precursor metabolites and energy|respiratory chain complex IV assembly	mitochondrial inner membrane	copper ion binding				0						AATCAATAACCACTGACCCAA	0.458													5	56	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18023401	18023401	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18023401G>A	uc010vxh.1	+	2	1625	c.1287G>A	c.(1285-1287)ATG>ATA	p.M429I		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	429	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					CCCACGCCATGGATGACATCG	0.652													17	21	---	---	---	---	PASS
CCDC144NL	339184	broad.mit.edu	37	17	20799191	20799191	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20799191C>A	uc002gyf.2	-	1	263	c.143G>T	c.(142-144)GGC>GTC	p.G48V	uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,	48											0						GTAGGAGAAGCCCAAGGACCA	0.617													19	64	---	---	---	---	PASS
MMP28	79148	broad.mit.edu	37	17	34100371	34100371	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34100371C>A	uc002hjy.1	-	4	676	c.417G>T	c.(415-417)CTG>CTT	p.L139L	MMP28_uc002hjw.1_RNA|MMP28_uc002hjz.1_RNA	NM_024302	NP_077278	Q9H239	MMP28_HUMAN	matrix metalloproteinase 28 isoform 1	139					proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GCCAGTTCACCAGGCGGTAGG	0.637													5	2	---	---	---	---	PASS
GGNBP2	79893	broad.mit.edu	37	17	34937844	34937844	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34937844G>T	uc002hnb.2	+	9	1340	c.1091G>T	c.(1090-1092)CGA>CTA	p.R364L	GGNBP2_uc002hna.2_Missense_Mutation_p.R364L|GGNBP2_uc002hnc.1_Missense_Mutation_p.R193L	NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403	364					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GAAGAGGAACGAGTAAGAGAA	0.368													4	83	---	---	---	---	PASS
KRT9	3857	broad.mit.edu	37	17	39724766	39724766	+	Silent	SNP	G	T	T	rs139934315		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39724766G>T	uc002hxe.3	-	5	1230	c.1164C>A	c.(1162-1164)CTC>CTA	p.L388L	JUP_uc010wfs.1_Intron	NM_000226	NP_000217	P35527	K1C9_HUMAN	keratin 9	388	Rod.|Coil 2.				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Breast(137;0.000307)				CAACCTTGCTGAGCTGAGACT	0.552													7	239	---	---	---	---	PASS
JUP	3728	broad.mit.edu	37	17	39913791	39913791	+	Intron	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39913791G>A	uc002hxq.2	-						JUP_uc010wfs.1_Intron|JUP_uc002hxr.2_Intron|JUP_uc002hxs.2_Intron	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GTAGGTGGCTGAGCAGAGAGG	0.627													14	21	---	---	---	---	PASS
AARSD1	80755	broad.mit.edu	37	17	41103875	41103875	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41103875C>G	uc002icc.2	-	11	1048	c.1045G>C	c.(1045-1047)GGT>CGT	p.G349R	AARSD1_uc002icd.2_Missense_Mutation_p.G462R|AARSD1_uc002ice.2_Missense_Mutation_p.G432R|AARSD1_uc002icf.2_Missense_Mutation_p.G523R|AARSD1_uc010whg.1_Missense_Mutation_p.G523R	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	349					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		AGTCCACCACCTTTCTCATCG	0.522													15	19	---	---	---	---	PASS
OR4D2	124538	broad.mit.edu	37	17	56247485	56247485	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56247485A>C	uc010wnp.1	+	1	469	c.469A>C	c.(469-471)ATT>CTT	p.I157L		NM_001004707	NP_001004707	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D,	157	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGTCCACTCTATTGTCCAGCT	0.567													14	54	---	---	---	---	PASS
PITPNC1	26207	broad.mit.edu	37	17	65683196	65683196	+	Intron	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65683196G>A	uc002jgc.2	+						PITPNC1_uc002jgb.2_Missense_Mutation_p.D233N	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GACAATGGATGATGTTCGGGA	0.418													47	56	---	---	---	---	PASS
TBC1D16	125058	broad.mit.edu	37	17	77925290	77925290	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77925290G>T	uc002jxj.2	-	5	1164	c.1048C>A	c.(1048-1050)CAG>AAG	p.Q350K	TBC1D16_uc002jxh.2_5'Flank|TBC1D16_uc002jxi.2_5'Flank|TBC1D16_uc002jxk.1_5'Flank	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	350						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			TTCCACTGCTGGAACACGTCA	0.632													5	79	---	---	---	---	PASS
METTL4	64863	broad.mit.edu	37	18	2539011	2539011	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2539011C>A	uc002klh.3	-	9	2187	c.1407G>T	c.(1405-1407)GAG>GAT	p.E469D	METTL4_uc010dkj.2_3'UTR	NM_022840	NP_073751	Q8N3J2	METL4_HUMAN	methyltransferase like 4	469					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		methyltransferase activity|nucleic acid binding			kidney(1)|skin(1)	2						AGCTTCCAGACTCCACAGCAA	0.353													14	40	---	---	---	---	PASS
KLHL14	57565	broad.mit.edu	37	18	30350180	30350180	+	Silent	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30350180C>A	uc002kxm.1	-	2	763	c.375G>T	c.(373-375)CTG>CTT	p.L125L		NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	125	BTB.					cytosol|endoplasmic reticulum membrane				ovary(1)	1						CCTGCAGCACCAGGTTGTTGA	0.567													5	64	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32438301	32438301	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32438301C>G	uc010dmn.1	+	15	1505	c.1504C>G	c.(1504-1506)CAG>GAG	p.Q502E	DTNA_uc010xbx.1_Missense_Mutation_p.Q252E|DTNA_uc002kxv.3_Missense_Mutation_p.Q445E|DTNA_uc002kxw.2_Missense_Mutation_p.Q445E|DTNA_uc010dmj.2_Missense_Mutation_p.Q442E|DTNA_uc002kxz.2_Missense_Mutation_p.Q442E|DTNA_uc002kxy.2_Missense_Mutation_p.Q442E|DTNA_uc010dml.2_Missense_Mutation_p.Q442E|DTNA_uc002kyb.3_Missense_Mutation_p.Q499E|DTNA_uc010dmm.2_Missense_Mutation_p.Q502E|DTNA_uc010xby.1_Missense_Mutation_p.Q192E|DTNA_uc010dmo.2_Missense_Mutation_p.Q124E|DTNA_uc002kyd.3_Missense_Mutation_p.Q124E|DTNA_uc010xbz.1_Missense_Mutation_p.Q211E|DTNA_uc010xca.1_Missense_Mutation_p.Q154E|DTNA_uc002kye.2_Missense_Mutation_p.Q150E	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	502	Potential.				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						ACAAGCTTCTCAGCCCACGCC	0.512													20	22	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56149153	56149153	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56149153T>A	uc002lhj.3	-	13	6629	c.6415A>T	c.(6415-6417)AAA>TAA	p.K2139*		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	2139							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						TGCTTCTGTTTCTGGTTGTTG	0.428													15	41	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59174738	59174738	+	Missense_Mutation	SNP	C	A	A	rs148517362		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59174738C>A	uc010dps.1	+	5	974	c.962C>A	c.(961-963)GCC>GAC	p.A321D	CDH20_uc002lif.2_Missense_Mutation_p.A315D	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	321	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				GGTGCAGATGCCTTTGACATT	0.423													12	33	---	---	---	---	PASS
SAFB2	9667	broad.mit.edu	37	19	5621405	5621405	+	Silent	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5621405C>T	uc002mcd.2	-	2	401	c.189G>A	c.(187-189)GCG>GCA	p.A63A	SAFB_uc010xiq.1_5'Flank|SAFB_uc002mcf.2_5'Flank|SAFB_uc002mcg.2_5'Flank|SAFB_uc002mce.3_5'Flank|SAFB_uc010xir.1_5'Flank|SAFB_uc010xis.1_5'Flank|SAFB_uc010xit.1_5'Flank|SAFB_uc010xiu.1_5'Flank|SAFB2_uc010xio.1_Silent_p.A63A|SAFB2_uc010xip.1_RNA	NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	63	SAP.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTTCTTTAACCGCCTATTAGG	0.443													13	397	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9026256	9026256	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9026256C>A	uc002mkp.2	-	14	36934	c.36730G>T	c.(36730-36732)GAG>TAG	p.E12244*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12246	SEA 2.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATGTCCTCCTCGTACTGCAGG	0.532													6	180	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9072230	9072230	+	Silent	SNP	G	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9072230G>C	uc002mkp.2	-	3	15420	c.15216C>G	c.(15214-15216)CTC>CTG	p.L5072L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5074	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGCCAGAGGTGAGAAGTGAAG	0.478													28	98	---	---	---	---	PASS
ZNF625	90589	broad.mit.edu	37	19	12256633	12256633	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12256633A>C	uc002mth.2	-	4	750	c.400T>G	c.(400-402)TTG>GTG	p.L134V	ZNF20_uc002mtg.1_Intron|ZNF625_uc010dyn.1_RNA|ZNF625_uc010dyo.1_Missense_Mutation_p.L168V	NM_145233	NP_660276	Q96I27	ZN625_HUMAN	zinc finger protein 625	134	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGACACATCAAGGCTTTCCCA	0.408													39	41	---	---	---	---	PASS
FBXW9	84261	broad.mit.edu	37	19	12800824	12800824	+	Silent	SNP	G	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12800824G>A	uc010dyx.2	-	6	1044	c.1044C>T	c.(1042-1044)ACC>ACT	p.T348T	FBXW9_uc010xmp.1_RNA|uc002mul.1_3'UTR|FBXW9_uc002mum.1_Silent_p.T328T|FBXW9_uc002mun.1_Silent_p.T165T	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	358	WD 4.						protein binding			ovary(1)	1						CCACCACCAGGGTGTGGTCCT	0.682													9	18	---	---	---	---	PASS
OR7A17	26333	broad.mit.edu	37	19	14991543	14991543	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14991543C>G	uc010xob.1	-	1	625	c.625G>C	c.(625-627)GGT>CGT	p.G209R		NM_030901	NP_112163	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Ovarian(108;0.203)					ACAAGGGGACCACCAGCCAGC	0.483													14	50	---	---	---	---	PASS
LPAR2	9170	broad.mit.edu	37	19	19735130	19735130	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19735130C>A	uc002nnb.3	-	3	1130	c.991G>T	c.(991-993)GGA>TGA	p.G331*	LPAR2_uc002nna.3_Nonsense_Mutation_p.G331*|LPAR2_uc002nnc.3_Nonsense_Mutation_p.G331*	NM_004720	NP_004711	Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	331	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration	cell surface|integral to plasma membrane	LIM domain binding|lipid binding			ovary(1)|breast(1)	2						CTGGCACCTCCCTGGGCAGAG	0.622													6	106	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30935742	30935742	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30935742A>T	uc002nsu.1	+	2	1411	c.1273A>T	c.(1273-1275)AAC>TAC	p.N425Y	ZNF536_uc010edd.1_Missense_Mutation_p.N425Y	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	425					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GGCCCACGCCAACCTGTACTC	0.637													8	21	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41071430	41071430	+	Missense_Mutation	SNP	G	C	C	rs139699793	byFrequency	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41071430G>C	uc002ony.2	+	28	6103	c.6017G>C	c.(6016-6018)CGA>CCA	p.R2006P	SPTBN4_uc002onz.2_Missense_Mutation_p.R2006P|SPTBN4_uc010egx.2_Missense_Mutation_p.R749P	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	2006	Spectrin 17.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAGCTGGGGCGATCTCTGCTG	0.632													10	8	---	---	---	---	PASS
ZNF234	10780	broad.mit.edu	37	19	44660428	44660428	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44660428G>T	uc002oym.2	+	6	566	c.259G>T	c.(259-261)GAG>TAG	p.E87*	ZNF234_uc002oyl.3_Nonsense_Mutation_p.E87*	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	87	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				AAGTGAGGTGGAGACTGTTCC	0.428													6	116	---	---	---	---	PASS
POLD1	5424	broad.mit.edu	37	19	50909578	50909578	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50909578A>T	uc002psb.3	+	11	1438	c.1382A>T	c.(1381-1383)CAG>CTG	p.Q461L	POLD1_uc002psc.3_Missense_Mutation_p.Q461L|POLD1_uc010enx.2_RNA|POLD1_uc010eny.2_Missense_Mutation_p.Q461L	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1	461					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GACATGCTGCAGGTATGGGCG	0.662								DNA_polymerases_(catalytic_subunits)					5	18	---	---	---	---	PASS
KLK1	3816	broad.mit.edu	37	19	51326971	51326971	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51326971G>T	uc002ptk.1	-	1	73	c.34C>A	c.(34-36)CTG>ATG	p.L12M	KLK1_uc010ycg.1_RNA	NM_002257	NP_002248	P06870	KLK1_HUMAN	kallikrein 1 preproprotein	12					proteolysis	nucleus	serine-type endopeptidase activity				0		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTCCCCCCCAGGGACAGGGCG	0.632													4	19	---	---	---	---	PASS
GP6	51206	broad.mit.edu	37	19	55539070	55539070	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55539070C>A	uc002qik.2	-	4	514	c.486G>T	c.(484-486)AGG>AGT	p.R162S	GP6_uc002qil.2_Missense_Mutation_p.R162S|GP6_uc010esq.2_Missense_Mutation_p.R162S|RDH13_uc010esr.1_RNA	NM_016363	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet) isoform 2	162	Ig-like C2-type 2.|Extracellular (Potential).				enzyme linked receptor protein signaling pathway|leukocyte migration|platelet activation	integral to plasma membrane	collagen binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		GAAAACTAGCCCTGTACCATC	0.572													16	44	---	---	---	---	PASS
NRSN2	80023	broad.mit.edu	37	20	333854	333854	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:333854A>G	uc002wdi.3	+	4	728	c.190A>G	c.(190-192)ATC>GTC	p.I64V	NRSN2_uc002wdj.2_RNA|NRSN2_uc002wdl.2_Intron	NM_024958	NP_079234	Q9GZP1	NRSN2_HUMAN	neurensin 2	64						integral to membrane|plasma membrane|transport vesicle					0		all_cancers(10;0.0834)				TTCTCCCTAGATCAGCCTGTC	0.622													8	44	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21367572	21367572	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21367572G>T	uc002wsf.1	+	29	2810	c.2715G>T	c.(2713-2715)CAG>CAT	p.Q905H	XRN2_uc002wsg.1_Missense_Mutation_p.Q829H|XRN2_uc010zsk.1_Missense_Mutation_p.Q851H|XRN2_uc002wsh.1_Missense_Mutation_p.Q43H	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	905					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						CAGCCTTCCAGCCAAACCAGT	0.527													4	49	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47269940	47269940	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47269940C>G	uc002xtw.1	-	20	2328	c.2305G>C	c.(2305-2307)GAG>CAG	p.E769Q	PREX1_uc002xtv.1_Missense_Mutation_p.E66Q	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	769					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)			TGGAAGTGCTCCAGGACCTCA	0.597													49	94	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62595205	62595205	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62595205G>T	uc002yhl.1	-	9	1596	c.1542C>A	c.(1540-1542)ACC>ACA	p.T514T		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	514					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCACGTTGCAGGTGGGGCAGA	0.652													6	86	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47957211	47957211	+	Intron	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47957211G>T	uc002zjo.2	+						DIP2A_uc011afy.1_Intron|DIP2A_uc011afz.1_Intron|DIP2A_uc002zjl.2_Intron|DIP2A_uc002zjm.2_Intron|DIP2A_uc010gql.2_Intron|DIP2A_uc002zjn.2_Intron|DIP2A_uc002zjp.1_Intron|DIP2A_uc002zjq.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		AGTGAGTGTTGTTTGCTGATG	0.443													65	120	---	---	---	---	PASS
TUBA8	51807	broad.mit.edu	37	22	18609318	18609318	+	Silent	SNP	C	A	A	rs150232320		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18609318C>A	uc002znv.1	+	4	646	c.573C>A	c.(571-573)ACC>ACA	p.T191T	TUBA8_uc002znr.2_Silent_p.T125T|TUBA8_uc002znw.1_Silent_p.T215T|TUBA8_uc002znx.1_Silent_p.T38T	NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	191					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0						TCCTGACCACCCACACCACAC	0.527													6	108	---	---	---	---	PASS
MYH9	4627	broad.mit.edu	37	22	36681312	36681312	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36681312G>T	uc003apg.2	-	38	5569	c.5338C>A	c.(5338-5340)CGG>AGG	p.R1780R		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1780	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						AGCTGCTGCCGAGCATTCTCG	0.592			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				4	87	---	---	---	---	PASS
SSTR3	6753	broad.mit.edu	37	22	37603528	37603528	+	Silent	SNP	G	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37603528G>T	uc003ara.2	-	2	377	c.315C>A	c.(313-315)GCC>GCA	p.A105A	SSTR3_uc003arb.2_Silent_p.A105A	NM_001051	NP_001042	P32745	SSR3_HUMAN	somatostatin receptor 3	105	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|induction of apoptosis by hormones|negative regulation of cell proliferation	integral to plasma membrane|nonmotile primary cilium	somatostatin receptor activity			lung(1)	1						AGTAGGACAGGGCGTTCTGGG	0.622													8	46	---	---	---	---	PASS
RANGAP1	5905	broad.mit.edu	37	22	41652071	41652071	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41652071C>T	uc003azs.2	-	9	2497	c.1027G>A	c.(1027-1029)GAG>AAG	p.E343K	RANGAP1_uc003azt.2_Missense_Mutation_p.E343K|RANGAP1_uc003azu.2_Missense_Mutation_p.E343K|RANGAP1_uc011aoz.1_Missense_Mutation_p.E288K	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	343	LRR 6.				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						TCCAGCACCTCCTGAAGCTGT	0.607													9	38	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45795000	45795000	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45795000C>A	uc003bgc.2	-	6	1140	c.1088G>T	c.(1087-1089)CGA>CTA	p.R363L	SMC1B_uc003bgd.2_Missense_Mutation_p.R363L|SMC1B_uc003bge.1_Missense_Mutation_p.R146L	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	363	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTCAATGTCTCGCTTTTTATG	0.353													4	81	---	---	---	---	PASS
EDA2R	60401	broad.mit.edu	37	X	65824983	65824983	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65824983C>A	uc004dwq.2	-	2	184	c.173G>T	c.(172-174)TGT>TTT	p.C58F	EDA2R_uc004dwr.2_Missense_Mutation_p.C58F|EDA2R_uc004dws.2_Missense_Mutation_p.C58F|EDA2R_uc011mpb.1_RNA|EDA2R_uc011mpc.1_Intron|EDA2R_uc010nkt.1_Missense_Mutation_p.C58F|EDA2R_uc004dwt.1_Missense_Mutation_p.C58F	NM_021783	NP_068555	Q9HAV5	TNR27_HUMAN	X-linked ectodysplasin receptor	58	Extracellular (Potential).|TNFR-Cys 2.				cell differentiation|embryo development|epidermis development|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	tumor necrosis factor receptor activity			upper_aerodigestive_tract(1)	1						GCAACTCTGACATCTGTGGTG	0.542													3	9	---	---	---	---	PASS
IL1RAPL2	26280	broad.mit.edu	37	X	104440271	104440271	+	Missense_Mutation	SNP	C	A	A	rs146735893		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104440271C>A	uc004elz.1	+	3	953	c.197C>A	c.(196-198)ACG>AAG	p.T66K		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	66	Ig-like C2-type 1.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						AACTATAGCACGGCCCAGAGC	0.468													9	17	---	---	---	---	PASS
FAM41C	284593	broad.mit.edu	37	1	812337	812338	+	5'Flank	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:812337_812338insT	uc001abt.3	-							NR_027055				Homo sapiens family with sequence similarity 41, member C, mRNA (cDNA clone IMAGE:5201580), partial cds.												0						TTGTTTACCTCTTGGGTGAGAG	0.569													4	2	---	---	---	---	
GNB1	2782	broad.mit.edu	37	1	1794370	1794370	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1794370delC	uc001aif.2	-						GNB1_uc009vky.2_Intron	NM_002074	NP_002065	P62873	GBB1_HUMAN	guanine nucleotide-binding protein, beta-1						cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		CTGAAGTCCACACAAATAACT	0.507													4	2	---	---	---	---	
MORN1	79906	broad.mit.edu	37	1	2256572	2256579	+	Intron	DEL	TCCCTCCC	-	-	rs113990186		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2256572_2256579delTCCCTCCC	uc001ajb.1	-							NM_024848	NP_079124	Q5T089	MORN1_HUMAN	MORN repeat containing 1											ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		cttccttccttccctccctccctccctt	0.139													5	5	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3318197	3318198	+	Intron	DEL	AT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3318197_3318198delAT	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GTTcacacacatattcacatgc	0.050			T	EVI1	MDS|AML								1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4371109	4371109	+	IGR	DEL	A	-	-	rs5772150		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4371109delA								LOC100133612 (537232 upstream) : LOC284661 (101002 downstream)																							GGCTTATGATAACACTACCTG	0.517													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5731457	5731477	+	IGR	DEL	AAAGTGGGGCAGATAAAAAAT	-	-	rs77279019		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5731457_5731477delAAAGTGGGGCAGATAAAAAAT								AJAP1 (887607 upstream) : NPHP4 (191393 downstream)																							GGAACCCAGGAAAGTGGGGCAGATAAAAAATGGGGTGGGCT	0.543													4	2	---	---	---	---	
KCNAB2	8514	broad.mit.edu	37	1	6112488	6112488	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6112488delA	uc009vlv.1	+						KCNAB2_uc001alv.1_Intron|KCNAB2_uc001alw.1_Intron|KCNAB2_uc001alx.1_Intron|KCNAB2_uc001aly.1_Intron|KCNAB2_uc009vlw.1_Intron|KCNAB2_uc001alu.2_Intron	NM_003636	NP_003627	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		tccattgcgcaaaaaaaaaaa	0.194													6	4	---	---	---	---	
CHD5	26038	broad.mit.edu	37	1	6235320	6235321	+	Intron	INS	-	TGGA	TGGA	rs150588853	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6235320_6235321insTGGA	uc001amb.1	-							NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		tggatggtgggtggatggatgg	0.000													3	3	---	---	---	---	
PARK7	11315	broad.mit.edu	37	1	8029645	8029646	+	Intron	DEL	TT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8029645_8029646delTT	uc001aou.3	+						PARK7_uc001aow.3_Intron|PARK7_uc001aox.3_Intron|PARK7_uc001aov.3_Intron	NM_001123377	NP_001116849	Q99497	PARK7_HUMAN	Parkinson disease protein 7						autophagy|cell death|cellular response to hydrogen peroxide|inflammatory response|mitochondrion organization|negative regulation of cell death|negative regulation of protein binding|neuroprotection|protein stabilization|regulation of androgen receptor signaling pathway|regulation of inflammatory response|single fertilization	mitochondrion|nucleus	mRNA binding|peptidase activity|peroxidase activity|protein homodimerization activity				0	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;1.28e-70)|GBM - Glioblastoma multiforme(8;3.05e-36)|Colorectal(212;6.83e-08)|COAD - Colon adenocarcinoma(227;7.51e-06)|Kidney(185;5.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000414)|KIRC - Kidney renal clear cell carcinoma(229;0.000967)|STAD - Stomach adenocarcinoma(132;0.00102)|READ - Rectum adenocarcinoma(331;0.0649)		TAACTCAAACtttttttttttt	0.129													3	5	---	---	---	---	
KIF1B	23095	broad.mit.edu	37	1	10436893	10436894	+	3'UTR	DEL	AC	-	-	rs111663673		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10436893_10436894delAC	uc001aqx.3	+	49					KIF1B_uc001aqw.3_3'UTR|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		ATGTTTTTAAacacacacacac	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14810413	14810413	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14810413delC								PRDM2 (658841 upstream) : KAZ (114800 downstream)																							agtctttaatccactttaaat	0.000													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15194463	15194464	+	Intron	INS	-	T	T	rs150668373		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15194463_15194464insT	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						TTGCATAGGCAGGCATCGCATA	0.426													4	2	---	---	---	---	
C1orf144	26099	broad.mit.edu	37	1	16693725	16693726	+	5'UTR	INS	-	G	G	rs142845497	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16693725_16693726insG	uc001aym.3	+	1					C1orf144_uc010ocb.1_5'UTR|C1orf144_uc001ayi.3_5'UTR|C1orf144_uc001ayk.3_5'UTR	NM_001114600	NP_001108072	Q7Z422	CA144_HUMAN	putative MAPK activating protein PM20,PM21												0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.12e-05)|Kidney(64;0.00018)|KIRC - Kidney renal clear cell carcinoma(64;0.00267)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GGGGAGGGGGTGGGGGAGGAGG	0.678													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16917461	16917462	+	Intron	DEL	CT	-	-	rs35460036		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16917461_16917462delCT	uc009vos.1	-						NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CACCAAGGTACTCTCTGCTTTT	0.282													4	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17230945	17230946	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17230945_17230946insA	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		atttGAAAAACAAAAAAACAAA	0.188													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17231626	17231626	+	Intron	DEL	C	-	-	rs67781706		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17231626delC	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGGTGGTGCTCGGGGCAAGTG	0.587													3	4	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18515871	18515871	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18515871delT	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		gtctccaacctttttggcacc	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20164825	20164825	+	IGR	DEL	T	-	-	rs112196639		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20164825delT								RNF186 (23054 upstream) : OTUD3 (44063 downstream)																							ttctttcttcttttttttttt	0.000													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21341917	21341917	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21341917delC	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		actcaatgaaccccacatagg	0.000													4	2	---	---	---	---	
WDTC1	23038	broad.mit.edu	37	1	27633122	27633122	+	3'UTR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27633122delC	uc009vst.2	+	16					WDTC1_uc001bno.2_3'UTR|WDTC1_uc001bnp.1_RNA|WDTC1_uc001bnq.2_3'UTR	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CCTCCATATGCCCCCCCCCAT	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30553981	30553981	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30553981delC								PTPRU (900666 upstream) : MATN1 (630145 downstream)																							TGGGTCTGATCCCAGCTCCAC	0.343													4	2	---	---	---	---	
OSCP1	127700	broad.mit.edu	37	1	36896765	36896765	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36896765delC	uc001cap.2	-						OSCP1_uc001caq.2_Intron|OSCP1_uc001car.2_Intron	NM_145047	NP_659484	Q8WVF1	OSCP1_HUMAN	oxidored-nitro domain-containing protein isoform						transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4						gaagtttcagcaaggtggtgg	0.000													4	2	---	---	---	---	
OSCP1	127700	broad.mit.edu	37	1	36900350	36900351	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36900350_36900351insA	uc001cap.2	-						OSCP1_uc001caq.2_Intron|OSCP1_uc001car.2_Intron	NM_145047	NP_659484	Q8WVF1	OSCP1_HUMAN	oxidored-nitro domain-containing protein isoform						transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4						gactttgtctcaaaaaaaaaaa	0.163													4	2	---	---	---	---	
PTPRF	5792	broad.mit.edu	37	1	44077103	44077104	+	Intron	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44077103_44077104delGA	uc001cjr.2	+						PTPRF_uc001cjs.2_Intron|PTPRF_uc001cju.2_Intron|PTPRF_uc009vwt.2_Intron|PTPRF_uc001cjv.2_Intron|PTPRF_uc001cjw.2_Intron	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				atgagcacctgagggtttctgc	0.054													4	2	---	---	---	---	
NASP	4678	broad.mit.edu	37	1	46054630	46054633	+	Intron	DEL	TGTT	-	-	rs66987604		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46054630_46054633delTGTT	uc001coi.1	+						NASP_uc010olq.1_Intron|NASP_uc001coh.1_Intron|NASP_uc001coj.1_Intron|NASP_uc010olr.1_Intron	NM_002482	NP_002473	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein isoform 2						blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GGTGGTCAAGtgtttgtttgtttg	0.167													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	47227731	47227732	+	IGR	INS	-	CTTC	CTTC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47227731_47227732insCTTC								KIAA0494 (42995 upstream) : CYP4B1 (36938 downstream)																							ttcctttctttcttccttcctt	0.000													2	6	---	---	---	---	
RNF11	26994	broad.mit.edu	37	1	51700060	51700061	+	5'Flank	DEL	TC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51700060_51700061delTC	uc001csi.3	+							NM_014372	NP_055187	Q9Y3C5	RNF11_HUMAN	ring finger protein 11						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0						ctgcctcccttctctctctctc	0.020													4	2	---	---	---	---	
PODN	127435	broad.mit.edu	37	1	53538579	53538579	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53538579delA	uc001cuv.2	+						PODN_uc001cuw.2_Intron|PODN_uc010onr.1_Intron|PODN_uc010ons.1_Intron	NM_153703	NP_714914	Q7Z5L7	PODN_HUMAN	podocan						negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2						ctaaaaatacaaaaaattatc	0.000													5	8	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55590788	55590789	+	Intron	DEL	TT	-	-	rs67888964		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55590788_55590789delTT	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						cacagaatgctttgtcttgtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56008207	56008208	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56008207_56008208delAC								USP24 (327445 upstream) : PPAP2B (952225 downstream)																							TCAGGAATGAacacacacacac	0.163													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58312494	58312495	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58312494_58312495delCA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						cacgtgcgtgcacacacacaca	0.094													5	4	---	---	---	---	
LEPR	3953	broad.mit.edu	37	1	66047133	66047133	+	Intron	DEL	T	-	-	rs150089956		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66047133delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Intron|LEPR_uc001dck.2_Intron	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		gttgaaaggcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84729072	84729072	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84729072delA								PRKACB (24893 upstream) : SAMD13 (34977 downstream)																							AGCATCAGATAAAAGAATAGG	0.453													4	2	---	---	---	---	
GBP7	388646	broad.mit.edu	37	1	89611588	89611588	+	Intron	DEL	T	-	-	rs59180604		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89611588delT	uc001dna.2	-						GBP2_uc001dmy.1_Intron	NM_207398	NP_997281	Q8N8V2	GBP7_HUMAN	guanylate binding protein 4-like							integral to membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		ctaaaaaaaatctacaggttt	0.000													4	3	---	---	---	---	
GBP6	163351	broad.mit.edu	37	1	89839665	89839665	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89839665delC	uc001dnf.2	+						GBP6_uc010ost.1_Intron	NM_198460	NP_940862	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6								GTP binding|GTPase activity			ovary(2)	2		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		gtgtttgcttccccttccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98932359	98932360	+	IGR	DEL	CA	-	-	rs71882802		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98932359_98932360delCA								MIR137 (420632 upstream) : SNX7 (194876 downstream)																							cacgcacatgcacacacacaca	0.144													3	3	---	---	---	---	
DBT	1629	broad.mit.edu	37	1	100657304	100657331	+	3'UTR	DEL	ATACACACACACACACACACACACACAC	-	-	rs112901689		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100657304_100657331delATACACACACACACACACACACACACAC	uc001dta.2	-	11					DBT_uc010oug.1_3'UTR	NM_001918	NP_001909	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase						branched chain family amino acid catabolic process|fatty-acyl-CoA biosynthetic process	microtubule cytoskeleton|mitochondrial alpha-ketoglutarate dehydrogenase complex|mitochondrial nucleoid	acyltransferase activity|cofactor binding|dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity|protein binding			pancreas(1)	1		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		GTGTGTGTGTATacacacacacacacacacacacacacacacacacac	0.088													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	107422447	107422447	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107422447delT								None (None upstream) : PRMT6 (176820 downstream)																							agcaacaaaattacctccttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108639887	108639887	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108639887delC								VAV3 (132342 upstream) : SLC25A24 (37562 downstream)																							CTCCCCCACACCCAGTCCAGA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108808936	108808936	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108808936delT	uc001dvp.1	-											Homo sapiens cDNA clone IMAGE:6167132.																		gcctggctaattttttacctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115640090	115640091	+	IGR	DEL	TT	-	-	rs35876057		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115640090_115640091delTT								TSPAN2 (7975 upstream) : NGF (188446 downstream)																							gcatggctaatttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142612809	142612810	+	IGR	INS	-	AC	AC	rs148296473		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142612809_142612810insAC								None (None upstream) : None (None downstream)																							catttatatatcttcttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142690566	142690567	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142690566_142690567delTG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		catgtgtgcctgtgtgtgtgtg	0.381													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142951514	142951514	+	Intron	DEL	C	-	-	rs143173818		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142951514delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		GGTTGTACTGCTGGGCTTAAG	0.378													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143123090	143123090	+	Intron	DEL	A	-	-	rs79390876		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143123090delA	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		atggttgcacatttttttttt	0.050													5	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144550341	144550342	+	Intron	DEL	AA	-	-	rs71252608		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144550341_144550342delAA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						CAGTTTTTGCAAAGTTACTAAA	0.386													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145033613	145033614	+	Intron	INS	-	AAA	AAA	rs141798859		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145033613_145033614insAAA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAAACAAAGTCAAAATTCTTAA	0.327			T	PDGFRB	MPD								2	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145048154	145048154	+	Intron	DEL	G	-	-	rs148993604		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145048154delG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tgcatggctcgggggggtcct	0.000													8	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145054268	145054269	+	Intron	INS	-	G	G	rs149978567		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145054268_145054269insG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TGTGGTTACCTTCATTCATTTA	0.386													4	4	---	---	---	---	
NBPF15	284565	broad.mit.edu	37	1	148556867	148556868	+	5'Flank	INS	-	TGTC	TGTC	rs111615504		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148556867_148556868insTGTC	uc001esb.1	+							NM_001102663	NP_001096133	Q8N660	NBPFF_HUMAN	hypothetical protein LOC728936							cytoplasm					0	all_hematologic(923;0.032)					TGATTTCCCTGTATCTGTCTTT	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149224233	149224234	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149224233_149224234insT								LOC645166 (271179 upstream) : LOC388692 (55242 downstream)																							AGCTCTTGCACCTCCGCCCCGC	0.297													4	2	---	---	---	---	
ETV3	2117	broad.mit.edu	37	1	157107302	157107303	+	Intron	DEL	AC	-	-	rs141722159		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157107302_157107303delAC	uc001fqr.2	-						ETV3_uc001fqt.2_Intron	NM_001145312	NP_001138784	P41162	ETV3_HUMAN	ets variant gene 3 isoform 1								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(266;0.158)	Prostate(1639;0.174)				ACAAGGAAAAacacacacacac	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157278190	157278191	+	IGR	DEL	CT	-	-	rs10531627		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157278190_157278191delCT								ETV3 (169807 upstream) : FCRL5 (204977 downstream)																							CCCTCCTTCCCTTCCACACTTT	0.465													3	3	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165188708	165188708	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165188708delA	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					GAAAGAAGGGAGGAATTTATG	0.453													4	2	---	---	---	---	
UCK2	7371	broad.mit.edu	37	1	165852581	165852581	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165852581delA	uc001gdp.2	+						UCK2_uc010plb.1_Intron	NM_012474	NP_036606	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					gCTAAAATTCAAGGACTgatg	0.090													4	2	---	---	---	---	
GPA33	10223	broad.mit.edu	37	1	167025869	167025870	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167025869_167025870delTG	uc001gea.1	-							NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor							integral to plasma membrane	receptor activity				0						gagtgtgtgatgtgtgtggtgt	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	171852619	171852620	+	Intron	DEL	TT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171852619_171852620delTT	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						tttttctttctttttttttttg	0.084													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175670052	175670053	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175670052_175670053insA	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					CTTCGTCCGCCTCCCCGAGCCT	0.490													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175679084	175679084	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175679084delG	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					agacagatgtgggtcaagatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178989290	178989297	+	IGR	DEL	ACACACAC	-	-	rs111366020		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178989290_178989297delACACACAC								RALGPS2 (100055 upstream) : FAM20B (5777 downstream)																							GTGTGTGTATacacacacacacacacac	0.346													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	180173206	180173207	+	IGR	INS	-	ATG	ATG	rs139518346	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180173206_180173207insATG								FLJ23867 (3349 upstream) : LHX4 (26235 downstream)																							ttggcaaagaaatgatgatgat	0.099													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181026257	181026257	+	IGR	DEL	A	-	-	rs34244742		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181026257delA								MR1 (1624 upstream) : IER5 (31381 downstream)																							ctctgtctccaaaaaaaaaaa	0.224													4	2	---	---	---	---	
PHLDA3	23612	broad.mit.edu	37	1	201436276	201436276	+	Intron	DEL	A	-	-	rs79500475		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201436276delA	uc001gwq.2	-						PHLDA3_uc009wzx.2_Intron	NM_012396	NP_036528	Q9Y5J5	PHLA3_HUMAN	pleckstrin homology-like domain, family A,						anatomical structure morphogenesis|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of protein kinase B signaling cascade	cytoplasm|intracellular membrane-bounded organelle|plasma membrane	identical protein binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-5-phosphate binding				0						ccaaatctacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RPS10P7	376693	broad.mit.edu	37	1	201485926	201485941	+	5'Flank	DEL	GAAGGAAGGAAGGAAA	-	-	rs61612301	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201485926_201485941delGAAGGAAGGAAGGAAA	uc009wzz.1	+											Homo sapiens cDNA FLJ31028 fis, clone HLUNG2000570, weakly similar to 40S RIBOSOMAL PROTEIN S10.												0						aggaaggaaggaaggaaggaaggaaagaaaggaggg	0.148													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208441958	208441959	+	IGR	DEL	TG	-	-	rs71699619		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208441958_208441959delTG								PLXNA2 (24293 upstream) : None (None downstream)																							GTTCTTGTATtgtgtgtgtgtg	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208442848	208442848	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208442848delG								PLXNA2 (25183 upstream) : None (None downstream)																							GTGAGACAATGAGAAATAAAA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208887925	208887926	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208887925_208887926insT								PLXNA2 (470260 upstream) : LOC642587 (714242 downstream)																							cttccaccacattttctatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219239584	219239585	+	IGR	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219239584_219239585delCA								TGFB2 (621625 upstream) : LYPLAL1 (107607 downstream)																							TTGACTGAATCACTTGAGACCA	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221693812	221693813	+	IGR	INS	-	TCATTCCC	TCATTCCC	rs149458916	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221693812_221693813insTCATTCCC								LOC400804 (184174 upstream) : DUSP10 (180953 downstream)																							tcctccttccttcctttcttct	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232679222	232679225	+	IGR	DEL	CTTT	-	-	rs138781683		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232679222_232679225delCTTT								SIPA1L2 (27979 upstream) : KIAA1383 (261413 downstream)																							atgtgaagacctttctttatagga	0.000													0	7	---	---	---	---	
TARBP1	6894	broad.mit.edu	37	1	234543947	234543947	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234543947delT	uc001hwd.2	-							NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TTAAGAAAGGTTTTTTTTTTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236288733	236288736	+	IGR	DEL	CACG	-	-	rs71705906		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236288733_236288736delCACG								NID1 (60252 upstream) : GPR137B (17096 downstream)																							cacacacacacacgcacacacaca	0.000													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237905570	237905571	+	Intron	INS	-	T	T	rs71656371		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237905570_237905571insT	uc001hyl.1	+						RYR2_uc010pya.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCCTGTCTCCttttttttttt	0.307													4	2	---	---	---	---	
GREM2	64388	broad.mit.edu	37	1	240704842	240704842	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240704842delT	uc001hys.2	-							NM_022469	NP_071914	Q9H772	GREM2_HUMAN	gremlin 2 precursor						BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			ATGGGTTTCATTTTACTGCTG	0.378													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241332021	241332022	+	Intron	DEL	TC	-	-	rs72385432		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241332021_241332022delTC	uc001hyv.2	-						RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			tctctctctgtctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242928320	242928321	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242928320_242928321insA								PLD5 (240322 upstream) : CEP170 (359410 downstream)																							cctgtctctacaaaaaaaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133389	133390	+	IGR	INS	-	A	A	rs34169697		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133389_133390insA								FAM110C (87004 upstream) : SH3YL1 (84748 downstream)																							cacaaaaaaggaaaaaaaaaaa	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	899215	899216	+	IGR	DEL	CT	-	-	rs146521649		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:899215_899216delCT								TMEM18 (221776 upstream) : SNTG2 (47339 downstream)																							ccacattttcctctcttgcttc	0.059													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2660865	2660865	+	IGR	DEL	T	-	-	rs66569182		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2660865delT								MYT1L (325820 upstream) : TSSC1 (531876 downstream)																							AGGTGTAGTCTTTTTTTTTTT	0.522													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	3778778	3778778	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3778778delG								ALLC (28520 upstream) : None (None downstream)																							AGGGTGCAGTGGGAGGGACAG	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11656438	11656439	+	IGR	DEL	GT	-	-	rs72035230		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11656438_11656439delGT								E2F6 (50141 upstream) : GREB1 (17803 downstream)																							TTTCCTGCAGgtgtgtgtgtgt	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15069811	15069812	+	IGR	INS	-	TT	TT			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15069811_15069812insTT								FAM84A (278878 upstream) : NBAS (237220 downstream)																							cCAACAGTAAATTTTTTTTTTT	0.233													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19330426	19330429	+	IGR	DEL	GTGT	-	-	rs113947912		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19330426_19330429delGTGT								NT5C1B (559588 upstream) : OSR1 (220818 downstream)																							TTTGTTTGGGgtgtgtgtgtgtgt	0.230													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23636185	23636185	+	IGR	DEL	C	-	-	rs112897052		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23636185delC								None (None upstream) : KLHL29 (119270 downstream)																							AACCATGGGGCCAGCCATTTC	0.522													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	25441663	25441664	+	IGR	INS	-	A	A	rs4665289		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25441663_25441664insA								POMC (50104 upstream) : DNMT3A (14182 downstream)																							aaaaaaaaaacaaaaaaaaaaa	0.183													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28443979	28443980	+	Intron	DEL	CT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28443979_28443980delCT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					cccttttttcctctctctctct	0.376													3	3	---	---	---	---	
EIF2AK2	5610	broad.mit.edu	37	2	37380268	37380268	+	Intron	DEL	T	-	-	rs76641313		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37380268delT	uc010ynh.1	-						EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)				accAttgtgattttttttttt	0.000													4	2	---	---	---	---	
SOS1	6654	broad.mit.edu	37	2	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)				tccaaaatccaaaaaaaaaac	0.045									Noonan_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41086309	41086309	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41086309delG								SLC8A1 (346734 upstream) : None (None downstream)																							CATGTAGCTTGGGGGGAGTGT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42164976	42164976	+	3'UTR	DEL	C	-	-	rs75454609		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42164976delC	uc002rsf.1	-	4										SubName: Full=cDNA FLJ42903 fis, clone BRHIP3013765;																		CTAAGGAGCACCAAGCTTTGC	0.502													3	3	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47656145	47656145	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47656145delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(1)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			tctttctgtcttttttttttt	0.174			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47986618	47986618	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47986618delA								MSH2 (80110 upstream) : MSH6 (23603 downstream)																							attttGggccaggcatgctgg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49558206	49558206	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49558206delA								FSHR (176576 upstream) : NRXN1 (587438 downstream)																							ggagaactgcaaaacactttg	0.000													4	2	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58346000	58346000	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58346000delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron|VRK2_uc010yph.1_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						aattacagtcaaaggaggttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66159047	66159048	+	Intron	INS	-	T	T	rs140910679		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66159047_66159048insT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		ATTGACTAGAATTTTTTTTTTT	0.361													3	3	---	---	---	---	
APLF	200558	broad.mit.edu	37	2	68756396	68756396	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68756396delA	uc002sep.2	+						APLF_uc002seq.1_5'Flank|APLF_uc010fdf.2_Intron	NM_173545	NP_775816	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor						double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2						ACCTGCCTGGAAAAGAAGGCC	0.632													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71758102	71758102	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71758102delA	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						CCAAGTTCCTAAGAAGATAGG	0.488													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845282	71845285	+	Intron	DEL	GTGT	-	-	rs151014845		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845282_71845285delGTGT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						ggtagaggtggtgtgtgtgtgtgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76670829	76670830	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76670829_76670830insG								C2orf3 (732718 upstream) : LRRTM4 (304028 downstream)																							GCAGTCTTACTGGGGaaaacaa	0.267													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77420225	77420225	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77420225delT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		attcaatgcattacctttgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85792018	85792018	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85792018delT								GGCX (3361 upstream) : VAMP8 (12630 downstream)																							cttcttcttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88980929	88980929	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88980929delT								EIF2AK3 (53935 upstream) : RPIA (10247 downstream)																							ttccagtggcttttgaagcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91769863	91769864	+	IGR	INS	-	TT	TT	rs144120667		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91769863_91769864insTT								None (None upstream) : LOC654342 (35328 downstream)																							CATTTTATATCTTTTTTTTTTC	0.446													4	3	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91829600	91829600	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91829600delT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0						GAGAGAGGTCTTTTTTTTTTT	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96605453	96605453	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96605453delA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		actccgtctcaaaaagaaaag	0.144													5	3	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111614957	111614957	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111614957delA	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						gtccattcctaaggccatcaa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	111926790	111926791	+	IGR	DEL	GT	-	-	rs72091170		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111926790_111926791delGT								BCL2L11 (768 upstream) : LOC541471 (38568 downstream)																							TTAATCTGCAgtgtgtgtgtgt	0.322													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113623397	113623397	+	IGR	DEL	A	-	-	rs34671850		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113623397delA								IL1B (29041 upstream) : IL1F7 (47151 downstream)																							TTCTAAGCTTAAAAAAAAAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118787406	118787406	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118787406delG								CCDC93 (15709 upstream) : INSIG2 (58644 downstream)																							ttagaaattaggatcccattt	0.174													4	2	---	---	---	---	
PCDP1	200373	broad.mit.edu	37	2	120342162	120342163	+	Intron	INS	-	A	A	rs71988922		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120342162_120342163insA	uc002tmb.2	+						PCDP1_uc010yyq.1_Intron	NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1							cilium	calmodulin binding				0	Colorectal(110;0.196)					gactgtgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
MKI67IP	84365	broad.mit.edu	37	2	122497211	122497224	+	5'Flank	DEL	GTGTGTGTGTGCGT	-	-	rs71426204		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122497211_122497224delGTGTGTGTGTGCGT	uc002tnk.2	-						MKI67IP_uc010fls.2_5'Flank	NM_032390	NP_115766	Q9BYG3	MK67I_HUMAN	MKI67 interacting nucleolar phosphoprotein						protein complex assembly|rRNA metabolic process|rRNA transcription	condensed nuclear chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						CCGTGTCCTCgtgtgtgtgtgcgtgtgtgtgtgt	0.393													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131652232	131652233	+	Intron	INS	-	T	T	rs143640301	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131652232_131652233insT	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																		AAAAAAGCAACTTTTTTTTTTG	0.381													4	2	---	---	---	---	
PLEKHB2	55041	broad.mit.edu	37	2	131868584	131868585	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131868584_131868585insT	uc002tsg.3	+						PLEKHB2_uc002tsh.2_Intron|PLEKHB2_uc002tsj.3_Intron|PLEKHB2_uc002tsf.3_Intron|PLEKHB2_uc010zao.1_Intron|PLEKHB2_uc010zap.1_Intron|PLEKHB2_uc010zaq.1_Intron	NM_001100623	NP_001094093	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)		tataagcagaattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132403233	132403236	+	IGR	DEL	ACAG	-	-	rs148619714		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132403233_132403236delACAG								CCDC74A (111996 upstream) : C2orf27A (76828 downstream)																							actgccacacacagacacaccgcc	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132773003	132773003	+	IGR	DEL	G	-	-	rs150347766	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132773003delG								C2orf27B (213769 upstream) : NCRNA00164 (132161 downstream)																							ATCGATTTCTGTTTTTTTTGA	0.100													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132977096	132977097	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132977096_132977097insT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						tcagaaacatcttgtgatgttt	0.000													3	3	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133009045	133009045	+	Intron	DEL	C	-	-	rs113324698		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133009045delC	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						gacacgttttcctccacccct	0.010													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133055010	133055011	+	IGR	INS	-	T	T	rs139949484	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133055010_133055011insT								NCRNA00164 (39468 upstream) : GPR39 (119136 downstream)																							TAATGGATGCAATTGCTGAAGG	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133072118	133072119	+	Intron	INS	-	C	C	rs148922808	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133072118_133072119insC	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		ggaaagacccgccccataattc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134867058	134867058	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134867058delC								NCKAP5 (541027 upstream) : MGAT5 (144772 downstream)																							ccgagccctgccccccaggga	0.000													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137634682	137634683	+	Intron	DEL	GG	-	-	rs67495613		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137634682_137634683delGG	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CTGTCCACTAGGGTTCCAGAAA	0.366													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	143436244	143436247	+	IGR	DEL	GTGT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143436244_143436247delGTGT								LRP1B (546974 upstream) : KYNU (198948 downstream)																							AGATAGATGAgtgtgtgtgtgtgt	0.309													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146395512	146395515	+	IGR	DEL	TGTG	-	-	rs66802338		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146395512_146395515delTGTG								None (None upstream) : PABPC1P2 (949110 downstream)																							TATGCAGTGAtgtgtgtgtgtgtg	0.240													5	4	---	---	---	---	
PLA2R1	22925	broad.mit.edu	37	2	160899604	160899605	+	Intron	INS	-	G	G	rs138155690	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160899604_160899605insG	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3						ccctctgggtagggagccaggg	0.000													4	3	---	---	---	---	
RBMS1	5937	broad.mit.edu	37	2	161263542	161263543	+	Intron	INS	-	AC	AC	rs147853303	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161263542_161263543insAC	uc002ubo.2	-						RBMS1_uc002ubl.2_Intron|RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	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						cagagacacagacacacacaca	0.366													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164009272	164009272	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164009272delA								KCNH7 (314032 upstream) : FIGN (454846 downstream)																							AGAAGTTGCCACCtttttttt	0.249													5	3	---	---	---	---	
MAP1D	254042	broad.mit.edu	37	2	172927365	172927366	+	Intron	INS	-	GCATTTGTGG	GCATTTGTGG	rs144652837	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172927365_172927366insGCATTTGTGG	uc002uhk.2	+						MAP1D_uc010zdw.1_Intron	NM_199227	NP_954697	Q6UB28	AMP1D_HUMAN	methionine aminopeptidase 1D precursor						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis	mitochondrion	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)			AGACCTGGTGAGCATTTGTGGG	0.520													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190384368	190384368	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190384368delA								WDR75 (44104 upstream) : SLC40A1 (40950 downstream)																							TAAGAGTTTGAAGTCACAGCT	0.279													4	2	---	---	---	---	
STAT4	6775	broad.mit.edu	37	2	191900806	191900811	+	Intron	DEL	TAGTAG	-	-	rs3024882	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191900806_191900811delTAGTAG	uc002usm.1	-						STAT4_uc002usn.1_Intron|STAT4_uc010zgk.1_Intron|STAT4_uc002uso.2_Intron	NM_003151	NP_003142	Q14765	STAT4_HUMAN	signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TCTTTATTATTAGTAGTAGTAATAGC	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192338292	192338292	+	IGR	DEL	T	-	-	rs68161186		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192338292delT								MYO1B (48177 upstream) : OBFC2A (204506 downstream)																							AAAAGGAGAAttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195374345	195374345	+	IGR	DEL	T	-	-	rs112587633		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195374345delT								None (None upstream) : None (None downstream)																							ccaaactttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	205052891	205052891	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205052891delT								ICOS (226595 upstream) : PARD3B (357625 downstream)																							TTCTCTAAAGTTTTTTTTTTT	0.368													3	3	---	---	---	---	
INO80D	54891	broad.mit.edu	37	2	206924465	206924466	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206924465_206924466delGT	uc002vaz.3	-							NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						AATCTACACCgtgtgtgtgtgt	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	211140566	211140567	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211140566_211140567insT								ACADL (50351 upstream) : MYL1 (14302 downstream)																							tgagcatggaatttttttttcc	0.000													4	2	---	---	---	---	
MARCH4	57574	broad.mit.edu	37	2	217182145	217182145	+	Intron	DEL	T	-	-	rs67522822		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217182145delT	uc002vgb.2	-							NM_020814	NP_065865	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TCCttttttgtttttttttag	0.224													4	3	---	---	---	---	
SPHKAP	80309	broad.mit.edu	37	2	229028924	229028924	+	Intron	DEL	A	-	-	rs35867399		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229028924delA	uc002vpq.2	-						SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein							cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ccttggacttaacaccagtgg	0.000													4	5	---	---	---	---	
SPATA3	130560	broad.mit.edu	37	2	231869725	231869726	+	Intron	INS	-	CAT	CAT	rs142539373	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231869725_231869726insCAT	uc010zmd.1	+						SPATA3_uc002vri.3_Intron|SPATA3_uc002vrk.2_Intron	NM_139073	NP_620712	Q8NHX4	SPTA3_HUMAN	testis and spermatogenesis cell apoptosis						apoptosis|spermatogenesis						0						atcatcaccaccatcatcacca	0.069													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232433679	232433679	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232433679delT								NMUR1 (38497 upstream) : C2orf57 (23933 downstream)																							TGCTAGCACATTTTTCCGTGG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236227482	236227482	+	IGR	DEL	A	-	-	rs68031119		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236227482delA								SH3BP4 (263126 upstream) : AGAP1 (175254 downstream)																							gtcacaaaagaaaaaaaaaaG	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238039711	238039712	+	IGR	DEL	TG	-	-	rs144613674		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238039711_238039712delTG								COPS8 (32224 upstream) : COL6A3 (192943 downstream)																							gtgcatatgatgtgagtgtaat	0.035													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238472162	238472162	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238472162delA								MLPH (8202 upstream) : PRLH (3055 downstream)																							AATGTGTTTTAAAACCACTTG	0.453													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238639563	238639566	+	Intron	DEL	ACAA	-	-	rs3835811		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238639563_238639566delACAA	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		tccatctcagacaaacaaacaaac	0.142													3	3	---	---	---	---	
ESPNL	339768	broad.mit.edu	37	2	239028088	239028089	+	Intron	INS	-	GAGGAGATG	GAGGAGATG	rs150026661	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239028088_239028089insGAGGAGATG	uc002vxq.3	+						ESPNL_uc010fyw.2_Intron	NM_194312	NP_919288	Q6ZVH7	ESPNL_HUMAN	espin-like											pancreas(1)	1		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		gaggtggaggagaggaggttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239676423	239676423	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239676423delA								ASB1 (315533 upstream) : TWIST2 (80250 downstream)																							CACATTGATTACTCCTCTGTT	0.413													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240144494	240144496	+	Intron	DEL	CTC	-	-	rs150672623		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240144494_240144496delCTC	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc002vyl.1_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GCTTTGTGATCTCCTTTCGTCCT	0.438													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240486803	240486803	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240486803delG								HDAC4 (163457 upstream) : NDUFA10 (413355 downstream)																							TTAATGAACTGGAGAAGAGAG	0.458													4	2	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2905967	2905969	+	Intron	DEL	TTG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2905967_2905969delTTG	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TAGTCTTACTTTGTTGTTGTTGT	0.227													4	2	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4806631	4806634	+	Intron	DEL	TGGA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4806631_4806634delTGGA	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		AGtgggtggctggatggatggatg	0.088													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	11766654	11766655	+	IGR	INS	-	CCT	CCT	rs143002672	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11766654_11766655insCCT								VGLL4 (4434 upstream) : C3orf31 (65265 downstream)																							ttgttctcttccctcttttgct	0.000													2	4	---	---	---	---	
SYN2	6854	broad.mit.edu	37	3	12232974	12232975	+	3'UTR	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12232974_12232975delGT	uc003bwm.2	+	17					SYN2_uc003bwn.2_3'UTR	NM_133625	NP_598328	Q92777	SYN2_HUMAN	synapsin II isoform IIa						neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2						TCCATGAGGGgtgtgtgtgtgt	0.243													4	2	---	---	---	---	
IQSEC1	9922	broad.mit.edu	37	3	12969056	12969056	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12969056delC	uc003bxt.2	-						IQSEC1_uc003bxu.3_Intron|IQSEC1_uc011auw.1_Intron	NM_014869	NP_055684	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform b						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1						TCTTTTTTTGCCCCCATCCAC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14422399	14422400	+	IGR	INS	-	AGGAAGGA	AGGAAGGA	rs140951888	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14422399_14422400insAGGAAGGA								LSM3 (182563 upstream) : SLC6A6 (21706 downstream)																							gggagggagggaggaaggaagT	0.084													4	2	---	---	---	---	
FGD5	152273	broad.mit.edu	37	3	14881441	14881444	+	Intron	DEL	AAAC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14881441_14881444delAAAC	uc003bzc.2	+						FGD5_uc011avk.1_Intron	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						ctgtctcaaaaaacaaacaaacaa	0.137													4	2	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16534743	16534743	+	Intron	DEL	T	-	-	rs11328406		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16534743delT	uc003cay.2	-							NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						aattcgttgcttttttttttt	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	20423649	20423650	+	IGR	DEL	TC	-	-	rs34658075		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20423649_20423650delTC								SGOL1 (195966 upstream) : None (None downstream)																							acagtgcttttctctctctcct	0.000													1	6	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	22010008	22010009	+	Intron	INS	-	GAGGA	GAGGA	rs149641003	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22010008_22010009insGAGGA	uc010hfb.1	-									Q9H6B1	Z385D_HUMAN	Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						tccttctgtctgaggagaggag	0.000													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41905839	41905843	+	Intron	DEL	TGTTT	-	-	rs146719807		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41905839_41905843delTGTTT	uc003ckv.3	-						ULK4_uc003ckw.2_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		aattcagaactgttttgttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43820269	43820269	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43820269delT								ABHD5 (56053 upstream) : MIR138-1 (335435 downstream)																							gtcactcttgtaatcatgtta	0.000													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54173783	54173783	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54173783delA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ACTGCCAAATAAAAAAAAAGC	0.438													4	2	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	56809828	56809829	+	Intron	INS	-	CA	CA	rs146595496	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56809828_56809829insCA	uc003dig.2	-						ARHGEF3_uc011bew.1_Intron|ARHGEF3_uc003dih.2_Intron|ARHGEF3_uc011bev.1_5'Flank|ARHGEF3_uc003dif.2_5'Flank|ARHGEF3_uc010hmy.1_Intron|ARHGEF3_uc003dii.2_Intron	NM_019555	NP_062455	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		acacgcgcaagcacacacacac	0.361													5	3	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57837080	57837080	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57837080delT	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		TTTTGGGTTGTTTTTTTTTTT	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	65335748	65335749	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65335748_65335749delAC								ADAMTS9 (662383 upstream) : MAGI1 (4158 downstream)																							atacagttatacacacacacac	0.084													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	67976106	67976107	+	Intron	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67976106_67976107delAC	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																		taatataaagacacacacacac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72002139	72002139	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72002139delT								PROK2 (167782 upstream) : RYBP (421612 downstream)																							ctttgttttgttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72724312	72724312	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72724312delT								RYBP (228538 upstream) : SHQ1 (74118 downstream)																							GGAAGAGTGGTTTTTTTTTGT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75905775	75905775	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75905775delA								ZNF717 (71105 upstream) : None (None downstream)																							AAGTGTTAATAAGCTGTATCT	0.303													4	2	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	79596518	79596518	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79596518delG	uc003dqe.2	-							NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GATTTTATATGAACGTGAGGA	0.303													4	2	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81662300	81662300	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81662300delT	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AGCTGCAGTCTTTTTTTTTTT	0.328									Glycogen_Storage_Disease_type_IV				6	3	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98619934	98619934	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98619934delC	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron|DCBLD2_uc003dtf.1_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						GACGGAGGTTCCCCCGCCGCT	0.532													4	2	---	---	---	---	
FILIP1L	11259	broad.mit.edu	37	3	99720941	99720941	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99720941delA	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						CTGCAAGTGGAAAACATGCCC	0.478													4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115426320	115426321	+	Intron	INS	-	AG	AG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115426320_115426321insAG	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		taattatttgtagaggctgagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117920210	117920211	+	IGR	INS	-	A	A	rs62929461		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117920210_117920211insA								None (None upstream) : IGSF11 (699270 downstream)																							AAGAGGCAGAGAAAAAAAAAAA	0.386													3	8	---	---	---	---	
ITGB5	3693	broad.mit.edu	37	3	124525643	124525644	+	Intron	INS	-	T	T	rs112269542		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124525643_124525644insT	uc003eho.2	-						ITGB5_uc010hrx.2_Intron	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		aagcattagtgttttttttttt	0.045													4	2	---	---	---	---	
SLC12A8	84561	broad.mit.edu	37	3	124935675	124935676	+	Intron	INS	-	TTT	TTT	rs142927713	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124935675_124935676insTTT	uc003ehw.3	-							NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0						gtatagtgttgttttaaaaagc	0.000													4	4	---	---	---	---	
ALDH1L1	10840	broad.mit.edu	37	3	125878066	125878067	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125878066_125878067delCA	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003eio.2_5'Flank|ALDH1L1_uc010hsf.1_Intron|ALDH1L1_uc003eip.1_5'Flank|ALDH1L1_uc011bkj.1_Intron	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1						10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	cacatgcgtgcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126401192	126401192	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126401192delG								TXNRD3IT1 (27247 upstream) : CHCHD6 (21926 downstream)																							TAACCAGGCTGCCTCCATTCC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127058151	127058152	+	Intron	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127058151_127058152delAC	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																		acatacatagacacacactaca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127273047	127273048	+	IGR	INS	-	GT	GT	rs72038427		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127273047_127273048insGT								PLXNA1 (516819 upstream) : TPRA1 (18860 downstream)																							AACCATTTGAAgtgtgtgtgtg	0.218													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128435152	128435152	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128435152delT								RPN1 (35234 upstream) : RAB7A (9827 downstream)																							atttttggtgttttttttttt	0.000													5	3	---	---	---	---	
NEK11	79858	broad.mit.edu	37	3	130798883	130798884	+	Intron	INS	-	TG	TG	rs145298747	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130798883_130798884insTG	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc003enw.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_5'Flank	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						gtgtgtgtgtttgtgtgtgtgt	0.139													6	5	---	---	---	---	
MSL2	55167	broad.mit.edu	37	3	135913505	135913505	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135913505delA	uc003eqx.1	-						MSL2_uc011bmb.1_5'Flank	NM_018133	NP_060603	Q9HCI7	MSL2_HUMAN	ring finger protein 184 isoform 1						histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1						AAGGTTTAAGAAAAAAAAAAA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	136829069	136829069	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136829069delT								IL20RB (99149 upstream) : SOX14 (654510 downstream)																							aacccaggagttttgagacca	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137779994	137779994	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137779994delC								CLDN18 (27500 upstream) : DZIP1L (840 downstream)																							TACGACAACACCCCCAGCCTG	0.378													4	2	---	---	---	---	
ARMC8	25852	broad.mit.edu	37	3	137993076	137993077	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137993076_137993077delTG	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2								binding				0						tgtatatacatgtgtgtgtgtg	0.228													4	2	---	---	---	---	
RBP2	5948	broad.mit.edu	37	3	139196518	139196518	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139196518delT	uc003eth.2	-							NM_004164	NP_004155	P50120	RET2_HUMAN	retinol binding protein 2, cellular						epidermis development|retinoid metabolic process|steroid metabolic process|vitamin A metabolic process	cytosol	retinal binding|retinol binding|transporter activity			skin(1)	1					Vitamin A(DB00162)	CACATTTATCTTTCAGTAAAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140616259	140616259	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140616259delC								TRIM42 (196268 upstream) : SLC25A36 (44403 downstream)																							gtgcaggcagccTACACACCT	0.020													2	5	---	---	---	---	
RASA2	5922	broad.mit.edu	37	3	141268326	141268327	+	Intron	INS	-	GT	GT	rs150308209	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141268326_141268327insGT	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.1_Intron	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						tgtgtgtgtgcgtgtgtgtgtg	0.069													3	3	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149387545	149387546	+	Intron	DEL	AA	-	-	rs3841102		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149387545_149387546delAA	uc003exh.2	-							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)			ACCAATCAAGAAAAAAAAATGA	0.243													4	2	---	---	---	---	
SELT	51714	broad.mit.edu	37	3	150340184	150340184	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150340184delT	uc011bnx.1	+	3	234	c.150delT	c.(148-150)GGTfs	p.G50fs		NM_016275	NP_057359	P62341	SELT_HUMAN	selenoprotein T precursor	50					cell redox homeostasis|selenocysteine incorporation		selenium binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTTCCTGAGGTTATAGGCGGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151865992	151865994	+	IGR	DEL	TCA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151865992_151865994delTCA								SUCNR1 (266342 upstream) : LOC401093 (114419 downstream)																							atttgccctttcattctttctct	0.039													2	4	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	172015272	172015273	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172015272_172015273insT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		ttccataagtgttttttttttg	0.000													5	3	---	---	---	---	
SPATA16	83893	broad.mit.edu	37	3	172736064	172736065	+	Intron	DEL	TT	-	-	rs72021279		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172736064_172736065delTT	uc003fin.3	-							NM_031955	NP_114161	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			ACAATGTCAAtttttttttttt	0.183													3	3	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174825298	174825301	+	Intron	DEL	ACAT	-	-	rs11921752		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174825298_174825301delACAT	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		acgaacacacacatacacacacac	0.020													1	5	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178546714	178546727	+	Intron	DEL	TGTGTGTGTGTGTG	-	-	rs9833033	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178546714_178546727delTGTGTGTGTGTGTG	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron|KCNMB2_uc011bqa.1_Intron|KCNMB2_uc011bqb.1_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			CCATGGTCACtgtgtgtgtgtgtgtgtgtgtgtg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180520234	180520235	+	Intron	INS	-	AA	AA	rs67834161		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180520234_180520235insAA	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																		cacacacacacacacaatgaaa	0.000													3	3	---	---	---	---	
SOX2OT	347689	broad.mit.edu	37	3	181368764	181368767	+	Intron	DEL	AGGA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181368764_181368767delAGGA	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0						ggaggaaaggaggaaggaaggaag	0.176													4	2	---	---	---	---	
KLHL24	54800	broad.mit.edu	37	3	183376597	183376598	+	Intron	INS	-	T	T	rs139060391		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183376597_183376598insT	uc003flv.2	+						KLHL24_uc003flw.2_Intron|KLHL24_uc003flx.2_Intron	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein							axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			ccttcctcccattttttttttt	0.000													4	2	---	---	---	---	
EPHB3	2049	broad.mit.edu	37	3	184283815	184283815	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184283815delG	uc003foz.2	+							NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TTGGGCAGCTGGGGGGGGTGA	0.582													4	2	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184661830	184661831	+	Intron	DEL	CA	-	-	rs111589895		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184661830_184661831delCA	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			gcagaggttgcacacacacaca	0.109													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186120363	186120364	+	IGR	INS	-	A	A	rs148047656	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186120363_186120364insA								DGKG (40340 upstream) : CRYGS (135869 downstream)																							tataataggataaaaaagaaga	0.000													4	2	---	---	---	---	
ST6GAL1	6480	broad.mit.edu	37	3	186784390	186784391	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186784390_186784391delGT	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron|ST6GAL1_uc003frd.2_Intron	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		gcgtgcgtgcgtgtgtgtgtgt	0.223													4	2	---	---	---	---	
LEPREL1	55214	broad.mit.edu	37	3	189804642	189804642	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189804642delC	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	caagtattttccccaaaagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195672006	195672006	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195672006delC								TNK2 (33190 upstream) : SDHAP1 (14786 downstream)																							atcagctcctccccgggtctg	0.000													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	61050	61051	+	Intron	INS	-	T	T	rs2362723		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61050_61051insT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ttctttttttcttttttttttt	0.045													6	5	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3223899	3223899	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3223899delG	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		catgtgtctcggacagtgcag	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3582206	3582207	+	Intron	DEL	TT	-	-	rs34752358		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3582206_3582207delTT	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		catccatccatttccatcctcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3582233	3582234	+	Intron	INS	-	GTTG	GTTG	rs4689994		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3582233_3582234insGTTG	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		tccatccatctgtccgtccatc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3628364	3628365	+	IGR	INS	-	C	C	rs144368206	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3628364_3628365insC								LRPAP1 (94140 upstream) : ADRA2C (139710 downstream)																							cctcagagccacgtgcttcctg	0.193													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4705715	4705715	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4705715delG	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																		CTGTGTGAGCGGTGCAGTCCG	0.532													4	2	---	---	---	---	
HMX1	3166	broad.mit.edu	37	4	8871595	8871595	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8871595delC	uc003izz.1	-							NM_018942	NP_061815	Q9NP08	HMX1_HUMAN	homeo box (H6 family) 1						multicellular organismal development|negative regulation of transcription, DNA-dependent		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						AGGGGATGCACCCCAGGGATG	0.587													4	2	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	16085683	16085683	+	5'Flank	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16085683delG	uc003gop.2	-						PROM1_uc003goq.3_5'Flank	NM_001145847	NP_001139319	O43490	PROM1_HUMAN	prominin 1 isoform 2						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						CCCGAGCCCTGGACGCACTCT	0.612													4	2	---	---	---	---	
SEL1L3	23231	broad.mit.edu	37	4	25804222	25804222	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25804222delG	uc003gru.3	-						SEL1L3_uc003grv.2_Intron	NM_015187	NP_056002	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3							integral to membrane	binding				0						Ctttttttttgagacggagcc	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26033293	26033294	+	IGR	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26033293_26033294delTG								C4orf52 (101793 upstream) : RBPJ (288038 downstream)																							TGTGCGTGCATGTGTGTGTGTG	0.178													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32277470	32277471	+	IGR	INS	-	G	G	rs146246949	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32277470_32277471insG								None (None upstream) : None (None downstream)																							caaataccattttttaggaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32496296	32496296	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32496296delT								None (None upstream) : None (None downstream)																							TAAGCCAACATAATGTGGGCT	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32780002	32780003	+	IGR	INS	-	C	C	rs72458410		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32780002_32780003insC								None (None upstream) : None (None downstream)																							cttctttctttttctttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	36403572	36403572	+	IGR	DEL	T	-	-	rs34598840		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36403572delT								DTHD1 (57614 upstream) : MIR1255B-1 (24416 downstream)																							gataatggcctctagctgcat	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38756323	38756326	+	IGR	DEL	CACA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38756323_38756326delCACA								KLF3 (53195 upstream) : TLR10 (17937 downstream)																							acacactctgcacacacacacaca	0.142													4	2	---	---	---	---	
TMEM156	80008	broad.mit.edu	37	4	38969639	38969639	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38969639delC	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219	Q8N614	TM156_HUMAN	transmembrane protein 156							integral to membrane				skin(1)	1						tataagagttcccAAAGTTGG	0.229													4	2	---	---	---	---	
N4BP2	55728	broad.mit.edu	37	4	40059067	40059067	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40059067delT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron|LOC344967_uc011byr.1_5'Flank	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						AGGCGGAGCCTTCTGGGAACT	0.587													4	2	---	---	---	---	
COX7B2	170712	broad.mit.edu	37	4	46770371	46770383	+	Intron	DEL	TCTAGCTGCTTCT	-	-	rs113702381		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46770371_46770383delTCTAGCTGCTTCT	uc003gxf.2	-						COX7B2_uc010ige.2_Intron	NM_130902	NP_570972	Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2 precursor							integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						gtctccaatatctagctgcttcttctcctctcg	0.000													3	4	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47365045	47365046	+	Intron	INS	-	TC	TC	rs71654871		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47365045_47365046insTC	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	GCgtgtgtgtgtgtgtgtgtgt	0.173													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	48458664	48458665	+	IGR	INS	-	CA	CA			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48458664_48458665insCA								SLAIN2 (30451 upstream) : SLC10A4 (26695 downstream)																							acacacacactcacacacacac	0.000													9	4	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48784901	48784904	+	5'Flank	DEL	CACA	-	-	rs67213172		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48784901_48784904delCACA	uc003gyh.1	-						FRYL_uc003gyk.2_5'Flank|FRYL_uc003gym.1_5'Flank|FRYL_uc003gyn.3_5'Flank	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						ctcactctgtcacacacacacaca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49094343	49094347	+	IGR	DEL	TGTTG	-	-	rs150471087		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49094343_49094347delTGTTG								CWH43 (30250 upstream) : None (None downstream)																							cattccgttctgttgcattccattc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49168321	49168322	+	IGR	INS	-	T	T	rs144632279	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49168321_49168322insT								CWH43 (104228 upstream) : None (None downstream)																							ATTGTTTTGGGTTCTGGTTTTA	0.446													17	9	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54872827	54872827	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54872827delA	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	agactgtctcaaaaaaaaaaa	0.159			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57741333	57741334	+	IGR	INS	-	A	A	rs139534083	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57741333_57741334insA								SPINK2 (53440 upstream) : REST (32708 downstream)																							aatcgcatgccaaaaaacgatc	0.000													2	7	---	---	---	---	
EPHA5	2044	broad.mit.edu	37	4	66331306	66331306	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66331306delA	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						gaaggaaaggaaagaaaggaa	0.154										TSP Lung(17;0.13)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72812386	72812387	+	IGR	INS	-	G	G	rs138550147	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72812386_72812387insG								GC (142628 upstream) : NPFFR2 (85134 downstream)																							TGGTCATCATTCCTCTGCTTCA	0.218													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	76213005	76213005	+	IGR	DEL	A	-	-	rs33945617		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76213005delA								PARM1 (237682 upstream) : RCHY1 (191350 downstream)																							ACCTCAAAGCAACACCAAATA	0.353													4	2	---	---	---	---	
SEPT11	55752	broad.mit.edu	37	4	77914212	77914214	+	Intron	DEL	TAT	-	-	rs3070493		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77914212_77914214delTAT	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						AGGGAGGAAGTATTAGAGAGGGT	0.463													3	5	---	---	---	---	
UNC5C	8633	broad.mit.edu	37	4	96178606	96178607	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96178606_96178607insA	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		GAGACAGGGAGAAAAAAAAAAT	0.297													4	2	---	---	---	---	
ADH5	128	broad.mit.edu	37	4	99995851	99995852	+	Intron	INS	-	AGG	AGG	rs148777339	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99995851_99995852insAGG	uc003hui.2	-						ADH5_uc003huj.2_Intron	NM_000671	NP_000662	P11766	ADHX_HUMAN	class III alcohol dehydrogenase, chi subunit						ethanol oxidation|response to redox state		alcohol dehydrogenase (NAD) activity|electron carrier activity|fatty acid binding|formaldehyde dehydrogenase activity|S-(hydroxymethyl)glutathione dehydrogenase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)	NADH(DB00157)	TCCTATGTTTCAGGTGAGCACC	0.411													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104189732	104189732	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104189732delG								CENPE (70166 upstream) : TACR3 (320893 downstream)																							gagggtccttggttgtgtttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117386467	117386468	+	IGR	INS	-	T	T	rs149991976	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117386467_117386468insT								MIR1973 (165543 upstream) : TRAM1L1 (618248 downstream)																							tccctggtgaatttttttgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120864976	120864977	+	IGR	INS	-	CTAA	CTAA	rs145044684	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120864976_120864977insCTAA								PDE5A (314995 upstream) : MAD2L1 (115602 downstream)																							TAAACGCTCGTCTATCCCCTGT	0.470													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122045969	122045970	+	IGR	INS	-	GA	GA	rs150229287	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122045969_122045970insGA								C4orf31 (52296 upstream) : TNIP3 (6596 downstream)																							agagagggagggagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	131185835	131185835	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131185835delC								None (None upstream) : None (None downstream)																							atgtaattatctaccgctcct	0.000													4	2	---	---	---	---	
CCRN4L	25819	broad.mit.edu	37	4	139956284	139956284	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139956284delT	uc003ihl.2	+						CCRN4L_uc003ihk.1_Intron	NM_012118	NP_036250	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like						rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)					actgtggacatttttttttta	0.005													4	2	---	---	---	---	
SCOC	60592	broad.mit.edu	37	4	141219406	141219406	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141219406delA	uc003iib.2	+						uc003iic.1_Intron	NM_032547	NP_115936	Q9UIL1	SCOC_HUMAN	short coiled-coil protein isoform 4							Golgi apparatus|nucleus	protein binding				0	all_hematologic(180;0.162)					tctctctctcagctacttcca	0.164													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143650666	143650667	+	Intron	INS	-	GAGT	GAGT	rs150450592	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143650666_143650667insGAGT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					atatagcagtggaaaaaggaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144220397	144220398	+	IGR	INS	-	C	C	rs147288013	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144220397_144220398insC								USP38 (77257 upstream) : GAB1 (37585 downstream)																							TTCTAAGACATCCCCCTCCTCT	0.446													3	3	---	---	---	---	
SMAD1	4086	broad.mit.edu	37	4	146420644	146420644	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146420644delT	uc003ikc.2	+						SMAD1_uc003ikd.2_Intron|SMAD1_uc010iov.2_Intron|uc003ike.2_Intron	NM_005900	NP_005891	Q15797	SMAD1_HUMAN	Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)					gagatggcacttgcccgtagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152259433	152259434	+	IGR	INS	-	T	T	rs141667646		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152259433_152259434insT								PRSS48 (46830 upstream) : FAM160A1 (70964 downstream)																							TTCTTTCTTtcttttttttttt	0.084													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154391182	154391182	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154391182delT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				TGATTAAGTCTTTTTTTTTTT	0.239													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157943040	157943040	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157943040delC								PDGFC (50494 upstream) : GLRB (54237 downstream)																							agagcagtagcaaaagaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	159669583	159669583	+	IGR	DEL	A	-	-	rs143774818		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159669583delA								PPID (25031 upstream) : FNIP2 (20599 downstream)																							acagcagcacaaaatggacta	0.000													4	4	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166835175	166835175	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166835175delA	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		ccttgtctccaaaaaaaaaaa	0.159													4	2	---	---	---	---	
GALNT7	51809	broad.mit.edu	37	4	174103889	174103890	+	Intron	INS	-	AC	AC	rs145116026	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174103889_174103890insAC	uc003isz.3	+							NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TTACTCTTAATacacacacaca	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174597314	174597315	+	IGR	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174597314_174597315delGA								MORF4 (59520 upstream) : FBXO8 (560497 downstream)																							caatctaagtgagagatgatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174630942	174630943	+	IGR	INS	-	AC	AC	rs139492186	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174630942_174630943insAC								MORF4 (93148 upstream) : FBXO8 (526869 downstream)																							gagtctacattacacacacaca	0.025													3	3	---	---	---	---	
GPM6A	2823	broad.mit.edu	37	4	176670363	176670363	+	Intron	DEL	G	-	-	rs34314997		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176670363delG	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		ccaaaaaaaaggtaatggcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182707851	182707851	+	IGR	DEL	T	-	-	rs146629166		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182707851delT								None (None upstream) : MGC45800 (352308 downstream)																							agacaatcacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190553383	190553386	+	IGR	DEL	AAAT	-	-	rs139151429		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190553383_190553386delAAAT								None (None upstream) : FRG1 (308588 downstream)																							aaaaaaaaaaaaaTGTTTATGTTG	0.186													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190567252	190567252	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190567252delG								None (None upstream) : FRG1 (294722 downstream)																							GGAGCGTGGCGGGGTGAACAG	0.657													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190598323	190598334	+	IGR	DEL	TGTGTGAAGTAT	-	-	rs72391922	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190598323_190598334delTGTGTGAAGTAT								None (None upstream) : FRG1 (263640 downstream)																							GTCAGGGTGCTGTGTGAAGTATTTTCATGTGT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1044767	1044770	+	IGR	DEL	TGAG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1044767_1044770delTGAG								NKD2 (5842 upstream) : SLC12A7 (5721 downstream)																							agtgtgtgaatgagtgagttcgtg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1140613	1140613	+	IGR	DEL	G	-	-	rs5865347		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1140613delG								SLC12A7 (28441 upstream) : SLC6A19 (61097 downstream)																							CTGCTGGTGAGGGGGGGTGCT	0.652											OREG0016477	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2531556	2531559	+	IGR	DEL	CACA	-	-	rs72185116		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2531556_2531559delCACA								IRX4 (648676 upstream) : IRX2 (214722 downstream)																							cacaaaagcgcacacacacacaca	0.054													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2894884	2894885	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2894884_2894885insT								C5orf38 (139372 upstream) : IRX1 (701283 downstream)																							AACATGGAGTGTTTTTTTTTTA	0.386													4	2	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5305440	5305441	+	Intron	INS	-	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5305440_5305441insC	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						cacacacacatccacaccacac	0.000													7	4	---	---	---	---	
PAPD7	11044	broad.mit.edu	37	5	6722819	6722820	+	Intron	INS	-	T	T	rs139998975	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6722819_6722820insT	uc003jdx.1	+							NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma						cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1						GTTGGTTAAGGTTTTTTTATTT	0.381													1	5	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7439906	7439906	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7439906delG	uc003jdz.1	+							NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						TGTCATGGATGAGGATGGAGA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7937555	7937556	+	IGR	INS	-	A	A	rs138668045	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7937555_7937556insA								MTRR (36322 upstream) : None (None downstream)																							accacaaggtcaggagatcgag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7979186	7979187	+	IGR	INS	-	T	T	rs11348245		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7979186_7979187insT								MTRR (77953 upstream) : None (None downstream)																							tttcttttttcttttttttttt	0.243													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8328684	8328685	+	IGR	INS	-	AA	AA			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8328684_8328685insAA								MTRR (427451 upstream) : SEMA5A (706453 downstream)																							TTTTTCTACTGAAAAAAAAAAA	0.312													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9178459	9178460	+	Intron	DEL	TG	-	-	rs57508382		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9178459_9178460delTG	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						tttttttttttgttgagatgga	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	9561094	9561095	+	IGR	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9561094_9561095delGT								SNORD123 (12068 upstream) : TAS2R1 (68014 downstream)																							CAGTGTAGAAgtgtgtgtgtgt	0.144													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10530902	10530903	+	IGR	DEL	GT	-	-	rs111992505		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10530902_10530903delGT								ROPN1L (65765 upstream) : DAP (148440 downstream)																							gtgtatgtccgtgtgtgtgtgt	0.183													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10648273	10648274	+	IGR	INS	-	GT	GT	rs140031407	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10648273_10648274insGT								ROPN1L (183136 upstream) : DAP (31069 downstream)																							CAGGATGAAACGTGTTGAGCAA	0.475													3	3	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14197413	14197413	+	Intron	DEL	T	-	-	rs71599603		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14197413delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.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)					ATCGAGGTGCTTCCTgtctgt	0.323													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14660957	14660957	+	IGR	DEL	T	-	-	rs79969140		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14660957delT								FAM105A (44672 upstream) : FAM105B (3826 downstream)																							tgtgtgtgtgtttttttttgg	0.000													4	3	---	---	---	---	
ANKH	56172	broad.mit.edu	37	5	14795967	14795967	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14795967delA	uc003jfm.3	-							NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1						actgtgtctcaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15370435	15370435	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15370435delT								ANKH (498548 upstream) : FBXL7 (129870 downstream)																							TTTTGTTTCATTTTTTTTTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28701784	28701785	+	IGR	DEL	CA	-	-	rs35481494	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28701784_28701785delCA								None (None upstream) : None (None downstream)																							cgcgcgcgcgcacacacacaca	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31137085	31137086	+	IGR	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31137085_31137086delGT								None (None upstream) : CDH6 (56710 downstream)																							AGTCgtgtgcgtgtgtgtgtgt	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	37086022	37086022	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37086022delA								NIPBL (20102 upstream) : C5orf42 (20308 downstream)																							AATTAATAGGAAAAAAAAaaa	0.204													6	3	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37430771	37430771	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37430771delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			taagcgattctcccacctcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40025219	40025220	+	IGR	INS	-	T	T	rs142234609	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40025219_40025220insT								DAB2 (599884 upstream) : PTGER4 (654812 downstream)																							gtgttgagagggagatctttaa	0.079													0	6	---	---	---	---	
TTC33	23548	broad.mit.edu	37	5	40753871	40753871	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40753871delT	uc003jma.2	-						TTC33_uc011cpm.1_Intron|TTC33_uc010ivg.2_Intron	NM_012382	NP_036514	Q6PID6	TTC33_HUMAN	tetratricopeptide repeat domain 33								binding			ovary(1)	1						GATGACCACGTTTTCCGGTTT	0.373													4	2	---	---	---	---	
CCDC152	100129792	broad.mit.edu	37	5	42757983	42757983	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42757983delA	uc003jmx.3	+						CCDC152_uc011cpr.1_Intron	NM_001134848	NP_001128320	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152												0						GTTAGGTACCAAAAAAAAAAG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42852049	42852049	+	IGR	DEL	T	-	-	rs71608670		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42852049delT								SEPP1 (26051 upstream) : C5orf39 (187134 downstream)																							TGAttttttcttttttttttt	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42939469	42939470	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42939469_42939470insT								SEPP1 (113471 upstream) : C5orf39 (99713 downstream)																							ttttctttacattttttttttt	0.040													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42963878	42963878	+	IGR	DEL	T	-	-	rs71608676		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42963878delT								SEPP1 (137880 upstream) : C5orf39 (75305 downstream)																							catggggtacttagggtagtc	0.000													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43047000	43047001	+	IGR	INS	-	GTGT	GTGT	rs35430600		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43047000_43047001insGTGT								LOC153684 (1630 upstream) : ZNF131 (73984 downstream)																							CTTCTAATGTAgtgtgtgtgtg	0.292													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43096084	43096084	+	IGR	DEL	G	-	-	rs139827310		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43096084delG								LOC153684 (50714 upstream) : ZNF131 (24901 downstream)																							TTTATCACGTGGGCAAAAACA	0.488													6	3	---	---	---	---	
SLC38A9	153129	broad.mit.edu	37	5	54998255	54998256	+	Intron	INS	-	T	T	rs113500611		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54998255_54998256insT	uc003jqf.2	-						SLC38A9_uc010ivy.2_Intron	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9						amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				atgcctggctattttttttttt	0.000													4	2	---	---	---	---	
ZSWIM6	57688	broad.mit.edu	37	5	60789974	60789975	+	Intron	DEL	GA	-	-	rs76684030		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60789974_60789975delGA	uc003jsr.2	+							NM_020928	NP_065979	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6								zinc ion binding				0						cacacacacGGAGAGAGAGAGA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	78652390	78652391	+	IGR	INS	-	T	T	rs111340488		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78652390_78652391insT								JMY (29354 upstream) : HOMER1 (17396 downstream)																							ttggttttttgttttttttttt	0.000													4	2	---	---	---	---	
RASA1	5921	broad.mit.edu	37	5	86679568	86679570	+	In_Frame_Del	DEL	TGA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86679568_86679570delTGA	uc003kiw.2	+	21	2847_2849	c.2729_2731delTGA	c.(2728-2733)CTGAAT>CAT	p.910_911LN>H	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_In_Frame_Del_p.733_734LN>H|RASA1_uc011ctv.1_In_Frame_Del_p.743_744LN>H|RASA1_uc011ctw.1_In_Frame_Del_p.744_745LN>H|RASA1_uc010jaw.2_In_Frame_Del_p.732_733LN>H	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	910_911	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCTGCCATCCTGAATCCACGGAT	0.296													16	9	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93261838	93261839	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93261838_93261839insT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						ATTTCCAAttcttttttttttt	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97654130	97654130	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97654130delG								None (None upstream) : RGMB (450869 downstream)																							GCTCCACACTGGTAATCTGTA	0.423													4	2	---	---	---	---	
LOC100133050	100133050	broad.mit.edu	37	5	99723843	99723844	+	Intron	INS	-	A	A	rs142327905	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99723843_99723844insA	uc011cuw.1	-						uc011cux.1_5'Flank|uc011cuy.1_5'Flank|uc003knh.2_5'Flank	NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGGAGAGCAGGAATCTTCAGTG	0.347													4	3	---	---	---	---	
TRIM36	55521	broad.mit.edu	37	5	114509220	114509221	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114509220_114509221delTG	uc003kqs.2	-						TRIM36_uc003kqt.2_Intron|TRIM36_uc003kqu.2_Intron	NM_018700	NP_061170	Q9NQ86	TRI36_HUMAN	tripartite motif-containing 36 isoform 1							acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding			ovary(4)|lung(2)|breast(2)	8		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		tgtatttgaatgtgtgtgtgtg	0.381													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119075685	119075686	+	IGR	INS	-	GT	GT	rs147608906	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119075685_119075686insGT								FAM170A (104169 upstream) : PRR16 (724333 downstream)																							ACAGAGTCAGGgtgtgtgtgtg	0.282													4	2	---	---	---	---	
PRR16	51334	broad.mit.edu	37	5	119805192	119805192	+	Intron	DEL	T	-	-	rs112912445		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119805192delT	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		taatttttaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123377707	123377707	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123377707delT								CSNK1G3 (425245 upstream) : ZNF608 (594903 downstream)																							catgctggccttccatgcccc	0.000													1	6	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127741038	127741038	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127741038delA	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACAATGAGGGAAATACAAGTG	0.438													4	2	---	---	---	---	
CHSY3	337876	broad.mit.edu	37	5	129283315	129283315	+	Intron	DEL	A	-	-	rs113595769		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129283315delA	uc003kvd.2	+							NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133976680	133976683	+	IGR	DEL	AAAA	-	-	rs35509090		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133976680_133976683delAAAA								SAR1B (8153 upstream) : SEC24A (7796 downstream)																							agactccgtcaaaaaaaaaaaaag	0.000													4	2	---	---	---	---	
DDX46	9879	broad.mit.edu	37	5	134153642	134153642	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134153642delT	uc003kzw.2	+							NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTGtttgttgttttttttttt	0.129													4	2	---	---	---	---	
TCERG1	10915	broad.mit.edu	37	5	145833987	145833988	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145833987_145833988insT	uc003lob.2	+						TCERG1_uc003loc.2_Intron|TCERG1_uc011dbt.1_Intron	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tatgtagagtgttttttttttc	0.000													4	2	---	---	---	---	
CAMK2A	815	broad.mit.edu	37	5	149670802	149670802	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149670802delT	uc003lru.2	-						CAMK2A_uc003lrt.2_5'Flank|CAMK2A_uc010jhe.2_5'Flank	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			agtgctaggattacaggtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153519981	153519981	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153519981delT								MFAP3 (82967 upstream) : GALNT10 (50314 downstream)																							CTTCAACTCCTACAGCCTCAG	0.498													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154287016	154287017	+	Intron	INS	-	GAAAAAAAA	GAAAAAAAA	rs145860358	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154287016_154287017insGAAAAAAAA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GAATAAAGCTTAACAAAAAAAA	0.356													2	4	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160855295	160855298	+	Intron	DEL	GTGT	-	-	rs71302909		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160855295_160855298delGTGT	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	agagagttacgtgtgtgtgtgtgt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164231021	164231022	+	IGR	INS	-	CA	CA	rs144381927	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164231021_164231022insCA								None (None upstream) : None (None downstream)																							TCTATCATCACcacacacacac	0.282													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165557698	165557698	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165557698delT								None (None upstream) : None (None downstream)																							ctttcatatctttaggtagag	0.204													4	2	---	---	---	---	
LOC257358	257358	broad.mit.edu	37	5	169757207	169757207	+	5'Flank	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169757207delC	uc011deu.1	+							NR_026945				Homo sapiens cDNA FLJ36406 fis, clone THYMU2010059.												0						tgtgatgagtcccaaatgata	0.000													2	4	---	---	---	---	
DOK3	79930	broad.mit.edu	37	5	176934190	176934190	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176934190delT	uc003mhk.2	-						DOK3_uc003mhh.3_Intron|DOK3_uc003mhi.3_Intron|DOK3_uc003mhj.3_Intron|DOK3_uc003mhl.2_Intron	NM_024872	NP_079148	Q7L591	DOK3_HUMAN	docking protein 3 isoform 1							cytoplasm|plasma membrane	insulin receptor binding				0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TCTTCttttcttttttttttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177407561	177407562	+	IGR	INS	-	GT	GT	rs147148558	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177407561_177407562insGT								LOC728554 (96294 upstream) : PROP1 (11674 downstream)																							TTTCTCCCTGGGTGTGTGTGTG	0.332													4	2	---	---	---	---	
ADAMTS2	9509	broad.mit.edu	37	5	178636628	178636638	+	Intron	DEL	TCCAGGGCCAC	-	-	rs113459243		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178636628_178636638delTCCAGGGCCAC	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GCAAGGACTTTCCAGGGCCACTCCAGGGACA	0.389													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179898863	179898863	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179898863delG								GFPT2 (118548 upstream) : CNOT6 (22554 downstream)																							ACAGGCCCGTGGGTCCCTAAC	0.403											OREG0016463	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
DUSP22	56940	broad.mit.edu	37	6	298881	298882	+	Intron	INS	-	GAAAGTAAG	GAAAGTAAG	rs139030879	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:298881_298882insGAAAGTAAG	uc003msx.2	+						DUSP22_uc011dhn.1_Intron	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		aagatcagtccgaaagtaagga	0.005													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1738924	1738927	+	Intron	DEL	TTAA	-	-	rs68060378		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1738924_1738927delTTAA	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GCTTTCTAGCTTAATTAATGGCAA	0.441													3	3	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1772218	1772219	+	Intron	INS	-	TGTAA	TGTAA	rs144564060	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1772218_1772219insTGTAA	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GAAGGTTTTTGTGTAATTTCCA	0.411													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3529126	3529127	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3529126_3529127insA								SLC22A23 (72333 upstream) : C6orf145 (193709 downstream)																							CTTATTTTTCTAAATGTTATCA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4356493	4356506	+	IGR	DEL	TGTGTGTGTGTGTG	-	-	rs112742652		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4356493_4356506delTGTGTGTGTGTGTG								PECI (220662 upstream) : CDYL (349887 downstream)																							agtattccattgtgtgtgtgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5049907	5049907	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5049907delT	uc003mwn.1	+											Homo sapiens cDNA FLJ37615 fis, clone BRCOC2011996.																		GGCAGTGTCAttttttttttt	0.080													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5853543	5853544	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5853543_5853544delAC								FARS2 (81727 upstream) : NRN1 (144691 downstream)																							taagccaccaacagtctgtggt	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7496884	7496884	+	IGR	DEL	G	-	-	rs11291955		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7496884delG								RIOK1 (78616 upstream) : DSP (44986 downstream)																							TCGAGTACGTGGAAGGACGTG	0.512													3	4	---	---	---	---	
GCNT2	2651	broad.mit.edu	37	6	10589123	10589124	+	Intron	INS	-	GTGTGTGTTGT	GTGTGTGTTGT	rs78524222	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10589123_10589124insGTGTGTGTTGT	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron|GCNT2_uc003mze.2_Intron	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		gtgtttgtagcgtgtgtgttgt	0.000													4	2	---	---	---	---	
RANBP9	10048	broad.mit.edu	37	6	13700720	13700723	+	Intron	DEL	GTAG	-	-	rs3831512		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13700720_13700723delGTAG	uc003nbb.2	-							NM_005493	NP_005484	Q96S59	RANB9_HUMAN	RAN binding protein 9						axon guidance|microtubule nucleation|protein complex assembly	cytosol|microtubule associated complex|nucleus	Ran GTPase binding			lung(1)|skin(1)	2	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			cttagcctgagtaggtaggtccta	0.000													6	5	---	---	---	---	
JARID2	3720	broad.mit.edu	37	6	15288541	15288542	+	Intron	INS	-	GGG	GGG	rs148026471	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15288541_15288542insGGG	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				aggtgggggttggagaaaaggg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18565945	18565946	+	Intron	INS	-	TTCC	TTCC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18565945_18565946insTTCC	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																		tccttccttcttgccttccttc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20017190	20017192	+	IGR	DEL	AAC	-	-	rs66465759		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20017190_20017192delAAC								ID4 (176276 upstream) : MBOAT1 (83743 downstream)																							GGGTTTTTCAAACAACAACAACA	0.355													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27244231	27244232	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27244231_27244232insT								PRSS16 (19982 upstream) : POM121L2 (32610 downstream)																							ttttcttttgcttttttttttt	0.094													4	2	---	---	---	---	
NCRNA00171	80862	broad.mit.edu	37	6	29982016	29982016	+	Intron	DEL	A	-	-	rs67161103		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29982016delA	uc011dme.1	-						uc011dmf.1_5'Flank	NR_026751				Homo sapiens clone HTEX4 mRNA, complete sequence.												0						AAATAACATCAAAAAAAACCA	0.373													1	5	---	---	---	---	
NCRNA00171	80862	broad.mit.edu	37	6	30024686	30024687	+	3'UTR	INS	-	A	A	rs145679846	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30024686_30024687insA	uc003rto.2	-	3					NCRNA00171_uc011dme.1_Intron|NCRNA00171_uc003nox.1_Intron					RecName: Full=Uncharacterized protein C6orf12; AltName: Full=Protein HTEX4;												0						ACGAGCATTTGAAAAAAAAAAG	0.312													4	2	---	---	---	---	
PSORS1C1	170679	broad.mit.edu	37	6	31107683	31107683	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31107683delC	uc003nsl.1	+	6	707	c.433delC	c.(433-435)CCTfs	p.P145fs	PSORS1C1_uc010jsj.1_Frame_Shift_Del_p.P94fs|PSORS1C1_uc003nsn.1_RNA|PSORS1C2_uc003nso.3_5'Flank	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein	145										ovary(1)	1						CTCCCATTCTCCTTTTGGTCT	0.448													68	38	---	---	---	---	
PACSIN1	29993	broad.mit.edu	37	6	34494236	34494236	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34494236delC	uc003ojo.2	+						PACSIN1_uc003ojp.2_Intron	NM_020804	NP_065855	Q9BY11	PACN1_HUMAN	protein kinase C and casein kinase substrate in						endocytosis		protein kinase activity				0						TGACCTCAGGCCCCACTCCGC	0.632													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34534550	34534551	+	IGR	INS	-	AAAC	AAAC	rs138100073	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34534550_34534551insAAAC								SPDEF (10459 upstream) : C6orf106 (20515 downstream)																							tcttaaataataaacaaacaaa	0.198													2	4	---	---	---	---	
ETV7	51513	broad.mit.edu	37	6	36347338	36347340	+	Intron	DEL	AAG	-	-	rs112110754		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36347338_36347340delAAG	uc003omb.2	-						ETV7_uc003olz.1_Intron|ETV7_uc003oma.1_Intron|ETV7_uc010jwg.2_Intron|ETV7_uc003omc.2_Intron|ETV7_uc010jwj.2_Intron|ETV7_uc010jwh.2_Intron|ETV7_uc010jwi.2_Intron|ETV7_uc011dtl.1_Intron	NM_016135	NP_057219	Q9Y603	ETV7_HUMAN	ets variant 7						organ morphogenesis|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						aaaaaaaaaaaagaagaagaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41418539	41418540	+	IGR	DEL	CA	-	-	rs67022603		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41418539_41418540delCA								NCR2 (99914 upstream) : FOXP4 (95624 downstream)																							GCAGCGCGCGcacacacacaca	0.495													4	2	---	---	---	---	
PTK7	5754	broad.mit.edu	37	6	43045225	43045225	+	Intron	DEL	C	-	-	rs2152049		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43045225delC	uc003oub.1	+						PTK7_uc003ouc.1_Intron|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_Intron|PTK7_uc011dve.1_Intron|PTK7_uc003oua.2_Intron	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a						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)			GACAGCACCGCCCCCCCAACT	0.547													4	2	---	---	---	---	
CRISP1	167	broad.mit.edu	37	6	49815176	49815177	+	Intron	DEL	CT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49815176_49815177delCT	uc003ozw.2	-						CRISP1_uc003ozx.2_Intron	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1						fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					caccccccaactctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49927996	49927996	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49927996delC								CRISP1 (93778 upstream) : DEFB114 (10 downstream)																							CAGAGGTATGCCTTTCTTTTC	0.328													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49950146	49950147	+	IGR	DEL	TC	-	-	rs112250956		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49950146_49950147delTC								DEFB113 (12808 upstream) : DEFB110 (26706 downstream)																							tgtgtgtgtgtctgtctgtctg	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50896318	50896318	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50896318delC								TFAP2B (80993 upstream) : PKHD1 (583827 downstream)																							ATTGATAACTCCATTGTGATT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	51163187	51163187	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51163187delC								TFAP2B (347862 upstream) : PKHD1 (316958 downstream)																							TTTCCAAGTTCTCCAGCTGCT	0.428													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51603719	51603720	+	Intron	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51603719_51603720delAC	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					tgcacacaagacACACACACAC	0.163													4	2	---	---	---	---	
TRAM2	9697	broad.mit.edu	37	6	52412822	52412822	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52412822delG	uc003paq.2	-							NM_012288	NP_036420	Q15035	TRAM2_HUMAN	translocation-associated membrane protein 2						collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding				0	Lung NSC(77;0.109)					TGTGCACAAAGCTGGCTGGTA	0.353													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57257973	57257974	+	Intron	INS	-	GTG	GTG	rs140385725	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57257973_57257974insGTG	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)		gatacccagtagtgttgctgga	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57402588	57402589	+	Intron	INS	-	GG	GG	rs78846932		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402588_57402589insGG	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)		TGTTGttttttttttttttttt	0.040													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404370	57404371	+	Intron	INS	-	A	A	rs139203387		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404370_57404371insA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		aaagaaacacgaaaagcagctc	0.104													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57474418	57474419	+	Intron	INS	-	AA	AA	rs143951527		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57474418_57474419insAA	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)		ATAACCTTTTCAAAAAATGTGT	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57608402	57608403	+	IGR	INS	-	GGA	GGA	rs146024593	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57608402_57608403insGGA								PRIM2 (95027 upstream) : GUSBL2 (637756 downstream)																							GTGGGGTGGATGGAGGAGATTT	0.411													2	4	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69709159	69709159	+	Intron	DEL	T	-	-	rs66662357		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69709159delT	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				TTCCCttttcttttttttttt	0.174													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69810856	69810859	+	Intron	DEL	AGAA	-	-	rs117995213	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69810856_69810859delAGAA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ggagggagggagaaagggaaggaa	0.157													4	2	---	---	---	---	
C6orf150	115004	broad.mit.edu	37	6	74152127	74152128	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74152127_74152128insT	uc003pgx.1	-							NM_138441	NP_612450	Q8N884	M21D1_HUMAN	hypothetical protein LOC115004												0						CCAGCCCAAACttttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	74225083	74225083	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74225083delT								MTO1 (13906 upstream) : EEF1A1 (392 downstream)																							agcacatgggttcttccttga	0.234													4	2	---	---	---	---	
KLHL32	114792	broad.mit.edu	37	6	97416987	97416987	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97416987delC	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		ccttactacacccccagggcc	0.000													4	2	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97615908	97615908	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97615908delT	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		AGTTTCAATATTTTTTTTTTA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	111815543	111815543	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111815543delT	uc003pvb.2	+											Homo sapiens cDNA clone IMAGE:5274708.																		ATGTGGTTGATTTTTTTTTTT	0.259													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115632674	115632675	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115632674_115632675insT								HS3ST5 (969134 upstream) : FRK (630018 downstream)																							ttctttctttctttctttcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115721659	115721659	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115721659delA								None (None upstream) : FRK (541034 downstream)																							gtctccactgaaaaaaaaata	0.000													4	2	---	---	---	---	
FAM184A	79632	broad.mit.edu	37	6	119427970	119427970	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119427970delA	uc003pyk.3	-						FAM184A_uc003pyl.3_Intron	NM_001100411	NP_001093881	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 2											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						tttggGAGGTAAGGTTTATTT	0.179													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124165406	124165406	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124165406delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		ATTCTGGCAGAGGGAACCAGA	0.299													4	2	---	---	---	---	
ARHGAP18	93663	broad.mit.edu	37	6	129945205	129945205	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129945205delA	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050	Q8N392	RHG18_HUMAN	Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		AACAGAGAAGAAAATGGCAGA	0.353													4	2	---	---	---	---	
MIR548A2	693126	broad.mit.edu	37	6	135557691	135557697	+	5'Flank	DEL	CCTTCTT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135557691_135557697delCCTTCTT	hsa-mir-548a-2|MI0003598	+																							0						tccttccctcccttcttccttcttcct	0.101													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	137662638	137662639	+	IGR	DEL	TG	-	-	rs10542869		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137662638_137662639delTG								IFNGR1 (122071 upstream) : OLIG3 (150697 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.272													5	3	---	---	---	---	
GRM1	2911	broad.mit.edu	37	6	146453957	146453957	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146453957delT	uc010khw.1	+						GRM1_uc010khu.1_Intron|GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	CAATCATTCCTTTGCAGGTCT	0.428													4	2	---	---	---	---	
ESR1	2099	broad.mit.edu	37	6	152308068	152308069	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152308068_152308069delGT	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Intron|ESR1_uc010kit.1_Intron|ESR1_uc011eey.1_Intron	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	acgcgagcacgtgtgtgtgtgt	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156815448	156815449	+	IGR	INS	-	TC	TC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156815448_156815449insTC								MIR1202 (547435 upstream) : ARID1B (283637 downstream)																							gtgtgtgtgtgtgtgtgtgtgt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158669306	158669306	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158669306delT								GTF2H5 (48940 upstream) : TULP4 (64386 downstream)																							aggcctcgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160319564	160319565	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160319564_160319565insT								PNLDC1 (77829 upstream) : MAS1 (8409 downstream)																							tcttcctcctcctccctcctcc	0.129													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166546300	166546307	+	IGR	DEL	GAGGGAGA	-	-	rs151120335		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166546300_166546307delGAGGGAGA								LOC441177 (143197 upstream) : T (24779 downstream)																							gagaaggggggagggagagagggaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166712168	166712168	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166712168delT								T (130037 upstream) : PRR18 (7000 downstream)																							CCAAAGTAGATTTGCAGGGAT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167898565	167898565	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167898565delA								TCP10 (100567 upstream) : C6orf123 (286656 downstream)																							ccaaaaaaagaaaaaaaaaaC	0.159													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169266055	169266058	+	IGR	DEL	AGTC	-	-	rs149293158		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169266055_169266058delAGTC								SMOC2 (197384 upstream) : THBS2 (349818 downstream)																							AGGAtatattagtcagggttctct	0.157													3	3	---	---	---	---	
FAM120B	84498	broad.mit.edu	37	6	170707740	170707741	+	Intron	DEL	CT	-	-	rs67356832		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170707740_170707741delCT	uc003qxp.2	+						FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B						cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TATGTCATAACTCTTAGGAGTG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	326057	326057	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:326057delA								FAM20C (25346 upstream) : PDGFA (210842 downstream)																							GGCCGTCGGGAAAGGCGTTTT	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	518871	518871	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:518871delA								FAM20C (218160 upstream) : PDGFA (18028 downstream)																							aggaggagggaaggagggaag	0.000													8	4	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	652495	652496	+	Intron	INS	-	TG	TG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:652495_652496insTG	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)		CACTGAAAAGATGTGTGTGTGT	0.342													4	3	---	---	---	---	
GET4	51608	broad.mit.edu	37	7	930048	930052	+	Intron	DEL	AGGAC	-	-	rs72198888		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:930048_930052delAGGAC	uc003sjl.1	+						GET4_uc003sjj.1_Intron	NM_015949	NP_057033	Q7L5D6	GET4_HUMAN	hypothetical protein LOC51608						tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	protein binding				0						AGCGGGTGTTAGGACGGGCCTGGGA	0.639													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	982855	982856	+	Intron	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:982855_982856delAG	uc003sjo.3	-						ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aggaggaggaagagagaggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1697870	1697870	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1697870delT								TFAMP1 (41543 upstream) : ELFN1 (50928 downstream)																							agatggacccttacctcacac	0.000													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3800392	3800392	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3800392delT	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		gacttttccgtttttgccttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6339472	6339473	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6339472_6339473insA								CYTH3 (27230 upstream) : C7orf70 (29568 downstream)																							acactgtctccaaaaaaaaaaa	0.074													4	2	---	---	---	---	
ICA1	3382	broad.mit.edu	37	7	8192519	8192521	+	Intron	DEL	ACT	-	-	rs138471164		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8192519_8192521delACT	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		ctccaccaccactaccaccatta	0.000													4	2	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8631477	8631477	+	Intron	DEL	T	-	-	rs111935394		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8631477delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CTGAGGTTTCTTTTTTTTTTT	0.358													4	2	---	---	---	---	
SCIN	85477	broad.mit.edu	37	7	12601996	12601998	+	Intron	DEL	TTT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12601996_12601998delTTT	uc003ssl.1	+									Q9Y6U3	ADSV_HUMAN	Homo sapiens cDNA clone IMAGE:30347465, with apparent retained intron.						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CTGACTTCTAttttttttttttt	0.172													1	5	---	---	---	---	
IGF2BP3	10643	broad.mit.edu	37	7	23435223	23435223	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23435223delC	uc003swg.2	-							NM_006547	NP_006538	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2						tctacCCCCACCCCCCCAAAA	0.085													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23531320	23531321	+	IGR	INS	-	TCC	TCC	rs139298885	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23531320_23531321insTCC								RPS2P32 (291 upstream) : TRA2A (13081 downstream)																							AGCTTTCTTCTtcctcctcctc	0.228													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30568336	30568337	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30568336_30568337delGT	uc003tbd.2	-											Homo sapiens full length insert cDNA clone ZC66C07.																		tccagcctgggtgacagagcaa	0.124													4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30900617	30900618	+	Intron	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30900617_30900618delAG	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_Intron|FAM188B_uc003tbu.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						ggccacacacagagacacacac	0.208													4	3	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42215217	42215218	+	Intron	INS	-	A	A	rs77528235		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42215217_42215218insA	uc011kbh.1	-							NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						actctgtctccaaaaaaaaaaa	0.035									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				4	2	---	---	---	---	
GCK	2645	broad.mit.edu	37	7	44224630	44224631	+	Intron	INS	-	ACAG	ACAG	rs61406576		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44224630_44224631insACAG	uc003tkl.2	-							NM_000162	NP_000153	P35557	HXK4_HUMAN	glucokinase isoform 1						cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4						cacacacacacagagaaaaaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46185608	46185609	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46185608_46185609insA								IGFBP3 (224737 upstream) : None (None downstream)																							gactcggtctcaaaaaaaaaaa	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46544281	46544282	+	IGR	INS	-	AAGT	AAGT	rs146558571	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46544281_46544282insAAGT								IGFBP3 (583410 upstream) : TNS3 (770471 downstream)																							agggaggaagggaggaaggaag	0.000													4	2	---	---	---	---	
TNS3	64759	broad.mit.edu	37	7	47430610	47430610	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47430610delG	uc003tnv.2	-						TNS3_uc003tnw.2_Intron	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3							focal adhesion	protein binding			ovary(4)	4						GCCAGGCTCAGGAAAGGAAGC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	47775653	47775654	+	IGR	INS	-	TCTT	TCTT	rs141462845	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47775653_47775654insTCTT								C7orf65 (74407 upstream) : PKD1L1 (38636 downstream)																							ctttctttctctctttcttttt	0.183													3	3	---	---	---	---	
PKD1L1	168507	broad.mit.edu	37	7	47985304	47985304	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47985304delC	uc003tny.1	-							NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						TAACCTCTGTCCACCACGTGC	0.522											OREG0018062	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49561920	49561922	+	IGR	DEL	CTA	-	-	rs143729561		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49561920_49561922delCTA								CDC14C (594871 upstream) : VWC2 (251335 downstream)																							GAGCAGAGTTCTACCAAGTCTCA	0.478													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52120439	52120440	+	IGR	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52120439_52120440delTG								COBL (735924 upstream) : POM121L12 (982909 downstream)																							Agtgtgtgcttgtgtgtgtgtg	0.168													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53224592	53224592	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53224592delT								POM121L12 (119975 upstream) : None (None downstream)																							TTCATAAAGATTAATTGGTAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53882486	53882487	+	IGR	INS	-	AGGT	AGGT	rs146360144	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53882486_53882487insAGGT								POM121L12 (777869 upstream) : HPVC1 (386430 downstream)																							ggaaggaaggaaggagggaagg	0.153													3	3	---	---	---	---	
GBAS	2631	broad.mit.edu	37	7	56062938	56062938	+	Intron	DEL	A	-	-	rs34820247		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56062938delA	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474	O75323	NIPS2_HUMAN	nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCCATGGAAGAAGGAGGCCAG	0.493													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57723992	57723993	+	IGR	DEL	AG	-	-	rs142987140		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57723992_57723993delAG								ZNF716 (190727 upstream) : None (None downstream)																							ATCCCAGGGCAGAGTctcatct	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57743995	57743995	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57743995delT								ZNF716 (210730 upstream) : None (None downstream)																							GTAAAAAAAATTATCTTCTGC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57983136	57983136	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57983136delT								ZNF716 (449871 upstream) : None (None downstream)																							tgaaactctctttttgtagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61761545	61761545	+	IGR	DEL	T	-	-	rs113286717		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61761545delT								None (None upstream) : LOC643955 (990127 downstream)																							CCTCCAAGAATTTTTTTTATC	0.184													4	5	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	73891693	73891694	+	Intron	INS	-	A	A	rs150000139	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73891693_73891694insA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						TTTTTGTGTCCAAAAAAAAAAG	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	74205184	74205184	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74205184delA								NCF1 (1526 upstream) : GTF2IRD2 (5300 downstream)																							gactccttccaaaaaaaaaaa	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75927635	75927635	+	IGR	DEL	A	-	-	rs74334483		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75927635delA								SRRM3 (11030 upstream) : HSPB1 (4240 downstream)																							actccgtctcaaaaaaaaaaa	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77093471	77093471	+	IGR	DEL	A	-	-	rs71524933		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77093471delA								PION (47754 upstream) : PTPN12 (73302 downstream)																							actccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	85455411	85455411	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85455411delG								SEMA3D (639240 upstream) : GRM3 (817819 downstream)																							gtaatcatgtggacccttaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	86504334	86504335	+	IGR	INS	-	CA	CA	rs147148775	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86504334_86504335insCA								GRM3 (10143 upstream) : KIAA1324L (4903 downstream)																							tgatacatatgcacacacacac	0.000													4	2	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87146680	87146681	+	Intron	INS	-	TC	TC	rs140059115	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87146680_87146681insTC	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	ctctctctctttctctctctct	0.040													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	91358480	91358481	+	IGR	INS	-	A	A	rs145178772	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91358480_91358481insA								FZD1 (460349 upstream) : MTERF (72979 downstream)																							gaagggaagggagggagggagg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	92073760	92073760	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92073760delA								ANKIB1 (43062 upstream) : GATAD1 (3005 downstream)																							CACGATTTCCAAAAAAAAAAA	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	92626455	92626456	+	IGR	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92626455_92626456delTG								CDK6 (160514 upstream) : SAMD9 (102376 downstream)																							tgtgtgtgcttgtgtgtgtgtg	0.282													4	2	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98743257	98743258	+	5'Flank	INS	-	TG	TG	rs138934252	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98743257_98743258insTG	uc003upu.1	-						SMURF1_uc003upv.1_5'Flank|SMURF1_uc003upt.2_5'Flank	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCTTTTAATACtgtgtgtgtgt	0.322													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101814720	101814720	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101814720delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						CAGTTTTGGGttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101967482	101967482	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967482delA								SH2B2 (5305 upstream) : SPDYE6 (18711 downstream)																							ACTCTGTCTCAAAAAAAAAAA	0.189													4	3	---	---	---	---	
MDFIC	29969	broad.mit.edu	37	7	114594292	114594292	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114594292delT	uc003vhf.2	+							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						CTCCCTGTCCTTTTCCTTAAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115116205	115116206	+	IGR	INS	-	GG	GG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115116205_115116206insGG								MDFIC (456942 upstream) : TFEC (458996 downstream)																							gaaaagagagagaagaaagaga	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	116970132	116970132	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116970132delT								WNT2 (6789 upstream) : ASZ1 (33144 downstream)																							attccatagcttttttttccc	0.000													4	2	---	---	---	---	
GPR37	2861	broad.mit.edu	37	7	124403621	124403622	+	Intron	INS	-	T	T	rs111336509		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124403621_124403622insT	uc003vli.2	-							NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37 precursor							endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|lung(1)|central_nervous_system(1)	3						AAATGCTAATGTTTTTTTTTTT	0.351													4	2	---	---	---	---	
CPA4	51200	broad.mit.edu	37	7	129949728	129949728	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129949728delC	uc003vpr.2	+						CPA4_uc011kpd.1_Intron|CPA4_uc011kpe.1_Intron	NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein						histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)					acctcagcctccctggtagct	0.000													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133610796	133610796	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133610796delA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				actccgtctcaaaaaaaaaaa	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140981112	140981113	+	IGR	INS	-	T	T	rs147111827	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140981112_140981113insT								MRPS33 (266331 upstream) : AGK (269965 downstream)																							CACAAGATAGATTTTTTTTTTC	0.376													4	2	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	144051238	144051238	+	Intron	DEL	A	-	-	rs71206340		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144051238delA	uc003wec.1	-						ARHGEF5_uc003wek.2_5'Flank|ARHGEF5_uc003wel.2_5'Flank					SubName: Full=Seven transmembrane helix receptor;												0						CAAGACTAACAGAACACAACG	0.383													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152099947	152099947	+	Intron	DEL	C	-	-	rs141377290		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152099947delC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		actctttactcccctttcact	0.060			N		medulloblastoma								3	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152104995	152104996	+	Intron	DEL	TT	-	-	rs145762454		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152104995_152104996delTT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		AAAATTTATCTTGTTAGAATAC	0.262			N		medulloblastoma								9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155128171	155128171	+	IGR	DEL	G	-	-	rs78957141		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155128171delG								INSIG1 (26229 upstream) : EN2 (122653 downstream)																							ATTACCCTCAGTCCTCATTGA	0.478													4	2	---	---	---	---	
CNPY1	285888	broad.mit.edu	37	7	155310970	155310971	+	Intron	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155310970_155310971insG	uc003wmc.1	-							NM_001103176	NP_001096646	Q3B7I2	CNPY1_HUMAN	canopy 1 homolog												0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		GTGCTAGTTTaggaagatgagg	0.243													4	2	---	---	---	---	
SHH	6469	broad.mit.edu	37	7	155604294	155604296	+	Intron	DEL	TCC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155604294_155604296delTCC	uc003wmk.1	-						SHH_uc003wmh.1_5'Flank|SHH_uc003wmi.1_5'Flank|SHH_uc003wmj.1_5'Flank	NM_000193	NP_000184	Q15465	SHH_HUMAN	sonic hedgehog preproprotein						androgen metabolic process|axon guidance|branching involved in ureteric bud morphogenesis|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment|embryonic digit morphogenesis|hindbrain development|intein-mediated protein splicing|lymphoid progenitor cell differentiation|metanephric mesenchymal cell proliferation involved in metanephros development|midbrain development|negative regulation of cell migration|negative regulation of kidney smooth muscle cell differentiation|negative regulation of ureter smooth muscle cell differentiation|negative thymic T cell selection|neural crest cell migration|neuroblast proliferation|patterning of blood vessels|positive regulation of alpha-beta T cell differentiation|positive regulation of immature T cell proliferation in thymus|positive regulation of kidney smooth muscle cell differentiation|positive regulation of mesenchymal cell proliferation involved in ureter development|positive regulation of T cell differentiation in thymus|positive regulation of ureter smooth muscle cell differentiation|positive thymic T cell selection|proteolysis|sclerotome development|stem cell development|thymus development|vasculogenesis|ventral midline development	cell surface|extracellular space|membrane raft|plasma membrane	calcium ion binding|laminin-1 binding|peptidase activity|signal transducer activity|zinc ion binding			central_nervous_system(3)|lung(1)	4	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTGTTACCGTCCTCACCCCCAC	0.571													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155935252	155935253	+	IGR	INS	-	A	A	rs143665593	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155935252_155935253insA								SHH (330285 upstream) : C7orf4 (397932 downstream)																							TATGTGGGCTGAAAAAAAAAAC	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156208976	156208976	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156208976delG								SHH (604009 upstream) : C7orf4 (124209 downstream)																							CTGAGGCCCTGGAGGAGAGAG	0.567													4	2	---	---	---	---	
LMBR1	64327	broad.mit.edu	37	7	156622253	156622254	+	Intron	INS	-	C	C	rs143633673	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156622253_156622254insC	uc003wmw.3	-						LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron|LMBR1_uc010lqo.2_Intron	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		tgcttgtacatctgcagaactg	0.035													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158036938	158036939	+	Intron	INS	-	AGGAAA	AGGAAA	rs146087801	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158036938_158036939insAGGAAA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTCAGAAGTGCAGGAAACTGAC	0.505													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158339723	158339723	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158339723delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CAGGCCCTCCTGCCAGGCAAG	0.612													4	2	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2047842	2047844	+	Intron	DEL	CTT	-	-	rs71993575		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2047842_2047844delCTT	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		tccttccttccttctttctttcc	0.123													5	4	---	---	---	---	
NAT1	9	broad.mit.edu	37	8	18028404	18028404	+	Intron	DEL	T	-	-	rs67694950		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18028404delT	uc010ltd.2	+							NM_001160179	NP_001153651	P18440	ARY1_HUMAN	N-acetyltransferase 1 isoform a						xenobiotic metabolic process	cytosol	arylamine N-acetyltransferase activity				0				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		ctctctctccttttttttttc	0.134													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20394163	20394163	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20394163delA								LZTS1 (281360 upstream) : None (None downstream)																							AATGAGGGGTAGTTGACCCAC	0.463													4	2	---	---	---	---	
EBF2	64641	broad.mit.edu	37	8	25801354	25801354	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25801354delT	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		CTCCCTCCCATTTTTTTTGTT	0.413													4	2	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27776023	27776031	+	Intron	DEL	GAGGAAAAG	-	-	rs139506235	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27776023_27776031delGAGGAAAAG	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		ggaggaaaaagaggaaaaggaggaaaagg	0.211													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32202826	32202827	+	Intron	INS	-	G	G	rs138001722	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32202826_32202827insG	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TTGGCTCTGTTGTCTGGAAGCT	0.431													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36831587	36831588	+	IGR	INS	-	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36831587_36831588insC								KCNU1 (37946 upstream) : ZNF703 (721713 downstream)																							cctcctacagtccggggacagc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37363792	37363792	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37363792delG								KCNU1 (570151 upstream) : ZNF703 (189509 downstream)																							gagggagggagggggggagga	0.164													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38336737	38336737	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38336737delG								FGFR1 (10385 upstream) : C8orf86 (31615 downstream)																							ttttttttttgagatggagtc	0.000													4	2	---	---	---	---	
RNF170	81790	broad.mit.edu	37	8	42721727	42721728	+	Intron	INS	-	A	A	rs77668327		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42721727_42721728insA	uc003xpo.2	-						RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Intron|RNF170_uc003xpm.2_Intron|RNF170_uc003xpp.2_Intron|RNF170_uc003xpn.2_Intron|RNF170_uc003xpq.3_Intron	NM_001160223	NP_001153695	Q96K19	RN170_HUMAN	ring finger protein 170 isoform a							integral to membrane	zinc ion binding				0	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			ctccgtctcagaaaaaaaaaaa	0.144													4	2	---	---	---	---	
HOOK3	84376	broad.mit.edu	37	8	42866593	42866594	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42866593_42866594delTG	uc003xpr.2	+							NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			agtaacagcatgtgtgtgtgtg	0.000			T	RET	papillary thyroid								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43142472	43142473	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43142472_43142473insA								HGSNAT (84503 upstream) : POTEA (5112 downstream)																							CATAATTACCCAAAAATAAATT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	46853299	46853299	+	IGR	DEL	G	-	-	rs8188615	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46853299delG								None (None upstream) : BEYLA (899209 downstream)																							acactctcctgttggaatctg	0.000													4	3	---	---	---	---	
PCMTD1	115294	broad.mit.edu	37	8	52730969	52730970	+	3'UTR	INS	-	A	A	rs35041148		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52730969_52730970insA	uc003xqx.3	-	6					PCMTD1_uc011ldm.1_3'UTR|PCMTD1_uc003xqw.3_3'UTR|PCMTD1_uc011ldn.1_3'UTR|PCMTD1_uc010lya.2_3'UTR	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				CAGCTCCAACCAAAAAAAAAAA	0.361													2	5	---	---	---	---	
LYN	4067	broad.mit.edu	37	8	56796421	56796421	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56796421delT	uc003xsk.3	+						LYN_uc003xsl.3_Intron	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene						erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)			AGTTGTTGGGTTTTTTTTTTC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64403238	64403239	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64403238_64403239insT								YTHDF3 (277893 upstream) : MIR124-2 (888467 downstream)																							tcttttctttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66912047	66912047	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66912047delC								PDE7A (158292 upstream) : DNAJC5B (21744 downstream)																							tgtgtggtgtcctggaaatta	0.000													4	2	---	---	---	---	
ADHFE1	137872	broad.mit.edu	37	8	67348644	67348645	+	Intron	INS	-	A	A	rs142094928	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67348644_67348645insA	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			ATGCAGAGGTGAAGCATACCTG	0.099													3	6	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68123279	68123279	+	Intron	DEL	A	-	-	rs112619283		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68123279delA	uc003xxo.1	-						ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxn.1_Intron	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			actccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70294501	70294502	+	IGR	INS	-	CAA	CAA	rs140758861	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70294501_70294502insCAA								C8orf34 (563245 upstream) : SULF1 (84357 downstream)																							cctccaaatgccaacacctctc	0.000													4	2	---	---	---	---	
NCOA2	10499	broad.mit.edu	37	8	71253317	71253318	+	Intron	INS	-	A	A	rs79461563		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71253317_71253318insA	uc003xyn.1	-							NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			ttaaaaagttgaaaaaaaaaaa	0.010			T	RUNXBP2	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77889387	77889387	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77889387delT								ZFHX4 (109867 upstream) : PEX2 (3109 downstream)																							aaaagttgaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78609768	78609769	+	IGR	INS	-	T	T	rs151047403	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78609768_78609769insT								PEX2 (697244 upstream) : PKIA (818567 downstream)																							gcaatccctgcttttttttgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79059403	79059403	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79059403delT								None (None upstream) : PKIA (368933 downstream)																							AGCACGTGCCTTTATTTTACT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81801197	81801198	+	IGR	DEL	TT	-	-	rs35952044		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81801197_81801198delTT								ZNF704 (14181 upstream) : PAG1 (78850 downstream)																							aattattgtatttttttttttt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89383327	89383327	+	IGR	DEL	T	-	-	rs112042731		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89383327delT								MMP16 (43610 upstream) : None (None downstream)																							TTTTCTCTACTTTTTTTTTTT	0.264													4	2	---	---	---	---	
NECAB1	64168	broad.mit.edu	37	8	91862813	91862814	+	Intron	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91862813_91862814delAG	uc011lgg.1	+							NM_022351	NP_071746	Q8N987	NECA1_HUMAN	N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)			ATGTGATACAAGAACACCATGC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98763282	98763282	+	IGR	DEL	A	-	-	rs112981702		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98763282delA								MTDH (20795 upstream) : LAPTM4B (24527 downstream)																							actccatctcaaaaaaaaaaa	0.015													4	3	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99574584	99574585	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99574584_99574585insA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		tattaagccacaaaaaaaacca	0.000													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99814021	99814021	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99814021delT	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		AGGATATGCCTTTTTTTTTTC	0.174													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99824339	99824339	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99824339delT	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		tgcctggccATTTTTTTTTTC	0.129													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100819906	100819907	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100819906_100819907delTG	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGGgtgtgtttgtgtgtgtgtg	0.267													8	4	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102980961	102980962	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102980961_102980962insA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			CACTCTCCTGTAAAAAAAAAAT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	105832650	105832651	+	IGR	INS	-	CA	CA	rs72476288		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105832650_105832651insCA								LRP12 (231430 upstream) : ZFPM2 (498496 downstream)																							atacacgtgcgcacacacacac	0.218													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106313555	106313555	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106313555delT								LRP12 (712335 upstream) : ZFPM2 (17592 downstream)																							atttttaaaattttttttgta	0.000													4	2	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106527960	106527961	+	Intron	INS	-	T	T	rs142466952	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106527960_106527961insT	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			CTACTTTGGGCTTTAGACTTAT	0.351													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112475865	112475865	+	IGR	DEL	A	-	-	rs148155175		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112475865delA								None (None upstream) : CSMD3 (759296 downstream)																							aggctaggggaaaaaaaaaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116741233	116741234	+	IGR	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116741233_116741234delGA								TRPS1 (60005 upstream) : EIF3H (915822 downstream)																							AAGAAGGAGCgagagagagaga	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122377523	122377523	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122377523delT								SNTB1 (553214 upstream) : HAS2 (247748 downstream)																							tcgtgtgaaattaccttatag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124068773	124068773	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124068773delA								DERL1 (14125 upstream) : WDR67 (16147 downstream)																							agactccatcaaaaaaaaaaa	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124635515	124635516	+	IGR	INS	-	T	T	rs140116381	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124635515_124635516insT								FBXO32 (82069 upstream) : KLHL38 (22399 downstream)																							TTCTGCTGAGCTTTTTTATTGA	0.411													4	3	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125050579	125050580	+	Intron	DEL	AT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125050579_125050580delAT	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTGCGTGCACATATTCTTATTT	0.267											OREG0018966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KIAA0196	9897	broad.mit.edu	37	8	126044154	126044154	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126044154delG	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron|KIAA0196_uc003yru.1_Intron	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			CAGGAGTGCAGGGGCTCGCTG	0.522													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127641165	127641168	+	IGR	DEL	GTGT	-	-	rs10531510		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127641165_127641168delGTGT								FAM84B (70699 upstream) : LOC727677 (660894 downstream)																							GTGCGCACTCgtgtgtgtgtgtgt	0.314													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128272219	128272220	+	IGR	INS	-	G	G	rs140279519	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128272219_128272220insG								FAM84B (701753 upstream) : LOC727677 (29842 downstream)																							tgttgtgagaattaaatggact	0.005													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128684168	128684169	+	IGR	INS	-	AA	AA	rs144934525		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128684168_128684169insAA								LOC727677 (189784 upstream) : MYC (63596 downstream)																							ctgggcgacagaAAAAAAAAAA	0.119													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128771280	128771280	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128771280delT								MYC (17602 upstream) : PVT1 (35499 downstream)																							aagtccttgattttttttttc	0.000													2	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129155276	129155277	+	IGR	INS	-	TATG	TATG	rs150429218	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129155276_129155277insTATG								PVT1 (41778 upstream) : MIR1208 (7085 downstream)																							TTTTTACCatttatgtatgtat	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130696294	130696295	+	IGR	INS	-	A	A	rs74384692		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130696294_130696295insA								None (None upstream) : GSDMC (64148 downstream)																							TCTTCATTGACAAAAAAAAAAA	0.426													3	4	---	---	---	---	
GSDMC	56169	broad.mit.edu	37	8	130788985	130788987	+	Intron	DEL	TGT	-	-	rs35034463		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130788985_130788987delTGT	uc003ysr.2	-							NM_031415	NP_113603	Q9BYG8	GSDMC_HUMAN	melanoma-derived leucine zipper, extra-nuclear							mitochondrion				ovary(2)|skin(1)	3						tggtttttgctgttgttgttgtt	0.000													6	6	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	131859134	131859134	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131859134delT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			ttcccttccctttccttcctt	0.080										HNSCC(32;0.087)			4	4	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133493789	133493795	+	5'Flank	DEL	TCCCTCT	-	-	rs3840713		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133493789_133493795delTCCCTCT	uc003ytj.2	-						KCNQ3_uc010mdt.2_5'Flank	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			AGCTCGTGACtccctcttccctcttcc	0.502													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	133577370	133577371	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133577370_133577371insG								HPYR1 (3644 upstream) : LRRC6 (7077 downstream)																							AGCTGTCACATGGGGGGCAGTC	0.564													5	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134415320	134415320	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134415320delT								NDRG1 (105773 upstream) : ST3GAL1 (51771 downstream)																							GTGAGGAGGCTGGAACAGTGT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134871223	134871224	+	IGR	INS	-	A	A	rs143874630	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134871223_134871224insA								ST3GAL1 (287040 upstream) : ZFAT (618809 downstream)																							CTTGGAAGGAGAAAAAAAACAA	0.401													3	3	---	---	---	---	
KHDRBS3	10656	broad.mit.edu	37	8	136645291	136645292	+	Intron	INS	-	TCT	TCT	rs150324119	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136645291_136645292insTCT	uc003yuv.2	+						KHDRBS3_uc003yuw.2_Intron|KHDRBS3_uc010mek.2_Intron	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			ctcttagctgctctaactctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138848819	138848820	+	IGR	INS	-	TCA	TCA	rs149041801	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138848819_138848820insTCA								None (None upstream) : FAM135B (293448 downstream)																							aaacattgaagtcatcattatg	0.000													6	4	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139152893	139152900	+	Intron	DEL	CACATATG	-	-	rs72491630		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139152893_139152900delCACATATG	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											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)			TTCTATGATACACATATGCACATATGCA	0.240										HNSCC(54;0.14)			2	5	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140997755	140997756	+	Intron	INS	-	AG	AG	rs138016791	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140997755_140997756insAG	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						ATgaaagaggcagagagagaga	0.173													2	4	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141307442	141307443	+	Intron	DEL	TG	-	-	rs62529376		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141307442_141307443delTG	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						tacacacacatgcatagacaca	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142873358	142873359	+	IGR	INS	-	T	T	rs147068020	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142873358_142873359insT								MIR1302-7 (5684 upstream) : NCRNA00051 (406358 downstream)																							GGACCTCCCTGTCCCCTGATGA	0.663													3	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144263965	144263966	+	IGR	INS	-	G	G	rs142415418	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144263965_144263966insG								LY6H (21912 upstream) : GPIHBP1 (31102 downstream)																							CATGTAAGCATTCtgtgtgtgc	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144264097	144264098	+	IGR	INS	-	TG	TG	rs148793675	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144264097_144264098insTG								LY6H (22044 upstream) : GPIHBP1 (30970 downstream)																							gtgtgtgtgtctgtgtgtgtgc	0.000													4	2	---	---	---	---	
ZC3H3	23144	broad.mit.edu	37	8	144597161	144597161	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144597161delC	uc003yyd.2	-							NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			CCGGCCAGTGCCCCCACCATC	0.667													4	2	---	---	---	---	
ZNF16	7564	broad.mit.edu	37	8	146172267	146172267	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146172267delG	uc003zet.2	-						ZNF16_uc003zeu.2_Intron	NM_001029976	NP_001025147	P17020	ZNF16_HUMAN	zinc finger protein 16						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		gtcctgctgtggggcctgtgt	0.065													4	2	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	4267945	4267952	+	Intron	DEL	CTGTGTGT	-	-	rs35447890		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4267945_4267952delCTGTGTGT	uc003zhx.1	-						GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron	NM_001042413	NP_001035878	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		ATAAAAATACCtgtgtgtgtgtgtgtgt	0.245													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6080407	6080408	+	IGR	INS	-	T	T	rs151004684	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6080407_6080408insT								RANBP6 (64767 upstream) : IL33 (135399 downstream)																							CTGGCCGCCCCGATCCCGCCCC	0.614													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6091477	6091478	+	IGR	INS	-	AAAC	AAAC	rs151077709	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6091477_6091478insAAAC								RANBP6 (75837 upstream) : IL33 (124329 downstream)																							agactctgtctaaacaaacaaa	0.119													4	3	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	8366675	8366676	+	Intron	INS	-	GTTA	GTTA	rs150745294	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8366675_8366676insGTTA	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	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)		TCATCTCATCTGTTATCTTTGG	0.431										TSP Lung(15;0.13)			2	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	12245522	12245523	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12245522_12245523insT								None (None upstream) : TYRP1 (447863 downstream)																							TAAAGAGACAAttttttttttg	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	13579889	13579889	+	IGR	DEL	A	-	-	rs140243325		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13579889delA								MPDZ (300326 upstream) : NFIB (501959 downstream)																							gttcatacttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NFIB	4781	broad.mit.edu	37	9	14098809	14098810	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14098809_14098810delCA	uc003zle.2	-						NFIB_uc003zld.2_Intron|NFIB_uc003zlf.2_Intron	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		CATGTGTGTGCACACACACaca	0.351			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16304228	16304228	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16304228delG								C9orf93 (332333 upstream) : BNC2 (105274 downstream)																							ATATGACTCTGGGGAAAGTGT	0.368													4	2	---	---	---	---	
MLLT3	4300	broad.mit.edu	37	9	20401053	20401053	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20401053delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		AAGCAGGAGGAGGAGAAAAAG	0.373			T	MLL	ALL								4	2	---	---	---	---	
SUGT1P1	441394	broad.mit.edu	37	9	33402932	33402933	+	Intron	INS	-	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33402932_33402933insC	uc010mjq.1	-						AQP7_uc003zst.2_5'Flank|AQP7_uc003zsu.1_5'Flank|AQP7_uc011lnx.1_5'Flank|AQP7_uc011lny.1_5'Flank|AQP7_uc003zss.3_5'Flank|AQP7_uc011lnz.1_5'Flank|AQP7_uc011loa.1_5'Flank	NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0						GGAGGGGACGGGGGAGGCCCTG	0.624													9	4	---	---	---	---	
CNTFR	1271	broad.mit.edu	37	9	34577648	34577649	+	Intron	INS	-	C	C	rs147372328	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34577648_34577649insC	uc003zup.1	-						CNTFR_uc003zuq.1_Intron|LOC415056_uc003zut.2_Intron|LOC415056_uc003zur.2_Intron|LOC415056_uc003zus.2_Intron	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor						nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		TCTCTCTGTAGCCCCCCTTCCA	0.619													6	3	---	---	---	---	
SIGMAR1	10280	broad.mit.edu	37	9	34637921	34637921	+	5'Flank	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34637921delG	uc003zvb.2	-						SIGMAR1_uc003zva.3_5'Flank|SIGMAR1_uc003zuz.2_5'Flank|SIGMAR1_uc003zvc.2_5'Flank|SIGMAR1_uc003zvd.2_5'Flank|SIGMAR1_uc011loo.1_5'Flank	NM_005866	NP_005857	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1						ergosterol biosynthetic process|lipid transport	cell junction|endoplasmic reticulum membrane|growth cone|integral to plasma membrane|lipid particle|nuclear inner membrane|nuclear outer membrane	C-8 sterol isomerase activity|drug binding				0					Dextromethorphan(DB00514)	GCGCAAGGGAGGCAAGGGGGC	0.577													4	2	---	---	---	---	
FBXO10	26267	broad.mit.edu	37	9	37538843	37538844	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37538843_37538844insA	uc004aab.2	-						FBXO10_uc004aac.2_Intron|FBXO10_uc004aad.2_Intron	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10							ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)		atgctaggcacaaacttagcac	0.233													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084624	44084624	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084624delT								FAM75A6 (453894 upstream) : FAM27C (905612 downstream)																							AACATAACTGTTAGAAACAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481125	66481125	+	IGR	DEL	G	-	-	rs2220719	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481125delG								FAM74A4 (986739 upstream) : LOC442421 (15345 downstream)																							ttaagggtttgttgtgtctct	0.000													4	3	---	---	---	---	
LOC442421	442421	broad.mit.edu	37	9	66495947	66495947	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66495947delT	uc004aed.1	+											Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						ttctttcttgttttttttttt	0.000													6	5	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67290547	67290547	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67290547delT	uc004aen.1	-						AQP7P1_uc004aeo.1_5'Flank|AQP7P1_uc004aep.1_5'Flank					Homo sapiens cDNA FLJ46364 fis, clone TESTI4051015.												0						CCTCTGCAGAttttttttttt	0.303													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68356752	68356752	+	IGR	DEL	C	-	-	rs75577840		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68356752delC								FAM27B (562563 upstream) : MIR1299 (645487 downstream)																							GAAGTCTCATCCCCATATTTT	0.368													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68491556	68491556	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68491556delC								FAM27B (697367 upstream) : MIR1299 (510683 downstream)																							ccctttctttctttctttctt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	71638126	71638127	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71638126_71638127insA								PRKACG (9087 upstream) : FXN (12352 downstream)																							gactctgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72748191	72748191	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72748191delC	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						AGTAACAGAACCAACTGAATC	0.423													4	2	---	---	---	---	
GCNT1	2650	broad.mit.edu	37	9	79100653	79100653	+	Intron	DEL	T	-	-	rs34832618		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79100653delT	uc010mpf.2	+						GCNT1_uc010mpg.2_Intron|GCNT1_uc010mph.2_Intron|GCNT1_uc004akf.3_Intron|GCNT1_uc010mpi.2_Intron	NM_001490	NP_001481	Q02742	GCNT1_HUMAN	beta-1,3-galactosyl-O-glycosyl-glycoprotein						protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity				0						tgtctcttccttttttttttt	0.000													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	79737574	79737574	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79737574delA								FOXB2 (101705 upstream) : VPS13A (54787 downstream)																							TCTTACAAAGAAAAAAAAGTG	0.338													4	2	---	---	---	---	
GNAQ	2776	broad.mit.edu	37	9	80501873	80501873	+	Intron	DEL	A	-	-	rs67836669		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80501873delA	uc004akw.2	-							NM_002072	NP_002063	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193						aaagaaatacaaaaaaaaaaa	0.000			Mis		uveal melanoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82450067	82450068	+	IGR	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82450067_82450068delGA								TLE4 (108410 upstream) : None (None downstream)																							AGTTAGGGGGGAGAGAGAGAGA	0.441													4	2	---	---	---	---	
FRMD3	257019	broad.mit.edu	37	9	86115413	86115414	+	Intron	INS	-	CA	CA			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86115413_86115414insCA	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2						TGGCGTGTATGCGCGcacacac	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	86841316	86841317	+	IGR	INS	-	GT	GT	rs138646993	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86841316_86841317insGT								RMI1 (222334 upstream) : SLC28A3 (51775 downstream)																							tgtgtgagtgcgtgtgtgtgtg	0.030													4	2	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87632926	87632926	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87632926delT	uc004aoa.1	+						NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						TGATTTCATCTTACCCATTTT	0.348										TSP Lung(25;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90326305	90326306	+	IGR	INS	-	TGG	TGG	rs148082384	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90326305_90326306insTGG								DAPK1 (2757 upstream) : CTSL1 (14668 downstream)																							tctggagggcatggtgatgatg	0.030													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90822397	90822398	+	IGR	INS	-	A	A	rs147587808		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90822397_90822398insA								CDK20 (232730 upstream) : SPIN1 (180442 downstream)																							cgtctgtacttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SPIN1	10927	broad.mit.edu	37	9	91088559	91088560	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91088559_91088560delTG	uc010mqj.2	+						SPIN1_uc004apy.2_Intron|SPIN1_uc004apz.2_Intron|SPIN1_uc010mqk.2_Intron	NM_006717	NP_006708	Q9Y657	SPIN1_HUMAN	spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0						TCTCCAAACTTGTGTGTGTGTG	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95467333	95467334	+	IGR	INS	-	A	A	rs146747788	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95467333_95467334insA								IPPK (34786 upstream) : BICD2 (6311 downstream)																							catccactttgaaatttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	96712934	96712935	+	IGR	INS	-	TTG	TTG	rs147876960	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96712934_96712935insTTG								PHF2 (271067 upstream) : BARX1 (976 downstream)																							CTGAATCTCTTttgttgttgtt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98514124	98514127	+	IGR	DEL	GGGA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98514124_98514127delGGGA								PTCH1 (234877 upstream) : C9orf130 (54245 downstream)																							gagggaggatgggagggagggagg	0.275													3	4	---	---	---	---	
LPPR1	54886	broad.mit.edu	37	9	104013909	104013910	+	Intron	INS	-	C	C	rs143204037	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104013909_104013910insC	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron|LPPR1_uc004bbc.2_Intron	NM_207299	NP_997182	Q8TBJ4	LPPR1_HUMAN	plasticity related gene 3							integral to membrane	catalytic activity				0						TTTTTGAGTTTCACCTGTTACT	0.421													5	3	---	---	---	---	
PTPN3	5774	broad.mit.edu	37	9	112154885	112154885	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112154885delT	uc004bed.2	-						PTPN3_uc004beb.2_Intron|PTPN3_uc004bec.2_Intron|PTPN3_uc010mtu.2_Intron|PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc011lwd.1_Intron|PTPN3_uc011lwe.1_Intron|PTPN3_uc011lwf.1_Intron	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3						ATACTGGCACtttttttttct	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115756541	115756541	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115756541delG								SLC46A2 (103348 upstream) : ZNF883 (2861 downstream)																							tgccttgtgtggcttccaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116892172	116892173	+	IGR	INS	-	CACT	CACT	rs146833162		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116892172_116892173insCACT								KIF12 (30665 upstream) : COL27A1 (26058 downstream)																							acacacacacacacacacatat	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120502212	120502213	+	IGR	INS	-	G	G	rs10759936	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120502212_120502213insG								TLR4 (22448 upstream) : None (None downstream)																							TATTTGGAtttttttttttttt	0.371													4	2	---	---	---	---	
C5	727	broad.mit.edu	37	9	123751833	123751833	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123751833delT	uc004bkv.2	-							NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	TGTGAAATACTTTTTTTTTTT	0.244													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126180165	126180166	+	Intron	INS	-	T	T	rs113918463		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126180165_126180166insT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron|DENND1A_uc010mwh.1_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						GCCATAGATTGGGGGGGGGGCA	0.604													4	2	---	---	---	---	
FAM129B	64855	broad.mit.edu	37	9	130337510	130337510	+	Intron	DEL	T	-	-	rs35853873		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130337510delT	uc004bri.2	-							NM_001035534	NP_001030611	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 2								protein binding				0						atatggattcttttttttttt	0.000													3	4	---	---	---	---	
SLC27A4	10999	broad.mit.edu	37	9	131116023	131116023	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131116023delT	uc004but.2	+						SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						TCATTCAttcttttttttttt	0.119													5	3	---	---	---	---	
ODF2	4957	broad.mit.edu	37	9	131236776	131236776	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131236776delA	uc011mbd.1	+						ODF2_uc011maz.1_Intron|ODF2_uc011mba.1_Intron|ODF2_uc010myb.2_Intron|ODF2_uc011mbb.1_Intron|ODF2_uc011mbc.1_Intron|ODF2_uc004bva.2_Intron|ODF2_uc004bvb.2_Intron|ODF2_uc011mbe.1_Intron|ODF2_uc004bvc.2_Intron|ODF2_uc010myc.2_Intron|ODF2_uc011mbf.1_Intron|ODF2_uc004bvd.3_Intron|ODF2_uc004bve.2_Intron	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1						catcttggggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	131307799	131307800	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131307799_131307800insA								GLE1 (3220 upstream) : SPTAN1 (7066 downstream)																							gactctgtctcaaaaaaaaaac	0.000													3	3	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586559	131586560	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586559_131586560delGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						GAGCtgtgtggtgtgtgtgtgt	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	131927105	131927106	+	IGR	DEL	GT	-	-	rs5900831		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131927105_131927106delGT								PPP2R4 (15882 upstream) : IER5L (10725 downstream)																							ccactctgtggtgtgtgtgtgt	0.322													4	2	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132727970	132727971	+	Intron	INS	-	AG	AG	rs3055539		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132727970_132727971insAG	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		AAAacacacacacacacgcgcg	0.015			T	MLL	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133443019	133443020	+	IGR	INS	-	TTG	TTG	rs72546215		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133443019_133443020insTTG								ASS1 (66359 upstream) : LOC100272217 (9719 downstream)																							tggttgttgttttgttgttgtt	0.005													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133872074	133872075	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133872074_133872075delAC								FIBCD1 (57619 upstream) : LAMC3 (12429 downstream)																							cacatcagagacacacacacac	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137361958	137361958	+	IGR	DEL	C	-	-	rs112698374	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137361958delC								RXRA (29527 upstream) : COL5A1 (171694 downstream)																							TTCTGAGCCTCGGGTCTTCCT	0.647													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137576922	137576929	+	Intron	DEL	CCATCCAC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137576922_137576929delCCATCCAC	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		atccatccatccatccacccaccatcca	0.000													4	2	---	---	---	---	
LCN12	286256	broad.mit.edu	37	9	139845477	139845478	+	5'Flank	INS	-	GGAGGAGGT	GGAGGAGGT	rs139924265		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139845477_139845478insGGAGGAGGT	uc004ckb.2	+						LCN12_uc004ckc.2_5'Flank	NM_178536	NP_848631	Q6JVE5	LCN12_HUMAN	lipocalcin 12 precursor						lipid metabolic process	extracellular region	binding|transporter activity				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GGGACCTGGGGGGCCTGGACAG	0.649													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2555435	2555437	+	IGR	DEL	GAG	-	-	rs71934388		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2555435_2555437delGAG								ADARB2 (775717 upstream) : PFKP (554315 downstream)																							CAGGTGTATTGAGGAGGAGTGGG	0.483													4	2	---	---	---	---	
PITRM1	10531	broad.mit.edu	37	10	3196646	3196646	+	Intron	DEL	G	-	-	rs11339937		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3196646delG	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						caggattgatggcatttggtg	0.000													3	4	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6263012	6263013	+	Intron	INS	-	TG	TG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6263012_6263013insTG	uc001ije.2	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron|PFKFB3_uc010qaw.1_Intron|PFKFB3_uc001ijf.2_Intron	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						ctgtatggctctgtgtgtgtgt	0.059													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	9402803	9402803	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9402803delC								None (None upstream) : None (None downstream)																							TCCCTTTTCTCCCCTTAGACA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	13404988	13404989	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13404988_13404989insT								SEPHS1 (14708 upstream) : BEND7 (75495 downstream)																							ggcgtggtggggggcgcctgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	17603910	17603910	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17603910delA								ST8SIA6 (107656 upstream) : PTPLA (28050 downstream)																							TTAAGGCCTGAAAACATAGCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30242042	30242042	+	IGR	DEL	A	-	-	rs67371686		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30242042delA								SVIL (216178 upstream) : KIAA1462 (59687 downstream)																							actccgtctcaaaaaaaaaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31925296	31925299	+	IGR	DEL	CACA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31925296_31925299delCACA								ZEB1 (107169 upstream) : ARHGAP12 (169926 downstream)																							TGTGCACGTGcacacacacacaca	0.206													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38561002	38561002	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38561002delG								LOC100129055 (57730 upstream) : HSD17B7P2 (84306 downstream)																							tagcctggatgacagagtgag	0.090													4	3	---	---	---	---	
HNRNPF	3185	broad.mit.edu	37	10	43893793	43893793	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43893793delT	uc009xmh.1	-						HNRNPF_uc001jar.2_5'Flank|HNRNPF_uc001jas.2_Intron|HNRNPF_uc001jat.2_Intron|HNRNPF_uc001jav.2_Intron|HNRNPF_uc001jau.2_Intron	NM_001098208	NP_001091678	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F						regulation of RNA splicing	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding				0						gttgttgttgttttttttttt	0.020													3	3	---	---	---	---	
HNRNPF	3185	broad.mit.edu	37	10	43896530	43896530	+	Intron	DEL	A	-	-	rs79222914		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43896530delA	uc001jas.2	-						HNRNPF_uc001jat.2_Intron|HNRNPF_uc001jav.2_Intron|HNRNPF_uc001jau.2_Intron	NM_001098206	NP_001091676	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F						regulation of RNA splicing	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding				0						actccgtctcaaaaaaaaaaa	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44579108	44579109	+	IGR	DEL	GT	-	-	rs112226175		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44579108_44579109delGT								HNRNPA3P1 (293243 upstream) : CXCL12 (286498 downstream)																							TGTGGTAGCCgtgtgtgtgtgt	0.371													6	4	---	---	---	---	
ALOX5	240	broad.mit.edu	37	10	45879087	45879087	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45879087delC	uc001jce.2	+						ALOX5_uc009xmt.2_Intron|ALOX5_uc010qfg.1_Intron	NM_000698	NP_000689	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)	atgactgttacccccatttta	0.254													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47094073	47094073	+	Intron	DEL	T	-	-	rs67692214		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47094073delT	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aaattaaatcttttttttttc	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65402008	65402008	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65402008delT								REEP3 (20037 upstream) : None (None downstream)																							ccttccttccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65620866	65620867	+	IGR	DEL	CA	-	-	rs144190724		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65620866_65620867delCA								REEP3 (238895 upstream) : ANXA2P3 (964418 downstream)																							tgtgtgtgtgcatgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67174059	67174060	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67174059_67174060insG								ANXA2P3 (587425 upstream) : CTNNA3 (505665 downstream)																							gattttcaaaaggggagggagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71420697	71420697	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71420697delA								C10orf35 (27350 upstream) : COL13A1 (140947 downstream)																							TAACATCCTGAAAGAAAGCAG	0.323													4	2	---	---	---	---	
ADAMTS14	140766	broad.mit.edu	37	10	72475314	72475314	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72475314delA	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						GGGCTATGGGAAAAACAATGA	0.532													4	2	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76134341	76134341	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76134341delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	TAGTTTTCTGTACACTGTTGC	0.279													4	2	---	---	---	---	
STAMBPL1	57559	broad.mit.edu	37	10	90731669	90731670	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90731669_90731670insT	uc010qmx.1	+						ACTA2_uc001kfq.2_Intron|FAS_uc010qna.1_RNA	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		aaggggactacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91890884	91890885	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91890884_91890885insT								KIF20B (356184 upstream) : HTR7 (609693 downstream)																							ATTAGAACATCTTTTTTTTTTT	0.361													4	2	---	---	---	---	
PCGF5	84333	broad.mit.edu	37	10	92953781	92953781	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92953781delA	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						gttatcaaccaagatgcagaa	0.000													4	2	---	---	---	---	
PDLIM1	9124	broad.mit.edu	37	10	97001574	97001575	+	Intron	INS	-	AG	AG	rs144578538	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97001574_97001575insAG	uc001kkh.2	-						PDLIM1_uc001kki.2_Intron|PDLIM1_uc009xuv.2_Intron|PDLIM1_uc001kkj.1_Intron	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1						response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TGAGAGGACTCGGGGCCTGGTC	0.535													4	3	---	---	---	---	
CPN1	1369	broad.mit.edu	37	10	101833791	101833792	+	Intron	INS	-	C	C	rs145901066	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101833791_101833792insC	uc001kql.2	-							NM_001308	NP_001299	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1 precursor						proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		ctgggccccatcccccccccac	0.000													4	3	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114842357	114842358	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114842357_114842358delTG	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TCATTCTGCTtgtgtgtgtgtg	0.292													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115563900	115563901	+	IGR	INS	-	CT	CT	rs147881792	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115563900_115563901insCT								C10orf81 (20713 upstream) : DCLRE1A (30583 downstream)																							TGCAAGCTAAACTCTGTAAATT	0.391													3	3	---	---	---	---	
FAM160B1	57700	broad.mit.edu	37	10	116642634	116642634	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116642634delA	uc001lcc.2	+							NM_001135051	NP_001128523	Q5W0V3	F16B1_HUMAN	hypothetical protein LOC57700 isoform b											lung(1)	1						actctgtctcaaaaaaaaaaa	0.174													3	3	---	---	---	---	
C10orf119	79892	broad.mit.edu	37	10	121613557	121613558	+	Intron	INS	-	T	T	rs111657130		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121613557_121613558insT	uc001ler.2	-						C10orf119_uc001leq.1_5'Flank|C10orf119_uc001les.1_Intron|C10orf119_uc001let.1_5'Flank	NM_024834	NP_079110	Q9BTE3	MCMBP_HUMAN	chromosome 10 open reading frame 119						cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.0044)		ttttccttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121843299	121843300	+	IGR	INS	-	AG	AG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121843299_121843300insAG								SEC23IP (142054 upstream) : PPAPDC1A (373166 downstream)																							TGGCTGTGTGAAGAGAGAGAGA	0.134													4	2	---	---	---	---	
ATE1	11101	broad.mit.edu	37	10	123558956	123558956	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123558956delA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				TTAGGAAAACAAAAAAAAAAA	0.443													4	2	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123799499	123799500	+	Intron	INS	-	C	C	rs146618788	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123799499_123799500insC	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCTCAGCCCAGCCCCTTGTGGG	0.540													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124417397	124417397	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124417397delG								DMBT1 (14145 upstream) : C10orf120 (39830 downstream)																							GTCTTGCTTTGGAGGCGTTCC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125015169	125015169	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125015169delT								BUB3 (90283 upstream) : GPR26 (410702 downstream)																							atcaccatcatcacaccacca	0.000													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132402313	132402313	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132402313delA								GLRX3 (419529 upstream) : TCERG1L (488343 downstream)																							tatggtttctaaatctggttg	0.000													4	2	---	---	---	---	
MUC2	4583	broad.mit.edu	37	11	1091940	1091940	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1091940delT	uc001lsx.1	+							NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor							inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGCACTCTGGTTTTTTGGCAA	0.577													4	2	---	---	---	---	
HBG2	3048	broad.mit.edu	37	11	5666274	5666275	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5666274_5666275insA	uc001mak.1	-						TRIM78P_uc009yer.2_Intron			P69892	HBG2_HUMAN	Homo sapiens hemoglobin gamma-G (HBG2) mRNA, partial cds.						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTATATTTGACAAAAAAAATTT	0.099													4	2	---	---	---	---	
WEE1	7465	broad.mit.edu	37	11	9593857	9593858	+	5'Flank	INS	-	A	A	rs150950933	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9593857_9593858insA	uc001mhs.2	+						WEE1_uc001mht.2_5'Flank	NM_003390	NP_003381	P30291	WEE1_HUMAN	WEE1 tyrosine kinase isoform 1						blood coagulation|cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|S phase of mitotic cell cycle	nucleoplasm	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	5				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		actccgtgtcgaaaaaaaccaa	0.119													7	6	---	---	---	---	
AMPD3	272	broad.mit.edu	37	11	10473719	10473719	+	5'Flank	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10473719delT	uc001mio.1	+						AMPD3_uc010rbz.1_Intron|AMPD3_uc001min.1_Intron|AMPD3_uc009yfw.1_Intron|AMPD3_uc009yfx.1_Intron	NM_001025389	NP_001020560	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3 isoform 1B						AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		AGAGATGAGGTTTTTTGTAGT	0.438													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	11281712	11281713	+	IGR	INS	-	CT	CT	rs140632996	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11281712_11281713insCT								ZBED5 (402092 upstream) : GALNTL4 (10708 downstream)																							gaaggacatgcctctatcctcc	0.000													2	8	---	---	---	---	
MICAL2	9645	broad.mit.edu	37	11	12260195	12260196	+	Intron	INS	-	ATCCTGGATTGA	ATCCTGGATTGA	rs150418430	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12260195_12260196insATCCTGGATTGA	uc001mjz.2	+						MICAL2_uc010rch.1_Intron|MICAL2_uc001mka.2_Intron|MICAL2_uc010rci.1_Intron|MICAL2_uc001mkb.2_Intron|MICAL2_uc001mkc.2_Intron|MICAL2_uc001mkd.2_Intron|MICAL2_uc010rcj.1_Intron|MICAL2_uc001mkf.2_5'Flank	NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		tgcagtgtgggatcctgggaca	0.000													3	3	---	---	---	---	
TEAD1	7003	broad.mit.edu	37	11	12905541	12905541	+	Intron	DEL	A	-	-	rs149582835		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12905541delA	uc001mkj.3	+						TEAD1_uc001mkk.3_Intron|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		actccgtctcaaaaaaaaaaa	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13206105	13206105	+	IGR	DEL	A	-	-	rs67619748		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13206105delA								RASSF10 (173458 upstream) : ARNTL (93220 downstream)																							AGAGAACTGGAAGGAGTCTGA	0.468													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15690758	15690758	+	IGR	DEL	C	-	-	rs66943967		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15690758delC								INSC (422006 upstream) : SOX6 (297238 downstream)																							ATACAGTGTGCccgggcgcag	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15867537	15867537	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15867537delA								INSC (598785 upstream) : SOX6 (120459 downstream)																							CCCCATCCCCAAATGGCAGAC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17709561	17709561	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17709561delA								USH1C (143598 upstream) : MYOD1 (31549 downstream)																							AGCCTCCCCCACCGCCTGCTC	0.647													4	2	---	---	---	---	
HTATIP2	10553	broad.mit.edu	37	11	20384886	20384887	+	5'Flank	INS	-	GT	GT	rs148422982	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20384886_20384887insGT	uc009yia.1	+						HTATIP2_uc009yib.1_5'Flank|HTATIP2_uc001mpx.2_5'Flank|HTATIP2_uc001mpz.2_5'Flank|HTATIP2_uc001mpy.3_5'Flank	NM_006410	NP_006401	Q9BUP3	HTAI2_HUMAN	HIV-1 Tat interactive protein 2, 30kDa isoform						angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0						tgtgtgtgtgcgtgtgtgtgtg	0.371													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	23425766	23425766	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23425766delC								SVIP (574384 upstream) : None (None downstream)																							CCCGAGCTATCCCCGAGCCCA	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28649654	28649655	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28649654_28649655delAC								METT5D1 (294600 upstream) : None (None downstream)																							acagacacagacacacacacac	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29265404	29265404	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29265404delT								METT5D1 (910350 upstream) : KCNA4 (766362 downstream)																							gagcaagttattttatctttc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33497241	33497242	+	IGR	INS	-	A	A	rs144554042		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33497241_33497242insA								HIPK3 (121302 upstream) : C11orf41 (66635 downstream)																							ctcgctctctcaaaaaaaaaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35088989	35088989	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35088989delC								PDHX (71315 upstream) : CD44 (71428 downstream)																							CTCTGTTGTTCAAAGAAATGG	0.433													4	2	---	---	---	---	
LDLRAD3	143458	broad.mit.edu	37	11	36146241	36146241	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36146241delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron|LDLRAD3_uc010rfa.1_Intron	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				ttttcctttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37203775	37203775	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37203775delG								C11orf74 (507385 upstream) : None (None downstream)																							CATATGGAGTGGATCTCCCAC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37731808	37731809	+	IGR	INS	-	A	A	rs138120899	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37731808_37731809insA								None (None upstream) : None (None downstream)																							CTTGGCACAGCACAGAGTGGAT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42116724	42116724	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42116724delC								LRRC4C (635401 upstream) : None (None downstream)																							ctaaaagaggccaaggtactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50033357	50033358	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50033357_50033358insA								OR4C12 (29320 upstream) : LOC441601 (205642 downstream)																							gactccacctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
PATL1	219988	broad.mit.edu	37	11	59425286	59425287	+	Intron	INS	-	T	T	rs137921547	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59425286_59425287insT	uc001noe.3	-						PATL1_uc009yms.1_Intron|PATL1_uc010rkw.1_Intron	NM_152716	NP_689929	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog						cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1						ACCTTAAGAAAtttttttaact	0.144													4	3	---	---	---	---	
SYT7	9066	broad.mit.edu	37	11	61323244	61323245	+	Intron	INS	-	GT	GT	rs144943454	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61323244_61323245insGT	uc001nrv.2	-						SYT7_uc009ynr.2_Intron|SYT7_uc001nrx.1_Intron	NM_004200	NP_004191	O43581	SYT7_HUMAN	synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4						GGAGGCAGGGCgtgtgtgtgtg	0.545													3	3	---	---	---	---	
SLC3A2	6520	broad.mit.edu	37	11	62643008	62643008	+	Intron	DEL	A	-	-	rs76996948		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62643008delA	uc001nwd.2	+						SLC3A2_uc001nwb.2_Intron|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c						blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0						acttcatctcaaaaaaaaaaG	0.030													4	2	---	---	---	---	
RTN3	10313	broad.mit.edu	37	11	63500633	63500633	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63500633delA	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1						ctaaaaatacaaaaaAAAAAA	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	65014050	65014051	+	IGR	DEL	AA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65014050_65014051delAA								SLC22A20 (4478 upstream) : POLA2 (15381 downstream)																							CTGTGTGTGGAAAAGAGAACTC	0.530													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69361811	69361812	+	IGR	INS	-	A	A	rs143867595	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69361811_69361812insA								MYEOV (205362 upstream) : CCND1 (94061 downstream)																							TGGAAGAAAAGACTGTGCAACT	0.525													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69814424	69814424	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69814424delG								FGF3 (180232 upstream) : ANO1 (109984 downstream)																							GGCCAAAGCAGGAACGACCCC	0.622													1	5	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70420770	70420772	+	Intron	DEL	AGA	-	-	rs149635432		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70420770_70420772delAGA	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GAGCAGGAAGAGAAGGAGGGGCT	0.635													0	10	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70873470	70873470	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70873470delC	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			aaaggccccacctccaatcaa	0.000													0	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71252622	71252623	+	IGR	INS	-	ACATG	ACATG	rs139432042	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71252622_71252623insACATG								KRTAP5-8 (2369 upstream) : KRTAP5-9 (6843 downstream)																							atctacattttacatgaggtaa	0.000													9	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71272311	71272312	+	IGR	INS	-	TTTG	TTTG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71272311_71272312insTTTG								KRTAP5-9 (11658 upstream) : KRTAP5-10 (4297 downstream)																							ttgcttgttgatttaagttcct	0.000													9	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	72918584	72918584	+	IGR	DEL	A	-	-	rs11350221		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72918584delA								FCHSD2 (65441 upstream) : P2RY2 (10760 downstream)																							actccgtctcaaaaaaaaaaa	0.020													4	2	---	---	---	---	
ARRB1	408	broad.mit.edu	37	11	75004244	75004245	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75004244_75004245insA	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032	P49407	ARRB1_HUMAN	arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2						AACAACAGCAGCAGCCACCACA	0.465													9	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76117191	76117192	+	Intron	INS	-	T	T	rs147796420	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76117191_76117192insT	uc001oxi.1	+											Homo sapiens cDNA FLJ30390 fis, clone BRACE2008308.																		taatttttgcattttttgtaga	0.000													3	6	---	---	---	---	
GDPD4	220032	broad.mit.edu	37	11	76993754	76993754	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76993754delA	uc001oyf.2	-							NM_182833	NP_878253	Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding			skin(1)	1						caacaacaacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77806280	77806281	+	IGR	INS	-	AC	AC	rs145828493	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77806280_77806281insAC								NDUFC2 (15015 upstream) : ALG8 (5707 downstream)																							taagcatacaaacacacacaca	0.000													7	4	---	---	---	---	
ALG8	79053	broad.mit.edu	37	11	77846401	77846401	+	Intron	DEL	A	-	-	rs111440035		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77846401delA	uc001oza.1	-						ALG8_uc001oyz.1_Intron|ALG8_uc009yux.1_Intron|ALG8_uc009yuy.1_Intron	NM_024079	NP_076984	Q9BVK2	ALG8_HUMAN	dolichyl pyrophosphate Glc1Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			accctgtttcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
GAB2	9846	broad.mit.edu	37	11	77962789	77962791	+	Intron	DEL	CTT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77962789_77962791delCTT	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			cctggacttgcttcttcttctgt	0.000													9	8	---	---	---	---	
GAB2	9846	broad.mit.edu	37	11	77981380	77981380	+	Intron	DEL	A	-	-	rs141850055		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77981380delA	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			actccgtcttaaaaaaaaaaa	0.179													5	5	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	79120105	79120112	+	Intron	DEL	TGTGTGTG	-	-	rs111495227		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79120105_79120112delTGTGTGTG	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						AGGGATATTTtgtgtgtgtgtgtgtgtg	0.264													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79316210	79316211	+	IGR	INS	-	A	A	rs5792865		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79316210_79316211insA								ODZ4 (164515 upstream) : None (None downstream)																							TCTTGGTCTGGAAAAAAAAAAA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	80191992	80191993	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80191992_80191993delAC								None (None upstream) : None (None downstream)																							acacatacatacacacacacac	0.342													8	6	---	---	---	---	
RAB30	27314	broad.mit.edu	37	11	82760451	82760452	+	Intron	INS	-	A	A	rs74770237		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82760451_82760452insA	uc001ozu.2	-						RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						gactccatatcaaaaaaaaaaa	0.193													4	3	---	---	---	---	
TMEM135	65084	broad.mit.edu	37	11	86795591	86795591	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86795591delG	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069	Q86UB9	TM135_HUMAN	transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ctcctatcttggcctcacaaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91879579	91879579	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91879579delC								None (None upstream) : FAT3 (205683 downstream)																							ctcctacctgcccccagacta	0.000													4	2	---	---	---	---	
FOLR4	390243	broad.mit.edu	37	11	94036171	94036174	+	5'Flank	DEL	CCTC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94036171_94036174delCCTC	uc010rud.1	+							NM_001080486	NP_001073955	A6ND01	FOLR4_HUMAN	folate receptor 4 (delta) homolog							extracellular region	folic acid binding|receptor activity			ovary(1)	1						GTAATTccttcctccctccctccc	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102387348	102387348	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102387348delA								TMEM123 (63573 upstream) : MMP7 (3892 downstream)																							AACCCAATTTAAATGTCCTGT	0.383													4	2	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107670620	107670621	+	Intron	DEL	TT	-	-	rs150391771		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107670620_107670621delTT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		tttgtttttgtttttttttttt	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114664326	114664327	+	IGR	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114664326_114664327delAG								FAM55B (86674 upstream) : CADM1 (375626 downstream)																							AGAGCAGAGCAGAGAAGATTGG	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114828705	114828705	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114828705delG								FAM55B (251053 upstream) : CADM1 (211248 downstream)																							TCAAAACTGTGGGGTTCCAGC	0.468													4	2	---	---	---	---	
CD3G	917	broad.mit.edu	37	11	118222930	118222931	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118222930_118222931insA	uc001psu.2	+						CD3G_uc009zaa.1_Intron	NM_000073	NP_000064	P09693	CD3G_HUMAN	CD3G antigen, gamma polypeptide precursor						establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		gactccgtctcaaaaaaaaaaa	0.168													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119661525	119661526	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119661525_119661526delAC								PVRL1 (62090 upstream) : TRIM29 (320469 downstream)																							ACACTTGCATACACACACACAC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119734808	119734808	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119734808delA								PVRL1 (135373 upstream) : TRIM29 (247187 downstream)																							AGGGCCTGGGAGGGGAGGATC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122452799	122452799	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122452799delC								LOC399959 (214332 upstream) : UBASH3B (73599 downstream)																							atgttcccctccttgtgtcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123585034	123585034	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123585034delT								SCN3B (59719 upstream) : ZNF202 (9963 downstream)																							tctggaatgctttttcatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129733504	129733504	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129733504delA								TMEM45B (3606 upstream) : NFRKB (167 downstream)																							ctctggccACAAaaacaaaca	0.010													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131468769	131468770	+	Intron	INS	-	C	C			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131468769_131468770insC	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						cttccttccttcttccttcctt	0.005													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131730766	131730766	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131730766delA	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CATACTTATGAAAAAGGCCTG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133428550	133428551	+	IGR	INS	-	T	T	rs113449743		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133428550_133428551insT								OPCML (26147 upstream) : SPATA19 (281966 downstream)																							CTTCTATGTCAttttttttttt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133734558	133734558	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133734558delA								SPATA19 (19166 upstream) : LOC283174 (31772 downstream)																							ATTGAACAGGAAAAAAAAAAA	0.542													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134936363	134936363	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134936363delC								B3GAT1 (654551 upstream) : None (None downstream)																							TAAAGAGGCACCGACAGAAGC	0.453													4	2	---	---	---	---	
IQSEC3	440073	broad.mit.edu	37	12	272470	272473	+	Intron	DEL	CCCT	-	-	rs35075594		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:272470_272473delCCCT	uc001qhw.1	+						IQSEC3_uc001qhu.1_Intron	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		ccctcccctcccctccctccacag	0.123													12	7	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	636809	636809	+	Intron	DEL	C	-	-	rs67294413		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:636809delC	uc001qii.1	+							NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TCCTCACTTGCCCCCCCACCA	0.587													4	3	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2743361	2743361	+	Intron	DEL	T	-	-	rs67384877		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2743361delT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	tttccataccttttttttttt	0.279													3	3	---	---	---	---	
PARP11	57097	broad.mit.edu	37	12	3943800	3943801	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3943800_3943801insA	uc001qml.2	-						PARP11_uc009zef.2_Intron|PARP11_uc001qmm.2_Intron|PARP11_uc001qmn.2_Intron	NM_020367	NP_065100	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11								NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			cactccatctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
NCAPD2	9918	broad.mit.edu	37	12	6630750	6630751	+	Intron	INS	-	G	G	rs146599711	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6630750_6630751insG	uc001qoo.2	+						NCAPD2_uc009zen.1_Intron|NCAPD2_uc010sfd.1_Intron	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2						cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						actgctcaggagctgaagtgag	0.000													6	5	---	---	---	---	
AICDA	57379	broad.mit.edu	37	12	8768166	8768166	+	5'Flank	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8768166delG	uc001qur.2	-							NM_020661	NP_065712	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase						B cell differentiation|DNA demethylation|mRNA processing|negative regulation of methylation-dependent chromatin silencing	cytoplasm	cytidine deaminase activity|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung SC(5;0.184)					AGCGTCAACTGGAAGGTGCAG	0.423									Immune_Deficiency_with_Hyper-IgM				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14170142	14170143	+	IGR	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14170142_14170143delAG								GRIN2B (37120 upstream) : ATF7IP (348468 downstream)																							CCAGATGTGTAGTCCTTCTCGC	0.510													4	2	---	---	---	---	
RERG	85004	broad.mit.edu	37	12	15281841	15281841	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15281841delT	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1						GGTCCAACACTTTTAGTTCTT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	18902424	18902425	+	IGR	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18902424_18902425delGT								CAPZA3 (10303 upstream) : PLEKHA5 (380223 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19032839	19032840	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19032839_19032840insA								CAPZA3 (140718 upstream) : PLEKHA5 (249808 downstream)																							GCCTACTGTTCAAAAAAAAAAG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	21265007	21265007	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21265007delT								SLCO1B3 (21969 upstream) : SLCO1B1 (19121 downstream)																							aaaaagcagcttcacatttca	0.000													4	2	---	---	---	---	
GYS2	2998	broad.mit.edu	37	12	21733560	21733560	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21733560delC	uc001rfb.2	-							NM_021957	NP_068776	P54840	GYS2_HUMAN	glycogen synthase 2						glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2						CATTTAGGATCCACTAAGCCC	0.303													4	2	---	---	---	---	
STK38L	23012	broad.mit.edu	37	12	27416461	27416461	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27416461delG	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815	Q9Y2H1	ST38L_HUMAN	serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)					CATTATCCCTGGTATAGGGCA	0.448													4	2	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29684055	29684055	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29684055delG	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_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)					cactccatgagggtaaccaca	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38142762	38142762	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38142762delC								None (None upstream) : ALG10B (567795 downstream)																							attcatctcacagagttgaac	0.000													4	2	---	---	---	---	
KIF21A	55605	broad.mit.edu	37	12	39789645	39789645	+	Intron	DEL	A	-	-	rs67156493		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39789645delA	uc001rly.2	-						KIF21A_uc001rlx.2_Intron|KIF21A_uc001rlz.2_Intron|KIF21A_uc010skl.1_Intron|KIF21A_uc001rma.1_Intron	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				actccgtctcaaaaaaaaaaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42195141	42195144	+	IGR	DEL	AGGG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42195141_42195144delAGGG								PDZRN4 (226757 upstream) : GXYLT1 (280506 downstream)																							aagggaaggaagggagggaaggga	0.127													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43395264	43395264	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43395264delC								PRICKLE1 (411692 upstream) : ADAMTS20 (352749 downstream)																							ATTCCTTTTTCCAAAATTTTC	0.284													4	2	---	---	---	---	
FKBP11	51303	broad.mit.edu	37	12	49317204	49317205	+	Intron	INS	-	G	G	rs150068728	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49317204_49317205insG	uc001rsp.2	-						FKBP11_uc010sma.1_Intron|FKBP11_uc001rsq.3_3'UTR|FKBP11_uc010smb.1_3'UTR	NM_016594	NP_057678	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11 isoform 1 precursor						protein folding	integral to membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0						AAGGAAGGGGTGGGGGGTGGCT	0.485													2	4	---	---	---	---	
DHH	50846	broad.mit.edu	37	12	49484450	49484451	+	Intron	INS	-	TATG	TATG	rs35343506		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49484450_49484451insTATG	uc001rtf.2	-							NM_021044	NP_066382	O43323	DHH_HUMAN	desert hedgehog preproprotein						cell-cell signaling|proteolysis	extracellular space|plasma membrane	calcium ion binding|peptidase activity|zinc ion binding			lung(1)|breast(1)	2						cttctcttttctatgtatgtat	0.173													4	2	---	---	---	---	
LIMA1	51474	broad.mit.edu	37	12	50607807	50607808	+	Intron	INS	-	CA	CA	rs143352147	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50607807_50607808insCA	uc001rwj.3	-						LIMA1_uc001rwh.3_Intron|LIMA1_uc001rwi.3_Intron|LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1						TATTATCTTACcacacacacac	0.292													4	3	---	---	---	---	
HOXC8	3224	broad.mit.edu	37	12	54401419	54401420	+	5'Flank	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54401419_54401420delGT	uc001ser.2	+							NM_022658	NP_073149	P31273	HXC8_HUMAN	homeobox C8							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGCACGTACAGTGTGTGTGTGT	0.485													4	2	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54475755	54475758	+	Intron	DEL	AACG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54475755_54475758delAACG	uc001sey.2	+						LOC100240735_uc010sor.1_5'Flank	NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						GGGGAAAAAAAACGATCGGAGAAG	0.534													4	2	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54502164	54502164	+	Intron	DEL	A	-	-	rs57897003		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54502164delA	uc001sey.2	+							NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						acacacacacacaccaccaca	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54621744	54621745	+	IGR	INS	-	T	T	rs28480968		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54621744_54621745insT								SMUG1 (38987 upstream) : CBX5 (2987 downstream)																							tctttttgttcttttttttttg	0.243													4	2	---	---	---	---	
IKZF4	64375	broad.mit.edu	37	12	56424513	56424514	+	Intron	INS	-	A	A	rs77831958		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56424513_56424514insA	uc001sjb.1	+						IKZF4_uc010sqa.1_Intron|IKZF4_uc001sjc.1_Intron|IKZF4_uc001sjd.1_Intron|IKZF4_uc009zoi.1_Intron|IKZF4_uc001sje.1_Intron	NM_022465	NP_071910	Q9H2S9	IKZF4_HUMAN	zinc finger protein, subfamily 1A, 4						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123)			aactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DTX3	196403	broad.mit.edu	37	12	58001040	58001040	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58001040delC	uc001sow.1	+	5	731	c.394delC	c.(394-396)CCCfs	p.P132fs	DTX3_uc001sov.1_Frame_Shift_Del_p.P125fs|DTX3_uc001sox.1_Frame_Shift_Del_p.P125fs|DTX3_uc001soy.1_Frame_Shift_Del_p.P125fs|GEFT_uc009zpy.2_5'Flank	NM_178502	NP_848597	Q8N9I9	DTX3_HUMAN	deltex homolog 3	132	Pro-rich.				Notch signaling pathway	cytoplasm	zinc ion binding			breast(1)|central_nervous_system(1)	2	Melanoma(17;0.122)					CCCACTTCTGCCCCCAGGAGC	0.547													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65929276	65929283	+	IGR	DEL	CATTCATT	-	-	rs71886244	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65929276_65929283delCATTCATT								MSRB3 (68596 upstream) : RPSAP52 (222520 downstream)																							GTGGATTTTAcattcattcattcattca	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65938069	65938069	+	RNA	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65938069delC	uc010ssu.1	-	3		c.674delG								Homo sapiens, clone IMAGE:5172510, mRNA.																		GAAAGACTGGCCTCAACTTCT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89524722	89524723	+	IGR	DEL	CA	-	-	rs111330847		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89524722_89524723delCA								KITLG (550484 upstream) : DUSP6 (217116 downstream)																							TACATGCCAGcacacacacaca	0.198													4	2	---	---	---	---	
NTN4	59277	broad.mit.edu	37	12	96080534	96080534	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96080534delA	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052	Q9HB63	NET4_HUMAN	netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2						actctgtctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111728672	111728673	+	Intron	DEL	TT	-	-	rs35377571		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111728672_111728673delTT	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						tcagccAACCtttttttttttt	0.010													3	3	---	---	---	---	
PITPNM2	57605	broad.mit.edu	37	12	123514375	123514378	+	Intron	DEL	TGTG	-	-	rs72405552		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123514375_123514378delTGTG	uc001uej.1	-						PITPNM2_uc001uek.1_Intron|PITPNM2_uc009zxu.1_Intron	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CATAtgtgtctgtgtgtgtgtgtg	0.284													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124719518	124719520	+	IGR	DEL	ATA	-	-	rs112028864		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124719518_124719520delATA								ZNF664 (219551 upstream) : FAM101A (54190 downstream)																							cattaccaccataatcatcatca	0.094													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	129248334	129248334	+	IGR	DEL	A	-	-	rs34907699		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129248334delA								TMEM132C (55871 upstream) : SLC15A4 (29405 downstream)																							ccttacatggaaaaaaaaaag	0.100													4	2	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131442752	131442753	+	Intron	INS	-	T	T	rs140573832	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131442752_131442753insT	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CCAATCCtttcttttttttttg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131723546	131723546	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131723546delG								LOC116437 (26071 upstream) : SFRS8 (472089 downstream)																							tcttgacgttggatttttttc	0.000													4	2	---	---	---	---	
FBRSL1	57666	broad.mit.edu	37	12	133126794	133126795	+	Intron	INS	-	C	C	rs139340505	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133126794_133126795insC	uc001ukf.2	+						uc001ukg.1_5'Flank	NM_001142641	NP_001136113	Q9HCM7	FBSL_HUMAN	fibrosin-like 1											central_nervous_system(2)	2						CAGCAGGGGAGGGAGAGGGGCT	0.683													4	2	---	---	---	---	
POLE	5426	broad.mit.edu	37	12	133246639	133246642	+	Intron	DEL	CTCA	-	-	rs67795875		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133246639_133246642delCTCA	uc001uks.1	-						POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		ACCTGCCCATCTCACTGTTTCTTA	0.338								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19728088	19728089	+	IGR	INS	-	GGGCCA	GGGCCA	rs145704745	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19728088_19728089insGGGCCA								DKFZp686A1627 (35665 upstream) : TUBA3C (19831 downstream)																							GGAGGCCACCGGGGCCAGGGCC	0.609													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19808402	19808402	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19808402delC								TUBA3C (52466 upstream) : LOC100101938 (28539 downstream)																							ccaggatatacaagaatctca	0.000													4	2	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24617813	24617813	+	Intron	DEL	T	-	-	rs34553109		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24617813delT	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TTTGAGGGAATTTTTTTTTGT	0.438													2	4	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24869749	24869750	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24869749_24869750insA	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc010tcy.1_Intron|SPATA13_uc010tcz.1_Intron|SPATA13_uc010tda.1_Intron|SPATA13_uc001uph.2_Intron|SPATA13_uc010tdb.1_Intron|SPATA13_uc009zzz.1_Intron|SPATA13_uc001upi.1_5'Flank	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		gactccgtctcaaaaaaaaaag	0.010													4	2	---	---	---	---	
PARP4	143	broad.mit.edu	37	13	25024443	25024443	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25024443delA	uc001upl.2	-							NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTGACATTTAAATGACAAGT	0.348													4	2	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25542607	25542608	+	5'UTR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25542607_25542608insG	uc010tdh.1	-	1					TPTE2P1_uc001upx.3_5'UTR	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						atcagcccattcctggggcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27425997	27425997	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27425997delT								GPR12 (91075 upstream) : USP12 (216441 downstream)																							gttttattacttagctcaagt	0.000													4	2	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31096874	31096875	+	Intron	DEL	TT	-	-	rs34360026		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31096874_31096875delTT	uc001usz.2	-							NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		TCTAAAAGTCtttttttttttt	0.193													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	34181236	34181237	+	Intron	DEL	TT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34181236_34181237delTT	uc001uux.2	-							NM_052851	NP_443083	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		gacagttttgTTTTTTTTTTTT	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35367371	35367371	+	IGR	DEL	A	-	-	rs11335222		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35367371delA								RFC3 (826677 upstream) : NBEA (149085 downstream)																							aggggtcatgaagccctggca	0.000													2	4	---	---	---	---	
LHFP	10186	broad.mit.edu	37	13	40082063	40082063	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40082063delC	uc001uxf.2	-							NM_005780	NP_005771	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		ttccctccctccctcccattt	0.100			T	HMGA2	lipoma								4	2	---	---	---	---	
PHF11	51131	broad.mit.edu	37	13	50102723	50102723	+	Frame_Shift_Del	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50102723delA	uc001vdb.2	+	10	1255	c.918delA	c.(916-918)TTAfs	p.L306fs	PHF11_uc001vdc.2_Frame_Shift_Del_p.L267fs|PHF11_uc001vdd.2_RNA	NM_001040443	NP_001035533	Q9UIL8	PHF11_HUMAN	PHD finger protein 11 isoform a	306					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		TTCAGGACTTAAAACAAACCT	0.343													32	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51135290	51135291	+	Intron	INS	-	AC	AC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51135290_51135291insAC	uc001vet.1	+											Homo sapiens mRNA for B-cell neoplasia associated transcript, (BCMS gene), splice variant D, non coding transcript.																		TGGATCcacatacacacacaca	0.297													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58309662	58309663	+	IGR	INS	-	TC	TC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58309662_58309663insTC								PCDH17 (6597 upstream) : None (None downstream)																							ttcttttctttttttttttttt	0.178													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59306973	59306973	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59306973delA								None (None upstream) : DIAPH3 (932752 downstream)																							cgaatctgccaaaaatgtatg	0.000													4	2	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60678700	60678701	+	Intron	INS	-	CA	CA	rs145153571	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60678700_60678701insCA	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CAGTATCAAGGcacacacacac	0.243													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77410192	77410192	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77410192delC								LMO7 (976188 upstream) : KCTD12 (44112 downstream)																							tgtgcgcactccaacctgggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87687818	87687818	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87687818delG								None (None upstream) : SLITRK5 (637052 downstream)																							TCTAGTACCTGGAGCATTGCC	0.299													4	2	---	---	---	---	
OXGR1	27199	broad.mit.edu	37	13	97639814	97639815	+	Frame_Shift_Ins	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97639814_97639815insT	uc001vmx.1	-	4	443_444	c.199_200insA	c.(199-201)AGCfs	p.S67fs	OXGR1_uc010afr.1_Frame_Shift_Ins_p.S67fs	NM_080818	NP_543008	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	67	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			GATGGTGCTGCTCTTCCAAGGT	0.470													13	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107466686	107466687	+	IGR	INS	-	AGGA	AGGA			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107466686_107466687insAGGA								ARGLU1 (246172 upstream) : FAM155A (354193 downstream)																							gaagggaagggaggaaggaagg	0.000													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108273338	108273339	+	Intron	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108273338_108273339delGT	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						gagtgtgtgcgtgtgtgtgtgt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111704445	111704445	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111704445delA								ANKRD10 (137029 upstream) : ARHGEF7 (63179 downstream)																							CTCACGTGAGAAGCAGGTCAC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114976330	114976331	+	IGR	INS	-	ACACACAC	ACACACAC	rs141932597	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114976330_114976331insACACACAC								RASA3 (78235 upstream) : CDC16 (24031 downstream)																							atttcattgatacacacacaca	0.267													4	2	---	---	---	---	
CDC16	8881	broad.mit.edu	37	13	115008296	115008296	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115008296delC	uc001vuk.1	+						CDC16_uc010tkm.1_3'UTR|CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894	Q13042	CDC16_HUMAN	anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|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 K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			ccgccccctgccccgggaaca	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19009534	19009534	+	IGR	DEL	G	-	-	rs61974093		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19009534delG								None (None upstream) : OR11H12 (368060 downstream)																							agttgagtgcgcacatcacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19040400	19040400	+	IGR	DEL	T	-	-	rs113500961		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19040400delT								None (None upstream) : OR11H12 (337194 downstream)																							ggttcaactctgtgagttgaa	0.000													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19327800	19327801	+	IGR	DEL	GT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19327800_19327801delGT								None (None upstream) : OR11H12 (49793 downstream)																							AGATTtgtgcgtgtgtgtgtgt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35845234	35845235	+	IGR	DEL	CA	-	-	rs57568570		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35845234_35845235delCA								KIAA0391 (58561 upstream) : NFKBIA (25482 downstream)																							cacgcgcgcgcacacacacaca	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	43978241	43978242	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43978241_43978242insA								None (None upstream) : FSCB (995113 downstream)																							aggaaggaaggagggagggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44249486	44249487	+	IGR	DEL	TG	-	-	rs12886619	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44249486_44249487delTG								None (None upstream) : FSCB (723868 downstream)																							cacacacacatgcacacacaca	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	52602184	52602185	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52602184_52602185insA								NID2 (66238 upstream) : PTGDR (132246 downstream)																							aatgaaaagtcaaaaaataaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56534461	56534461	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56534461delT								C14orf34 (271069 upstream) : PELI2 (50632 downstream)																							CCTGTGGCCCTTTTAACCCAG	0.398													4	2	---	---	---	---	
C14orf135	64430	broad.mit.edu	37	14	60579417	60579417	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60579417delA	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		GTCTTGGGGGAAAAAAAAGTG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62722939	62722944	+	IGR	DEL	TTGTTG	-	-	rs113403049		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62722939_62722944delTTGTTG								FLJ43390 (125707 upstream) : KCNH5 (451003 downstream)																							GTATAGCTTTttgttgttgttgttgt	0.228													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62918563	62918564	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62918563_62918564insT								FLJ43390 (321331 upstream) : KCNH5 (255383 downstream)																							CTGCTAACttcttttttttttg	0.198													4	2	---	---	---	---	
PPP2R5E	5529	broad.mit.edu	37	14	63954624	63954625	+	Intron	INS	-	A	A	rs150918365	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63954624_63954625insA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		ATCAAGGTTTTAGTAACTTCCT	0.342													1	5	---	---	---	---	
TMEM229B	161145	broad.mit.edu	37	14	67943884	67943884	+	Intron	DEL	A	-	-	rs33935509		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67943884delA	uc001xjk.2	-						TMEM229B_uc001xjj.1_Intron	NM_182526	NP_872332	Q8NBD8	T229B_HUMAN	transmembrane protein 229B							integral to membrane				central_nervous_system(1)	1						actccatctcaaaaaaaaaaa	0.184													3	3	---	---	---	---	
SLC39A9	55334	broad.mit.edu	37	14	69912739	69912741	+	Intron	DEL	GTT	-	-	rs111347808		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69912739_69912741delGTT	uc001xle.2	+						SLC39A9_uc010aqx.2_Intron|SLC39A9_uc001xlf.3_Intron|SLC39A9_uc001xlg.3_Intron	NM_018375	NP_060845	Q9NUM3	S39A9_HUMAN	solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		tactgaactcgttgttgttgttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	89426325	89426325	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89426325delC								TTC8 (81991 upstream) : FOXN3 (196192 downstream)																							TTCAAGTGATCCAAGGAAGCT	0.478													1	5	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89895876	89895876	+	Intron	DEL	T	-	-	rs66521722		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89895876delT	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						ACACAACTGATTTTTTTTTTT	0.443													3	4	---	---	---	---	
TTC7B	145567	broad.mit.edu	37	14	91258920	91258922	+	Intron	DEL	CAA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91258920_91258922delCAA	uc001xyp.2	-							NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)				gactctgtctcaacaacaacaac	0.192													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95273528	95273528	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95273528delT								GSC (37029 upstream) : DICER1 (279037 downstream)																							GCTTGTCCCCTTTTTCCTACT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96060926	96060927	+	IGR	INS	-	G	G	rs145048453	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96060926_96060927insG								GLRX5 (49871 upstream) : TCL6 (55908 downstream)																							agcttctctcatttccttcctc	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97181919	97181919	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97181919delG								PAPOLA (148473 upstream) : VRK1 (81765 downstream)																							tgctttttttgaagacagggt	0.154													4	2	---	---	---	---	
CCDC85C	317762	broad.mit.edu	37	14	100034090	100034090	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100034090delA	uc010avr.2	-							NM_001144995	NP_001138467	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C												0						tgaacttgggaggaggagctt	0.010													4	2	---	---	---	---	
WDR25	79446	broad.mit.edu	37	14	100950800	100950801	+	Intron	DEL	GG	-	-	rs140989477	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100950800_100950801delGG	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25												0		Melanoma(154;0.212)				ACAGAGAATTGgtgtgtgtgtg	0.381													4	2	---	---	---	---	
RAGE	5891	broad.mit.edu	37	14	102750421	102750421	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102750421delG	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041	Q9UQ07	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						aactttccctgggtgtgctgc	0.000													4	2	---	---	---	---	
CINP	51550	broad.mit.edu	37	14	102821856	102821856	+	Intron	DEL	A	-	-	rs113572507		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102821856delA	uc001ylv.1	-						CINP_uc001ylu.1_Intron	NM_032630	NP_116019	Q9BW66	CINP_HUMAN	cyclin-dependent kinase 2-interacting protein						cell cycle|cell division|DNA repair|DNA replication	nucleus	protein binding			large_intestine(1)	1						catatcatggaaaaaaaaaaa	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104671002	104671005	+	IGR	DEL	TCTG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104671002_104671005delTCTG								KIF26A (23768 upstream) : C14orf180 (375051 downstream)																							catccatccatctgtccatccatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20012963	20012963	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20012963delA								None (None upstream) : GOLGA6L6 (724131 downstream)																							tcttgtttttatgtgaagata	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21903812	21903812	+	IGR	DEL	A	-	-	rs71399695		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21903812delA								NF1P1 (769187 upstream) : LOC646214 (28702 downstream)																							ATTGCAGGAGAAAGGGGGAGA	0.299													2	7	---	---	---	---	
TUBGCP5	114791	broad.mit.edu	37	15	22862068	22862068	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22862068delT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron|TUBGCP5_uc010axz.1_Intron	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		ttctttttccttttttttttt	0.159													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25882051	25882051	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25882051delA								UBE3A (197923 upstream) : ATP10A (41811 downstream)																							cggcacactgaaaaaggcata	0.000													4	2	---	---	---	---	
OCA2	4948	broad.mit.edu	37	15	28233296	28233297	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28233296_28233297insA	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CAGGGATGGGGGTAAATGGTCC	0.545									Oculocutaneous_Albinism				4	2	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41308143	41308143	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41308143delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						actctgtctcaaaaaaaaaaa	0.149													6	3	---	---	---	---	
CASC4	113201	broad.mit.edu	37	15	44677105	44677106	+	Intron	INS	-	A	A	rs137866986		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44677105_44677106insA	uc001zto.1	+						CASC4_uc001ztp.2_Intron|CASC4_uc001ztq.2_Intron	NM_138423	NP_612432	Q6P4E1	CASC4_HUMAN	cancer susceptibility candidate 4 isoform a							integral to membrane				ovary(1)	1		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)		gactgcatcttaaaaaaaaaaa	0.000													5	3	---	---	---	---	
SLC12A1	6557	broad.mit.edu	37	15	48526949	48526950	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48526949_48526950insA	uc001zwn.3	+						SLC12A1_uc010uew.1_Intron|SLC12A1_uc010bem.2_Intron|SLC12A1_uc010uex.1_Intron|SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	gactctgtctcaaaaaaaaaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	51410187	51410187	+	IGR	DEL	A	-	-	rs36107143		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51410187delA								TNFAIP8L3 (12714 upstream) : CYP19A1 (90068 downstream)																							AGCTTAGCCCAAAAATTGAAG	0.408													4	2	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52796251	52796251	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52796251delC	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		Gtttctccttctttttttttt	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60002644	60002644	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60002644delC								BNIP2 (21002 upstream) : FOXB1 (293777 downstream)																							tttctagagtcccactgtgag	0.104													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61447223	61447223	+	Intron	DEL	A	-	-	rs34780771		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61447223delA	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						gtggagttctaatatacagta	0.139													2	4	---	---	---	---	
PLEKHO2	80301	broad.mit.edu	37	15	65155719	65155722	+	Intron	DEL	TGTG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65155719_65155722delTGTG	uc002anv.2	+						PLEKHO2_uc010bgz.2_Intron|PLEKHO2_uc002anw.2_Intron	NM_025201	NP_079477	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O											ovary(1)|lung(1)	2						tgtgtgtgtttgtgtgtgtgtgtg	0.441													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82052996	82052996	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82052996delC								TMC3 (386578 upstream) : MEX3B (281132 downstream)																							TGTGGCCTAACCCCAGGCTTT	0.502													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86561755	86561756	+	IGR	DEL	TG	-	-	rs10564091		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86561755_86561756delTG								KLHL25 (223566 upstream) : AGBL1 (123486 downstream)																							TGCATCCTTCtgtgtgtgtgtg	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96918836	96918836	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96918836delT								NR2F2 (35346 upstream) : SPATA8 (407843 downstream)																							ACCTGGGttcttttttttttt	0.124													5	3	---	---	---	---	
NPRL3	8131	broad.mit.edu	37	16	139928	139928	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:139928delC	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc010uuc.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN	conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1						TGAGGCTGGTCCCCCTCCCCA	0.637													4	2	---	---	---	---	
TPSG1	25823	broad.mit.edu	37	16	1276602	1276602	+	5'Flank	DEL	A	-	-	rs67870503		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1276602delA	uc002ckw.2	-							NM_012467	NP_036599	Q9NRR2	TRYG1_HUMAN	transmembrane tryptase preproprotein						proteolysis	integral to plasma membrane	serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)				GGTGCCGTTCACCCCCACCAT	0.642													4	2	---	---	---	---	
C16orf91	283951	broad.mit.edu	37	16	1479113	1479114	+	Intron	INS	-	G	G	rs147810748	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1479113_1479114insG	uc010uvd.1	-							NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951							integral to membrane					0						CACCTGGCTGTGGGTCACTGGG	0.663													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	2832420	2832420	+	IGR	DEL	A	-	-	rs78380471		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2832420delA								TCEB2 (5123 upstream) : PRSS33 (1534 downstream)																							CCTTATTTGTAAGAGTGTTTT	0.209													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6172769	6172769	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6172769delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TTCTGCTGGGTTGCGGAATAT	0.299													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6822860	6822861	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6822860_6822861delTG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_5'Flank	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		GGGATGCATTtgtgtgtgtgtg	0.084													4	2	---	---	---	---	
ABAT	18	broad.mit.edu	37	16	8838229	8838229	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8838229delT	uc002czc.3	+						ABAT_uc002czd.3_Intron|ABAT_uc010buh.2_Intron|ABAT_uc010bui.2_Intron	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	gagccacacatttttttttct	0.000													2	4	---	---	---	---	
ABAT	18	broad.mit.edu	37	16	8846378	8846378	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8846378delG	uc002czc.3	+						ABAT_uc002czd.3_Intron|ABAT_uc010buh.2_Intron|ABAT_uc010bui.2_Intron	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	cactttgggaggccaagggaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9285452	9285454	+	IGR	DEL	TAT	-	-	rs142524514		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9285452_9285454delTAT								C16orf72 (71907 upstream) : GRIN2A (561813 downstream)																							atgatagtgatattgttgatgat	0.005													4	3	---	---	---	---	
TXNDC11	51061	broad.mit.edu	37	16	11804830	11804831	+	Intron	INS	-	CAG	CAG	rs145213289	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11804830_11804831insCAG	uc010buu.1	-						TXNDC11_uc002dbg.1_Intron	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0						TATTAGTGCAACAGCAGCTCCA	0.446													5	3	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12079691	12079691	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12079691delT	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						TTGCCTTATCttttttttttt	0.269			T	CIITA	PMBL|Hodgkin Lymphona|								4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12419065	12419065	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12419065delT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						ACTATAGCCCTTCCAGTGTGA	0.403													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12645304	12645304	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12645304delT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						cccagcatgcttttaaaaata	0.134													4	2	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12889207	12889207	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12889207delT	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						GTCATGCAACttttttttttt	0.279													4	2	---	---	---	---	
SHISA9	729993	broad.mit.edu	37	16	13297154	13297155	+	Intron	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13297154_13297155insG	uc010uyy.1	+							NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						CCCTAAAGGGTGGGGAGAGTTT	0.505													5	4	---	---	---	---	
C16orf88	400506	broad.mit.edu	37	16	19727868	19727869	+	Intron	INS	-	AT	AT	rs139515325	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19727868_19727869insAT	uc002dgq.2	-						IQCK_uc002dgr.2_Intron|IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_5'Flank|IQCK_uc010bwc.2_5'Flank|IQCK_uc010vau.1_5'Flank	NM_001012991	NP_001013009	Q1ED39	CP088_HUMAN	hypothetical protein LOC400506							nucleolus					0						TGGACAGGTGAATATATATGGA	0.475													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22424222	22424223	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22424222_22424223insT								CDR2 (38284 upstream) : RRN3P3 (6644 downstream)																							CTCAttcttccttttttttgag	0.084													4	2	---	---	---	---	
COG7	91949	broad.mit.edu	37	16	23462151	23462152	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23462151_23462152insA	uc002dlo.2	-							NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)		gaccctgtctcaaaaaaaaaaa	0.124													5	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	24085456	24085456	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24085456delA	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	actccatctcaaaaaaaaaaa	0.194													4	3	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	25939696	25939696	+	Intron	DEL	T	-	-	rs57863281		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25939696delT	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		tattaaaaaataaaatagaaG	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29081118	29081119	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29081118_29081119insA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		gagattctgtcaaaaaaaaaaa	0.178													5	3	---	---	---	---	
ITGAL	3683	broad.mit.edu	37	16	30489046	30489047	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30489046_30489047insA	uc002dyi.3	+						ITGAL_uc010veu.1_Intron|ITGAL_uc002dyj.3_Intron|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor						blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)	gccatctctacaaaaaaaaaaa	0.020													4	2	---	---	---	---	
ITGAM	3684	broad.mit.edu	37	16	31343193	31343196	+	3'UTR	DEL	TGTC	-	-	rs4990418		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31343193_31343196delTGTC	uc002ebq.2	+	30					ITGAM_uc002ebr.2_3'UTR|ITGAM_uc010can.2_3'UTR	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						tgtgtgcaagtgtctgtgtgcaag	0.230													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32847247	32847247	+	IGR	DEL	T	-	-	rs112612876		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32847247delT								TP53TG3B (158369 upstream) : SLC6A10P (41550 downstream)																							ctgcttaaccttttttgattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33522699	33522699	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33522699delT								SLC6A10P (626236 upstream) : MIR1826 (442809 downstream)																							ATATTTACCCTTACCTACAAG	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33530019	33530019	+	IGR	DEL	T	-	-	rs111564755		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33530019delT								SLC6A10P (633556 upstream) : MIR1826 (435489 downstream)																							AACAGCACTGTTTTTAAAGAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33860412	33860413	+	IGR	DEL	AA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33860412_33860413delAA								SLC6A10P (963949 upstream) : MIR1826 (105095 downstream)																							GGTTGAACTCAAAGTCATTGCT	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33919622	33919622	+	IGR	DEL	C	-	-	rs138108780		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33919622delC								None (None upstream) : MIR1826 (45886 downstream)																							aggttcaactctttgggatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33951847	33951847	+	IGR	DEL	T	-	-	rs78456927	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33951847delT								None (None upstream) : MIR1826 (13661 downstream)																							gcctcccaaattgctgggatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33952323	33952323	+	IGR	DEL	A	-	-	rs62026796	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33952323delA								None (None upstream) : MIR1826 (13185 downstream)																							CATTCAGAAGATTTTACATGC	0.552													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33976749	33976749	+	IGR	DEL	G	-	-	rs111283986		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33976749delG								MIR1826 (11157 upstream) : UBE2MP1 (427053 downstream)																							ggcctatggtgaaaaaaggaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46466141	46466142	+	IGR	INS	-	T	T	rs143190748	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46466141_46466142insT								None (None upstream) : ANKRD26P1 (37107 downstream)																							ACACTCTAATCTTTAAAAAATA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49305152	49305153	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49305152_49305153insA								N4BP1 (661032 upstream) : CBLN1 (7058 downstream)																							TACCACTCCCCAAAAAAAAACA	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49971170	49971171	+	IGR	INS	-	GC	GC	rs112385465		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49971170_49971171insGC								ZNF423 (110252 upstream) : TMEM188 (88018 downstream)																							AAGCTGTGTGTGCGCGcacaca	0.401													4	2	---	---	---	---	
GPR97	222487	broad.mit.edu	37	16	57715290	57715295	+	Intron	DEL	GCGCGT	-	-	rs148784081	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57715290_57715295delGCGCGT	uc002emh.2	+						GPR97_uc010vhv.1_Intron|GPR97_uc010cdd.2_Intron|GPR97_uc010cde.2_Intron	NM_170776	NP_740746	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1						gtgtgtgtgcgcgcgtgcgtgCGCGc	0.019													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63095669	63095669	+	IGR	DEL	C	-	-	rs72787829	byFrequency	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63095669delC								None (None upstream) : None (None downstream)																							ttgtctggtgccccaaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66902528	66902528	+	IGR	DEL	A	-	-	rs112635603		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66902528delA								CA7 (14481 upstream) : PDP2 (11908 downstream)																							cttcatctccaaaaaaaaaaa	0.000													3	5	---	---	---	---	
PLA2G15	23659	broad.mit.edu	37	16	68285760	68285760	+	Intron	DEL	C	-	-	rs76383204		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68285760delC	uc002evr.2	+						PLA2G15_uc010vld.1_Intron|PLA2G15_uc010vle.1_Intron|PLA2G15_uc010vlf.1_Intron	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)						fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						gagactgtctcaaaaaaaaaa	0.234													4	2	---	---	---	---	
ZFP90	146198	broad.mit.edu	37	16	68598744	68598745	+	3'UTR	INS	-	TTT	TTT	rs34979386		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68598744_68598745insTTT	uc010cff.2	+	5					ZFP90_uc002ewb.2_3'UTR|ZFP90_uc002ewc.2_3'UTR|ZFP90_uc002ewd.2_3'UTR|ZFP90_uc002ewe.2_3'UTR	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CAGTAGACAGATTTTTTTTTTT	0.371													3	3	---	---	---	---	
CLEC18A	348174	broad.mit.edu	37	16	69989687	69989690	+	Intron	DEL	TGAT	-	-	rs138298265		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69989687_69989690delTGAT	uc010vlo.1	+						CLEC18C_uc002exy.2_Intron|CLEC18A_uc002exz.2_Intron|CLEC18A_uc002eya.2_Intron|CLEC18A_uc010vlp.1_Intron	NM_001136214	NP_001129686	A5D8T8	CL18A_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						GTTCAGGAGCTGATATCACTGCCA	0.324													4	2	---	---	---	---	
ATXN1L	342371	broad.mit.edu	37	16	71877778	71877779	+	5'Flank	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71877778_71877779delTG	uc002fbd.2	+						ATXN1L_uc010vmi.1_5'Flank	NM_001137675	NP_001131147	P0C7T5	ATX1L_HUMAN	ataxin 1-like							dendrite|nucleus	binding				0						tgtgtgtgtctgtgtgtgtgtc	0.252													4	2	---	---	---	---	
PKD1L3	342372	broad.mit.edu	37	16	71987960	71987961	+	Intron	INS	-	C	C	rs9888745	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71987960_71987961insC	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0						aaaaaaaaaaaGGATTGCTTAC	0.213													8	8	---	---	---	---	
HTA	283902	broad.mit.edu	37	16	73125135	73125135	+	5'Flank	DEL	A	-	-	rs71692673		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73125135delA	uc010vmq.1	+							NR_027756				Homo sapiens cDNA clone IMAGE:4544545, partial cds.												0						gaaagcggggaaaaaaaaaaa	0.229													4	2	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74643616	74643617	+	5'Flank	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74643616_74643617insT	uc002fcy.3	-						GLG1_uc002fcx.2_5'Flank|GLG1_uc002fcw.3_5'Flank|GLG1_uc002fcz.3_5'Flank	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						TGAACAttttcttttttttttt	0.163													5	3	---	---	---	---	
CFDP1	10428	broad.mit.edu	37	16	75345669	75345671	+	Intron	DEL	TTT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75345669_75345671delTTT	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1						ACCTTTACAAttttttttttttt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76606505	76606505	+	IGR	DEL	T	-	-	rs67122453		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76606505delT								CNTNAP4 (13370 upstream) : MON1B (618331 downstream)																							gttttttgtgttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85401451	85401451	+	IGR	DEL	T	-	-	rs141841583		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85401451delT								FAM92B (255337 upstream) : KIAA0182 (243578 downstream)																							AATAAGAttcttttttttttt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87255527	87255529	+	Intron	DEL	CAC	-	-	rs143019650		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87255527_87255529delCAC	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		tcatcataatcaccaccatcacc	0.000													3	3	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89402181	89402181	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89402181delG	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GACAGTGAGAGGCCCCAGTGT	0.567													4	2	---	---	---	---	
MYO1C	4641	broad.mit.edu	37	17	1385975	1385976	+	Intron	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1385975_1385976insG	uc002fsp.2	-						MYO1C_uc002fsn.2_Intron|MYO1C_uc002fso.2_Intron|MYO1C_uc010vqj.1_Intron|MYO1C_uc010vqk.1_Intron	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a						mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		cctcccctcccctcccgcactg	0.272													2	4	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2739927	2739936	+	Intron	DEL	AAAACAAAAC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2739927_2739936delAAAACAAAAC	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						ctcagtctcaaaaacaaaacaaaacaaaac	0.000													2	4	---	---	---	---	
KIF1C	10749	broad.mit.edu	37	17	4906333	4906334	+	Intron	INS	-	T	T	rs79714052		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4906333_4906334insT	uc002gan.1	+							NM_006612	NP_006603	O43896	KIF1C_HUMAN	kinesin family member 1C						microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2						Gtttgcttgtcttttttttttt	0.267													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9859754	9859754	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9859754delT	uc002gmg.1	-						GAS7_uc010vvc.1_Intron|GAS7_uc002gmh.1_Intron|GAS7_uc010vvd.1_Intron|GAS7_uc002gmi.2_Intron|GAS7_uc002gmj.1_Intron|GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						CAAATTCCTCTTTCCAGGTGA	0.582			T	MLL	AML*								4	2	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11539310	11539313	+	Intron	DEL	TTTA	-	-	rs5819330		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11539310_11539313delTTTA	uc002gne.2	+							NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		tttttgtttgtttatttgtttgtt	0.162													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13382064	13382065	+	IGR	DEL	AG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13382064_13382065delAG								ELAC2 (460705 upstream) : HS3ST3A1 (16941 downstream)																							ggagaaacgaagagagagagag	0.297													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16759980	16759981	+	IGR	INS	-	GT	GT	rs2882121		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16759980_16759981insGT								LOC162632 (52161 upstream) : TNFRSF13B (72868 downstream)																							cagagaggaaagactgagaccc	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16885575	16885575	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16885575delC								TNFRSF13B (10173 upstream) : MPRIP (60532 downstream)																							AGAGAGTGGACTTAGTACACT	0.572													4	2	---	---	---	---	
LRRC48	83450	broad.mit.edu	37	17	17875942	17875942	+	5'Flank	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17875942delG	uc010vxd.1	+						TOM1L2_uc002grz.3_5'Flank|TOM1L2_uc002gry.3_5'Flank|TOM1L2_uc010vwy.1_5'Flank|TOM1L2_uc010cpr.2_5'Flank|TOM1L2_uc010vwz.1_5'Flank|TOM1L2_uc010vxa.1_5'Flank|TOM1L2_uc010vxb.1_5'Flank|LRRC48_uc002gsa.2_5'Flank|LRRC48_uc010vxc.1_5'Flank|LRRC48_uc002gsb.2_5'Flank	NM_001130090	NP_001123562	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48 isoform a							cytoplasm				pancreas(1)	1	all_neural(463;0.228)					CGCCCCCAAAGGGGAAGCTGC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21237414	21237417	+	IGR	DEL	CCCT	-	-	rs10587360		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21237414_21237417delCCCT								MAP2K3 (18865 upstream) : KCNJ12 (42282 downstream)																							gagcagagacccctccctcttaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21248150	21248151	+	IGR	INS	-	C	C	rs142379650		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21248150_21248151insC								MAP2K3 (29601 upstream) : KCNJ12 (31548 downstream)																							ACAACAGTGGTCatacctctgg	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21327654	21327655	+	IGR	DEL	AC	-	-	rs5819767		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21327654_21327655delAC								KCNJ12 (4475 upstream) : C17orf51 (103917 downstream)																							GCCCGCCCCAACCCCCAGCCCC	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22246412	22246413	+	IGR	INS	-	T	T	rs141289874		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22246412_22246413insT								FLJ36000 (333342 upstream) : None (None downstream)																							tcagaatcttcttgtgatgttt	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25289537	25289538	+	IGR	INS	-	T	T	rs147625618		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25289537_25289538insT								None (None upstream) : WSB1 (331568 downstream)																							CCCACCGTGGCTTTTGCCCCCG	0.639													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25304776	25304777	+	IGR	INS	-	AC	AC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25304776_25304777insAC								None (None upstream) : WSB1 (316329 downstream)																							tgcatatatatacaTGAATTTA	0.119													4	2	---	---	---	---	
KIAA0100	9703	broad.mit.edu	37	17	26950601	26950601	+	Intron	DEL	A	-	-	rs35696171		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26950601delA	uc002hbu.2	-						KIAA0100_uc002hbt.2_5'Flank	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)					CACCATGAGGAAAAAAAAAAA	0.368													2	5	---	---	---	---	
UNC45B	146862	broad.mit.edu	37	17	33502526	33502526	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33502526delA	uc002hja.2	+						UNC45B_uc002hjb.2_Intron|UNC45B_uc002hjc.2_Intron|UNC45B_uc010cto.2_Intron	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1						cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				caggagagggaaggttccagg	0.000													4	2	---	---	---	---	
CWC25	54883	broad.mit.edu	37	17	36962070	36962070	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36962070delT	uc002hqu.2	-						CWC25_uc010wdv.1_Intron|CWC25_uc010wdw.1_Intron	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49												0						GTTAAGAGACttttttttttt	0.030													3	3	---	---	---	---	
THRA	7067	broad.mit.edu	37	17	38243668	38243669	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38243668_38243669delCA	uc002htw.2	+						THRA_uc010cwp.1_Intron|THRA_uc002htv.2_Intron|THRA_uc002htx.2_Intron	NM_003250	NP_003241	P10827	THA_HUMAN	thyroid hormone receptor, alpha isoform 2						negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter	cytosol|nucleoplasm	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding				0	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Levothyroxine(DB00451)|Liothyronine(DB00279)	agcacacaggcacacacacaca	0.025													3	3	---	---	---	---	
TNS4	84951	broad.mit.edu	37	17	38638838	38638839	+	Intron	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38638838_38638839delAC	uc010cxb.2	-						TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			tctactaaagacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42675844	42675845	+	IGR	DEL	TA	-	-	rs150952024		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42675844_42675845delTA								FZD2 (38937 upstream) : C17orf104 (58137 downstream)																							cagccatccctagaccacccct	0.139													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46092485	46092485	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46092485delG								CDK5RAP3 (33339 upstream) : COPZ2 (11050 downstream)																							GAGAGTGGAAGGAAGAAGAGA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46103486	46103487	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46103486_46103487delAC								CDK5RAP3 (44340 upstream) : COPZ2 (48 downstream)																							CCTTATATGAacacacacacac	0.490											OREG0024510	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46485216	46485217	+	Intron	INS	-	A	A	rs71366874		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46485216_46485217insA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						actttgtctccaaaaaaaaaaa	0.183													4	2	---	---	---	---	
PHOSPHO1	162466	broad.mit.edu	37	17	47305609	47305616	+	Intron	DEL	TCCTTCCT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47305609_47305616delTCCTTCCT	uc010wlv.1	-						PHOSPHO1_uc002ios.2_Intron	NM_178500	NP_848595	Q8TCT1	PHOP1_HUMAN	phosphatase, orphan 1 isoform 2						regulation of bone mineralization		metal ion binding|phosphoethanolamine/phosphocholine phosphatase activity				0			Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)		Choline(DB00122)	cctgtctctctccttccttccttccttc	0.192													6	3	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	58777535	58777535	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58777535delA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			accctgtctcaaaaaaaaaaa	0.199													4	2	---	---	---	---	
TEX2	55852	broad.mit.edu	37	17	62271891	62271891	+	Intron	DEL	T	-	-	rs11352763		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62271891delT	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)		TACCGCAGAATCACCACACAT	0.279													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70916586	70916586	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70916586delA	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						tgggccttccacctggaatgc	0.000													4	2	---	---	---	---	
C17orf77	146723	broad.mit.edu	37	17	72585440	72585440	+	Intron	DEL	T	-	-	rs35927928		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72585440delT	uc002jla.1	+						CD300LD_uc002jkz.2_Intron	NM_152460	NP_689673	Q96MU5	CQ077_HUMAN	hypothetical protein LOC146723							extracellular region					0						TTAATCACCCTGAATGAATCC	0.453													2	4	---	---	---	---	
FADS6	283985	broad.mit.edu	37	17	72878071	72878071	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72878071delT	uc002jmd.1	-						FADS6_uc010wrn.1_Intron	NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6						fatty acid biosynthetic process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)					CTGCAAAGCAttttttttttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76665779	76665779	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76665779delC								DNAH17 (196923 upstream) : CYTH1 (4352 downstream)																							CTGGGGTTAGCCCCCCACACC	0.468													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77299934	77299935	+	Intron	DEL	TG	-	-	rs67071194		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77299934_77299935delTG	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			catgtctgcctgtgtgtgtgtg	0.337													4	2	---	---	---	---	
BAIAP2	10458	broad.mit.edu	37	17	79048067	79048068	+	Intron	INS	-	GTGCCTGT	GTGCCTGT	rs138162499	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79048067_79048068insGTGCCTGT	uc002jzg.2	+						BAIAP2_uc002jyz.3_Intron|BAIAP2_uc002jza.2_Intron|BAIAP2_uc002jzc.2_Intron|BAIAP2_uc002jzb.2_Intron|BAIAP2_uc002jzd.2_Intron|BAIAP2_uc002jzf.2_Intron|BAIAP2_uc002jze.2_Intron|BAIAP2_uc010wuh.1_Intron	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2						axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ggctgaaaaaagtgcctgtgtg	0.000													5	4	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80091962	80091963	+	Frame_Shift_Ins	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80091962_80091963insA	uc002kdy.2	-	2	162_163	c.148_149insT	c.(148-150)CATfs	p.H50fs	CCDC57_uc002kdx.1_Intron			Q2TAC2	CCD57_HUMAN	SubName: Full=cDNA FLJ23754 fis, clone HEP17288;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment										ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			AGATGTAAAATGGGGCTGCACC	0.500													4	2	---	---	---	---	
ENOSF1	55556	broad.mit.edu	37	18	685704	685704	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:685704delC	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982	Q7L5Y1	ENOF1_HUMAN	enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1						GGATCCTTAACCCCAAACTTA	0.408													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3596554	3596554	+	Intron	DEL	T	-	-	rs113973080		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3596554delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|FLJ35776_uc010wza.1_Intron|FLJ35776_uc010wzb.1_RNA	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TTAGGAGAACTTTTTTTTTTT	0.224													5	3	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8006022	8006023	+	Intron	INS	-	AAG	AAG	rs142033704	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8006022_8006023insAAG	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				GCAAGAGGTGAAAGGATTCATG	0.505													2	4	---	---	---	---	
TWSG1	57045	broad.mit.edu	37	18	9364647	9364647	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9364647delC	uc002knz.2	+						TWSG1_uc002koa.2_Intron	NM_020648	NP_065699	Q9GZX9	TWSG1_HUMAN	twisted gastrulation precursor											ovary(1)|pancreas(1)	2						caaaaattagccaggtgtggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11114668	11114668	+	IGR	DEL	A	-	-	rs146709465		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11114668delA								FAM38B (412689 upstream) : GNAL (574468 downstream)																							tgtcttaaacaaaaaaaaaaa	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14213076	14213076	+	IGR	DEL	C	-	-	rs75328904		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14213076delC								ZNF519 (80647 upstream) : LOC284233 (124346 downstream)																							GCTAACCTCACTCTCTAAGTC	0.408													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20509327	20509327	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20509327delT								CTAGE1 (511449 upstream) : RBBP8 (3968 downstream)																							ggataacagattttttttttt	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27885735	27885735	+	IGR	DEL	A	-	-	rs35573648		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27885735delA								MIR302F (6809 upstream) : DSC3 (684318 downstream)																							CAACAACAACAAAAAAAAAAA	0.318													2	6	---	---	---	---	
REEP6	92840	broad.mit.edu	37	19	1496700	1496701	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1496700_1496701delTG	uc002ltc.2	+							NM_138393	NP_612402	Q96HR9	REEP6_HUMAN	receptor accessory protein 6							integral to membrane					0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGATAGGAGCtgtgtgtgtgtg	0.431													4	4	---	---	---	---	
ONECUT3	390874	broad.mit.edu	37	19	1768998	1768999	+	Intron	INS	-	GGA	GGA	rs138220122	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1768998_1768999insGGA	uc010xgr.1	+							NM_001080488	NP_001073957	O60422	ONEC3_HUMAN	one cut homeobox 3						endocrine pancreas development		sequence-specific DNA binding				0		Acute lymphoblastic leukemia(61;4.66e-11)|all_hematologic(61;4.59e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gtggaggtgatggtggaggtgg	0.000											OREG0025124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
CSNK1G2	1455	broad.mit.edu	37	19	1968049	1968050	+	Intron	INS	-	T	T	rs113542067	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1968049_1968050insT	uc002lul.3	+						CSNK1G2_uc010dsu.2_5'Flank	NM_001319	NP_001310	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2						sphingolipid metabolic process|Wnt receptor signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity			stomach(1)	1		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCTGCCCCCACCACCCTTC	0.698													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4750055	4750058	+	IGR	DEL	CACA	-	-	rs71930528	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4750055_4750058delCACA								DPP9 (26200 upstream) : C19orf30 (19059 downstream)																							catgcgcgtgcacacacacacaca	0.211													6	3	---	---	---	---	
TMEM146	257062	broad.mit.edu	37	19	5766300	5766301	+	Intron	INS	-	A	A	rs10645590		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5766300_5766301insA	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						cgtctctactgaaaaaaaaaaa	0.000													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6129105	6129105	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6129105delC								RFX2 (18441 upstream) : ACSBG2 (6546 downstream)																							TGCTTCTGTTCAATTCATTCT	0.318													4	2	---	---	---	---	
TNFSF9	8744	broad.mit.edu	37	19	6530031	6530034	+	5'Flank	DEL	AGAC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6530031_6530034delAGAC	uc002mfh.2	+							NM_003811	NP_003802	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily,						apoptosis|cell proliferation|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding			central_nervous_system(1)	1						agagagaaagagacagacagacat	0.000													2	4	---	---	---	---	
PNPLA6	10908	broad.mit.edu	37	19	7609916	7609916	+	Intron	DEL	T	-	-	rs112232890		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7609916delT	uc010xjq.1	+						PNPLA6_uc002mgq.1_Intron|PNPLA6_uc010xjp.1_Intron|PNPLA6_uc002mgr.1_Intron|PNPLA6_uc002mgs.2_Intron	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b						cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						TCCTTGAAACttttttttttt	0.279													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13100121	13100121	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13100121delT								DAND5 (14554 upstream) : NFIX (6463 downstream)																							aaggctggggtgtgtgtgtgt	0.070													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14484571	14484571	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14484571delT								LPHN1 (167574 upstream) : CD97 (7642 downstream)																							agttacttaattttttttttt	0.000													3	4	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17124695	17124698	+	Intron	DEL	TTCC	-	-	rs77591148		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17124695_17124698delTTCC	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						CACTACACAAttccttccttcctt	0.074													3	3	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17994332	17994332	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994332delG	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						GCAGGAACAAGGGGGGGGGGT	0.542													4	2	---	---	---	---	
UPF1	5976	broad.mit.edu	37	19	18973650	18973650	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18973650delA	uc002nkg.2	+						UPF1_uc002nkf.2_Intron|UPF1_uc002nkh.2_Intron	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1						cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2						tctccaaaggaaaaaaaaaaa	0.284													4	2	---	---	---	---	
NCAN	1463	broad.mit.edu	37	19	19362000	19362000	+	3'UTR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19362000delA	uc002nlz.2	+	15					NCAN_uc002nma.2_3'UTR	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor						axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			GATCAGGGTTAAAAAAGCACC	0.453													4	2	---	---	---	---	
ZNF826	664701	broad.mit.edu	37	19	20501708	20501709	+	Intron	INS	-	TTT	TTT	rs111650842		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20501708_20501709insTTT	uc002now.1	-						ZNF826_uc010ecl.1_Intron					Homo sapiens cDNA FLJ44894 fis, clone BRAMY3000692, moderately similar to Zinc finger protein 91.												0						ACGCtttttgcttttttttttt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27865506	27865507	+	IGR	DEL	TC	-	-	rs71224979		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27865506_27865507delTC								None (None upstream) : LOC148189 (415895 downstream)																							gttgaacgtatcttttTTTTTt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29795744	29795744	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29795744delT	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		ATGCCTCTCCTGCCTGCATCA	0.488													4	2	---	---	---	---	
WDR88	126248	broad.mit.edu	37	19	33637298	33637298	+	Intron	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33637298delG	uc002nui.2	+							NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing											ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)					GAAGAGTACTGGGGATGATTG	0.254													6	3	---	---	---	---	
SIPA1L3	23094	broad.mit.edu	37	19	38602538	38602539	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38602538_38602539delCA	uc002ohk.2	+							NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			caggcacatgcacacacacaca	0.168													4	2	---	---	---	---	
NCCRP1	342897	broad.mit.edu	37	19	39686510	39686511	+	5'Flank	INS	-	AG	AG	rs150591748	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39686510_39686511insAG	uc002okq.1	+							NM_001001414	NP_001001414	Q6ZVX7	NCRP1_HUMAN	non-specific cytotoxic cell receptor protein 1						protein catabolic process					ovary(1)	1						gagactccatcagagagagaga	0.248													3	3	---	---	---	---	
NUMBL	9253	broad.mit.edu	37	19	41195371	41195372	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41195371_41195372delCA	uc002oon.2	-						NUMBL_uc010xvq.1_Intron|NUMBL_uc002ooo.2_Intron|NUMBL_uc010xvr.1_Intron	NM_004756	NP_004747	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like						cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process	cytoplasm	protein binding			lung(3)|ovary(1)|breast(1)	5			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CGTACGCGTGcacacacacaca	0.302													4	2	---	---	---	---	
CYP2S1	29785	broad.mit.edu	37	19	41702549	41702549	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41702549delT	uc002opw.2	+						CYP2F1_uc010xvw.1_Intron|CYP2S1_uc010xvx.1_Intron	NM_030622	NP_085125	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity			skin(1)	1						CTTAGGCCACTTTGGAACACA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42749818	42749818	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42749818delA								GSK3A (3082 upstream) : ERF (1900 downstream)																							gaaaaaaaagaaaaaaaaaaa	0.239											OREG0025499	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44209094	44209094	+	IGR	DEL	T	-	-	rs112090823		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44209094delT								PLAUR (34592 upstream) : IRGC (11120 downstream)																							ATGCttttgattttttttttt	0.065													3	3	---	---	---	---	
ZNF284	342909	broad.mit.edu	37	19	44578522	44578522	+	Intron	DEL	A	-	-	rs34757324		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44578522delA	uc002oyg.1	+						ZNF284_uc010ejd.2_Intron	NM_001037813	NP_001032902	Q2VY69	ZN284_HUMAN	zinc finger protein 284						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				tcccggtctcaaaaaaaaaaa	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47514063	47514063	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47514063delA								GRLF1 (5740 upstream) : NPAS1 (9038 downstream)																							aaaaagaaagaaaaaaaaaGT	0.055													4	2	---	---	---	---	
RASIP1	54922	broad.mit.edu	37	19	49240662	49240662	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49240662delC	uc002pki.2	-							NM_017805	NP_060275	Q5U651	RAIN_HUMAN	Ras-interacting protein 1						signal transduction	Golgi stack|perinuclear region of cytoplasm				pancreas(1)	1		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)		CCAGGCCCCACCCCTGCCAGG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49581575	49581576	+	IGR	INS	-	A	A	rs146838826	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49581575_49581576insA								KCNA7 (5377 upstream) : SNRNP70 (6889 downstream)																							aataaaaaatcaaaaaaaaaga	0.000													3	5	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50801658	50801659	+	Intron	INS	-	AC	AC	rs144135989	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50801658_50801659insAC	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		cacacacacatacacacacaca	0.188													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55633620	55633620	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55633620delT								PPP1R12C (4693 upstream) : TNNT1 (10542 downstream)																							ttttctttgcttttttttttt	0.000													4	2	---	---	---	---	
ZNF542	147947	broad.mit.edu	37	19	56889273	56889274	+	3'UTR	INS	-	AGTCCTTT	AGTCCTTT	rs143807509	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56889273_56889274insAGTCCTTT	uc002qmu.3	+	7					ZNF542_uc010ygj.1_3'UTR|ZNF542_uc010ygk.1_3'UTR|ZNF542_uc002qmv.3_3'UTR|ZNF542_uc010etk.2_3'UTR|ZNF542_uc010etj.2_RNA	NR_003127				SubName: Full=cDNA FLJ58906;												0						TCAATGCGGGAAGTCCTTTAGC	0.371													3	3	---	---	---	---	
ZNF586	54807	broad.mit.edu	37	19	58281192	58281193	+	5'UTR	INS	-	C	C	rs140430529	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58281192_58281193insC	uc002qqd.2	+	1					ZNF587_uc002qqb.2_Intron|ZNF586_uc002qqe.2_5'UTR|ZNF586_uc010euh.2_5'UTR|ZNF586_uc002qqf.1_RNA	NM_017652	NP_060122	Q9NXT0	ZN586_HUMAN	zinc finger protein 586						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GAGCCCGCGTTCCCCCCCCGCC	0.698													4	2	---	---	---	---	
RPS5	6193	broad.mit.edu	37	19	58905673	58905674	+	Intron	DEL	TG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58905673_58905674delTG	uc002qsn.2	+						RPS5_uc002qso.2_Intron	NM_001009	NP_001000	P46782	RS5_HUMAN	ribosomal protein S5						endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)		AACTTCAGCCTGTGTGTGTGTG	0.426													4	2	---	---	---	---	
ZNF584	201514	broad.mit.edu	37	19	58926242	58926242	+	Intron	DEL	T	-	-	rs35582780		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58926242delT	uc002qsp.2	+						ZNF584_uc010yia.1_Intron|ZNF584_uc002qsr.2_Intron|ZNF584_uc010yib.1_Intron	NM_173548	NP_775819	Q8IVC4	ZN584_HUMAN	zinc finger protein 584						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		atAGAAAGGCTTTtttttttc	0.020													4	2	---	---	---	---	
VPS16	64601	broad.mit.edu	37	20	2834054	2834055	+	Intron	DEL	AA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2834054_2834055delAA	uc002whe.2	+						VPS16_uc002whf.2_Intron|VPS16_uc002whd.2_Intron	NM_022575	NP_072097	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 isoform 1						intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)|skin(1)	4						aaacaacaacaaaaaaaaaaaa	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20808790	20808791	+	IGR	INS	-	TGA	TGA			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20808790_20808791insTGA								RALGAPA2 (115524 upstream) : PLK1S1 (297833 downstream)																							aaggaaggaagggagggaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22586629	22586630	+	IGR	INS	-	AA	AA	rs145423056	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22586629_22586630insAA								FOXA2 (20528 upstream) : SSTR4 (429427 downstream)																							AGCATTGGCACAGGGGTGTGGT	0.455													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23129495	23129496	+	IGR	DEL	AC	-	-	rs112339727		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23129495_23129496delAC								CD93 (62518 upstream) : NXT1 (201877 downstream)																							AAACAAAACAacacacacacac	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25742238	25742239	+	IGR	INS	-	GAC	GAC			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25742238_25742239insGAC								ZNF337 (64769 upstream) : FAM182B (1863 downstream)																							atgatgatgatggtgatggtga	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26075417	26075418	+	IGR	INS	-	TCC	TCC	rs147363891		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26075417_26075418insTCC								FAM182A (7865 upstream) : C20orf191 (8635 downstream)																							tctcaccatcatcatcctcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29431750	29431750	+	IGR	DEL	G	-	-	rs112192023		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29431750delG								None (None upstream) : FRG1B (180129 downstream)																							gtgtagatgtgtttttctctt	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29439508	29439508	+	IGR	DEL	A	-	-	rs111942506		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29439508delA								None (None upstream) : FRG1B (172371 downstream)																							actccgtctcaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29562213	29562215	+	IGR	DEL	GTG	-	-	rs73620363		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29562213_29562215delGTG								None (None upstream) : FRG1B (49664 downstream)																							AGCTCCCTCTGTGGTAAGGCTGC	0.389													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29595858	29595859	+	IGR	DEL	AA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29595858_29595859delAA								None (None upstream) : FRG1B (16020 downstream)																							ttgtccctacaaaaaaAAAATC	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29602221	29602222	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29602221_29602222insG								None (None upstream) : FRG1B (9657 downstream)																							aaacattcaattgggaaagaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29604164	29604164	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29604164delC								None (None upstream) : FRG1B (7715 downstream)																							CAATTTGTTTCAGGAGAAAAT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29604550	29604553	+	IGR	DEL	AAAC	-	-	rs77273072		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29604550_29604553delAAAC								None (None upstream) : FRG1B (7326 downstream)																							caaatgagttaaacaaaaatctta	0.010													6	3	---	---	---	---	
C20orf112	140688	broad.mit.edu	37	20	31067749	31067749	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31067749delC	uc002wxu.3	-						C20orf112_uc010gec.2_Intron|C20orf112_uc002wxv.3_Intron|C20orf112_uc002wxw.1_Intron	NM_080616	NP_542183	Q96MY1	CT112_HUMAN	hypothetical protein LOC140688												0						CAGTCTCTCTCCACCCAGCTT	0.567													4	2	---	---	---	---	
CBFA2T2	9139	broad.mit.edu	37	20	32161289	32161290	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32161289_32161290insT	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_5'Flank	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2						tcttcttcttcttttttttttt	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32493773	32493773	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32493773delT								CHMP4B (51604 upstream) : RALY (87959 downstream)																							tttttattaattttttttttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32914668	32914669	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32914668_32914669insA								AHCY (15060 upstream) : ITCH (36393 downstream)																							ctccatctcacaaaaaaaaaaa	0.094													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34107499	34107499	+	IGR	DEL	T	-	-	rs11475353		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34107499delT								CEP250 (7697 upstream) : C20orf173 (1073 downstream)																							GTAttgtttcttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	35163517	35163517	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35163517delA	uc002xfk.3	-											Homo sapiens, clone IMAGE:5165100, mRNA.																		atccaaatgcaaaaaaaagga	0.000													4	2	---	---	---	---	
SAMHD1	25939	broad.mit.edu	37	20	35555435	35555436	+	Intron	DEL	AT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35555435_35555436delAT	uc002xgh.1	-							NM_015474	NP_056289	Q9Y3Z3	SAMH1_HUMAN	SAM domain- and HD domain-containing protein 1						defense response to virus|innate immune response|regulation of innate immune response	nucleus	metal ion binding|phosphoric diester hydrolase activity				0		Myeloproliferative disorder(115;0.00878)				aaacaaaagcatatatatatat	0.094													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42123180	42123181	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42123180_42123181insA								SFRS6 (30938 upstream) : L3MBTL (13169 downstream)																							aagattgtctcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
SLC2A10	81031	broad.mit.edu	37	20	45339517	45339517	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45339517delT	uc002xsl.2	+							NM_030777	NP_110404	O95528	GTR10_HUMAN	solute carrier family 2 member 10							endomembrane system|integral to membrane|perinuclear region of cytoplasm|plasma membrane	D-glucose transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				ttatcttttcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46570817	46570817	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46570817delA								SULF2 (155457 upstream) : LOC284749 (417837 downstream)																							ttttgtcaataaagttttatt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46890561	46890561	+	IGR	DEL	T	-	-	rs3092760		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46890561delT								SULF2 (475201 upstream) : LOC284749 (98093 downstream)																							CCAGTTAATATCACGGTTCTG	0.388													3	4	---	---	---	---	
ARFGEF2	10564	broad.mit.edu	37	20	47537357	47537358	+	5'Flank	INS	-	CTCA	CTCA	rs139629508	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47537357_47537358insCTCA	uc002xtx.3	+							NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			ctgtctttctcctttttctttt	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49615503	49615504	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49615503_49615504delAC								MOCS3 (37683 upstream) : KCNG1 (4690 downstream)																							tggagctgagacacacaggggc	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49940718	49940727	+	IGR	DEL	TTGGCCCAGC	-	-	rs67157158		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49940718_49940727delTTGGCCCAGC								KCNG1 (301043 upstream) : NFATC2 (67039 downstream)																							tagggttgatttggcccagcttggcttggg	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50688865	50688865	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50688865delT								SALL4 (269817 upstream) : ZFP64 (11686 downstream)																							gtgttgttGGttttttttttt	0.010													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51041980	51041981	+	IGR	INS	-	C	C	rs146372523	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51041980_51041981insC								ZFP64 (233456 upstream) : TSHZ2 (546896 downstream)																							CGAGGACGCCTCCTGCAGGTTT	0.500													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51088392	51088392	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51088392delA								ZFP64 (279868 upstream) : TSHZ2 (500485 downstream)																							ACCATGAGTTAAAAAAAAAAA	0.308													4	3	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51878763	51878763	+	Intron	DEL	C	-	-	rs2426480	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51878763delC	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			TTGTCTTTTTCTTTTTTTAAC	0.353													4	2	---	---	---	---	
GNAS	2778	broad.mit.edu	37	20	57440031	57440032	+	Intron	DEL	CT	-	-	rs113376325		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57440031_57440032delCT	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			cgcacgcacactctctctctct	0.084			Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59232405	59232405	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59232405delA								MIR646 (348780 upstream) : CDH4 (595154 downstream)																							GACCAGGAAGAAAAAAAAAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59767379	59767379	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59767379delT								MIR646 (883754 upstream) : CDH4 (60180 downstream)																							tattttttCCTTTTTTTTTTA	0.224													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60010931	60010938	+	Intron	DEL	GCCCATGT	-	-	rs113283438		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60010931_60010938delGCCCATGT	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CATCCTGTTGGCCCATGTGCTGGGGAGG	0.529													4	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60274582	60274582	+	Intron	DEL	C	-	-	rs66505986		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60274582delC	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TTCTGGCTCTCCGAGTTGTTG	0.532													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	60804722	60804723	+	5'Flank	DEL	CA	-	-	rs150906642		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60804722_60804723delCA	uc002ycj.1	+											Homo sapiens cDNA FLJ44790 fis, clone BRACE3039288.																		ctccccattccacacacacaaa	0.054													6	3	---	---	---	---	
DIDO1	11083	broad.mit.edu	37	20	61535568	61535569	+	Intron	INS	-	CT	CT	rs150895162	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61535568_61535569insCT	uc002ydr.1	-						DIDO1_uc002yds.1_Intron|DIDO1_uc002ydt.1_Intron|DIDO1_uc002ydu.1_Intron	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c						apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					ATTAAAAATCCCTCTCTGCATT	0.391													6	3	---	---	---	---	
EEF1A2	1917	broad.mit.edu	37	20	62123710	62123713	+	Intron	DEL	GATG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62123710_62123713delGATG	uc002yfd.1	-						EEF1A2_uc002yfe.1_Intron|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			tgggtcaatagatggatggataga	0.000													4	2	---	---	---	---	
PCMTD2	55251	broad.mit.edu	37	20	62884055	62884056	+	5'Flank	INS	-	C	C	rs146601331	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62884055_62884056insC	uc002yil.3	+						PCMTD2_uc002yim.3_5'Flank	NM_018257	NP_060727	Q9NV79	PCMD2_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					cttccctccgtccgaggctcct	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9667741	9667742	+	IGR	DEL	CT	-	-	rs145219527	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9667741_9667742delCT								None (None upstream) : None (None downstream)																							TCATCTGCCCCTCCCCCCGACA	0.515													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9832226	9832227	+	IGR	INS	-	CG	CG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9832226_9832227insCG								None (None upstream) : None (None downstream)																							catcccctagcagagaaccctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10588349	10588349	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10588349delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		acaaatgttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10786167	10786171	+	IGR	DEL	GGAAT	-	-	rs28970962		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10786167_10786171delGGAAT								None (None upstream) : TPTE (120572 downstream)																							ggacacgaaaggaatggaatggaat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10789086	10789090	+	IGR	DEL	TGGAG	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10789086_10789090delTGGAG								None (None upstream) : TPTE (117653 downstream)																							tggaattgaatggagtggagtggag	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10805533	10805537	+	IGR	DEL	AGTGG	-	-	rs150709766		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10805533_10805537delAGTGG								None (None upstream) : TPTE (101206 downstream)																							agtggattgtagtggagtggagtgg	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10815870	10815874	+	IGR	DEL	GATTT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10815870_10815874delGATTT								None (None upstream) : TPTE (90869 downstream)																							gaatggaatggatttgaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10851518	10851518	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10851518delA								None (None upstream) : TPTE (55225 downstream)																							aatggaatggaaaaggaatgg	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10857683	10857687	+	IGR	DEL	GAATA	-	-	rs113195832		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10857683_10857687delGAATA								None (None upstream) : TPTE (49056 downstream)																							gactcaaatggaatagaatggaatc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14360253	14360254	+	IGR	INS	-	A	A	rs151198233		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360253_14360254insA								None (None upstream) : C21orf99 (50233 downstream)																							gcagattctacaaaaaaaaatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14360853	14360853	+	IGR	DEL	A	-	-	rs113034034		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360853delA								None (None upstream) : C21orf99 (49634 downstream)																							aaaactgctcaaaaaaagaaa	0.000													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14373147	14373147	+	IGR	DEL	A	-	-	rs112293037		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14373147delA								None (None upstream) : C21orf99 (37340 downstream)																							aaaactgtctaaaaaaaaaaa	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14493164	14493165	+	IGR	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14493164_14493165insT								C21orf99 (2595 upstream) : POTED (489333 downstream)																							TACATAGTAGAACTATATCTGA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15224593	15224594	+	IGR	DEL	AA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15224593_15224594delAA								C21orf15 (3908 upstream) : C21orf81 (91502 downstream)																							atgccttttcaaaagtttccaa	0.000													5	3	---	---	---	---	
CXADR	1525	broad.mit.edu	37	21	18901656	18901657	+	Intron	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18901656_18901657insG	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron	NM_001338	NP_001329	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		gctttttttttgagacacagtt	0.000													4	2	---	---	---	---	
SYNJ1	8867	broad.mit.edu	37	21	34102684	34102685	+	5'Flank	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34102684_34102685delGA	uc002yqh.2	-						SYNJ1_uc002yqf.2_5'Flank|SYNJ1_uc002yqg.2_5'Flank|SYNJ1_uc002yqi.2_5'Flank|uc002yqj.1_RNA|uc002yqk.2_RNA	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a								inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						acgcacacaggagagagagaga	0.000													4	2	---	---	---	---	
IFNGR2	3460	broad.mit.edu	37	21	34793638	34793639	+	Intron	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34793638_34793639insA	uc002yrp.3	+						IFNGR2_uc002yrq.3_Intron|IFNGR2_uc010gma.2_Intron|IFNGR2_uc002yrr.3_Intron	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)	aactccatctcaaaaaaaaaaa	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35813055	35813056	+	IGR	INS	-	AG	AG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35813055_35813056insAG								FAM165B (37981 upstream) : KCNE1 (5933 downstream)																							gtttttgtgacagagtctcact	0.000													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37192940	37192941	+	Intron	DEL	TG	-	-	rs113454419		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37192940_37192941delTG	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						acaataggtctgtgtgtgtgtg	0.050			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				3	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37204035	37204036	+	Intron	DEL	CT	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37204035_37204036delCT	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						TTTCTACCTCCTCTCTCTCTCT	0.599			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37334429	37334430	+	Intron	DEL	CA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37334429_37334430delCA	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						TCCCTTTACCCACACTCTCAAT	0.391			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				6	3	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37851460	37851460	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37851460delA	uc002yvn.1	-						CLDN14_uc002yvo.1_Intron|CLDN14_uc002yvl.1_Intron|CLDN14_uc002yvm.1_Intron	NM_001146078	NP_001139550	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CTGTGGCCTCAAAACACTGAA	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40276370	40276371	+	IGR	INS	-	GT	GT	rs143157681	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40276370_40276371insGT								ETS2 (79494 upstream) : PSMG1 (271019 downstream)																							GTGGGTGGTCAGTGTGTGCAGT	0.540													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42151669	42151669	+	Intron	DEL	G	-	-	rs67324555		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42151669delG	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				agggacagccgggcctggcaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	43086668	43086669	+	IGR	DEL	CA	-	-	rs3033572		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43086668_43086669delCA								TMPRSS2 (183625 upstream) : NCRNA00111 (12793 downstream)																							CTCTCCTCCTCACACACACATG	0.589													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43270422	43270422	+	Intron	DEL	A	-	-	rs78217838		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43270422delA	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GTGCCCCCCCAACACTCTCCT	0.577													3	3	---	---	---	---	
C2CD2	25966	broad.mit.edu	37	21	43312777	43312777	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43312777delC	uc002yzw.2	-						C2CD2_uc002yzs.2_Intron|C2CD2_uc002yzt.2_Intron|C2CD2_uc002yzu.2_Intron|C2CD2_uc002yzv.2_Intron	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1						gagcatttttcaaaagttccc	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44722244	44722245	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44722244_44722245insA								CRYAA (129331 upstream) : SIK1 (112153 downstream)																							CCACCTGCCCCTGAGGCTGAGG	0.639													4	2	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	17843937	17843937	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17843937delT	uc010gqv.1	+							NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		TTCCttcttcttttttttttt	0.214													3	4	---	---	---	---	
SCARF2	91179	broad.mit.edu	37	22	20789460	20789460	+	Intron	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20789460delT	uc002zsj.1	-						SCARF2_uc002zsk.1_Intron	NM_153334	NP_699165	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2 isoform 1						cell adhesion	integral to membrane	protein binding|receptor activity			breast(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			cagataaccctgcctgtcctt	0.000													2	7	---	---	---	---	
PPM1F	9647	broad.mit.edu	37	22	22283231	22283232	+	Intron	INS	-	C	C	rs146075500	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22283231_22283232insC	uc002zvp.1	-						PPM1F_uc011aik.1_Intron|PPM1F_uc002zvq.2_Intron	NM_014634	NP_055449	P49593	PPM1F_HUMAN	protein phosphatase 1F						apoptosis|protein dephosphorylation	protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(2)|large_intestine(1)|breast(1)|kidney(1)	5	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GCCTCATCCTGCCAGGTCCTTG	0.342													0	9	---	---	---	---	
UPB1	51733	broad.mit.edu	37	22	24926804	24926805	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24926804_24926805insT	uc011ajt.1	+							NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					agaagatgtacttttttttttt	0.020													4	5	---	---	---	---	
PIWIL3	440822	broad.mit.edu	37	22	25149193	25149193	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25149193delA	uc003abd.1	-						PIWIL3_uc011ajx.1_Intron|PIWIL3_uc011ajy.1_Intron|PIWIL3_uc010gut.1_Intron	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3						cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4						tccctagctcaaagtcaaaaa	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25381747	25381748	+	IGR	DEL	GA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25381747_25381748delGA								TMEM211 (46433 upstream) : KIAA1671 (42193 downstream)																							atggtgaggggagagagagaga	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	26821715	26821718	+	IGR	DEL	TCTT	-	-	rs112521148		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26821715_26821718delTCTT								SEZ6L (45281 upstream) : ASPHD2 (3562 downstream)																							cctccctctctctttctttctttc	0.049													4	2	---	---	---	---	
SLC5A1	6523	broad.mit.edu	37	22	32499713	32499714	+	Intron	INS	-	T	T			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32499713_32499714insT	uc003amc.2	+						SLC5A1_uc011alz.1_Intron	NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1						ttgccTCTTGATTTTTTTTTCC	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35997870	35997871	+	IGR	INS	-	TG	TG	rs147336697		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35997870_35997871insTG								RASD2 (47827 upstream) : MB (4941 downstream)																							gtctgtgtatttgtgtgtatgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37348344	37348344	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37348344delA								CSF2RB (11867 upstream) : C22orf33 (38817 downstream)																							CTCTGGTTCCAGTGGCTTAAT	0.557													4	2	---	---	---	---	
ELFN2	114794	broad.mit.edu	37	22	37821409	37821409	+	Intron	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37821409delC	uc003asq.3	-							NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)					GGAAAGGGGTCCCATGCCCAC	0.597													4	2	---	---	---	---	
APOBEC3F	200316	broad.mit.edu	37	22	39451083	39451083	+	3'UTR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39451083delT	uc003aww.2	+	7						NM_145298	NP_660341	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						base conversion or substitution editing|DNA cytosine deamination|innate immune response|interspecies interaction between organisms|negative regulation of retroviral genome replication|negative regulation of transposition|positive regulation of defense response to virus by host|response to virus|viral reproduction	apolipoprotein B mRNA editing enzyme complex|cytosol|mitochondrion	cytidine deaminase activity|dCTP deaminase activity|protein homodimerization activity|RNA binding|zinc ion binding				0	Melanoma(58;0.04)					TCCAAATAtcttttttttttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41383974	41383974	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41383974delA								RBX1 (15308 upstream) : MIR1281 (104543 downstream)																							aactccgtctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41406640	41406640	+	IGR	DEL	A	-	-	rs68116641		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41406640delA								RBX1 (37974 upstream) : MIR1281 (81877 downstream)																							atgctgtctcaaaaaaaaaaa	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41468206	41468207	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41468206_41468207insA								RBX1 (99540 upstream) : MIR1281 (20310 downstream)																							acaagaaattgaaaaaaaaact	0.045													4	2	---	---	---	---	
RANGAP1	5905	broad.mit.edu	37	22	41676099	41676099	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41676099delA	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						actccatctcaaaaaaaaaaa	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	43126338	43126338	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43126338delA								A4GALT (9052 upstream) : ARFGAP3 (66194 downstream)																							GGAAGATACCAAAATCCCATC	0.254													4	2	---	---	---	---	
PARVG	64098	broad.mit.edu	37	22	44590595	44590598	+	Intron	DEL	CATC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44590595_44590598delCATC	uc011aqe.1	+						PARVG_uc003bep.2_Intron|PARVG_uc011aqf.1_Intron|PARVG_uc003beq.2_Intron|PARVG_uc003ber.2_Intron	NM_001137605	NP_001131077	Q9HBI0	PARVG_HUMAN	parvin, gamma						cell-matrix adhesion	cytoplasm|cytoskeleton|focal adhesion	actin binding				0		Ovarian(80;0.024)|all_neural(38;0.0299)				tccacgcattcatccatccatcca	0.000													4	2	---	---	---	---	
KIAA1644	85352	broad.mit.edu	37	22	44676620	44676621	+	Intron	INS	-	C	C	rs141049619	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44676620_44676621insC	uc003bet.2	-							NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				GAGGATGTCAGCCcccatcagg	0.327													4	5	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46856226	46856226	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46856226delA	uc003bhw.1	-							NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		aggaagcttcaagggaggaaa	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47009751	47009752	+	IGR	INS	-	TCG	TCG	rs148719926	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47009751_47009752insTCG								CELSR1 (76684 upstream) : GRAMD4 (12906 downstream)																							CTCAGGAACTCTTTTGCATTTA	0.614													3	5	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47263465	47263466	+	Intron	DEL	CC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47263465_47263466delCC	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		aagaagtcttccacatcgataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47788379	47788380	+	IGR	DEL	CA	-	-	rs75138474		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47788379_47788380delCA								TBC1D22A (218657 upstream) : None (None downstream)																							atcatacacccacacacacaca	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48773315	48773316	+	IGR	INS	-	G	G	rs148696819	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48773315_48773316insG								None (None upstream) : FAM19A5 (111972 downstream)																							GGGGAGGCCATGGGGGGTCctc	0.262													3	5	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	49001148	49001149	+	Intron	INS	-	TGGTGG	TGGTGG	rs147933897	by1000genomes	TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49001148_49001149insTGGTGG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		gatggtgatgatggtgatggcg	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	51072126	51072126	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51072126delC								ARSA (5519 upstream) : SHANK3 (40944 downstream)																							ggattgcagtcccatttactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1895220	1895221	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1895220_1895221insA								ASMT (133247 upstream) : DHRSX (242336 downstream)																							caggtctctgcaaatgtaatga	0.030													4	2	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2232513	2232514	+	Intron	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2232513_2232514insG	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				gaaggggagaaggaaggaagga	0.000													4	10	---	---	---	---	
SCML1	6322	broad.mit.edu	37	X	17756326	17756326	+	Intron	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17756326delA	uc004cyb.2	+						SCML1_uc004cyc.2_Intron|SCML1_uc004cyd.2_Intron|SCML1_uc004cye.2_Intron	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a						anatomical structure morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)					TTGGGAGCAGAGGCGGGAGGC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61804789	61804789	+	IGR	DEL	C	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61804789delC								None (None upstream) : SPIN4 (762319 downstream)																							atttggagcgctttgaggcct	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61805340	61805340	+	IGR	DEL	A	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61805340delA								None (None upstream) : SPIN4 (761768 downstream)																							atcttcaaataaaatctacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68700532	68700533	+	IGR	DEL	AC	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68700532_68700533delAC								PJA1 (315192 upstream) : FAM155B (24545 downstream)																							gtgctaacggacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115392333	115392333	+	IGR	DEL	T	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115392333delT								AGTR2 (86110 upstream) : SLC6A14 (175441 downstream)																							tgtggcagagtttttggctcc	0.000													4	2	---	---	---	---	
IL9R	3581	broad.mit.edu	37	X	155238775	155238776	+	Intron	DEL	TA	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155238775_155238776delTA	uc004fnv.1	+						IL9R_uc004fnu.1_Intron	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor						cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					tgtgtgtgtttatgtgtctgtg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9941533	9941533	+	IGR	DEL	T	-	-	rs111836903		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9941533delT								TTTY22 (290679 upstream) : None (None downstream)																							TATAATTCCCTTCTTTTAACC	0.289													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9985025	9985026	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9985025_9985026insG								TTTY22 (334171 upstream) : None (None downstream)																							GACAAGGGGAAGGAAGTGGCCT	0.540													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10008563	10008564	+	IGR	INS	-	G	G			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10008563_10008564insG								TTTY22 (357709 upstream) : None (None downstream)																							ttccaaggtcctcctttcatcc	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13267778	13267779	+	IGR	INS	-	A	A			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13267778_13267779insA								None (None upstream) : None (None downstream)																							TTCCTCCCCCCCtttttttgag	0.277													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13292384	13292384	+	IGR	DEL	T	-	-	rs112305521		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13292384delT								None (None upstream) : None (None downstream)																							ctctcccccctccagatatta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13482679	13482680	+	IGR	INS	-	T	T	rs145303557		TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13482679_13482680insT								None (None upstream) : None (None downstream)																							tgtaccaatgcccctgtaggca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28792854	28792855	+	IGR	INS	-	TGGAG	TGGAG			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28792854_28792855insTGGAG								None (None upstream) : None (None downstream)																							atgaaattgaatggagtggggt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28807116	28807116	+	IGR	DEL	G	-	-			TCGA-66-2744-01	TCGA-66-2744-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28807116delG								None (None upstream) : None (None downstream)																							cgaatcgaacggaaAATTATG	0.015													4	2	---	---	---	---	
