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
ACOT7	11332	broad.mit.edu	37	1	6418892	6418892	+	Intron	SNP	A	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6418892A>T	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron|ACOT7_uc001amq.2_Missense_Mutation_p.L5Q|ACOT7_uc001amr.2_Intron	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		GTACCTGCTCAGCTGGAAAGC	0.582													4	116	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11177077	11177077	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11177077A>C	uc001asd.2	-	50	7121	c.7000T>G	c.(7000-7002)TTA>GTA	p.L2334V	MTOR_uc001asc.2_Missense_Mutation_p.L539V	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2334	PI3K/PI4K.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						CCCAGGCCTAAAATATACCCA	0.378													39	287	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	T	T	rs367060		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946434C>T	uc010ocf.1	-	3		c.464G>A			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CTCAGCCTTCCGCCGGGCCAG	0.672													9	27	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946438	16946438	+	RNA	SNP	G	A	A	rs28392876	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946438G>A	uc010ocf.1	-	3		c.460C>T			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GCCTTCCGCCGGGCCAGCAGC	0.672													9	24	---	---	---	---	PASS
TMEM57	55219	broad.mit.edu	37	1	25818030	25818030	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25818030T>C	uc001bkk.2	+	10	1949	c.1747T>C	c.(1747-1749)TTC>CTC	p.F583L	TMEM57_uc009vru.2_Missense_Mutation_p.F356L|TMEM57_uc009vrv.2_Missense_Mutation_p.F225L	NM_018202	NP_060672	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	583						axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGGACCTGTTCTCCGCACT	0.552													4	65	---	---	---	---	PASS
NFIA	4774	broad.mit.edu	37	1	61743222	61743222	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61743222C>T	uc001czw.2	+	3	1074	c.590C>T	c.(589-591)CCA>CTA	p.P197L	NFIA_uc001czy.2_Missense_Mutation_p.P189L|NFIA_uc010oos.1_Missense_Mutation_p.P242L|NFIA_uc001czv.2_Missense_Mutation_p.P197L	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	197					DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						CCCAGCCAGCCAAGTGACGCT	0.473													21	123	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62330046	62330046	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62330046C>A	uc001dab.2	+	20	2690	c.2576C>A	c.(2575-2577)CCT>CAT	p.P859H	INADL_uc009waf.1_Missense_Mutation_p.P859H|INADL_uc001daa.2_Missense_Mutation_p.P859H|INADL_uc001dad.3_Missense_Mutation_p.P556H|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	859					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TTTCTGACTCCTAGATTGCAG	0.413													5	176	---	---	---	---	PASS
DOCK7	85440	broad.mit.edu	37	1	62958389	62958389	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62958389C>T	uc001daq.2	-	41	5354	c.5320G>A	c.(5320-5322)GCT>ACT	p.A1774T	DOCK7_uc001dan.2_Missense_Mutation_p.A1635T|DOCK7_uc001dao.2_Missense_Mutation_p.A1635T|DOCK7_uc001dap.2_Missense_Mutation_p.A1752T|DOCK7_uc001dam.2_Missense_Mutation_p.A954T|DOCK7_uc010oov.1_Missense_Mutation_p.A513T	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1783	DHR-2.				activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						GAGAAGGAAGCAGCTGCTTGT	0.403													5	214	---	---	---	---	PASS
WDR78	79819	broad.mit.edu	37	1	67358977	67358977	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67358977T>G	uc001dcx.2	-	3	521	c.465A>C	c.(463-465)GAA>GAC	p.E155D	WDR78_uc001dcy.2_Missense_Mutation_p.E155D|WDR78_uc001dcz.2_Missense_Mutation_p.E155D|WDR78_uc009wax.2_5'Flank	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	155										ovary(2)	2						AAGATATAAATTCTGATCCAA	0.363													104	313	---	---	---	---	PASS
FAM72B	653820	broad.mit.edu	37	1	120839743	120839743	+	5'UTR	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120839743C>T	uc009whp.2	+	1					FAM72B_uc001ein.3_5'UTR	NM_001100910	NP_001094380	Q86X60	FA72B_HUMAN	hypothetical protein LOC653820												0	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)		GGTCCCGCAACTTGAATTTTA	0.403													4	124	---	---	---	---	PASS
RBM8A	9939	broad.mit.edu	37	1	145509177	145509177	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145509177G>T	uc001ent.1	+	6	520	c.491G>T	c.(490-492)AGA>ATA	p.R164I	NBPF10_uc001emp.3_Intron|RBM8A_uc001enu.1_Missense_Mutation_p.R163I|RBM8A_uc001enw.1_5'Flank	NM_005105	NP_005096	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	164					mRNA 3'-end processing|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|exon-exon junction complex|nuclear speck	mRNA binding|nucleotide binding|protein binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGTGGCCGAAGACGCAGCAGA	0.498													17	113	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152280762	152280762	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152280762T>C	uc001ezu.1	-	3	6636	c.6600A>G	c.(6598-6600)GGA>GGG	p.G2200G		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2200	Ser-rich.				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)			TAGAGCCATCTCCTGATTGTT	0.547									Ichthyosis				6	228	---	---	---	---	PASS
BCAN	63827	broad.mit.edu	37	1	156617869	156617869	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156617869T>C	uc001fpp.2	+	5	1072	c.736T>C	c.(736-738)TAT>CAT	p.Y246H	BCAN_uc001fpo.2_Missense_Mutation_p.Y246H	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	246	Link 1.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGATGACCTCTATGATGTGTA	0.557													4	165	---	---	---	---	PASS
FCRL5	83416	broad.mit.edu	37	1	157497598	157497598	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157497598G>A	uc001fqu.2	-	9	1927	c.1769C>T	c.(1768-1770)CCG>CTG	p.P590L	FCRL5_uc009wsm.2_Missense_Mutation_p.P590L|FCRL5_uc010phv.1_Missense_Mutation_p.P590L|FCRL5_uc010phw.1_Missense_Mutation_p.P505L	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	590	Extracellular (Potential).|Ig-like C2-type 6.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				AGAGCCTCTCGGGGCCTCACA	0.592													9	43	---	---	---	---	PASS
RBM34	23029	broad.mit.edu	37	1	235295228	235295228	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235295228T>G	uc001hwn.2	-	11	1123	c.1093A>C	c.(1093-1095)AAA>CAA	p.K365Q	TOMM20_uc001hwl.2_5'Flank|RBM34_uc001hwo.2_RNA|ARID4B_uc001hwp.2_RNA	NM_015014	NP_055829	P42696	RBM34_HUMAN	RNA binding motif protein 34 isoform 1	365						nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			AATTTTTCTTTATTAACAGAA	0.338													51	174	---	---	---	---	PASS
ROCK2	9475	broad.mit.edu	37	2	11348011	11348011	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11348011T>A	uc002rbd.1	-	20	2839	c.2390A>T	c.(2389-2391)GAG>GTG	p.E797V		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	797	Potential.				axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		AGTTTCTTGCTCTATTTTTAA	0.308													96	432	---	---	---	---	PASS
ROCK2	9475	broad.mit.edu	37	2	11348012	11348012	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11348012C>T	uc002rbd.1	-	20	2838	c.2389G>A	c.(2389-2391)GAG>AAG	p.E797K		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	797	Potential.				axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		GTTTCTTGCTCTATTTTTAAT	0.308													97	429	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33534615	33534615	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33534615C>G	uc002ros.2	+	23	3599	c.3599C>G	c.(3598-3600)ACA>AGA	p.T1200R	LTBP1_uc002rot.2_Missense_Mutation_p.T874R|LTBP1_uc002rou.2_Missense_Mutation_p.T873R|LTBP1_uc002rov.2_Missense_Mutation_p.T820R|LTBP1_uc010ymz.1_Missense_Mutation_p.T873R|LTBP1_uc010yna.1_Missense_Mutation_p.T820R|LTBP1_uc010ynb.1_Missense_Mutation_p.T139R	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1199	EGF-like 11; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GACAATAAAACATGTCAAGGT	0.408													68	231	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84912547	84912547	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84912547T>C	uc010fgb.2	+	43	7151	c.7014T>C	c.(7012-7014)ATT>ATC	p.I2338I	DNAH6_uc002sor.2_Intron	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	2338					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						ATCGCTTGATTAATAATGAAG	0.338													38	189	---	---	---	---	PASS
CD28	940	broad.mit.edu	37	2	204591374	204591374	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204591374A>G	uc002vah.3	+	2	293	c.71A>G	c.(70-72)AAG>AGG	p.K24R	CD28_uc002vag.1_RNA|CD28_uc010zio.1_RNA|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_RNA	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor	24	Extracellular (Potential).				cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0						ATTTTGGTGAAGCAGTCGCCC	0.393													4	55	---	---	---	---	PASS
FANCD2	2177	broad.mit.edu	37	3	10116259	10116259	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10116259T>C	uc003buw.2	+	29	2839	c.2761T>C	c.(2761-2763)TCC>CCC	p.S921P	FANCD2_uc003bux.1_Missense_Mutation_p.S921P|FANCD2_uc003buy.1_Missense_Mutation_p.S921P|FANCD2_uc010hcw.1_RNA	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform	921					DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		ACTACATAATTCCCATGCTTT	0.373			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				5	248	---	---	---	---	PASS
BOC	91653	broad.mit.edu	37	3	112969550	112969550	+	Silent	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112969550G>T	uc003dzx.2	+	4	867	c.246G>T	c.(244-246)CTG>CTT	p.L82L	BOC_uc010hqi.2_Silent_p.L82L|BOC_uc003dzy.2_Silent_p.L82L|BOC_uc003dzz.2_Silent_p.L82L|BOC_uc003dzw.1_Silent_p.L82L|BOC_uc003eaa.1_Silent_p.L82L	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	82	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			ATGATGCTCTGGGTGTCCTCA	0.602													33	103	---	---	---	---	PASS
CDV3	55573	broad.mit.edu	37	3	133302937	133302937	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133302937T>C	uc003epq.2	+	3	864	c.409T>C	c.(409-411)TCT>CCT	p.S137P	CDV3_uc003epp.3_Missense_Mutation_p.S137P|CDV3_uc003epr.2_Missense_Mutation_p.S35P	NM_017548	NP_060018	Q9UKY7	CDV3_HUMAN	carnitine deficiency-associated gene expressed	137					cell proliferation	cytoplasm					0						TATGGAAAAATCTTCAGGTCC	0.403													61	273	---	---	---	---	PASS
USO1	8615	broad.mit.edu	37	4	76711836	76711836	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76711836A>G	uc003hiu.2	+	11	1301	c.1126A>G	c.(1126-1128)AGG>GGG	p.R376G	USO1_uc003hiv.2_Missense_Mutation_p.R211G|USO1_uc003hiw.2_Missense_Mutation_p.R211G	NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein	376	ARM 7.|Globular head.				intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GGTTAATGAAAGGCAGCCATT	0.368													6	359	---	---	---	---	PASS
FBXO8	26269	broad.mit.edu	37	4	175162270	175162270	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175162270T>C	uc003itp.2	-	4	1406	c.556A>G	c.(556-558)AGA>GGA	p.R186G	FBXO8_uc003itq.2_Missense_Mutation_p.R145G	NM_012180	NP_036312	Q9NRD0	FBX8_HUMAN	F-box only protein 8	186	SEC7.				regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity			breast(2)	2		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		AGATAGATTCTCAGTTTTTTC	0.308													7	341	---	---	---	---	PASS
STARD4	134429	broad.mit.edu	37	5	110843054	110843054	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110843054T>C	uc003kph.1	-	2	162	c.78A>G	c.(76-78)GAA>GAG	p.E26E	STARD4_uc010jbw.1_5'UTR|STARD4_uc010jbx.1_Intron|STARD4_uc003kpi.1_RNA|STARD4_uc003kpj.2_Silent_p.E26E	NM_139164	NP_631903	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain	26	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)		GCCACTTATCTTCTTCAATGC	0.343													7	583	---	---	---	---	PASS
KIF3A	11127	broad.mit.edu	37	5	132039254	132039254	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132039254T>C	uc003kxo.2	-	10	1440	c.1286A>G	c.(1285-1287)GAG>GGG	p.E429G	KIF3A_uc003kxm.2_Missense_Mutation_p.E11G|KIF3A_uc003kxn.2_Missense_Mutation_p.E414G|KIF3A_uc011cxf.1_Missense_Mutation_p.E456G|KIF3A_uc003kxp.2_Missense_Mutation_p.E432G	NM_007054	NP_008985	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	429	Potential.				blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGCTTTTCTCTCCTCATCAAT	0.353													8	775	---	---	---	---	PASS
LRRTM2	26045	broad.mit.edu	37	5	138209538	138209538	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138209538A>C	uc011cyz.1	-	2	1169	c.712T>G	c.(712-714)TGG>GGG	p.W238G	CTNNA1_uc003ldh.2_Intron|CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|LRRTM2_uc010jez.2_Intron|LRRTM2_uc011cza.1_Missense_Mutation_p.W104G|CTNNA1_uc003ldl.2_5'Flank	NM_015564	NP_056379	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	238	Extracellular (Potential).|LRR 8.					cell junction|integral to membrane|postsynaptic membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATTTTGTTCCATTGTAAGAAG	0.443													34	169	---	---	---	---	PASS
GALNT10	55568	broad.mit.edu	37	5	153709212	153709212	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153709212T>C	uc003lvh.2	+	4	614	c.482T>C	c.(481-483)CTC>CCC	p.L161P	GALNT10_uc003lvg.1_Missense_Mutation_p.L161P|GALNT10_uc010jic.2_RNA|GALNT10_uc010jid.2_Missense_Mutation_p.L64P	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	161	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TGGTCCTCCCTCCTCCGCACC	0.582													19	127	---	---	---	---	PASS
SERPINB1	1992	broad.mit.edu	37	6	2836102	2836102	+	Silent	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2836102C>T	uc003mub.2	-	6	767	c.723G>A	c.(721-723)ACG>ACA	p.T241T	SERPINB1_uc003muc.2_Silent_p.T90T	NM_030666	NP_109591	P30740	ILEU_HUMAN	serine (or cysteine) proteinase inhibitor, clade	241					regulation of proteolysis	cytoplasm|extracellular space	serine-type endopeptidase inhibitor activity			breast(4)|ovary(1)	5	Ovarian(93;0.0412)			OV - Ovarian serous cystadenocarcinoma(45;0.0717)		TCTTCAGGCCCGTGGACTCGT	0.542													15	41	---	---	---	---	PASS
OR2J2	26707	broad.mit.edu	37	6	29141782	29141782	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29141782T>C	uc011dlm.1	+	1	472	c.370T>C	c.(370-372)TAT>CAT	p.Y124H		NM_030905	NP_112167	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ATATGATCGTTATGTAGCTGT	0.448													45	160	---	---	---	---	PASS
CUL7	9820	broad.mit.edu	37	6	43019452	43019452	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43019452C>G	uc003otq.2	-	3	933	c.630G>C	c.(628-630)GAG>GAC	p.E210D	CUL7_uc011dvb.1_Missense_Mutation_p.E294D|CUL7_uc010jyh.2_Intron|KLC4_uc003otr.1_Intron	NM_014780	NP_055595	Q14999	CUL7_HUMAN	cullin 7	210					interspecies interaction between organisms|ubiquitin-dependent protein catabolic process|vasculogenesis	anaphase-promoting complex|mitochondrion	ubiquitin protein ligase binding			ovary(3)|kidney(1)	4			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCAGGTGTTTCTCAATGGCTT	0.532													25	124	---	---	---	---	PASS
C6orf103	79747	broad.mit.edu	37	6	147045502	147045502	+	Intron	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147045502T>C	uc010khx.2	+						C6orf103_uc003qlp.2_5'UTR|C6orf103_uc003qlq.2_Intron	NM_024694	NP_078970	Q8N7X0	CAN7L_HUMAN	hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)		TAAAAATTGTTTGAAGGCTTG	0.289													20	73	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168344647	168344647	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168344647G>T	uc003qwd.2	+	25	3384	c.3242G>T	c.(3241-3243)AGC>ATC	p.S1081I	MLLT4_uc003qwb.1_Missense_Mutation_p.S1066I|MLLT4_uc003qwc.1_Missense_Mutation_p.S1082I|MLLT4_uc003qwg.1_Missense_Mutation_p.S391I	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1082	PDZ.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ACAAGAACAAGCTCTGTGGTG	0.493			T	MLL	AL								20	82	---	---	---	---	PASS
ANLN	54443	broad.mit.edu	37	7	36445891	36445891	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36445891G>A	uc003tff.2	+	4	793	c.589G>A	c.(589-591)GGC>AGC	p.G197S	ANLN_uc011kaz.1_Missense_Mutation_p.G109S|ANLN_uc003tfg.2_Missense_Mutation_p.G197S|ANLN_uc010kxe.2_Missense_Mutation_p.G197S	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	197	Nuclear localization.				cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						AACTCCAGTTGGCAGAAGGGG	0.488													6	77	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101926034	101926034	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101926034A>T	uc003uyt.2	+	22	1952	c.1933A>T	c.(1933-1935)ATG>TTG	p.M645L	CUX1_uc011kkn.1_Missense_Mutation_p.M606L|CUX1_uc003uyw.2_Missense_Mutation_p.M599L|CUX1_uc003uyv.2_Missense_Mutation_p.M629L|CUX1_uc003uyu.2_Missense_Mutation_p.M643L|CUX1_uc003uyz.2_RNA|SH2B2_uc011kko.1_5'Flank	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b	Error:Variant_position_missing_in_P39880_after_alignment					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						GAGCGAGAGCATGGAGAGGGA	0.682													9	26	---	---	---	---	PASS
C7orf58	79974	broad.mit.edu	37	7	120782148	120782148	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120782148C>T	uc003vjq.3	+	16	2455	c.2008C>T	c.(2008-2010)CCA>TCA	p.P670S	C7orf58_uc003vjs.3_Missense_Mutation_p.P670S|C7orf58_uc003vjt.3_Missense_Mutation_p.P450S	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	670						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					AGAAGACCGCCCAAGTCTGCC	0.433													52	153	---	---	---	---	PASS
KEL	3792	broad.mit.edu	37	7	142658079	142658079	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142658079T>C	uc003wcb.2	-	4	546	c.336A>G	c.(334-336)AAA>AAG	p.K112K		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	112	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					TATTGGTCTCTTTGGCCCTTC	0.507													5	171	---	---	---	---	PASS
IDO2	169355	broad.mit.edu	37	8	39845470	39845470	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39845470A>G	uc010lwy.1	+	7	811	c.569A>G	c.(568-570)GAA>GGA	p.E190G	IDO2_uc003xno.1_RNA|IDO2_uc010lwz.1_Intron|IDO2_uc003xnp.1_5'UTR	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1	177					tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2						GTAGAGAAAGAAGCAGTGCCT	0.473													5	241	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86037088	86037088	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86037088A>C	uc003ycw.2	+	8	1340	c.1186A>C	c.(1186-1188)AAC>CAC	p.N396H	LRRCC1_uc010lzz.1_RNA|LRRCC1_uc010maa.1_Missense_Mutation_p.N97H|LRRCC1_uc003ycx.2_Missense_Mutation_p.N303H|LRRCC1_uc003ycy.2_Missense_Mutation_p.N376H	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	396					cell division|mitosis	centriole|nucleus					0						ATCTTTAGCAAACTGTCCTAT	0.308													33	122	---	---	---	---	PASS
CA1	759	broad.mit.edu	37	8	86240870	86240870	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86240870T>C	uc003ydh.2	-	9	905	c.705A>G	c.(703-705)GAA>GAG	p.E235E	CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Silent_p.E235E|CA1_uc003ydi.2_Silent_p.E235E	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I	235					one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	CGTTATCACCTTCAACATTTG	0.378													5	227	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414338	68414338	+	RNA	SNP	G	T	T	rs62545747		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414338G>T	uc004aex.2	+	1		c.893G>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		gcttagtgaagatgtagaatt	0.000													3	5	---	---	---	---	PASS
C9orf85	138241	broad.mit.edu	37	9	74526670	74526670	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74526670A>T	uc004ain.2	+	1	248	c.20A>T	c.(19-21)AAC>ATC	p.N7I	C9orf85_uc004aio.2_RNA|C9orf85_uc010mou.2_RNA|C9orf85_uc010mov.2_RNA|FAM108B1_uc004ail.2_5'Flank|FAM108B1_uc004aim.1_5'Flank	NM_182505	NP_872311	Q96MD7	CI085_HUMAN	hypothetical protein LOC138241	7											0						CAGAAAGGCAACGTGGCTCGT	0.502													20	100	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90534072	90534072	+	Intron	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90534072A>G	uc010mqi.2	+						FAM75C1_uc004apq.3_Missense_Mutation_p.K14R	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						TCCCTGAGCAAGACAGACAGA	0.507													4	33	---	---	---	---	PASS
NCBP1	4686	broad.mit.edu	37	9	100418302	100418302	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100418302T>C	uc004axq.2	+	14	1767	c.1308T>C	c.(1306-1308)TGT>TGC	p.C436C		NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	436					gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				GGTCAGATTGTCTTAGTCAAG	0.313													7	400	---	---	---	---	PASS
GAPVD1	26130	broad.mit.edu	37	9	128092444	128092444	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128092444T>C	uc010mwx.2	+	13	2446	c.2120T>C	c.(2119-2121)ATA>ACA	p.I707T	GAPVD1_uc011lzs.1_Missense_Mutation_p.I707T|GAPVD1_uc004bpp.2_Missense_Mutation_p.I707T|GAPVD1_uc004bpq.2_Missense_Mutation_p.I707T|GAPVD1_uc004bpr.2_Missense_Mutation_p.I686T|GAPVD1_uc004bps.2_Missense_Mutation_p.I707T|GAPVD1_uc010mwy.1_Missense_Mutation_p.I566T	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	707					endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						GGTTCTACCATATCAGAGACA	0.448													5	328	---	---	---	---	PASS
POMT1	10585	broad.mit.edu	37	9	134379711	134379711	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134379711T>C	uc004cav.2	+	2	308	c.106T>C	c.(106-108)TAC>CAC	p.Y36H	POMT1_uc011mci.1_Missense_Mutation_p.Y36H|POMT1_uc004cax.2_Missense_Mutation_p.Y36H|POMT1_uc011mcj.1_Intron|POMT1_uc004cau.2_Missense_Mutation_p.Y36H|POMT1_uc004caw.2_Intron|POMT1_uc011mck.1_Intron|POMT1_uc011mcl.1_Intron|POMT1_uc011mcm.1_Missense_Mutation_p.Y36H	NM_007171	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1 isoform a	36					multicellular organismal development|protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GCGACTCACCTACCCGCGGGC	0.537											OREG0019563	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	55	213	---	---	---	---	PASS
ARMC4	55130	broad.mit.edu	37	10	28229610	28229610	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28229610G>A	uc009xky.2	-	13	1966	c.1868C>T	c.(1867-1869)ACG>ATG	p.T623M	ARMC4_uc010qds.1_Missense_Mutation_p.T148M|ARMC4_uc010qdt.1_Missense_Mutation_p.T315M|ARMC4_uc001itz.2_Missense_Mutation_p.T623M|ARMC4_uc010qdu.1_Missense_Mutation_p.T315M	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	623	ARM 3.						binding			ovary(4)|skin(2)	6						TTCTTTATTCGTATGACTCTT	0.532													9	64	---	---	---	---	PASS
OPN4	94233	broad.mit.edu	37	10	88422065	88422065	+	Missense_Mutation	SNP	G	A	A	rs142050572		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88422065G>A	uc001kdq.2	+	8	1357	c.1130G>A	c.(1129-1131)CGG>CAG	p.R377Q	OPN4_uc001kdp.2_Missense_Mutation_p.R388Q|OPN4_uc010qmk.1_Missense_Mutation_p.R388Q|OPN4_uc009xsx.1_Missense_Mutation_p.R47Q	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 1	377	Cytoplasmic (Potential).				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1						GTATCACGCCGGCACAGTCGC	0.677													4	11	---	---	---	---	PASS
CYP17A1	1586	broad.mit.edu	37	10	104595107	104595107	+	Missense_Mutation	SNP	A	G	G	rs104894147		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104595107A>G	uc001kwg.2	-	2	512	c.340T>C	c.(340-342)TTC>CTC	p.F114L		NM_000102	NP_000093	P05093	CP17A_HUMAN	cytochrome P450, family 17	114			F -> V (in AH5).		androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)	GAGTCAGCGAAGGCGATACCC	0.557											OREG0020487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	55	---	---	---	---	PASS
IPO7	10527	broad.mit.edu	37	11	9459375	9459375	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9459375G>A	uc001mho.2	+	21	2485	c.2343G>A	c.(2341-2343)ATG>ATA	p.M781I		NM_006391	NP_006382	O95373	IPO7_HUMAN	importin 7	781					interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTCGAACTATGTGTCTGCAAG	0.373													34	161	---	---	---	---	PASS
NELL1	4745	broad.mit.edu	37	11	21596638	21596638	+	3'UTR	SNP	C	T	T	rs80344018	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21596638C>T	uc001mqe.2	+	20					NELL1_uc001mqf.2_3'UTR|NELL1_uc009yid.2_3'UTR|NELL1_uc010rdo.1_3'UTR|NELL1_uc010rdp.1_3'UTR|NELL1_uc001mqh.2_3'UTR	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						GGATAGGAATCGGTAGTTTGG	0.388													4	216	---	---	---	---	PASS
OR10G4	390264	broad.mit.edu	37	11	123887117	123887117	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887117C>T	uc010sac.1	+	1	836	c.836C>T	c.(835-837)ACG>ATG	p.T279M		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	279	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		ACTGTGCTGACGCCCCTTCTC	0.473													10	107	---	---	---	---	PASS
A2ML1	144568	broad.mit.edu	37	12	9008181	9008181	+	Silent	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9008181G>A	uc001quz.3	+	23	2939	c.2841G>A	c.(2839-2841)ACG>ACA	p.T947T	A2ML1_uc001qva.1_Silent_p.T527T|A2ML1_uc010sgm.1_Silent_p.T447T	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	791						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						CTTATGTTACGGTTCTGGGTA	0.512													26	124	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9225272	9225272	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9225272C>T	uc001qvk.1	-	30	4065	c.3952G>A	c.(3952-3954)GGA>AGA	p.G1318R	A2M_uc001qvj.1_Missense_Mutation_p.G360R|A2M_uc009zgk.1_Missense_Mutation_p.G1168R	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1318					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	CATCCTTCTCCTGTCACTTTC	0.502													4	239	---	---	---	---	PASS
KLRC4	8302	broad.mit.edu	37	12	10561535	10561535	+	Silent	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10561535A>G	uc001qye.2	-	2	444	c.262T>C	c.(262-264)TTA>CTA	p.L88L	KLRK1_uc001qyc.2_5'Flank|KLRK1_uc009zhk.2_5'UTR|KLRK1_uc001qyd.2_5'UTR	NM_013431	NP_038459	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C,	88	Helical; Signal-anchor for type II membrane protein; (Potential).				cellular defense response	integral to membrane	binding|receptor activity				0						ATTGTTTTTAACACAGTGGCC	0.403													7	451	---	---	---	---	PASS
PRB4	5545	broad.mit.edu	37	12	11461568	11461568	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11461568G>T	uc001qzf.1	-	3	383	c.349C>A	c.(349-351)CCA>ACA	p.P117T	PRB4_uc001qzt.2_Missense_Mutation_p.P117T	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	180	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.|7.		Missing (in allele S).			extracellular region				ovary(1)	1						GGCTTTCCTGGAGGAGGTGGG	0.597										HNSCC(22;0.051)			12	48	---	---	---	---	PASS
PRB4	5545	broad.mit.edu	37	12	11461694	11461694	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11461694G>T	uc001qzf.1	-	3	257	c.223C>A	c.(223-225)CCA>ACA	p.P75T	PRB4_uc001qzt.2_Missense_Mutation_p.P75T	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	75	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.|2.			Missing (in Ref. 7; CAA30542).		extracellular region				ovary(1)	1						GGCTTTCCTGGAGGAGGTGGG	0.607										HNSCC(22;0.051)			6	99	---	---	---	---	PASS
CASC1	55259	broad.mit.edu	37	12	25348052	25348052	+	5'UTR	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25348052G>A	uc001rgl.2	-	1					CASC1_uc001rgk.2_5'UTR|CASC1_uc001rgm.3_5'UTR|CASC1_uc001rgj.2_5'UTR|CASC1_uc010sje.1_5'UTR|CASC1_uc010sjf.1_5'UTR|CASC1_uc010sjg.1_5'UTR|CASC1_uc010sjh.1_RNA|LYRM5_uc001rgn.2_5'Flank|LYRM5_uc001rgo.2_5'Flank	NM_001082973	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1 isoform b											ovary(2)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			CAGAGTCGGAGCAGAAATTGT	0.607													4	49	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27081163	27081163	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27081163T>C	uc001rhk.3	-	5	1096	c.559A>G	c.(559-561)AAC>GAC	p.N187D	C12orf11_uc010sjk.1_Missense_Mutation_p.N86D	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	187					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					GCAAGCTTGTTATGTTCATGA	0.299													35	169	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32134198	32134198	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32134198A>C	uc001rks.2	+	4	723	c.309A>C	c.(307-309)CAA>CAC	p.Q103H		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	103										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			GACCCAAACAACTAACTCACA	0.393													16	93	---	---	---	---	PASS
RASSF9	9182	broad.mit.edu	37	12	86230146	86230146	+	5'UTR	SNP	G	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86230146G>C	uc001taf.1	-	1						NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						GTTGCTGGAAGTTGTGCAACT	0.537													4	13	---	---	---	---	PASS
C12orf50	160419	broad.mit.edu	37	12	88390211	88390211	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88390211T>C	uc001tam.1	-	6	589	c.421A>G	c.(421-423)ACA>GCA	p.T141A	C12orf50_uc001tan.2_Missense_Mutation_p.T195A	NM_152589	NP_689802	Q8NA57	CL050_HUMAN	hypothetical protein LOC160419	141										skin(2)|ovary(1)	3						GCTGTAGGTGTCATGCTTTTT	0.338													8	722	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19411895	19411895	+	RNA	SNP	A	G	G	rs7334605	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19411895A>G	uc010tcj.1	-	1		c.34215T>C				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						cagagatcccaccactgcact	0.149													6	68	---	---	---	---	PASS
CENPJ	55835	broad.mit.edu	37	13	25482183	25482183	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25482183G>C	uc001upt.3	-	5	1200	c.947C>G	c.(946-948)TCC>TGC	p.S316C	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	316					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		CACTTCTGAGGAATCATCATG	0.323													6	683	---	---	---	---	PASS
NUDT15	55270	broad.mit.edu	37	13	48615262	48615262	+	Intron	SNP	T	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48615262T>G	uc001vbw.1	+						NUDT15_uc001vbv.2_Missense_Mutation_p.I122S	NM_018283	NP_060753	Q9NV35	NUD15_HUMAN	nudix-type motif 15								hydrolase activity|metal ion binding				0		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		AGTAAGAGAATTATATATAAT	0.289													20	64	---	---	---	---	PASS
LOC643677	643677	broad.mit.edu	37	13	103392046	103392046	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103392046T>C	uc001vpm.2	-	4	11141	c.11001A>G	c.(10999-11001)AAA>AAG	p.K3667K		NM_001146197	NP_001139669			hypothetical protein LOC643677												0						TATCCATTGCTTTTACTCTAT	0.328													6	453	---	---	---	---	PASS
CARS2	79587	broad.mit.edu	37	13	111340142	111340142	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111340142G>T	uc001vrd.2	-	5	537	c.497C>A	c.(496-498)ACC>AAC	p.T166N	CARS2_uc010tjm.1_RNA	NM_024537	NP_078813	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial	166					cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AATATTTTCGGTTACCCTCAG	0.458													45	85	---	---	---	---	PASS
NFATC4	4776	broad.mit.edu	37	14	24845299	24845299	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24845299T>G	uc001wpc.2	+	8	2369	c.2048T>G	c.(2047-2049)TTT>TGT	p.F683C	NFATC4_uc010tok.1_Missense_Mutation_p.F746C|NFATC4_uc010tol.1_Missense_Mutation_p.F746C|NFATC4_uc010alr.2_Missense_Mutation_p.F746C|NFATC4_uc010tom.1_Missense_Mutation_p.F696C|NFATC4_uc010ton.1_Missense_Mutation_p.F696C|NFATC4_uc010too.1_Missense_Mutation_p.F696C|NFATC4_uc010alt.2_Missense_Mutation_p.F715C|NFATC4_uc010top.1_Missense_Mutation_p.F715C|NFATC4_uc010toq.1_Missense_Mutation_p.F715C|NFATC4_uc010tor.1_Missense_Mutation_p.F683C|NFATC4_uc010tos.1_Missense_Mutation_p.F613C|NFATC4_uc010tot.1_Missense_Mutation_p.F671C|NFATC4_uc010tou.1_Missense_Mutation_p.F613C|NFATC4_uc010tov.1_Missense_Mutation_p.F671C|NFATC4_uc010tow.1_Missense_Mutation_p.F613C|NFATC4_uc010alv.2_Missense_Mutation_p.F671C|NFATC4_uc010tox.1_Missense_Mutation_p.F613C|NFATC4_uc001wpd.2_Missense_Mutation_p.F218C|NFATC4_uc010toy.1_Missense_Mutation_p.F218C|NFATC4_uc010toz.1_Missense_Mutation_p.F218C|NFATC4_uc010tpa.1_5'UTR|NFATC4_uc010tpb.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	683	IPT/TIG.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)		AGTTTCAGGTTTCTGCCTGGT	0.577													21	54	---	---	---	---	PASS
WDHD1	11169	broad.mit.edu	37	14	55468905	55468905	+	Splice_Site	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55468905T>C	uc001xbm.1	-	8	679	c.601_splice	c.e8-1	p.L201_splice	WDHD1_uc001xbn.1_Splice_Site_p.L78_splice	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1						TGCCAGTAACTATTAGAAAAG	0.289													4	162	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22383016	22383016	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22383016C>T	uc001yuc.1	+	7	1525	c.544C>T	c.(544-546)CGA>TGA	p.R182*	LOC727924_uc001yub.1_Intron|OR4N4_uc010tzv.1_Nonsense_Mutation_p.R182*	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTGTGATGTCCGACAGGTCAT	0.527													8	135	---	---	---	---	PASS
OCA2	4948	broad.mit.edu	37	15	28000341	28000341	+	3'UTR	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28000341A>G	uc001zbh.3	-	24					OCA2_uc010ayv.2_3'UTR	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)		AAGGACACACAGAGGAGGTCA	0.428									Oculocutaneous_Albinism				4	13	---	---	---	---	PASS
NARG2	79664	broad.mit.edu	37	15	60740179	60740179	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60740179T>A	uc002agp.2	-	11	2520	c.2285A>T	c.(2284-2286)AAA>ATA	p.K762I	NARG2_uc002ago.2_Missense_Mutation_p.K625I|NARG2_uc002agq.3_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a	762						nucleus				ovary(1)|lung(1)	2						TCTTCTGATTTTCTTCCGTTT	0.343													48	181	---	---	---	---	PASS
GSPT1	2935	broad.mit.edu	37	16	11981534	11981534	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11981534A>G	uc002dbr.2	-	5	463	c.436T>C	c.(436-438)TAT>CAT	p.Y146H	GSPT1_uc002dbu.2_Missense_Mutation_p.Y283H|GSPT1_uc002dbt.2_Missense_Mutation_p.Y284H|GSPT1_uc010bux.2_Missense_Mutation_p.Y146H	NM_001130007	NP_001123479	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 3	146					G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						GTTTCAAAATAGGCACGACCC	0.408													6	324	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902088	21902088	+	RNA	SNP	C	T	T	rs55647608	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902088C>T	uc002djs.3	-	2		c.157G>A			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		GTCTTACTGTCAGCTAAAAGG	0.373													5	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902089	21902089	+	RNA	SNP	A	G	G	rs56214519	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902089A>G	uc002djs.3	-	2		c.156T>C			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		TCTTACTGTCAGCTAAAAGGC	0.373													5	14	---	---	---	---	PASS
ZNF720	124411	broad.mit.edu	37	16	31724708	31724708	+	5'UTR	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31724708C>T	uc002ecn.3	+	1					ZNF720_uc010vfs.1_5'UTR|ZNF720_uc002eco.2_RNA|ZNF720_uc002ecp.1_5'UTR|ZNF720_uc002ecq.2_5'UTR	NM_001130913	NP_001124385	Q7Z2F6	ZN720_HUMAN	zinc finger protein 720						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0						CGGCAGGCACCGGGAGATCCG	0.617													7	26	---	---	---	---	PASS
MMP2	4313	broad.mit.edu	37	16	55519518	55519518	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55519518G>A	uc002ehz.3	+	5	972	c.661G>A	c.(661-663)GTC>ATC	p.V221I	MMP2_uc010vhd.1_Missense_Mutation_p.V145I|MMP2_uc010ccc.2_Missense_Mutation_p.V171I	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	221	Collagenase-like 1.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)	CTCTTTAGTGGTCCGTGTGAA	0.542													11	33	---	---	---	---	PASS
ADAMTS18	170692	broad.mit.edu	37	16	77353798	77353798	+	Missense_Mutation	SNP	C	T	T	rs149031657	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77353798C>T	uc002ffc.3	-	16	2899	c.2480G>A	c.(2479-2481)CGC>CAC	p.R827H	ADAMTS18_uc010chc.1_Missense_Mutation_p.R415H|ADAMTS18_uc002ffe.1_Missense_Mutation_p.R523H	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	827	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						ACGTTCCGGGCGGTTGAAAGA	0.542													8	23	---	---	---	---	PASS
RABEP1	9135	broad.mit.edu	37	17	5257716	5257716	+	Silent	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5257716A>G	uc002gbm.3	+	8	1250	c.1026A>G	c.(1024-1026)GAA>GAG	p.E342E	RABEP1_uc010clc.1_Silent_p.E335E|RABEP1_uc010cld.1_Silent_p.E299E|RABEP1_uc010vsw.1_Silent_p.E299E|RABEP1_uc002gbl.3_Silent_p.E342E	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	342	Potential.				apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						ATGTTGAGGAAGAAATAAAAA	0.318													6	398	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8052099	8052099	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8052099C>A	uc002gkd.2	-	8	1149	c.911G>T	c.(910-912)GGT>GTT	p.G304V	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Missense_Mutation_p.G288V	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	304					circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						CCGGTCAGGACCTCCTCTAGC	0.587			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					9	42	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	40004451	40004451	+	Silent	SNP	A	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40004451A>C	uc010cxr.2	+	5	1861	c.1719A>C	c.(1717-1719)CCA>CCC	p.P573P	KLHL10_uc010wfw.1_Silent_p.P485P	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	573	Kelch 6.					cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				GTGTAGTACCAGGGCTGGCCA	0.463													29	126	---	---	---	---	PASS
ATXN7L3	56970	broad.mit.edu	37	17	42272825	42272825	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42272825T>C	uc002iga.2	-	8	674	c.583A>G	c.(583-585)ACC>GCC	p.T195A	ATXN7L3_uc010wiv.1_5'UTR|ATXN7L3_uc002ifz.2_Missense_Mutation_p.T202A	NM_001098833	NP_001092303	Q14CW9	AT7L3_HUMAN	ataxin 7-like 3 isoform b	195					histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|metal ion binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GGCCCCAGGGTCTCATAGCTG	0.567													4	78	---	---	---	---	PASS
MYCBPAP	84073	broad.mit.edu	37	17	48605625	48605625	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48605625G>T	uc010wmr.1	+	16	2692	c.2530G>T	c.(2530-2532)GAG>TAG	p.E844*	MYCBPAP_uc002iqz.2_RNA	NM_032133	NP_115509	Q8TBZ2	MYBPP_HUMAN	Myc-binding protein-associated protein	807					cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGTGCCTGAAGAGCAAGGTCA	0.542													5	168	---	---	---	---	PASS
S1PR4	8698	broad.mit.edu	37	19	3179916	3179916	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3179916T>C	uc002lxg.2	+	1	1151	c.1126T>C	c.(1126-1128)TCC>CCC	p.S376P		NM_003775	NP_003766	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4 precursor	376	Cytoplasmic (By similarity).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			lung(1)|skin(1)	2						GGAGCCCCTGTCCAGCATCTC	0.652													3	11	---	---	---	---	PASS
GDF15	9518	broad.mit.edu	37	19	18497194	18497194	+	Silent	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18497194C>A	uc002niv.2	+	1	227	c.195C>A	c.(193-195)ACC>ACA	p.T65T	hsa-mir-3189|MI0014233_5'Flank	NM_004864	NP_004855	Q99988	GDF15_HUMAN	growth differentiation factor 15	65					cell-cell signaling|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)	1						ACCTGCTAACCAGGCTGCGGG	0.602													7	14	---	---	---	---	PASS
LIG1	3978	broad.mit.edu	37	19	48634399	48634399	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48634399C>A	uc002pia.1	-	19	1875	c.1755G>T	c.(1753-1755)AAG>AAT	p.K585N	LIG1_uc010xze.1_Missense_Mutation_p.K278N|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Missense_Mutation_p.K517N|LIG1_uc010xzg.1_Missense_Mutation_p.K554N	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	585					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|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	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	TGCTGAAGATCTTCACCTCCC	0.582								NER					24	106	---	---	---	---	PASS
FCGRT	2217	broad.mit.edu	37	19	50017370	50017370	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50017370T>A	uc002poe.2	+	3	791	c.305T>A	c.(304-306)TTC>TAC	p.F102Y	FCGRT_uc002pod.2_RNA|FCGRT_uc002pog.2_Missense_Mutation_p.F102Y|FCGRT_uc002pof.1_5'UTR|FCGRT_uc010yax.1_Missense_Mutation_p.F102Y|FCGRT_uc002poh.1_5'Flank	NM_001136019	NP_001129491	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	102	Extracellular (Potential).|Alpha-1.			Missing (in Ref. 3; AAG31421).	antigen processing and presentation|female pregnancy|immune response	integral to membrane|MHC class I protein complex	IgG binding|receptor activity			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		CTGGAAGCTTTCAAAGCTTTG	0.587													10	47	---	---	---	---	PASS
KIR2DS4	3809	broad.mit.edu	37	19	55351066	55351066	+	Silent	SNP	C	T	T	rs1130503		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55351066C>T	uc002qhm.1	+	5	622	c.576C>T	c.(574-576)CAC>CAT	p.H192H	KIR2DS4_uc010yfj.1_Missense_Mutation_p.T178M|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Missense_Mutation_p.T185M|KIR2DS4_uc002qhn.1_Intron	NM_012314	NP_036446	P43632	KI2S4_HUMAN	killer cell immunoglobulin-like receptor, two	192	Extracellular (Potential).|Ig-like C2-type 2.					integral to plasma membrane	receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		CTGCCACCCACGGAGGGACCT	0.587													54	168	---	---	---	---	PASS
ZSCAN18	65982	broad.mit.edu	37	19	58597544	58597544	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58597544G>T	uc002qri.2	-	6	1144	c.835C>A	c.(835-837)CCA>ACA	p.P279T	ZSCAN18_uc002qrj.3_Missense_Mutation_p.P279T|ZSCAN18_uc010yhs.1_Missense_Mutation_p.P144T|ZSCAN18_uc002qrh.2_Missense_Mutation_p.P279T|ZSCAN18_uc010yht.1_Missense_Mutation_p.P335T|ZSCAN18_uc002qrk.1_3'UTR|ZSCAN18_uc002qrl.2_3'UTR	NM_001145543	NP_001139015	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	279					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		ACCTCACCTGGGAGGCTGCTT	0.597													10	41	---	---	---	---	PASS
IDH3B	3420	broad.mit.edu	37	20	2644110	2644110	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2644110T>C	uc002wgp.2	-	4	328	c.319A>G	c.(319-321)AAC>GAC	p.N107D	IDH3B_uc002wgq.2_Missense_Mutation_p.N107D|IDH3B_uc002wgr.2_5'UTR|IDH3B_uc010zpz.1_Missense_Mutation_p.N107D	NM_006899	NP_008830	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3, beta subunit isoform	107					isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	electron carrier activity|isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0					NADH(DB00157)	GCCACTTTGTTCTCCTTCATG	0.498													4	86	---	---	---	---	PASS
MKKS	8195	broad.mit.edu	37	20	10393381	10393381	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10393381A>G	uc002wnt.1	-	3	1669	c.782T>C	c.(781-783)GTG>GCG	p.V261A	MKKS_uc002wnu.1_Missense_Mutation_p.V261A|MKKS_uc010zrd.1_Intron	NM_018848	NP_061336	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome protein	261	Substrate-binding apical domain.				brain morphogenesis|cerebral cortex development|convergent extension involved in gastrulation|detection of mechanical stimulus involved in sensory perception of sound|fat cell differentiation|flagellum assembly|gonad development|heart looping|hippocampus development|intracellular transport|melanosome transport|photoreceptor cell maintenance|pigment granule aggregation in cell center|protein folding|regulation of cilium beat frequency involved in ciliary motility|sensory perception of smell|social behavior|spermatid development|striatum development	cytosol|microtubule organizing center|motile cilium	ATP binding|unfolded protein binding				0						ATAACTGACCACCACAGTTCC	0.458									Bardet-Biedl_syndrome				17	190	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21321460	21321460	+	Silent	SNP	A	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21321460A>T	uc002wsf.1	+	15	1475	c.1380A>T	c.(1378-1380)GCA>GCT	p.A460A	XRN2_uc002wsg.1_Silent_p.A384A|XRN2_uc010zsk.1_Silent_p.A406A	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	460					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						CGAGACAAGCAGCCTATGAAA	0.428													44	139	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29628252	29628252	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628252A>G	uc010ztl.1	+	3	196	c.164A>G	c.(163-165)AAT>AGT	p.N55S	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.N7S					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TTGGCCTCAAATAGCTGCTTT	0.358													8	650	---	---	---	---	PASS
SUN5	140732	broad.mit.edu	37	20	31571646	31571646	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31571646G>A	uc002wyi.2	-	13	1187	c.1094C>T	c.(1093-1095)CCG>CTG	p.P365L		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	365					spermatogenesis					skin(1)	1						CTCTCTGGGCGGGGCCACAGA	0.557													11	56	---	---	---	---	PASS
ZHX3	23051	broad.mit.edu	37	20	39832047	39832047	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39832047C>A	uc002xjs.1	-	3	1888	c.1510G>T	c.(1510-1512)GAA>TAA	p.E504*	ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Nonsense_Mutation_p.E504*|ZHX3_uc002xjt.1_Nonsense_Mutation_p.E504*|ZHX3_uc002xju.1_Nonsense_Mutation_p.E504*|ZHX3_uc002xjv.1_Nonsense_Mutation_p.E504*|ZHX3_uc002xjw.1_Nonsense_Mutation_p.E504*|ZHX3_uc010ggg.1_Nonsense_Mutation_p.E504*	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	504	Required for nuclear localization.|Homeobox 2.				negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)				GACAGCTGTTCATGAGATTTC	0.527													22	92	---	---	---	---	PASS
CDH4	1002	broad.mit.edu	37	20	60511821	60511821	+	Silent	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60511821C>T	uc002ybn.1	+	16	2585	c.2571C>T	c.(2569-2571)CCC>CCT	p.P857P	CDH4_uc002ybp.1_Silent_p.P783P|uc002ybr.1_5'Flank	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	857	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ACAACGACCCCACGGCACCCC	0.647													8	28	---	---	---	---	PASS
MIRLET7C	406885	broad.mit.edu	37	21	17912220	17912220	+	RNA	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17912220T>C	hsa-let-7c|MI0000064	+			c.73T>C			C21orf34_uc002ykb.2_Intron|C21orf34_uc010glc.2_Intron|C21orf34_uc002ykc.2_Intron|uc002yke.2_RNA																	0						ACCTTCTAGCTTTCCTTGGAG	0.443													6	357	---	---	---	---	PASS
DOPEY2	9980	broad.mit.edu	37	21	37635872	37635872	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37635872T>C	uc002yvg.2	+	25	5423	c.5344T>C	c.(5344-5346)TTT>CTT	p.F1782L	DOPEY2_uc011aeb.1_Missense_Mutation_p.F1731L	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	1782					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						GCAAGAGAACTTTTCTTCACT	0.373													6	257	---	---	---	---	PASS
TRAPPC10	7109	broad.mit.edu	37	21	45494928	45494928	+	Silent	SNP	C	T	T	rs36041631		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45494928C>T	uc002zea.2	+	9	1363	c.1194C>T	c.(1192-1194)TCC>TCT	p.S398S	TRAPPC10_uc010gpo.2_Silent_p.S109S	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	398					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2						AGTTAAAGTCCTTGGGCTATC	0.388													4	294	---	---	---	---	PASS
LGALS2	3957	broad.mit.edu	37	22	37967936	37967936	+	Silent	SNP	C	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37967936C>T	uc003ata.2	-	2	121	c.9G>A	c.(7-9)GGG>GGA	p.G3G		NM_006498	NP_006489	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	3										breast(1)|skin(1)	2	Melanoma(58;0.0574)					CCTCAAGTTCCCCCTGGGCCA	0.547													4	133	---	---	---	---	PASS
FAM47C	442444	broad.mit.edu	37	X	37028223	37028223	+	Silent	SNP	C	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37028223C>A	uc004ddl.1	+	1	1754	c.1740C>A	c.(1738-1740)TCC>TCA	p.S580S		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	580										ovary(3)	3						CTGGAGTGTCCCATCTCTGCC	0.657													13	28	---	---	---	---	PASS
LPAR4	2846	broad.mit.edu	37	X	78011222	78011222	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78011222G>T	uc010nme.2	+	2	1261	c.856G>T	c.(856-858)GAA>TAA	p.E286*		NM_005296	NP_005287	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	286	Extracellular (Potential).					integral to plasma membrane	lipid binding|purinergic nucleotide receptor activity, G-protein coupled			ovary(3)	3						TTGCTTTTTGGAAAGATTTGC	0.418													86	268	---	---	---	---	PASS
NDUFA1	4694	broad.mit.edu	37	X	119005937	119005937	+	Silent	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119005937G>A	uc004esc.3	+	1	204	c.63G>A	c.(61-63)CTG>CTA	p.L21L	RNF113A_uc004esb.2_5'Flank	NM_004541	NP_004532	O15239	NDUA1_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	21	Helical; (Potential).				mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			large_intestine(1)	1					NADH(DB00157)	TTCCAGGACTGGCTACTGCGT	0.602													14	72	---	---	---	---	PASS
CCDC160	347475	broad.mit.edu	37	X	133379666	133379666	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133379666G>A	uc011mvj.1	+	2	1157	c.836G>A	c.(835-837)AGT>AAT	p.S279N		NM_001101357	NP_001094827	A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	279	Potential.									skin(1)	1						GGAGAGCTCAGTGTCATCAAG	0.383													16	76	---	---	---	---	PASS
F8	2157	broad.mit.edu	37	X	154157808	154157808	+	Silent	SNP	T	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154157808T>C	uc004fmt.2	-	14	4428	c.4257A>G	c.(4255-4257)AGA>AGG	p.R1419R		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1419	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GATATATAGGTCTAATAGATG	0.413													6	225	---	---	---	---	PASS
BRCC3	79184	broad.mit.edu	37	X	154344345	154344345	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154344345G>A	uc004fna.2	+	9	730	c.637G>A	c.(637-639)GAA>AAA	p.E213K	BRCC3_uc004fnb.2_Missense_Mutation_p.E188K	NM_024332	NP_077308	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	213					double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|positive regulation of DNA repair|response to X-ray	BRCA1-A complex|BRISC complex|nuclear ubiquitin ligase complex	enzyme regulator activity|metal ion binding|metallopeptidase activity|polyubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(3)|ovary(1)|large_intestine(1)|breast(1)	6	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)					TGAGAGAATCGAAATCCCAAT	0.438													30	143	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2534	2534	+	5'Flank	SNP	G	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2534G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TCACCAGTATTAGAGGCACCG	0.383													6	65	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4869549	4869550	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4869549_4869550delCA								AJAP1 (25699 upstream) : None (None downstream)																							ccaaaagagtcacacacacaca	0.000													4	2	---	---	---	---	
PTCHD2	57540	broad.mit.edu	37	1	11588347	11588347	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11588347delA	uc001ash.3	+							NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCCGAGTCAGAGGCTGCATTC	0.358													4	2	---	---	---	---	
DDI2	84301	broad.mit.edu	37	1	15952852	15952852	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15952852delA	uc001awx.1	+						DDI2_uc001aww.2_Intron	NM_032341	NP_115717	Q5TDH0	DDI2_HUMAN	DNA-damage inducible protein 2						proteolysis		aspartic-type endopeptidase activity				0		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		acgtaaaaggaaaaaaatgag	0.000													4	2	---	---	---	---	
ALDH4A1	8659	broad.mit.edu	37	1	19207210	19207210	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19207210delC	uc001bbb.2	-						ALDH4A1_uc010ocu.1_Intron|ALDH4A1_uc001bbc.2_Intron	NM_170726	NP_733844	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4A1 isoform a precursor						proline biosynthetic process|proline catabolic process	mitochondrial matrix	1-pyrroline-5-carboxylate dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	NADH(DB00157)	GCATCCAGGTCCAGGGGACCA	0.289													4	2	---	---	---	---	
KIAA0090	23065	broad.mit.edu	37	1	19548906	19548906	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19548906delA	uc001bbo.2	-						KIAA0090_uc001bbn.2_5'Flank|KIAA0090_uc001bbp.2_Intron|KIAA0090_uc001bbq.2_Intron|KIAA0090_uc001bbr.2_Intron	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor							integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)		ctcgaaaaacaaaaaaaagaT	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20602826	20602826	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20602826delC								UBXN10 (82885 upstream) : VWA5B1 (14586 downstream)																							actgatggctccctcctccac	0.000													4	2	---	---	---	---	
MDS2	259283	broad.mit.edu	37	1	23952853	23952853	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23952853delG	uc001bhi.3	+						MDS2_uc001bhj.3_5'Flank					Homo sapiens MDS2 gene.											ovary(2)	2						tgatgatgatGGGgatgatga	0.020			T	ETV6	MDS								4	2	---	---	---	---	
MAN1C1	57134	broad.mit.edu	37	1	26102233	26102233	+	Intron	DEL	C	-	-	rs35990149		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26102233delC	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		ggaggcgcagcaccagctaag	0.035													3	3	---	---	---	---	
GPN2	54707	broad.mit.edu	37	1	27215784	27215784	+	Intron	DEL	C	-	-	rs910048	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27215784delC	uc001bnd.1	-							NM_018066	NP_060536	Q9H9Y4	GPN2_HUMAN	ATP binding domain 1 family, member B								GTP binding				0						TAGGAGTCATCTTTTTTTTCT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31102922	31102922	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31102922delC								None (None upstream) : MATN1 (81204 downstream)																							GGTTTAATTTCCATATAGGTT	0.313													4	2	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39848006	39848008	+	Intron	DEL	TAT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39848006_39848008delTAT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCAAAAACTCTATTATTATTATT	0.207													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	44836604	44836604	+	IGR	DEL	C	-	-	rs34606208		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44836604delC								ERI3 (15665 upstream) : RNF220 (34356 downstream)																							ggtatcccagccccccatgtc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	46040195	46040195	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46040195delC								AKR1A1 (4475 upstream) : NASP (9522 downstream)																							attgagtcctcccccaacaag	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49134105	49134109	+	Intron	DEL	ACCAT	-	-	rs148523321		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49134105_49134109delACCAT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		cttagcctagaccataccatccctg	0.000													2	4	---	---	---	---	
SSBP3	23648	broad.mit.edu	37	1	54863217	54863218	+	Intron	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54863217_54863218delAG	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	NM_145716	NP_663768	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0						GTGGGAGAGCAGAGTCTTGCTG	0.564													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56076332	56076332	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56076332delA	uc001cyi.1	+											SubName: Full=cDNA FLJ45337 fis, clone BRHIP3007960;																		ATCAGATAAGAGGGTGGTGTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61138342	61138342	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61138342delC	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																		atgtgcttctccctttccagc	0.000													4	2	---	---	---	---	
TM2D1	83941	broad.mit.edu	37	1	62149067	62149068	+	Intron	INS	-	AT	AT	rs149969652	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62149067_62149068insAT	uc001czz.1	-							NM_032027	NP_114416	Q9BX74	TM2D1_HUMAN	beta-amyloid binding protein precursor						apoptosis					ovary(1)	1						TAAGATATTACATATATATATA	0.252													7	5	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72287701	72287701	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72287701delG	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		gtttccagaagggtttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	86070950	86070950	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86070950delC								CYR61 (21304 upstream) : ZNHIT6 (47542 downstream)																							ACATATAATTCCCTGCAGAAG	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91659744	91659744	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91659744delT								ZNF644 (172073 upstream) : HFM1 (66580 downstream)																							CACATACCCATTGCCCCTAAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	107383769	107383769	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107383769delA								None (None upstream) : PRMT6 (215498 downstream)																							gttcacacataaaagccctgg	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116063766	116063767	+	IGR	DEL	CT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116063766_116063767delCT								NGF (182909 upstream) : VANGL1 (120807 downstream)																							TTTATTTATCCTCTAAGACCCT	0.396													4	2	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153894069	153894070	+	Intron	INS	-	AC	AC			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153894069_153894070insAC	uc001fdb.3	-						uc001fdc.1_5'Flank	NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTCTCTCTCTTacacacacaca	0.376													4	2	---	---	---	---	
IQGAP3	128239	broad.mit.edu	37	1	156532119	156532120	+	Intron	INS	-	C	C	rs138515696	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156532119_156532120insC	uc001fpf.2	-						IQGAP3_uc009wsb.1_Intron	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAGTCCAACTGCCCCCCCGGCA	0.569													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163409738	163409738	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163409738delT								NUF2 (84185 upstream) : None (None downstream)																							GTGGATTCTGTTTAGGATGGC	0.408													4	2	---	---	---	---	
ILDR2	387597	broad.mit.edu	37	1	166944274	166944277	+	Intron	DEL	CACA	-	-	rs67253020		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166944274_166944277delCACA	uc001gdx.1	-							NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1						CTCTCTCTCTcacacacacacaca	0.441													4	2	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169492282	169492282	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169492282delT	uc001ggg.1	-							NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ACCTATCATATTACTGCTTTT	0.294													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171203826	171203826	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171203826delT								FMO2 (22004 upstream) : FMO1 (13807 downstream)																							GATTAAACTATTTTTTTAAAT	0.174													4	2	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179416621	179416621	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179416621delT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						GAAATATTCATTAGGAATAGG	0.284													4	2	---	---	---	---	
LHX4	89884	broad.mit.edu	37	1	180211340	180211340	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180211340delT	uc001goe.1	+							NM_033343	NP_203129	Q969G2	LHX4_HUMAN	LIM homeobox protein 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						CAGAATTGGCTTTTTTTTTCC	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	190641394	190641395	+	IGR	INS	-	T	T	rs142491978	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190641394_190641395insT								FAM5C (194635 upstream) : None (None downstream)																							tggaagaaatgctcgacaggcc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195054303	195054304	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195054303_195054304delCA								None (None upstream) : None (None downstream)																							TAAACAGAGTCACACACCCACA	0.376													4	2	---	---	---	---	
CRB1	23418	broad.mit.edu	37	1	197415484	197415484	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197415484delG	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						acttgagggagttaggctgtg	0.000													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202319372	202319372	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202319372delT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			TTTGTACCCATTTTTTTTTCC	0.234													4	2	---	---	---	---	
DSTYK	25778	broad.mit.edu	37	1	205179817	205179817	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205179817delG	uc001hbw.2	-						DSTYK_uc001hbx.2_Intron	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1						GCAATTCCGTGGCACCCATCA	0.473													4	2	---	---	---	---	
TMCC2	9911	broad.mit.edu	37	1	205197541	205197541	+	5'UTR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205197541delT	uc001hbz.1	+	2					TMCC2_uc010prf.1_5'Flank	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2							integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCTTTAAGAATTTTTTTTTTA	0.478													4	2	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206524555	206524555	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206524555delA	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					AGAAGAGGAGAAGTGGTGACC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209326249	209326250	+	IGR	INS	-	A	A	rs147512631	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209326249_209326250insA								PLXNA2 (908584 upstream) : LOC642587 (275918 downstream)																							ttttataactgaaaaaaaattg	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215416008	215416009	+	IGR	INS	-	C	C	rs72509568		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215416008_215416009insC								KCNK2 (5573 upstream) : KCTD3 (324726 downstream)																							ggaaatcaatgtgaggggatgc	0.040													2	4	---	---	---	---	
SUSD4	55061	broad.mit.edu	37	1	223470659	223470659	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223470659delC	uc001hnx.2	-						SUSD4_uc001hny.3_Intron|SUSD4_uc010puw.1_Intron|SUSD4_uc001hnz.2_Intron|SUSD4_uc010pux.1_Intron	NM_017982	NP_060452	Q5VX71	SUSD4_HUMAN	sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)		ATGGACTAGGCCCAAGGGATG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232449370	232449370	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232449370delC								DISC1 (272354 upstream) : SIPA1L2 (84344 downstream)																							cccagtctcacgcattccgtt	0.124													4	2	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236697905	236697905	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236697905delA	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCTCATAGTTAAAAAAAAAAA	0.413													6	5	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242016438	242016439	+	Intron	DEL	TG	-	-	rs35698447		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242016438_242016439delTG	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			ATGGTAATCTTGTGTGTGTGTG	0.356								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247573343	247573345	+	IGR	DEL	AGC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247573343_247573345delAGC								ZNF496 (78181 upstream) : NLRP3 (6113 downstream)																							AAGAGGGAAGAGCAGCAGCAGCA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	3061710	3061711	+	Intron	INS	-	GTA	GTA			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3061710_3061711insGTA	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		ttatgataatggtggtgatggt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8231503	8231504	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8231503_8231504delGT	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		GATCAGGATAGTGTGTGTGTTT	0.396													4	2	---	---	---	---	
PQLC3	130814	broad.mit.edu	37	2	11318191	11318192	+	3'UTR	INS	-	AGA	AGA	rs148190616	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11318191_11318192insAGA	uc002rbc.2	+	7					PQLC3_uc010yjk.1_3'UTR	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor							integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		CTGCAGTGTTGAGGCCAGTCAC	0.406													3	3	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15686862	15686862	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15686862delA	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						aaaacaaaacaaaaaaaaCAA	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20085187	20085187	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20085187delA								OSR1 (526815 upstream) : TTC32 (11331 downstream)																							AGGGACTCCTAATAAGATAGA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20380766	20380766	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20380766delT								LAPTM4A (128977 upstream) : SDC1 (19792 downstream)																							AAGTTGTGCCTTTTTTTGTCC	0.542													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31344425	31344425	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31344425delT	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					AACGGCTTTATTTTTTAACTT	0.448													4	2	---	---	---	---	
XDH	7498	broad.mit.edu	37	2	31609007	31609007	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31609007delA	uc002rnv.1	-							NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	atccccatataaaaaacagaa	0.100													4	2	---	---	---	---	
MEMO1	51072	broad.mit.edu	37	2	32172885	32172886	+	Intron	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32172885_32172886delCA	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1 isoform 1						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					ACTAAATACGCACACACACACA	0.332													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33487628	33487628	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33487628delG	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ttttttttttGTAATTTCACA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37947254	37947254	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37947254delT								CDC42EP3 (47928 upstream) : FAM82A1 (205208 downstream)																							AGTTCATTGCTTTTTGCAGAG	0.348													4	2	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42738175	42738175	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42738175delC	uc002rso.1	+							NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						ACCCTTCTGTCCCTCTAACAA	0.438													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	45924520	45924522	+	Intron	DEL	CTT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45924520_45924522delCTT	uc002rut.2	+						PRKCE_uc002ruu.2_Intron	NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			GCGCTCTGACCTTCTATTGTTTT	0.453													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47126500	47126500	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47126500delA								LOC100134259 (40355 upstream) : MCFD2 (2517 downstream)																							ATTATTTGGCAAAAAAATTAT	0.468													4	2	---	---	---	---	
PUS10	150962	broad.mit.edu	37	2	61242903	61242903	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61242903delT	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron|PUS10_uc002sap.1_5'Flank|PUS10_uc002saq.1_Intron|PEX13_uc010fcj.1_5'Flank|PEX13_uc002sau.3_5'Flank|PEX13_uc002sas.2_5'Flank|PEX13_uc002sat.2_5'Flank	NM_144709	NP_653310	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TCTGGATCCCTTTTCCCAGCC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69184326	69184326	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69184326delT								GKN2 (4224 upstream) : GKN1 (17379 downstream)																							ttggtttgccttttttttagt	0.000													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71798314	71798315	+	Intron	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71798314_71798315delCA	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						tcacacccagcacacacacaca	0.000													4	2	---	---	---	---	
ALMS1	7840	broad.mit.edu	37	2	73613032	73613037	+	In_Frame_Del	DEL	GGAGGA	-	-	rs72319667		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73613032_73613037delGGAGGA	uc002sje.1	+	1	147_152	c.36_41delGGAGGA	c.(34-42)CTGGAGGAG>CTG	p.EE27del	ALMS1_uc002sjf.1_In_Frame_Del_p.EE27del	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	27_28	Glu-rich.				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						CGGGCGAGCTggaggaggaggaggag	0.403													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78563294	78563295	+	IGR	DEL	TC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78563294_78563295delTC								SNAR-H (381142 upstream) : REG3G (689531 downstream)																							tctttttctttcccagcttccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89168959	89168960	+	Intron	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89168959_89168960delAG	uc010ytr.1	-											Parts of antibodies, mostly variable regions.																		agaaagagaaagagagagagag	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91694606	91694607	+	IGR	INS	-	GT	GT	rs55687190		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91694606_91694607insGT								None (None upstream) : LOC654342 (110585 downstream)																							agtgtgtgtacgtgtgtgtgtg	0.292													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91801453	91801454	+	IGR	INS	-	T	T	rs149695974		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801453_91801454insT								None (None upstream) : LOC654342 (3738 downstream)																							tgatttcattcttttttaaggc	0.000													4	2	---	---	---	---	
MRPS5	64969	broad.mit.edu	37	2	95767130	95767131	+	Intron	DEL	AA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95767130_95767131delAA	uc002sub.2	-						MRPS5_uc002suc.2_Intron	NM_031902	NP_114108	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5						translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3						acaacgtctcaaaaaaaaaaaa	0.045													4	2	---	---	---	---	
SNRNP200	23020	broad.mit.edu	37	2	96965417	96965417	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96965417delC	uc002svu.2	-							NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						TGGATCATAGCCTCTCTCTAA	0.428													4	2	---	---	---	---	
LYG1	129530	broad.mit.edu	37	2	99909376	99909376	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99909376delT	uc002szy.2	-						MRPL30_uc002szl.1_Intron|LYG1_uc010yvo.1_Intron	NM_174898	NP_777558	Q8N1E2	LYG1_HUMAN	lysozyme g-like protein 1 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity				0						TCTGGTGCCCTTTGATGTTGT	0.373													4	2	---	---	---	---	
EIF5B	9669	broad.mit.edu	37	2	99964742	99964742	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99964742delG	uc002tab.2	+							NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3						ATCGTAAGCTGGGAGGGTTTT	0.363													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100272715	100272715	+	Intron	DEL	A	-	-	rs11337782		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100272715delA	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						GTTCTAAGAGAAAAAGATTTA	0.294													4	2	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101587760	101587761	+	Intron	INS	-	AA	AA	rs35040339		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101587760_101587761insAA	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4						gactctatctcaaaaaaaaaaa	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106212606	106212606	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106212606delA	uc002tdf.2	-											Homo sapiens hypothetical protein LOC285000, mRNA (cDNA clone IMAGE:3925223), partial cds.																		ATAAGCTGGGAAAAGCAAGGG	0.473													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109803818	109803818	+	Intron	DEL	T	-	-	rs5833319		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109803818delT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						AACCACAGACTTTTTTTTTTT	0.284													4	2	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125564492	125564493	+	Intron	INS	-	T	T	rs34184441		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125564492_125564493insT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTTTATTTTACTTTTTTTTTTT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	125999045	125999045	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125999045delG								CNTNAP5 (326184 upstream) : None (None downstream)																							aaccaggtatgggtaatggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136487985	136487985	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136487985delA								R3HDM1 (5149 upstream) : UBXN4 (11204 downstream)																							cgtctcagctaataagtgatg	0.075													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138050039	138050039	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138050039delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		GCAACTGCCCTTGGAAGCCTA	0.353													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138222821	138222821	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138222821delA	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CCCCATTCATAAAAAAAAAAA	0.398													4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	144895623	144895624	+	Intron	DEL	AA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144895623_144895624delAA	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		ccaaccccttaagtgtcaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	167514623	167514623	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167514623delG								SCN7A (163906 upstream) : XIRP2 (230374 downstream)																							ttgagtaactggattaatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173399696	173399696	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173399696delC								ITGA6 (28515 upstream) : PDK1 (20405 downstream)																							gggtacatggcccagtcataa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	180277204	180277204	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180277204delG								SESTD1 (147854 upstream) : ZNF385B (29516 downstream)																							tattgtgtctggggctcaggg	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203867213	203867214	+	IGR	DEL	GA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203867213_203867214delGA								ALS2CR8 (16153 upstream) : NBEAL1 (12388 downstream)																							accaaaattggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	205086035	205086035	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205086035delG								ICOS (259739 upstream) : PARD3B (324481 downstream)																							CAAGGCATCAGGAGCATCTAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210253944	210253944	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210253944delA								PTH2R (549126 upstream) : MAP2 (34827 downstream)																							ATCTTTTACTAACCGAGTGCA	0.423													4	2	---	---	---	---	
XRCC5	7520	broad.mit.edu	37	2	216983452	216983452	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216983452delG	uc002vfy.2	+						XRCC5_uc002vfz.2_Intron	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II						double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		AGAGTATGCTGGGAGAATTCT	0.408								Direct_reversal_of_damage|NHEJ					4	2	---	---	---	---	
BCS1L	617	broad.mit.edu	37	2	219524287	219524287	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219524287delC	uc002vio.2	+						ZNF142_uc002vin.2_5'Flank|ZNF142_uc010fvt.2_5'Flank|ZNF142_uc002vim.2_5'Flank|BCS1L_uc002vip.2_5'Flank|BCS1L_uc002viq.2_5'Flank|BCS1L_uc010fvu.2_5'Flank|BCS1L_uc010fvv.2_5'Flank|BCS1L_uc002vir.2_5'Flank|BCS1L_uc002vis.2_5'Flank	NM_004328	NP_004319	Q9Y276	BCS1_HUMAN	BCS1-like						mitochondrial respiratory chain complex I assembly|mitochondrial respiratory chain complex III assembly|mitochondrial respiratory chain complex IV assembly	integral to membrane|mitochondrial respiratory chain complex III	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGCCCTCCACCCCCACTCCA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229493626	229493626	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229493626delA								SPHKAP (447265 upstream) : PID1 (395064 downstream)																							cagaggctggaaaaatgccag	0.000													4	2	---	---	---	---	
FBXO36	130888	broad.mit.edu	37	2	230886032	230886032	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230886032delC	uc010fxi.1	+							NM_174899	NP_777559	Q8NEA4	FBX36_HUMAN	F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		TAACCTGCGTCCCTTACTGCC	0.498													4	2	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234066313	234066314	+	Intron	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234066313_234066314insG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		aaagaaatttcaacctcatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239648064	239648065	+	IGR	INS	-	GT	GT			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239648064_239648065insGT								ASB1 (287174 upstream) : TWIST2 (108608 downstream)																							GATGTTGGGCAGTGTGTGTTGT	0.327													4	2	---	---	---	---	
LMCD1	29995	broad.mit.edu	37	3	8575224	8575224	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8575224delT	uc003bqq.2	+						LMCD1_uc011atd.1_Intron|LMCD1_uc011ate.1_Intron	NM_014583	NP_055398	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1						positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.124)		AAAGAAAGAGTTTTTATCACC	0.502													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191499	10191499	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191499delG	uc003bvc.2	+	3	705	c.492delG	c.(490-492)CAGfs	p.Q164fs	VHL_uc003bvd.2_Frame_Shift_Del_p.Q123fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	164	Interaction with Elongin BC complex.		Q -> R (in VHLD; type II).|Q -> H (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.Q164*(4)|p.Q164P(3)|p.Q164H(3)|p.Q164fs*9(1)|p.Q164R(1)|p.V165fs*5(1)|p.Q164fs*10(1)|p.Q164L(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATGCCTCCAGGTTGTCCGGA	0.507		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				97	42	---	---	---	---	
SYN2	6854	broad.mit.edu	37	3	12223942	12223942	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12223942delT	uc003bwm.2	+						SYN2_uc003bwl.1_Intron|SYN2_uc003bwn.2_Intron	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						AATACAAGCATTAGACAAACT	0.488													4	2	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16461102	16461102	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16461102delT	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						TTTCCCATAATTTTATGAACC	0.413													4	2	---	---	---	---	
TRIM71	131405	broad.mit.edu	37	3	32886440	32886440	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32886440delT	uc003cff.2	+							NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71						multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3						GAAGACTGAGTTTTTGGGCTG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	36960947	36960947	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36960947delA								TRANK1 (58536 upstream) : EPM2AIP1 (66411 downstream)																							atatatcagtaactcctttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	41018672	41018672	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41018672delA								ZNF621 (437629 upstream) : CTNNB1 (217729 downstream)																							GGTTTGGTTTAAAAAAAAAAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	47891745	47891746	+	IGR	DEL	AA	-	-	rs62835861		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47891745_47891746delAA								DHX30 (60 upstream) : MAP4 (434 downstream)																							ACGGTTCCCCAAAGAGGAAGGA	0.500											OREG0015550	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PHF7	51533	broad.mit.edu	37	3	52448283	52448283	+	Intron	DEL	A	-	-	rs3832250		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52448283delA	uc003ddy.2	+						PHF7_uc003ddz.2_Intron	NM_016483	NP_057567	Q9BWX1	PHF7_HUMAN	PHD finger protein 7 isoform 1							nucleus	zinc ion binding			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		AAACAAAACCAAAAAAAAATG	0.348													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	59101674	59101674	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59101674delA								C3orf67 (65916 upstream) : FHIT (633364 downstream)																							TTTCACTTTCAAAAAAAGAAA	0.413													4	2	---	---	---	---	
ADAMTS9	56999	broad.mit.edu	37	3	64609410	64609410	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64609410delT	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc003dmk.1_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1						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)		tggcactttgtttatactctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	68029410	68029411	+	IGR	INS	-	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68029410_68029411insC								SUCLG2 (324372 upstream) : FAM19A1 (11323 downstream)																							cacatcaaatgcccccagtatc	0.188													4	2	---	---	---	---	
FRMD4B	23150	broad.mit.edu	37	3	69232088	69232088	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69232088delA	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnu.2_Intron|FRMD4B_uc011bga.1_Intron	NM_015123	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		ATATGTAGGGAAAAAAAGGAC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72329198	72329198	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72329198delG								PROK2 (494841 upstream) : RYBP (94553 downstream)																							AGGTACGACAGGGAGAGGGCA	0.338													4	2	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85672058	85672058	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85672058delC	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		ATGGGATGGGCTTTAGGCTAT	0.388													4	2	---	---	---	---	
CRYBG3	131544	broad.mit.edu	37	3	97620941	97620941	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97620941delC	uc003drx.2	+							NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0						CGTTCAATAACTAGAAAGTAT	0.383													4	2	---	---	---	---	
GPR128	84873	broad.mit.edu	37	3	100371623	100371624	+	Intron	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100371623_100371624delAC	uc003duc.2	+						GPR128_uc011bhc.1_Intron|GPR128_uc003dud.2_5'Flank	NM_032787	NP_116176	Q96K78	GP128_HUMAN	G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4						atacacacatacacacacacac	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106321748	106321748	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106321748delT								CBLB (733482 upstream) : LOC100302640 (233912 downstream)																							ttatttctcctttttttttga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112842004	112842004	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112842004delT								C3orf17 (103449 upstream) : BOC (88408 downstream)																							GAGCAGGTCCTTTCCCTGTCC	0.413													4	2	---	---	---	---	
WDR52	55779	broad.mit.edu	37	3	113046242	113046243	+	Intron	INS	-	AATT	AATT			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113046242_113046243insAATT	uc003ead.1	-						WDR52_uc010hqk.1_Intron			Q96MT7	WDR52_HUMAN	RecName: Full=WD repeat protein 52.; Flags: Fragment;											central_nervous_system(1)	1						CTTACAGAATATCAGACCAAAT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	114889563	114889564	+	IGR	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114889563_114889564delAG								ZBTB20 (23436 upstream) : GAP43 (452587 downstream)																							gtcctgacacagagagagagat	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117210461	117210463	+	IGR	DEL	AGA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117210461_117210463delAGA								LOC285194 (774576 upstream) : None (None downstream)																							GGATGACTTTAGAAGAAGAAAGT	0.177													4	2	---	---	---	---	
AMOTL2	51421	broad.mit.edu	37	3	134093744	134093745	+	Intron	DEL	TG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134093744_134093745delTG	uc003eqf.2	-						AMOTL2_uc003eqg.1_5'Flank|AMOTL2_uc003eqh.1_5'Flank	NM_016201	NP_057285	Q9Y2J4	AMOL2_HUMAN	angiomotin like 2											large_intestine(1)	1						GGACTCCGGCtgtgtgtgtgtg	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138137086	138137087	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138137086_138137087delAC								MRAS (12710 upstream) : ESYT3 (16328 downstream)																							CAGGCTTCATACACACACACAC	0.554											OREG0015834	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142226181	142226182	+	Intron	INS	-	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142226181_142226182insC	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						ACCGGCACTTGCCCCCACTAAC	0.441								Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147410031	147410031	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147410031delC								ZIC1 (275527 upstream) : None (None downstream)																							tgtactgtcaccccattttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152745287	152745287	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152745287delC								P2RY1 (189446 upstream) : RAP2B (134742 downstream)																							CTAAGAACTGCCTCAGTGTTG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159674107	159674107	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159674107delT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		TTACAGAAGATTTGTGGATTG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166009079	166009079	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166009079delC								BCHE (453826 upstream) : ZBBX (949002 downstream)																							CTGCCAGCTTCAAATTGACTG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168686117	168686117	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168686117delA								C3orf50 (137745 upstream) : MECOM (115170 downstream)																							attccaaaagaaaaaaaaagg	0.000													4	3	---	---	---	---	
LRRC31	79782	broad.mit.edu	37	3	169575041	169575041	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169575041delA	uc003fgc.1	-						LRRC31_uc010hwp.1_Intron	NM_024727	NP_079003	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31											ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			GATAGAAGTGAGGCAAAGCAG	0.393													4	2	---	---	---	---	
TBL1XR1	79718	broad.mit.edu	37	3	176755297	176755298	+	Intron	INS	-	G	G	rs142109121	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176755297_176755298insG	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			caatgggcggcggggggggcat	0.000													4	2	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183526058	183526058	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183526058delT	uc003fly.2	+						uc003fma.1_5'Flank	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TTCCTTCTGATTTTTAAATGG	0.393													4	2	---	---	---	---	
KNG1	3827	broad.mit.edu	37	3	186436788	186436788	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186436788delA	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)	ACTTTAGCAGAAAAAAAAAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35910	35910	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35910delG								None (None upstream) : ZNF595 (17317 downstream)																							TCCAGGAAATGGGACAGGATG	0.368													4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3101357	3101358	+	Intron	INS	-	TG	TG	rs10665872		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3101357_3101358insTG	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)		TGGAGGTGCTCTTGTATGGTTT	0.475													4	3	---	---	---	---	
WDR1	9948	broad.mit.edu	37	4	10110324	10110325	+	Intron	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10110324_10110325insA	uc003gmf.2	-						WDR1_uc003gmg.2_Intron	NM_017491	NP_059830	O75083	WDR1_HUMAN	WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		TGAATGACAGCAAAAAACCTCA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12961761	12961761	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12961761delA								None (None upstream) : HSP90AB2P (373276 downstream)																							aaccaaaggtaatcctatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22340948	22340948	+	Intron	DEL	C	-	-	rs34486445		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22340948delC	uc003gqk.2	-											Homo sapiens, clone IMAGE:3922198, mRNA.																		ccagcccagaccctgcagcta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27188445	27188446	+	IGR	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27188445_27188446insT								STIM2 (162637 upstream) : None (None downstream)																							acaaatattgatttttttcaca	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35562075	35562075	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35562075delT								None (None upstream) : ARAP2 (387769 downstream)																							CTTCTTTTGGTTTTCCCTTTA	0.299													4	2	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	41057154	41057154	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41057154delA	uc003gvl.2	-						APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						cttggtctgtaatgggctttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49088320	49088320	+	IGR	DEL	A	-	-	rs149932191		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49088320delA								CWH43 (24227 upstream) : None (None downstream)																							tgaaaactagaaaaaaactac	0.000													1	6	---	---	---	---	
KIAA1211	57482	broad.mit.edu	37	4	57037007	57037007	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57037007delA	uc003hbk.2	+							NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)					cctatctcttaaaaaaCTATT	0.154													4	2	---	---	---	---	
LOC550112	550112	broad.mit.edu	37	4	68829342	68829342	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68829342delT	uc003hdl.3	+						TMPRSS11A_uc003hdr.1_5'Flank|TMPRSS11A_uc003hds.1_5'Flank					Homo sapiens chromosome 4 cDNA.												0						GAAAGCAATATTTTTTTAGTA	0.333													4	2	---	---	---	---	
TMEM150C	441027	broad.mit.edu	37	4	83472106	83472107	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83472106_83472107delGT	uc003hmy.1	-						TMEM150C_uc011ccj.1_Intron	NM_001080506	NP_001073975	B9EJG8	T150C_HUMAN	transmembrane protein 150C							integral to membrane				ovary(1)	1						TTGAGAGTGAGTAGGTATGGTT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	94872876	94872877	+	IGR	DEL	TA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94872876_94872877delTA								ATOH1 (121734 upstream) : SMARCAD1 (255882 downstream)																							acagcagatctatacagaacat	0.000													4	2	---	---	---	---	
TSPAN5	10098	broad.mit.edu	37	4	99582700	99582700	+	5'Flank	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99582700delA	uc003hub.2	-							NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		cagcagatggaaaaagttata	0.030													4	2	---	---	---	---	
LEF1	51176	broad.mit.edu	37	4	109088507	109088508	+	Intron	INS	-	ACAC	ACAC			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109088507_109088508insACAC	uc003hyt.1	-						LEF1_uc011cfj.1_5'Flank|LEF1_uc011cfk.1_5'Flank|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		CCTCCCATCCTacacacacaca	0.446													3	3	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	109870694	109870694	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109870694delT	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		TAAAtttttcttttttttttt	0.010													4	2	---	---	---	---	
CASP6	839	broad.mit.edu	37	4	110617197	110617198	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110617197_110617198insT	uc003hzn.1	-						CASP6_uc003hzo.1_Intron	NM_001226	NP_001217	P55212	CASP6_HUMAN	caspase 6 isoform alpha preproprotein						cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis	cytosol|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		aaccaacactatttggaaacCA	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	112951594	112951594	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112951594delT								None (None upstream) : C4orf32 (114959 downstream)																							CAATTGTCCCTTTCATGCCTC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190550470	190550470	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190550470delA								None (None upstream) : FRG1 (311504 downstream)																							GCCAGACTCCAAAAAAAATTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190565740	190565741	+	IGR	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565740_190565741insT								None (None upstream) : FRG1 (296233 downstream)																							acatgactgTATATAAGCTGCA	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190581823	190581823	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190581823delT								None (None upstream) : FRG1 (280151 downstream)																							AGCTGTTTCATTTTTTTGCAG	0.403													6	3	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190883957	190883957	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190883957delA	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		CAGCATTCTCACCCTGTTAAA	0.318													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190894277	190894277	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190894277delT								FRG1 (9919 upstream) : TUBB4Q (9402 downstream)																							AAAAGATATGTAGGCTGAGCA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190894279	190894279	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190894279delG								FRG1 (9921 upstream) : TUBB4Q (9400 downstream)																							AAGATATGTAGGCTGAGCAAA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1545776	1545777	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1545776_1545777delAC								LPCAT1 (21700 upstream) : SDHAP3 (22860 downstream)																							acacatacctacacacacacct	0.223													4	2	---	---	---	---	
SDHAP3	728609	broad.mit.edu	37	5	1587435	1587438	+	Intron	DEL	AAAC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1587435_1587438delAAAC	uc011cme.1	-							NR_003263				Homo sapiens cDNA FLJ58919 complete cds, moderately similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC1.3.5.1).												0						aaaaGTTGAAaaacaaacaaacaa	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4268136	4268136	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4268136delA								IRX1 (666620 upstream) : LOC340094 (766336 downstream)																							TATTCCATGGAAAAAAAATGT	0.343													4	2	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6606701	6606701	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6606701delT	uc003jdu.2	-						NSUN2_uc003jds.2_5'Flank|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						cccggtcCAGTTTTTTTTTAT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6674477	6674477	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6674477delA								SRD5A1 (4804 upstream) : PAPD7 (40241 downstream)																							taaatctattaaAAAAAAAAC	0.219													4	2	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16512692	16512692	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16512692delT	uc003jfs.2	-							NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						TCAGTCCGAGTTTTTTTTTTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17670208	17670209	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17670208_17670209insA								BASP1 (393273 upstream) : None (None downstream)																							TGAAAGAAGAGAAAAAAAAAAC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24155739	24155749	+	Intron	DEL	GAGAAGGAAAC	-	-	rs75075313		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24155739_24155749delGAGAAGGAAAC	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		ccactctgaagagaaggaaacggttctggct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27881519	27881520	+	IGR	INS	-	T	T	rs10651453		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27881519_27881520insT								CDH9 (842830 upstream) : None (None downstream)																							acatgagagtgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31366827	31366828	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31366827_31366828insA								CDH6 (41590 upstream) : RNASEN (33774 downstream)																							CTAATCAATCTAAAAAAGAACA	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32976422	32976422	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32976422delG								C5orf23 (184603 upstream) : TARS (464380 downstream)																							TTGGGGGGTTGGGGCATGCAT	0.333													4	2	---	---	---	---	
PRLR	5618	broad.mit.edu	37	5	35057005	35057005	+	3'UTR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35057005delA	uc003jjm.2	-	10					PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_3'UTR	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	GGAGGCAGAGAAGAACTTGGA	0.358													4	2	---	---	---	---	
FYB	2533	broad.mit.edu	37	5	39252812	39252813	+	Intron	INS	-	A	A	rs142356372	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39252812_39252813insA	uc011cpl.1	-							NM_001465	NP_001456	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 1						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)			GGGTTGGTGCCTTTCTTTTTAC	0.272													2	4	---	---	---	---	
PLCXD3	345557	broad.mit.edu	37	5	41326657	41326657	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41326657delC	uc003jmm.1	-							NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						cttgtattttccccaaaacat	0.065													4	2	---	---	---	---	
PLCXD3	345557	broad.mit.edu	37	5	41396103	41396104	+	Intron	INS	-	AA	AA	rs113198555		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41396103_41396104insAA	uc003jmm.1	-							NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						gcccatcaaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	45037315	45037315	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45037315delA								MRPS30 (221701 upstream) : HCN1 (222038 downstream)																							CTGTCCTTGGAAAAAAAAAAT	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46095283	46095283	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46095283delT								HCN1 (399063 upstream) : None (None downstream)																							gagttgaacctttcttttgat	0.000													5	3	---	---	---	---	
GPX8	493869	broad.mit.edu	37	5	54460230	54460230	+	3'UTR	DEL	T	-	-	rs77476120		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54460230delT	uc003jpq.2	+	3					CDC20B_uc003jpn.1_Intron|CDC20B_uc010ivu.1_Intron|CDC20B_uc003jpo.1_Intron|CDC20B_uc010ivv.1_Intron|CDC20B_uc003jpp.2_Intron|GPX8_uc003jpr.2_3'UTR|GPX8_uc003jps.2_RNA|GPX8_uc003jpt.2_3'UTR	NM_001008397	NP_001008398	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8						response to oxidative stress	integral to membrane	glutathione peroxidase activity				0					Glutathione(DB00143)	CAATGAAGGATTTTTTTTTAA	0.214													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59053040	59053040	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59053040delC	uc003jsa.2	-						PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	AGTCTGAGAGCCCAAGGAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	75133504	75133505	+	IGR	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75133504_75133505insT								POC5 (120191 upstream) : SV2C (245800 downstream)																							tctactttctattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77092080	77092080	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77092080delA								TBCA (19895 upstream) : AP3B1 (206071 downstream)																							tatgttctataaaatgtcact	0.000													4	2	---	---	---	---	
XRCC4	7518	broad.mit.edu	37	5	82451129	82451129	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82451129delG	uc003kib.2	+						XRCC4_uc003kia.1_Intron|XRCC4_uc003kid.2_Intron|XRCC4_uc003kic.2_Intron|XRCC4_uc003kie.2_Intron|XRCC4_uc003kif.1_Intron	NM_022406	NP_071801	Q13426	XRCC4_HUMAN	X-ray repair cross complementing protein 4						DNA ligation involved in DNA repair|double-strand break repair via nonhomologous end joining|initiation of viral infection|positive regulation of ligase activity|provirus integration|response to X-ray	cytosol|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|nucleoplasm	DNA binding|protein C-terminus binding			skin(3)	3		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TATTTCTAAAGGGGAAAAGTT	0.358								NHEJ					4	2	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108081735	108081735	+	5'Flank	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108081735delT	uc003kop.1	+						FER_uc011cve.1_5'Flank|FER_uc011cvf.1_5'Flank|FER_uc003koq.2_5'Flank|FER_uc011cvg.1_5'Flank	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTTTCAATCATTTTTTATTAC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	113840730	113840730	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113840730delA	uc003kqr.1	-											Homo sapiens cDNA FLJ40367 fis, clone TESTI2034785.																		CATATCACACACAGTGAAACT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	118601307	118601307	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118601307delG								DMXL1 (16485 upstream) : TNFAIP8 (3111 downstream)																							TTGAGGACATGGTAAAAAGAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122607464	122607464	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122607464delA								PRDM6 (83720 upstream) : CEP120 (73116 downstream)																							agagggaaggaagtgtcaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129192974	129192974	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129192974delC								ADAMTS19 (118598 upstream) : CHSY3 (47549 downstream)																							tttctcacttccccacttccc	0.000													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142592989	142592989	+	Intron	DEL	T	-	-	rs11331984		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142592989delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCCCTCCCCTGGGGGTTGGA	0.557													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144661142	144661142	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144661142delT								KCTD16 (804198 upstream) : PRELID2 (477440 downstream)																							AATAAGACAGTAATGACAACA	0.413													4	2	---	---	---	---	
PPARGC1B	133522	broad.mit.edu	37	5	149128704	149128704	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149128704delC	uc003lrc.2	+						PPARGC1B_uc003lrb.1_Intron|PPARGC1B_uc003lrd.2_Intron	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor						estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GGGCCAGGCACCACAGAACCA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151443433	151443433	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151443433delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																		AATCAGAGGATTGGCTGGGGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153222656	153222656	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153222656delC								GRIA1 (29228 upstream) : FAM114A2 (148615 downstream)																							gacactaactcccaggtggta	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154864206	154864206	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154864206delC								KIF4B (466521 upstream) : SGCD (270857 downstream)																							CTTCCCTTATCCCATGATAAG	0.383													4	2	---	---	---	---	
HAVCR1	26762	broad.mit.edu	37	5	156468154	156468154	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156468154delA	uc010jij.1	-						HAVCR1_uc011ddl.1_Intron|HAVCR1_uc003lwi.2_Intron	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1						interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTCACTGAGAAAAAAAGTAT	0.254													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156710446	156710446	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156710446delT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwp.2_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAAGACAGTCTTTTTTTTTTC	0.393													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158851352	158851352	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158851352delA								IL12B (93871 upstream) : LOC285627 (24212 downstream)																							gtcaaggattaactgtacagt	0.000													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166979924	166979925	+	Intron	INS	-	AATG	AATG	rs148946193	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166979924_166979925insAATG	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		ggtaagttaataatgaatgaat	0.045													3	3	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167835971	167835971	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167835971delT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CTTTCTCTGGTTTTTTTTTTC	0.418													4	2	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167848817	167848818	+	Intron	DEL	AT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167848817_167848818delAT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		agagtgcctgatatataTATAT	0.188													3	4	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168117807	168117808	+	Intron	INS	-	AA	AA	rs146726218	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168117807_168117808insAA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTCATTGAGCAACCAGAGCCT	0.480													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173070819	173070820	+	IGR	INS	-	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173070819_173070820insC								BOD1 (27153 upstream) : CPEB4 (244511 downstream)																							TTCAAATCCAACCCCCTACCCC	0.545													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173256706	173256706	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173256706delT								BOD1 (213040 upstream) : CPEB4 (58625 downstream)																							TTGAAATCCCTTTTTTTGCTC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174615810	174615811	+	IGR	INS	-	T	T	rs5873473		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174615810_174615811insT								MSX2 (457909 upstream) : DRD1 (251865 downstream)																							ttttgtttttgttttttttttt	0.099													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174768181	174768182	+	IGR	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174768181_174768182delAG								MSX2 (610280 upstream) : DRD1 (99494 downstream)																							tgtaggggctaggtgggagagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177393688	177393689	+	IGR	INS	-	GTG	GTG	rs144895247	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177393688_177393689insGTG								LOC728554 (82421 upstream) : PROP1 (25547 downstream)																							TCTGGGGAATCGGGTGGCGTGC	0.272													1	6	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5312054	5312054	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5312054delA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	AATGAGAGATAAAAAGCCACT	0.368													4	2	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5564652	5564652	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5564652delT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	tacccatcccttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	6803283	6803283	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6803283delG								LY86 (148067 upstream) : RREB1 (304905 downstream)																							GAGACAGCGTGGGCCAAGCTG	0.622													4	2	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17516372	17516373	+	Intron	DEL	CC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17516372_17516373delCC	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			tccatcagctccccatctgggt	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22586605	22586605	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22586605delA								HDGFL1 (15856 upstream) : None (None downstream)																							CATCAAATGGAAAAAAAAAAG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22628032	22628032	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22628032delT								HDGFL1 (57283 upstream) : None (None downstream)																							ttgagggtcctttttttagtc	0.000													4	2	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25559800	25559800	+	Intron	DEL	T	-	-	rs3840100		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25559800delT	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						CAGATGGAGCTTACAGCACTG	0.393													2	4	---	---	---	---	
FANCE	2178	broad.mit.edu	37	6	35426416	35426417	+	Intron	INS	-	T	T	rs71794281		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35426416_35426417insT	uc003oko.1	+						FANCE_uc010jvw.1_Intron	NM_021922	NP_068741	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E						DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3						TGGCATCTAACttttttttttt	0.292			N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
SLC26A8	116369	broad.mit.edu	37	6	35927057	35927057	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35927057delT	uc003olm.2	-						SLC26A8_uc010jwa.2_Intron|SLC26A8_uc003olk.2_Intron|SLC26A8_uc003oln.2_Intron|SLC26A8_uc003oll.2_Intron	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a						cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						ATCTTGTGCCTTTTTTTTTTC	0.413													5	3	---	---	---	---	
CPNE5	57699	broad.mit.edu	37	6	36805247	36805247	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36805247delG	uc003omr.1	-							NM_020939	NP_065990	Q9HCH3	CPNE5_HUMAN	copine V											skin(1)	1						GACTCAGGGTGGGAATCCCTG	0.363													4	2	---	---	---	---	
MDGA1	266727	broad.mit.edu	37	6	37659294	37659294	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37659294delC	uc003onu.1	-							NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing						brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2						AAAACCATGACCAAACgaatg	0.179													4	2	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39760930	39760930	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39760930delG	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					GTAATTTTGTGAAGAGGATGA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40268113	40268113	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40268113delT								MOCS1 (365859 upstream) : TDRG1 (78050 downstream)																							agatagtatattttgggaggg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40844691	40844692	+	IGR	INS	-	T	T	rs149678124	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40844691_40844692insT								LRFN2 (289565 upstream) : UNC5CL (150080 downstream)																							ttttactttgctttttttttac	0.000													4	2	---	---	---	---	
GLYATL3	389396	broad.mit.edu	37	6	49479979	49479979	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49479979delC	uc003ozi.2	+							NM_001010904	NP_001010904	Q5SZD4	GLYL3_HUMAN	glycine N-acyltransferase-like protein 3							mitochondrion	glycine N-acyltransferase activity				0						ttacacttttctttttttttt	0.000													4	2	---	---	---	---	
GLYATL3	389396	broad.mit.edu	37	6	49479980	49479980	+	Intron	DEL	T	-	-	rs11358799		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49479980delT	uc003ozi.2	+							NM_001010904	NP_001010904	Q5SZD4	GLYL3_HUMAN	glycine N-acyltransferase-like protein 3							mitochondrion	glycine N-acyltransferase activity				0						tacacttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57518368	57518369	+	IGR	INS	-	TGTT	TGTT	rs146375109		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57518368_57518369insTGTT								PRIM2 (4993 upstream) : GUSBL2 (727790 downstream)																							tgtttcccttatgttttatagt	0.000													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69694979	69694980	+	Intron	INS	-	A	A	rs139995520	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69694979_69694980insA	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)				aagtctgaaatacagaatttag	0.000													1	6	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73859727	73859727	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73859727delG	uc003pgk.2	+						KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		aaacaccacaggggaaaaaaa	0.000													4	2	---	---	---	---	
COL12A1	1303	broad.mit.edu	37	6	75798722	75798722	+	Intron	DEL	C	-	-	rs672648		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75798722delC	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						gtctcaaaaacaaaaaaaaga	0.184													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85583200	85583200	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85583200delG								TBX18 (109301 upstream) : NT5E (576102 downstream)																							ACCCAGATGTGGGAAGCCCAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87539232	87539232	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87539232delA								None (None upstream) : HTR1E (107792 downstream)																							accaggatacaaaaccaatag	0.000													4	2	---	---	---	---	
GABRR1	2569	broad.mit.edu	37	6	89908138	89908138	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89908138delG	uc003pna.2	-						GABRR1_uc011dzv.1_Intron	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1						gamma-aminobutyric acid signaling pathway|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			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)	TGCAGGGGGCGGGGGGCGGGG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92363268	92363269	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92363268_92363269insT	uc003pod.2	-											Homo sapiens cDNA clone IMAGE:5284581.																		GGTTTTTAACATTTTTTTTTCC	0.371													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	93697671	93697671	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93697671delC								None (None upstream) : EPHA7 (252071 downstream)																							TAGAAATGTTCTTCCAATTCT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	97198493	97198494	+	IGR	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97198493_97198494delGT								FHL5 (133981 upstream) : GPR63 (47395 downstream)																							TCACTGCTCAGTAATGTGGGGC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104779955	104779955	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104779955delT								None (None upstream) : HACE1 (396013 downstream)																							CTTGGGGACATTTTTTTTGCA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	105100223	105100223	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105100223delA								None (None upstream) : HACE1 (75745 downstream)																							TCTCAAGTTGAAAAAAAAAAA	0.303													4	2	---	---	---	---	
BVES	11149	broad.mit.edu	37	6	105577833	105577833	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105577833delC	uc003pqw.2	-						BVES_uc003pqx.2_Intron|BVES_uc003pqy.2_Intron	NM_147147	NP_671488	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance isoform 5						epithelial cell-cell adhesion|muscle organ development|positive regulation of locomotion|positive regulation of receptor recycling|regulation of Cdc42 GTPase activity|regulation of cell shape|regulation of Rac GTPase activity|substrate adhesion-dependent cell spreading|vesicle-mediated transport	integral to membrane|lateral plasma membrane|tight junction	structural molecule activity				0		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TTTAGAACTACCTAAGCCAAA	0.159													4	2	---	---	---	---	
ATG5	9474	broad.mit.edu	37	6	106762600	106762600	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106762600delA	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		ACTTGTTTGGAAAAAAAAAAT	0.274													4	2	---	---	---	---	
PDSS2	57107	broad.mit.edu	37	6	107531364	107531364	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107531364delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_3'UTR	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		AAGCCTTTAGAAAAAAAAAGT	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112891356	112891356	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112891356delT								RFPL4B (218858 upstream) : None (None downstream)																							ccccacaccctttttttttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119784216	119784216	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119784216delC	uc003pyn.1	-											Homo sapiens cDNA FLJ39782 fis, clone SPLEN2002175.																		AACTCAAGTGCCCACATCTCT	0.483													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124567906	124567907	+	Intron	INS	-	TC	TC			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124567906_124567907insTC	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)		atcacccgttttctctccctca	0.025													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	125061275	125061276	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125061275_125061276insT	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		GGTTGCCCCTGTTTTTTTTTTT	0.366													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138297693	138297694	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138297693_138297694delCA								TNFAIP3 (93248 upstream) : PERP (111948 downstream)																							CACTCACACTCACACACACAcc	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138435805	138435805	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138435805delT								PERP (7145 upstream) : KIAA1244 (47419 downstream)																							ctgccagggattttttttttc	0.025													4	2	---	---	---	---	
HIVEP2	3097	broad.mit.edu	37	6	143163880	143163880	+	Intron	DEL	A	-	-	rs78058099		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143163880delA	uc003qjd.2	-							NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ACTTTAAGTGAAAAAAAAAAA	0.323													4	2	---	---	---	---	
C6orf103	79747	broad.mit.edu	37	6	147048400	147048400	+	Intron	DEL	C	-	-	rs76466411		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147048400delC	uc010khx.2	+						C6orf103_uc003qlp.2_Intron|C6orf103_uc003qlq.2_Intron	NM_024694	NP_078970	Q8N7X0	CAN7L_HUMAN	hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)		AAGCAGATTGCCCCCACACAT	0.239													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147489718	147489718	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147489718delA	uc003qlt.1	-						uc003qlu.1_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		cacagggattaaaaaaaaAAA	0.239													4	2	---	---	---	---	
CYP2W1	54905	broad.mit.edu	37	7	1023995	1023996	+	Intron	INS	-	G	G	rs140406976	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1023995_1023996insG	uc003sjq.1	+						CYP2W1_uc003sjr.1_Intron	NM_017781	NP_060251	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W,						xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		AGGGGACCTAAGGGGGGTCTTG	0.678													6	4	---	---	---	---	
RNF216	54476	broad.mit.edu	37	7	5736716	5736717	+	Intron	INS	-	A	A	rs151191940	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5736716_5736717insA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TATTTATCTTCAAAGTCCTGCT	0.505													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23969855	23969855	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23969855delC								STK31 (25490 upstream) : NPY (353954 downstream)																							GATGCCTGTTCAGATGCTGTG	0.493													4	2	---	---	---	---	
LOC441204	441204	broad.mit.edu	37	7	26527114	26527114	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26527114delT	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0						TCAAATGCCCTTGTCTCTCTG	0.413													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28444832	28444832	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28444832delG	uc003szo.2	+							NM_182899	NP_878902	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						ACTTCCCAATGGGACGATAGC	0.358													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33597989	33597989	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33597989delA	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			gatggatgggaaggagccagc	0.000									Bardet-Biedl_syndrome				4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37235678	37235678	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37235678delT	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						CCCTCACTGCTTTGCCCTGGT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41853641	41853641	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41853641delA								LOC285954 (34667 upstream) : GLI3 (146909 downstream)																							GATGGTGGTTAAGAATGTAGG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45965764	45965764	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45965764delC								IGFBP3 (4893 upstream) : None (None downstream)																							tttgtattttccagaatttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46905063	46905063	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46905063delA								IGFBP3 (944192 upstream) : TNS3 (409690 downstream)																							ctgaagtctcaaaaaaagagg	0.000													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48585156	48585156	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48585156delT	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						tcatatatcattttttttcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49742863	49742863	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49742863delC								CDC14C (775814 upstream) : VWC2 (70394 downstream)																							GTCTGTTTTTCTGTGACTTCT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53682780	53682780	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53682780delT								POM121L12 (578163 upstream) : HPVC1 (586137 downstream)																							AACAGCTGCATTTTTTTTTCT	0.403													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54534910	54534910	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54534910delA								HPVC1 (264796 upstream) : VSTM2A (75109 downstream)																							AAAGAAAGACAAAAGGGTGCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54538011	54538011	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54538011delC								HPVC1 (267897 upstream) : VSTM2A (72008 downstream)																							TTCTAGACTTCCCCAGCCTGG	0.493													4	2	---	---	---	---	
GBAS	2631	broad.mit.edu	37	7	56062938	56062938	+	Intron	DEL	A	-	-	rs34820247		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									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													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57660364	57660364	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57660364delT								ZNF716 (127099 upstream) : None (None downstream)																							tagttgcacgtttttttttga	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57768869	57768869	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768869delT								ZNF716 (235604 upstream) : None (None downstream)																							GATCACAAAGttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61816553	61816553	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61816553delG								None (None upstream) : LOC643955 (935119 downstream)																							TATCTACTTTGGTTTATGCTC	0.403													6	4	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70917808	70917808	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70917808delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AAGCATCTTGTTTTTTTGTTG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75729556	75729557	+	IGR	INS	-	A	A	rs145035384	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75729556_75729557insA								MDH2 (33628 upstream) : SRRM3 (101659 downstream)																							CAGATATAATTAAAAAAAAACC	0.173													4	2	---	---	---	---	
DYNC1I1	1780	broad.mit.edu	37	7	95652522	95652522	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95652522delT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			TCAGCCACCATTTAACAGCAT	0.458													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101968582	101968582	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101968582delT								SH2B2 (6405 upstream) : SPDYE6 (17611 downstream)																							GGATAAAGtcttttttttttt	0.174													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	110013476	110013476	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110013476delG								EIF3IP1 (413206 upstream) : IMMP2L (289634 downstream)																							TCTTCATATTGGAAAATCACT	0.388													4	2	---	---	---	---	
CAV1	857	broad.mit.edu	37	7	115949576	115949576	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115949576delT	uc010lkd.1	+						CAV2_uc003vhv.2_Intron|CAV2_uc003vhw.2_Intron|CAV2_uc003vhx.2_Intron|CAV2_uc010lkb.1_Intron|CAV2_uc010lkc.2_Intron|CAV2_uc003vib.2_Intron|CAV2_uc003vhz.2_Intron|CAV2_uc003via.2_Intron|CAV1_uc010lke.1_Intron|uc003vhu.1_Intron|uc003vhs.1_Intron|uc003vht.1_Intron|uc003vhy.1_Intron	NM_001753	NP_001744	Q03135	CAV1_HUMAN	caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			gagtcttaccttcatggggag	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	130623405	130623406	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130623405_130623406delAC								MIR29B1 (61107 upstream) : FLJ43663 (5515 downstream)																							TAAAATTAGTACACACACACAC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142134072	142134072	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142134072delC	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc010lnz.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		TGAAATTTGGCCACAAAATAA	0.363													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	145949569	145949569	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145949569delA	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTCCCTGCTGAAAACCACTTC	0.443										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147726199	147726200	+	Intron	DEL	TT	-	-	rs67892131		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147726199_147726200delTT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GGCAACACACTTTTAACCTCTC	0.327										HNSCC(39;0.1)			0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148319554	148319554	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148319554delG								C7orf33 (6603 upstream) : CUL1 (75452 downstream)																							ctaagagcttggtaacatatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152764781	152764782	+	IGR	INS	-	A	A	rs678338	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152764781_152764782insA								ACTR3B (212318 upstream) : DPP6 (819637 downstream)																							TTTTTTTTTTTAAATGTGTCAG	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153261673	153261674	+	IGR	DEL	TC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153261673_153261674delTC								ACTR3B (709210 upstream) : DPP6 (322745 downstream)																							TTCAACCGTGTctagcaccctc	0.272													4	2	---	---	---	---	
LMBR1	64327	broad.mit.edu	37	7	156586702	156586705	+	Intron	DEL	TCCT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156586702_156586705delTCCT	uc003wmw.3	-						LMBR1_uc003wmv.3_Intron|LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		CCCATCTCCCTCCTTCCTTTAACG	0.456													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1282525	1282525	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1282525delC								ERICH1 (601299 upstream) : DLGAP2 (167044 downstream)																							CCACCTGTCACCAACCCAAAA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1957274	1957274	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1957274delG								KBTBD11 (2166 upstream) : MYOM2 (35884 downstream)																							CGGGCCACCTGGGCTTCTTTC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12445086	12445086	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12445086delG	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		gcagataacagggggttactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19971206	19971206	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19971206delT								LPL (146437 upstream) : SLC18A1 (31161 downstream)																							TGAAGGCCTCTTTTGCCACCA	0.353													4	2	---	---	---	---	
ADAM28	10863	broad.mit.edu	37	8	24191374	24191374	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24191374delT	uc003xdy.2	+						ADAM28_uc003xdx.2_Intron|ADAM28_uc011kzz.1_Intron|ADAM28_uc011laa.1_Intron|ADAM28_uc010lua.2_Intron	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1						proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		ATTGTGAGGGTTTGTTTCCAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	27124050	27124050	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27124050delA								STMN4 (8147 upstream) : TRIM35 (18354 downstream)																							AGCAAATGACAAAAACCCACC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37169289	37169289	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37169289delA								KCNU1 (375648 upstream) : ZNF703 (384012 downstream)																							AGACTCCCCTAAAAATGGGAG	0.398													4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40581577	40581577	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40581577delT	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			TTATGTGAGGTTTTTTTTTTC	0.443													2	5	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63560434	63560434	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63560434delA	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				TGCTCCATGCAAAATGGactg	0.174													4	2	---	---	---	---	
LRRC67	286187	broad.mit.edu	37	8	67929733	67929733	+	Intron	DEL	A	-	-	rs78422147		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67929733delA	uc003xxc.2	-							NM_001013626	NP_001013648	Q7Z4L9	LRC67_HUMAN	leucine rich repeat containing 67												0						actctatctcaaaaaaaaaaG	0.085													4	2	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68164072	68164072	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68164072delA	uc003xxo.1	-						ARFGEF1_uc003xxl.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)			atttcacctcaaAAAAAAAAA	0.194													3	3	---	---	---	---	
SLCO5A1	81796	broad.mit.edu	37	8	70748495	70748496	+	5'Flank	INS	-	A	A	rs58344044		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70748495_70748496insA	uc003xyl.2	-						SLCO5A1_uc003xyk.2_5'Flank|SLCO5A1_uc010lzc.2_5'Flank	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			GATGATAACTGAAAAAAAAAAA	0.450													4	2	---	---	---	---	
UBE2W	55284	broad.mit.edu	37	8	74712685	74712685	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74712685delA	uc003xzv.2	-						UBE2W_uc003xzt.2_Intron|UBE2W_uc003xzu.2_Intron|UBE2W_uc003xzw.2_Intron	NM_018299	NP_060769	Q96B02	UBE2W_HUMAN	ubiquitin-conjugating enzyme E2W (putative)						protein K11-linked ubiquitination|protein monoubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0	Breast(64;0.0311)		Epithelial(68;0.0235)|all cancers(69;0.0687)|BRCA - Breast invasive adenocarcinoma(89;0.069)			TCTGTAAATGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104590402	104590402	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104590402delA	uc003ylp.2	+							NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			caaggcacataatcaaattct	0.000										HNSCC(12;0.0054)			4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	105212125	105212126	+	Intron	DEL	TT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105212125_105212126delTT	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TAAAGTGTGCTTTAAAGAGGAA	0.465										HNSCC(12;0.0054)			4	2	---	---	---	---	
TRHR	7201	broad.mit.edu	37	8	110109735	110109735	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110109735delG	uc003ymz.3	+							NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor							integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			ACTCTCCTCTGGAACATTCAG	0.279													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	114183506	114183506	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114183506delA	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	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						CAGTATAGCTAAAAAAAAAAT	0.189										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129154538	129154538	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129154538delT								PVT1 (41040 upstream) : MIR1208 (7824 downstream)																							TCCACTGTGCTTGGAATTTGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132901612	132901615	+	IGR	DEL	ATGA	-	-	rs139997982		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132901612_132901615delATGA								ADCY8 (848777 upstream) : EFR3A (14744 downstream)																							gcccatcAGTatgaatgaatgaat	0.162													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134177786	134177786	+	IGR	DEL	C	-	-	rs66512720		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134177786delC								TG (30645 upstream) : WISP1 (25526 downstream)																							ACTGCTGAGGCCTCCCCTCCA	0.259													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136063716	136063717	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136063716_136063717delCA								MIR30D (246528 upstream) : LOC286094 (182657 downstream)																							TCCCAGCTTCCACAGTGTCCTC	0.337													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2382845	2382845	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2382845delT								SMARCA2 (189224 upstream) : FLJ35024 (39857 downstream)																							ccagcatatCTTTTTTTTTTC	0.169													2	4	---	---	---	---	
MPDZ	8777	broad.mit.edu	37	9	13150910	13150910	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13150910delA	uc010mia.1	-						MPDZ_uc010mhx.2_Intron|MPDZ_uc011lmm.1_Intron|MPDZ_uc003zkz.3_Intron|MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		agtatctgctaataacatatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16282794	16282794	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16282794delT								C9orf93 (310899 upstream) : BNC2 (126708 downstream)																							CCTTTTCCTCTTTTTCGTCTT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16287975	16287975	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16287975delA								C9orf93 (316080 upstream) : BNC2 (121527 downstream)																							TTCACCATGCAAAAAACGTGT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25611183	25611183	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25611183delT								None (None upstream) : TUSC1 (65211 downstream)																							GACTGCAAGCTTTGATCATGA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25991918	25991918	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25991918delT								TUSC1 (313062 upstream) : C9orf82 (848766 downstream)																							GAATCCCAGATTTTTTTTCTG	0.333													4	2	---	---	---	---	
C9orf72	203228	broad.mit.edu	37	9	27565290	27565291	+	Intron	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27565290_27565291insA	uc003zqq.2	-						C9orf72_uc003zqr.1_Intron	NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a											ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		TGGGCAAACAGAAAAAAAAAGG	0.297													4	2	---	---	---	---	
PAX5	5079	broad.mit.edu	37	9	36860338	36860339	+	Intron	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36860338_36860339insA	uc003zzo.1	-						PAX5_uc011lpt.1_Intron|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Intron|PAX5_uc011lqa.1_Intron|PAX5_uc010mlq.1_Intron|PAX5_uc011lqb.1_Intron|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Intron	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5						cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(10)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		tctcaaaaaagaaaaaaaaatc	0.000			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68332862	68332862	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68332862delA								FAM27B (538673 upstream) : MIR1299 (669377 downstream)																							cattcagggcaaaaacaccac	0.000													4	2	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78588841	78588841	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78588841delT	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						ACACATCATATTTCCGTGAAC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81876097	81876097	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81876097delC								PSAT1 (931090 upstream) : TLE4 (310781 downstream)																							ttccattcatcccagtacctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84124633	84124633	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84124633delC								None (None upstream) : TLE1 (73967 downstream)																							TCAGCCCAAGCAAATAGCAGG	0.567													4	2	---	---	---	---	
PHF2	5253	broad.mit.edu	37	9	96377049	96377050	+	Intron	INS	-	G	G	rs144742789		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96377049_96377050insG	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CCAGCAAAAAAAAGtgatgatg	0.233													4	2	---	---	---	---	
TBC1D2	55357	broad.mit.edu	37	9	100985923	100985926	+	Intron	DEL	AGTT	-	-	rs10558626		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100985923_100985926delAGTT	uc011lvb.1	-						TBC1D2_uc004ayq.2_Intron|TBC1D2_uc004ayr.2_Intron|TBC1D2_uc004ayo.3_Intron	NM_018421	NP_060891	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2							cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CAATTTGGGGAGTTAGTTGACTCT	0.500													4	2	---	---	---	---	
SMC2	10592	broad.mit.edu	37	9	106888729	106888729	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106888729delT	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_5'Flank	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						TTACACATACTTTTTTTTTTG	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	114370698	114370698	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114370698delA	uc004bfk.3	-											Homo sapiens chromosome 9 open reading frame 29, mRNA (cDNA clone MGC:39589 IMAGE:4838739), complete cds.																		TTTTAGTGAGAAAAAAAAAAG	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118227832	118227832	+	IGR	DEL	T	-	-	rs113859926		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118227832delT								DEC1 (62909 upstream) : C9orf27 (422714 downstream)																							gttATAATTATTTTTTTAAGT	0.179													4	2	---	---	---	---	
DDX31	64794	broad.mit.edu	37	9	135513406	135513406	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135513406delA	uc004cbq.1	-						DDX31_uc010mzu.1_Intron|DDX31_uc004cbr.1_3'UTR	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		CTTCAAGCGGAAAAAAATACG	0.507													4	2	---	---	---	---	
TSC1	7248	broad.mit.edu	37	9	135798260	135798260	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135798260delA	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron|TSC1_uc004ccc.1_Intron|TSC1_uc004ccd.2_Intron|TSC1_uc004cce.1_Intron	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding			lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CCGATAGGGGAAAAAAAAAAA	0.448			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	2	---	---	---	---	
ABO	28	broad.mit.edu	37	9	136139838	136139838	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136139838delT	uc004cda.1	-						ABO_uc010naf.1_Intron|ABO_uc011mcz.1_Intron|ABO_uc010nag.1_Intron	NM_020469	NP_065202	P16442	BGAT_HUMAN	ABO blood group (alpha						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	fucosylgalactoside 3-alpha-galactosyltransferase activity|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		tgtgttttcatttcccttgag	0.000													4	2	---	---	---	---	
REXO4	57109	broad.mit.edu	37	9	136278227	136278227	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136278227delT	uc004cdm.2	-						ADAMTS13_uc004cdp.3_5'Flank|REXO4_uc011mde.1_Intron|REXO4_uc011mdf.1_Intron|REXO4_uc004cdn.2_Intron|REXO4_uc004cdo.2_Intron	NM_020385	NP_065118	Q9GZR2	REXO4_HUMAN	XPMC2 prevents mitotic catastrophe 2 homolog							nucleolus	exonuclease activity|nucleic acid binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		GGCAttttccttttttttttg	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138090341	138090341	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138090341delA								OLFM1 (77310 upstream) : KIAA0649 (281307 downstream)																							tgtcttgagtaactcctccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30687271	30687271	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30687271delC								MTPAP (23894 upstream) : MAP3K8 (35595 downstream)																							ATGTTACTCTCCCCACCACCT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36091695	36091695	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36091695delT								FZD8 (161333 upstream) : None (None downstream)																							cttcatgttgttttttttttc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50347395	50347395	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50347395delC	uc001jhi.1	+						uc001jhk.1_Intron					Homo sapiens cDNA FLJ35736 fis, clone TESTI2003545.																		TTCTTCAGCTCCCCCAAGCAA	0.448													4	2	---	---	---	---	
CISD1	55847	broad.mit.edu	37	10	60029526	60029526	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60029526delT	uc001jkc.3	+						IPMK_uc001jkb.2_5'Flank	NM_018464	NP_060934	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1							integral to membrane|mitochondrial outer membrane	2 iron, 2 sulfur cluster binding|metal ion binding				0						GTTTTGCAGATTTTTTTTTAA	0.443													4	2	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61068355	61068360	+	Intron	DEL	CAGCAT	-	-	rs78950813	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61068355_61068360delCAGCAT	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						caccaccaaccagcatcaccatcacc	0.117													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71325624	71325624	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71325624delC								TSPAN15 (58201 upstream) : NEUROG3 (6168 downstream)																							agcagaggttcccacccacct	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77343531	77343531	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77343531delT								MIR606 (31220 upstream) : C10orf11 (198988 downstream)																							CAGTCTCACATTGCACCAAAT	0.453													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	78835935	78835935	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78835935delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	TGGACAGTGGAAAAAAAAAGC	0.368													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	79009168	79009168	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79009168delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	AGTAGACTGTAAAAAAAGACA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85921609	85921610	+	IGR	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85921609_85921610delAG								GHITM (8298 upstream) : C10orf99 (11944 downstream)																							CAGAAACTCCAGAGAGAGAGAG	0.520													3	3	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95125795	95125796	+	Intron	INS	-	TG	TG	rs145681166	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95125795_95125796insTG	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						atctgtgaaactgacgggggac	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107719767	107719767	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107719767delG								SORCS3 (694774 upstream) : SORCS1 (613655 downstream)																							caatggtactggtgttcctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109550225	109550225	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109550225delA								SORCS1 (625933 upstream) : None (None downstream)																							tcaaaggtctaacacacgtat	0.000													4	2	---	---	---	---	
SEC23IP	11196	broad.mit.edu	37	10	121662074	121662076	+	Intron	DEL	ATC	-	-	rs72318530		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121662074_121662076delATC	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		gcaatgtgtaatcatcacatcag	0.054													4	2	---	---	---	---	
DMBT1	1755	broad.mit.edu	37	10	124357135	124357135	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124357135delT	uc001lgk.1	+						DMBT1_uc001lgl.1_Intron|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Intron|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_5'Flank	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b						epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TTGATACCCCTTTGGTCAGCT	0.488													4	2	---	---	---	---	
ODF3	113746	broad.mit.edu	37	11	194812	194812	+	5'Flank	DEL	C	-	-	rs113267557		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:194812delC	uc001lob.2	+						ODF3_uc010qvk.1_5'Flank|ODF3_uc001loc.2_5'Flank	NM_053280	NP_444510	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm				ovary(1)	1		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTGCGAAAGTCCCCCACAGAG	0.552													6	3	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1465901	1465901	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1465901delC	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		tccctccgctccccaggcccc	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	8367014	8367014	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8367014delG								LMO1 (76832 upstream) : STK33 (46404 downstream)																							gcaggatgccggggaaaatgc	0.214													4	2	---	---	---	---	
MRVI1	10335	broad.mit.edu	37	11	10672209	10672209	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10672209delC	uc010rcc.1	-						MRVI1_uc001miw.2_Intron|MRVI1_uc010rcb.1_Intron|MRVI1_uc009ygb.1_Intron|MRVI1_uc001mix.2_Intron|MRVI1_uc001miz.2_Intron|MRVI1_uc009ygc.1_Intron|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Intron	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c						platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TTTCCTTAATCCCCAAGCTTT	0.527													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11575227	11575228	+	Intron	INS	-	C	C	rs142968783	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11575227_11575228insC	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		AGCACCAAGCTCCCCCCCAGCA	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15379901	15379901	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15379901delT								INSC (111149 upstream) : SOX6 (608095 downstream)																							agaatggctgttaccaaaaag	0.000													4	2	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	16815724	16815725	+	Intron	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16815724_16815725delCA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron|PLEKHA7_uc001mmm.2_5'Flank|PLEKHA7_uc010rcv.1_Intron|PLEKHA7_uc001mmn.2_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						CGTCCACAGCCACACACCTCTC	0.406													4	2	---	---	---	---	
ANO3	63982	broad.mit.edu	37	11	26584943	26584950	+	Intron	DEL	TGTGTGTG	-	-	rs61877025		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26584943_26584950delTGTGTGTG	uc001mqt.3	+						ANO3_uc010rdr.1_Intron|ANO3_uc010rds.1_Intron|ANO3_uc010rdt.1_Intron|MUC15_uc001mqw.2_Intron|MUC15_uc001mqx.2_Intron|MUC15_uc001mqy.2_Intron	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTTCTCTCTCtgtgtgtgtgtgtgtgtg	0.226													6	4	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33597512	33597512	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33597512delG	uc001mup.3	+						C11orf41_uc001mun.1_Intron	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758							integral to membrane				ovary(2)	2						AAGCTTAATTGGTCAGCAGTG	0.483													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40944383	40944383	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40944383delT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				AATGTGATACtttttttttca	0.154													4	2	---	---	---	---	
EXT2	2132	broad.mit.edu	37	11	44196917	44196917	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44196917delT	uc001mxz.2	+						EXT2_uc010rfo.1_Intron|EXT2_uc001mxy.2_Intron|EXT2_uc009ykt.2_Intron|EXT2_uc001mya.2_Intron	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5						TCTACCtttctttttttttct	0.383			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				4	2	---	---	---	---	
OR8H2	390151	broad.mit.edu	37	11	55872323	55872323	+	5'Flank	DEL	G	-	-	rs113669153		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55872323delG	uc010riy.1	+							NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)					Gtttttttttgtttgtttttt	0.109										HNSCC(53;0.14)			4	4	---	---	---	---	
OSBP	5007	broad.mit.edu	37	11	59386517	59386517	+	5'Flank	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59386517delT	uc001noc.1	-							NM_002556	NP_002547	P22059	OSBP1_HUMAN	oxysterol binding protein						lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		TTTCCAGTCCttttttttttt	0.234													4	2	---	---	---	---	
LRP5	4041	broad.mit.edu	37	11	68121610	68121610	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68121610delA	uc001ont.2	+						LRP5_uc009ysg.2_Intron	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein						adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						GCCCTTCCCTAAAATAACACA	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	80251332	80251332	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80251332delA								None (None upstream) : None (None downstream)																							tcccagcagtaaaaaaaaagt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	85813446	85813446	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85813446delC								PICALM (32546 upstream) : EED (142369 downstream)																							TAGTGGGGAGCCATGGTCAGT	0.418													4	2	---	---	---	---	
GRM5	2915	broad.mit.edu	37	11	88770346	88770346	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88770346delG	uc001pcq.2	-						GRM5_uc009yvm.2_Intron|GRM5_uc009yvn.1_Intron	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	gtgtatgtgtgggggggagtt	0.000													4	2	---	---	---	---	
NOX4	50507	broad.mit.edu	37	11	89223956	89223956	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89223956delT	uc001pct.2	-						NOX4_uc009yvr.2_5'Flank|NOX4_uc001pcu.2_Intron|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_Intron|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Intron|NOX4_uc009yvs.1_Intron|NOX4_uc001pcy.2_Intron	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				ATAGGTTTCCTAAATGATTTA	0.393													4	2	---	---	---	---	
HEPHL1	341208	broad.mit.edu	37	11	93839460	93839460	+	Intron	DEL	T	-	-	rs144455207		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93839460delT	uc001pep.2	+						uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor						copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				Atttcttttcttttttttttt	0.179													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	94485272	94485272	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94485272delT								PIWIL4 (130686 upstream) : AMOTL1 (16236 downstream)																							CTCAAATCAGTTTTGCCCAGT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	98667867	98667868	+	IGR	DEL	AA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98667867_98667868delAA								None (None upstream) : CNTN5 (224003 downstream)																							GTTACATTCTAAATCTTTATCT	0.297													4	2	---	---	---	---	
ARHGAP42	143872	broad.mit.edu	37	11	100728818	100728819	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100728818_100728819delGT	uc001pge.2	+							NM_152432	NP_689645	A6NI28	RHG42_HUMAN	Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0						CTGGATAGGGgtgtgtgtgtgt	0.287													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	113394290	113394291	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113394290_113394291insA								DRD2 (47877 upstream) : TMPRSS5 (163978 downstream)																							cctctcaaattaaaaaaaaaaa	0.054													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114199573	114199573	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114199573delT								NNMT (16335 upstream) : C11orf71 (62597 downstream)																							CAACAGAAGATTTTTTTTTCT	0.318													4	2	---	---	---	---	
LOC399959	399959	broad.mit.edu	37	11	122093288	122093288	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122093288delA	uc009zbb.1	-											Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0						TTTGAAGGAGAAAAAAGTTTT	0.343													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	132119173	132119174	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132119173_132119174delGT	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron|NTM_uc001qgr.2_Intron	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						tgatgagagggtgtgtgtgtat	0.351													4	2	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	1980067	1980068	+	Intron	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1980067_1980068delAG	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TGTGAGGGGAAGAGAGAGAGAG	0.515													4	2	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3307516	3307517	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3307516_3307517delGT	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			acagctcaccgtaccagcacag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	3871765	3871765	+	IGR	DEL	A	-	-	rs113070202		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3871765delA								EFCAB4B (9399 upstream) : PARP11 (46262 downstream)																							catattcaggaaaaaaaaaaa	0.000													4	3	---	---	---	---	
PLBD1	79887	broad.mit.edu	37	12	14659645	14659645	+	Intron	DEL	T	-	-	rs78906132		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14659645delT	uc001rcc.1	-							NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0						TTACAGATGATTTTTTTTTTT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22957994	22957994	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22957994delA								ETNK1 (114387 upstream) : SOX5 (727238 downstream)																							GCTCCACTACAAACATATCAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	23098007	23098008	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23098007_23098008delCA								ETNK1 (254400 upstream) : SOX5 (587224 downstream)																							TCAAATGGGCCACACACAGACT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25559747	25559747	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25559747delA								KRAS (155884 upstream) : IFLTD1 (69269 downstream)																							ttcaatgactaaaaaaaatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29107891	29107891	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29107891delG								CCDC91 (404793 upstream) : FAR2 (194341 downstream)																							GTTGCATTATGGAAAAGCAGC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30234080	30234081	+	IGR	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30234080_30234081insG								TMTC1 (296388 upstream) : IPO8 (547842 downstream)																							GGACCATGACAGGGGGCATCAT	0.391													4	2	---	---	---	---	
IPO8	10526	broad.mit.edu	37	12	30801830	30801831	+	Intron	INS	-	T	T	rs143565540	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30801830_30801831insT	uc001rjd.2	-						IPO8_uc001rje.1_Intron|IPO8_uc010sjt.1_Intron	NM_006390	NP_006381	O15397	IPO8_HUMAN	importin 8						intracellular protein transport|signal transduction	cytoplasm|nucleus	protein transporter activity|Ran GTPase binding			skin(2)|central_nervous_system(1)	3	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTCCTTCATTATTTTTTTGATA	0.342													1	5	---	---	---	---	
FGD4	121512	broad.mit.edu	37	12	32714931	32714932	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32714931_32714932delGT	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rkx.3_Intron	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GGGCGAGAGGGTGTGTGTGTGG	0.465													4	2	---	---	---	---	
CNTN1	1272	broad.mit.edu	37	12	41349766	41349766	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41349766delG	uc001rmm.1	+						CNTN1_uc009zjy.1_Intron|CNTN1_uc001rmn.1_Intron|CNTN1_uc001rmo.2_Intron	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				cactgtggctggggcacagga	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42170379	42170379	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42170379delG								PDZRN4 (201995 upstream) : GXYLT1 (305271 downstream)																							CCTGAACTCCGAACCTGCCTA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45962849	45962850	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45962849_45962850insA								ANO6 (128662 upstream) : LOC400027 (156960 downstream)																							ATGTGTTGGGTAAAAAAAAAGG	0.391													4	2	---	---	---	---	
SLC48A1	55652	broad.mit.edu	37	12	48171470	48171470	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48171470delT	uc001rqd.2	+						SLC48A1_uc001rqc.2_Intron	NM_017842	NP_060312	Q6P1K1	HRG1_HUMAN	heme-responsive gene 1						transport	endosome membrane|integral to membrane|lysosomal membrane					0						ttatgaaatattttaggcaca	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48903208	48903208	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48903208delC								C12orf54 (13043 upstream) : OR8S1 (16207 downstream)																							tggtctgcttccccacgagaa	0.000													4	2	---	---	---	---	
KRT83	3889	broad.mit.edu	37	12	52710075	52710078	+	Intron	DEL	AGAT	-	-	rs78013851		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52710075_52710078delAGAT	uc001saf.2	-							NM_002282	NP_002273	P78385	KRT83_HUMAN	keratin 83						epidermis development	keratin filament	structural molecule activity			skin(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		cacaccacacagatacacacacac	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54084317	54084318	+	IGR	INS	-	T	T	rs142689710		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54084317_54084318insT								ATP5G2 (13805 upstream) : CALCOCO1 (20585 downstream)																							ttttcttttacttttttctttc	0.213													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54601247	54601247	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54601247delC								SMUG1 (18490 upstream) : CBX5 (23485 downstream)																							CAGGAGTTAGCCCCAGCAGTG	0.557											OREG0021887	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
DPY19L2	283417	broad.mit.edu	37	12	64005820	64005820	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64005820delA	uc001srp.1	-						DPY19L2_uc009zqk.1_Intron	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		atagctagagaagtaacatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67488572	67488572	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67488572delA								GRIP1 (290678 upstream) : CAND1 (174489 downstream)																							GTCAGACTGGAAGGATCATGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80613335	80613335	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80613335delT								PPP1R12A (284100 upstream) : PTPRQ (224791 downstream)																							GACCTTTGAATTGCTTGAAAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	84218131	84218131	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84218131delA								TMTC2 (690068 upstream) : None (None downstream)																							ttcagactttaaacgtatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89571571	89571571	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89571571delC								KITLG (597333 upstream) : DUSP6 (170268 downstream)																							tcagtggcatccccagagcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90619327	90619327	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90619327delT								LOC338758 (513599 upstream) : C12orf12 (726666 downstream)																							TTTCATTCTATTTTTTTTTCC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93517619	93517619	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93517619delA								EEA1 (194512 upstream) : NUDT4 (254082 downstream)																							aaaaataaataaaaaaaaaaG	0.149													4	2	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104147634	104147635	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104147634_104147635insT	uc001tjw.2	+						STAB2_uc009zug.2_Intron	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						AAACAGTGGAGTTTCCCTGGAA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	109158940	109158941	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109158940_109158941delAC								CORO1C (33645 upstream) : SSH1 (17526 downstream)																							AACACCCCCGACACACACACAT	0.342													4	2	---	---	---	---	
PTPN11	5781	broad.mit.edu	37	12	112913857	112913857	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112913857delC	uc001ttx.2	+						PTPN11_uc001ttw.1_Intron	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						tatcctcctgccttggcttcc	0.124			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115828543	115828543	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115828543delC								TBX3 (706574 upstream) : MED13L (567840 downstream)																							GACCACCTGTCCCTACCCACC	0.294													4	2	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117281511	117281511	+	Intron	DEL	G	-	-	rs34567723		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117281511delG	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		GCTGGGCCCTGGGGTAAACCT	0.443													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	118247949	118247949	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118247949delT	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCTCGgtttgttttttttgtc	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127297570	127297570	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127297570delG								LOC100128554 (340240 upstream) : None (None downstream)																							TATATGGGGTGGGAGCCTGCG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128290214	128290214	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128290214delC								None (None upstream) : TMEM132C (609077 downstream)																							TTTGTGCTTTCCCCAGGCAAT	0.488													4	2	---	---	---	---	
POLE	5426	broad.mit.edu	37	12	133248568	133248568	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133248568delT	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)		AGGACCCACCTTCCATGTTAC	0.483								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
FGF9	2254	broad.mit.edu	37	13	22248847	22248847	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22248847delT	uc001uog.2	+							NM_002010	NP_002001	P31371	FGF9_HUMAN	fibroblast growth factor 9 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|male gonad development|positive regulation of cell division	extracellular space	growth factor activity|heparin binding				0		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		TCCATGAGCATTTTTTTTTTT	0.502													3	3	---	---	---	---	
ATP5EP2	432369	broad.mit.edu	37	13	28519646	28519646	+	RNA	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28519646delA	uc001uru.2	+	1		c.304delA				NR_002162				Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2 (ATP5EP2), transcript variant 6, non-coding RNA.											ovary(1)	1						ATTTCATGGGAAAAAAAAATC	0.284													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29146278	29146278	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29146278delA								FLT1 (77013 upstream) : POMP (86963 downstream)																							TGTGGCATGTAAAAAAAAGGA	0.264													4	2	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	29836047	29836048	+	Intron	INS	-	A	A	rs138600620	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29836047_29836048insA	uc001usl.3	+							NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						AGAGGAATGGTAAAAAGTTGCC	0.332													2	4	---	---	---	---	
EPSTI1	94240	broad.mit.edu	37	13	43537898	43537898	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43537898delT	uc001uyw.1	-						EPSTI1_uc001uyx.1_Intron	NM_001002264	NP_001002264	Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 isoform 1											ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		ATCCATATTCTTAGAACCAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43734614	43734615	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43734614_43734615delAC								DNAJC15 (51310 upstream) : ENOX1 (53065 downstream)																							GTTCATCATTACAAGCCAAGAA	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	52886985	52886985	+	IGR	DEL	T	-	-	rs147923511	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52886985delT								THSD1P1 (21305 upstream) : THSD1 (64320 downstream)																							TGAAATGTCATTTTTTTTTCA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54816398	54816398	+	5'Flank	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54816398delT	uc001vho.2	+											Homo sapiens cDNA clone IMAGE:5263207.																		TCGACTCTTATTTTGATGTGA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	62617913	62617914	+	IGR	INS	-	TACTT	TACTT	rs140174592	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62617913_62617914insTACTT								PCDH20 (615834 upstream) : None (None downstream)																							CAAATACTGAATATAGGTTTGT	0.366													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73065411	73065411	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73065411delA								DACH1 (624081 upstream) : C13orf37 (217084 downstream)																							TCAGAGGCAGAAAAAAAAAAA	0.323													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75590893	75590894	+	IGR	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75590893_75590894insG								KLF12 (882499 upstream) : LOC647288 (220996 downstream)																							GTTATAGGAGTGGGGAAATGGG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85751192	85751193	+	IGR	DEL	GA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85751192_85751193delGA								None (None upstream) : SLITRK6 (615729 downstream)																							TTATCCAGTTGAGAGAGAGTGG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90705746	90705746	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90705746delC								None (None upstream) : MIR622 (177690 downstream)																							ATGGACACTACCTAATTCCAC	0.254													1	6	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94075302	94075303	+	Intron	INS	-	C	C	rs138840911	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94075302_94075303insC	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				tggtggtcacaccccaccagct	0.109													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95210479	95210479	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95210479delA								DCT (78543 upstream) : TGDS (15830 downstream)																							CTTCCCCCACAAAAAATGCAA	0.333													4	2	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97164802	97164803	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97164802_97164803insT	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					tattgtgggtgttttttttgtt	0.000													4	2	---	---	---	---	
TM9SF2	9375	broad.mit.edu	37	13	100179081	100179081	+	Intron	DEL	G	-	-	rs34587513		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100179081delG	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					ccagtgacctggggttggtag	0.000													5	3	---	---	---	---	
ITGBL1	9358	broad.mit.edu	37	13	102321464	102321464	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102321464delA	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTTTTTCGTTAAAAAAAAAAG	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106924682	106924682	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106924682delA								DAOA (781300 upstream) : EFNB2 (217416 downstream)																							AACAAAAAACAAAAAAAAAAA	0.398													4	2	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109736705	109736706	+	Intron	INS	-	GACA	GACA			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109736705_109736706insGACA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGCAGGTTGATGACTTGATGAT	0.406													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114301312	114301313	+	IGR	INS	-	G	G	rs149002740	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114301312_114301313insG								TFDP1 (5526 upstream) : ATP4B (1810 downstream)																							GGGCTCTGTGTGGGTGCATGTG	0.530													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114907866	114907867	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114907866_114907867delCA								RASA3 (9771 upstream) : CDC16 (92495 downstream)																							cccccatgctcacacacacact	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22853889	22853889	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22853889delG	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AGGATTAAGTGAACAATATAA	0.318													4	2	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25306700	25306700	+	Intron	DEL	A	-	-	rs80119201		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25306700delA	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		CAAAAGCAGGAAAAAAAATAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32026685	32026685	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32026685delA								HEATR5A (100005 upstream) : NUBPL (3906 downstream)																							TGACTGGTACAAGAACCCATG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34508206	34508206	+	IGR	DEL	G	-	-	rs71433641		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34508206delG								EGLN3 (87919 upstream) : C14orf147 (393939 downstream)																							GCTTGCTATTGGTGGAGTGCT	0.493													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50395249	50395249	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50395249delA								ARF6 (31478 upstream) : C14orf182 (53181 downstream)																							aatcttacataaaactataaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53866060	53866060	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53866060delG								DDHD1 (246014 upstream) : BMP4 (550397 downstream)																							ATGCTATGTAGGGGGGGTCAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	61615199	61615200	+	IGR	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61615199_61615200delGT								SLC38A6 (64749 upstream) : PRKCH (39087 downstream)																							gtgcatgtgagtgtgtgtgtgt	0.406													3	4	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67031668	67031668	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67031668delG	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TTGTGATGCTGGGACTAGCAT	0.259			T	MLL	AL								4	2	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67313167	67313167	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67313167delA	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		gacatttaacaaaaaaaATGC	0.179			T	MLL	AL								4	2	---	---	---	---	
C14orf179	112752	broad.mit.edu	37	14	76499270	76499270	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76499270delG	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron|C14orf179_uc001xse.2_Intron	NM_001102564	NP_001096034	Q96FT9	IFT43_HUMAN	hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)		GTGTCTGGTTGGGTCATGGTG	0.303													4	2	---	---	---	---	
SPTLC2	9517	broad.mit.edu	37	14	78063942	78063943	+	Intron	INS	-	C	C	rs151275919	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78063942_78063943insC	uc001xub.2	-							NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	acatggtgaaacctgtctctac	0.000													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79116948	79116948	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79116948delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ATCAAGACCCTTCTCCTTCCC	0.398													4	2	---	---	---	---	
DDX24	57062	broad.mit.edu	37	14	94526303	94526303	+	Intron	DEL	A	-	-	rs36013055		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94526303delA	uc001ycj.2	-						DDX24_uc010twq.1_Intron|DDX24_uc010twr.1_Intron	NM_020414	NP_065147	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24						RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		AATGCTGTGCAAAAAAAAAAA	0.393													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97718018	97718018	+	IGR	DEL	T	-	-	rs34980470		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97718018delT								VRK1 (370068 upstream) : C14orf64 (673929 downstream)																							TATGACACAATTTTTTTTTTC	0.398													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98717505	98717506	+	IGR	DEL	TC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98717505_98717506delTC								C14orf64 (273044 upstream) : C14orf177 (460444 downstream)																							CGCCTATGTGTCTCTCTTTTTT	0.168													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99212762	99212763	+	IGR	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99212762_99212763delCA								C14orf177 (28665 upstream) : BCL11B (422864 downstream)																							AAGCTGAAGCCACACACACACC	0.495													4	2	---	---	---	---	
C14orf79	122616	broad.mit.edu	37	14	105454673	105454674	+	Intron	DEL	TT	-	-	rs141732032		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105454673_105454674delTT	uc001ypy.1	+						C14orf79_uc001ypz.1_Intron|C14orf79_uc010tym.1_Intron	NM_174891	NP_777551	Q96F83	CN079_HUMAN	hypothetical protein LOC122616												0		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)			gtataatttctttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	105464590	105464590	+	IGR	DEL	A	-	-	rs113438254		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105464590delA								C14orf79 (2735 upstream) : CDCA4 (11320 downstream)																							acaaaaaagtaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20019051	20019051	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20019051delC								None (None upstream) : GOLGA6L6 (718043 downstream)																							gaatatatttccttttctaac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20126859	20126860	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20126859_20126860insA								None (None upstream) : GOLGA6L6 (610234 downstream)																							aaaatttatagaaaaaaataga	0.000													4	2	---	---	---	---	
OR4N4	283694	broad.mit.edu	37	15	22348002	22348005	+	Intron	DEL	AAAT	-	-	rs71414238		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22348002_22348005delAAAT	uc001yuc.1	+						LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		GCATTAAAAGAAATAAAACAAGTA	0.157													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23098652	23098655	+	Intron	DEL	TTCT	-	-	rs3057778		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23098652_23098655delTTCT	uc001yvf.2	-											Homo sapiens cDNA clone IMAGE:5275816.																		tgagtcctacttctctctccatct	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26754303	26754303	+	IGR	DEL	C	-	-	rs146769421		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26754303delC								ATP10A (643986 upstream) : GABRB3 (34392 downstream)																							gacaaaaaaacatgattattt	0.000													3	4	---	---	---	---	
BUB1B	701	broad.mit.edu	37	15	40492787	40492788	+	Intron	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40492787_40492788insA	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		ATACTGTTTTTAAAAAACAAAA	0.307			Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				4	2	---	---	---	---	
TP53BP1	7158	broad.mit.edu	37	15	43737951	43737951	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43737951delA	uc001zrs.2	-						TP53BP1_uc010udp.1_Intron|TP53BP1_uc001zrq.3_Intron|TP53BP1_uc001zrr.3_Intron|TP53BP1_uc010udq.1_Intron	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CTCGCTCCTCAAATTCATCCC	0.403								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46812395	46812395	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46812395delA								SQRDL (828917 upstream) : SEMA6D (664008 downstream)																							tggtaaccacaaaaaaaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48659250	48659250	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48659250delT								DUT (23682 upstream) : FBN1 (41255 downstream)																							gggattctgcttttttttgct	0.134													4	2	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52646487	52646488	+	Intron	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52646487_52646488insG	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010ugd.1_5'Flank|MYO5A_uc002aca.1_5'Flank|MYO5A_uc002acb.1_5'Flank|MYO5A_uc002acc.1_5'Flank	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)		atgatattggtggaagtaaaag	0.000													4	2	---	---	---	---	
CGNL1	84952	broad.mit.edu	37	15	57743970	57743971	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57743970_57743971insT	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TGTCCAAAGAATTTTTTTTTTT	0.366													4	2	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58471708	58471709	+	Intron	INS	-	TGTG	TGTG	rs147605496	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58471708_58471709insTGTG	uc010ugw.1	-						AQP9_uc010ugx.1_Intron|AQP9_uc002aez.2_Intron	NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	TTGTGGTATGAtgtgtgtgtgt	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61766638	61766639	+	IGR	INS	-	TGTT	TGTT	rs140022570	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61766638_61766639insTGTT								RORA (245136 upstream) : VPS13C (377953 downstream)																							TCTCATTTGTCTGTCTTTTCTG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62772186	62772186	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62772186delC								C2CD4B (314704 upstream) : MGC15885 (157185 downstream)																							CTTGAGCAGACCCAGGAGTGG	0.453													4	2	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63645314	63645314	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63645314delA	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	agaccagtgtaagagactgat	0.000													4	2	---	---	---	---	
LOC145837	145837	broad.mit.edu	37	15	69801840	69801841	+	Intron	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69801840_69801841insG	uc002asf.1	+						LOC145837_uc002asg.1_Intron|LOC145837_uc010bij.1_Intron					Homo sapiens cDNA clone IMAGE:5189446.												0						AAGTGAGAAAAAAAAGGTTATT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70228992	70228992	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70228992delG								C15orf50 (93687 upstream) : TLE3 (111551 downstream)																							aaatcacaaaggaagatggaa	0.000													4	2	---	---	---	---	
MYO9A	4649	broad.mit.edu	37	15	72181374	72181375	+	Intron	DEL	AG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72181374_72181375delAG	uc002atl.3	-						MYO9A_uc002atk.2_Intron|MYO9A_uc002atm.1_Intron	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3						gctgtgatgcagagaggaggaa	0.000													4	2	---	---	---	---	
DNM1P35	100128285	broad.mit.edu	37	15	76024223	76024224	+	Intron	DEL	CT	-	-	rs35247110		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76024223_76024224delCT	uc002bay.1	-											Homo sapiens cDNA FLJ33925 fis, clone CTONG2017292.												0						ACCAGGTTTCctctctctctct	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78197768	78197768	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78197768delG								LINGO1 (209293 upstream) : LOC645752 (8791 downstream)																							GAGGCTGCGTGGGCATCTGGA	0.612													4	2	---	---	---	---	
WHAMM	123720	broad.mit.edu	37	15	83480604	83480604	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83480604delA	uc002bje.2	+							NM_001080435	NP_001073904	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi							cytoplasmic vesicle membrane|ER-Golgi intermediate compartment|Golgi apparatus	actin binding				0						GCTTTCACTTAAAAAAAAAAC	0.299													5	3	---	---	---	---	
SEC11A	23478	broad.mit.edu	37	15	85213776	85213776	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85213776delT	uc002blb.1	-						SEC11A_uc002blc.1_Intron	NM_014300	NP_055115	P67812	SC11A_HUMAN	SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)			agGCTAATAAttttttttttt	0.010													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86068215	86068215	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86068215delT	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						AAATAAAGTATTTTAAGCGTA	0.224													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87141098	87141098	+	Intron	DEL	T	-	-	rs5814251		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87141098delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						atgtgattggtttggggagga	0.000													4	2	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89372234	89372234	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89372234delG	uc010upo.1	+						ACAN_uc002bmx.2_Intron|ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCCAATCCTAGACAAAAGTAT	0.507													4	2	---	---	---	---	
SOLH	6650	broad.mit.edu	37	16	603028	603063	+	Splice_Site	DEL	CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:603028_603063delCCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	uc002chi.2	+	13	3446	c.3083_splice	c.e13+1	p.R1028_splice	SOLH_uc002chj.2_Splice_Site_p.R88_splice	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				GGATAGCGTGCCACCCCTGCACAGGTGcgcccccgcccctgcccccccacccctgc	0.318													7	5	---	---	---	---	
HAGH	3029	broad.mit.edu	37	16	1865248	1865248	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1865248delG	uc002cna.2	-						HAGH_uc002cmz.2_Intron|HAGH_uc010uvp.1_Intron|HAGH_uc002cnb.1_Intron	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1						glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)	aagcattggtgggggactgta	0.000													4	2	---	---	---	---	
ABCA3	21	broad.mit.edu	37	16	2382818	2382818	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2382818delT	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron|ABCA3_uc002cpz.1_5'Flank	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3						response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				CTATGTGCCCttttttttttt	0.234													4	2	---	---	---	---	
C16orf90	646174	broad.mit.edu	37	16	3546141	3546141	+	5'Flank	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3546141delA	uc002cvi.2	-							NM_001080524	NP_001073993	A8MZG2	CP090_HUMAN	hypothetical protein LOC646174												0						actccgtctcaaaaaaaaaaa	0.234													5	6	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4958446	4958447	+	Intron	INS	-	CA	CA	rs138719548		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4958446_4958447insCA	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						tctctctctctcACACACATAC	0.277													4	2	---	---	---	---	
SEC14L5	9717	broad.mit.edu	37	16	5042213	5042213	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5042213delC	uc002cye.2	+							NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5							integral to membrane|intracellular	transporter activity				0						CCATCCTGGTCCAAGAGCAGA	0.348													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6766910	6766910	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6766910delG	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	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)		ccaatgtgatggtattaggag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8418398	8418398	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8418398delT								A2BP1 (655058 upstream) : TMEM114 (201105 downstream)																							TTCTTCTGTATTTTTTTTTGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16931532	16931532	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16931532delT								LOC339047 (487095 upstream) : XYLT1 (264651 downstream)																							TGTTGCTTTCTTTTTTTTTTT	0.378													2	4	---	---	---	---	
ZP2	7783	broad.mit.edu	37	16	21225785	21225786	+	5'Flank	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21225785_21225786insA	uc002dii.2	-						ZP2_uc010bwn.1_5'Flank|ZP2_uc010bwo.2_5'Flank	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein						binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(48;0.0573)		ttataagtgggagctgaacaat	0.134													4	2	---	---	---	---	
NSMCE1	197370	broad.mit.edu	37	16	27237503	27237503	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27237503delA	uc002doi.1	-						NSMCE1_uc002doj.1_Intron	NM_145080	NP_659547	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog						DNA recombination|DNA repair|intracellular signal transduction	nucleus	zinc ion binding				0						aaaagctttcaaaaaaaaagt	0.124													4	3	---	---	---	---	
KIAA0556	23247	broad.mit.edu	37	16	27657223	27657223	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27657223delC	uc002dow.2	+						KIAA0556_uc002dox.1_Intron	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						gctgcaagggCCCCCAGCAAT	0.279													4	2	---	---	---	---	
TMEM188	255919	broad.mit.edu	37	16	50067803	50067803	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50067803delT	uc002efu.2	+						TMEM188_uc002eft.2_Intron|TMEM188_uc002efv.2_Intron			Q8N9A8	TM188_HUMAN	SubName: Full=TMP125; SubName: Full=Putative uncharacterized protein FLJ38101;							integral to membrane					0						ACGCtttgtgttttttttttg	0.025													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52226355	52226355	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52226355delA								None (None upstream) : TOX3 (245563 downstream)																							AAAAGAAAAGAAAAAAAAAAG	0.383													2	4	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55854626	55854626	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55854626delC	uc002eim.2	-						CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	AATCCCCAATCCCAGCAGGAC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66096196	66096196	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66096196delT								LOC283867 (485993 upstream) : CDH5 (304329 downstream)																							GTCTTACTCCTCAGTGTCCCC	0.443													4	2	---	---	---	---	
CFDP1	10428	broad.mit.edu	37	16	75442210	75442210	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75442210delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron|CFDP1_uc002fea.1_Intron	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1						atcccatgttaaaaaaaaaat	0.000													4	2	---	---	---	---	
DNAH2	146754	broad.mit.edu	37	17	7646597	7646597	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7646597delT	uc002giu.1	+						DNAH2_uc002git.2_Frame_Shift_Del_p.F763fs|DNAH2_uc010vuk.1_Frame_Shift_Del_p.F681fs	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GTCATTTTACTTTTTTTTTTC	0.338													5	3	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10308044	10308045	+	Intron	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10308044_10308045delAC	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGCAGGCTTTacacacacacac	0.307									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				4	2	---	---	---	---	
MPRIP	23164	broad.mit.edu	37	17	17087914	17087915	+	Intron	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17087914_17087915insT	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron|MPRIP_uc002gqw.1_Intron|MPRIP_uc002gqx.1_Intron|MPRIP_uc002gqy.1_Intron|MPRIP_uc010cpl.1_Intron|MPRIP_uc010cpm.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0						TGTCTCTCTGATTTTTTTTTCC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21247082	21247083	+	IGR	INS	-	G	G	rs113371593		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21247082_21247083insG								MAP2K3 (28533 upstream) : KCNJ12 (32616 downstream)																							tcagatgggaaggggtagagct	0.139													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21249572	21249573	+	IGR	INS	-	A	A	rs151227449		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21249572_21249573insA								MAP2K3 (31023 upstream) : KCNJ12 (30126 downstream)																							tgtcatggatgaaagacattcc	0.000													6	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21310811	21310812	+	Intron	INS	-	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21310811_21310812insC	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	actcattcactcacccatccat	0.000										Prostate(3;0.18)			6	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21310823	21310823	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21310823delC	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	acccatccatccacccaatca	0.000										Prostate(3;0.18)			5	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21311067	21311068	+	Intron	INS	-	CATC	CATC			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21311067_21311068insCATC	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	atccatccattcatccatccat	0.000										Prostate(3;0.18)			2	4	---	---	---	---	
ATAD5	79915	broad.mit.edu	37	17	29157795	29157798	+	5'Flank	DEL	CAAA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29157795_29157798delCAAA	uc002hfs.1	+							NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ccgtctcaagcaaacaaacaaaca	0.103													9	4	---	---	---	---	
TAF15	8148	broad.mit.edu	37	17	34161246	34161246	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34161246delA	uc002hkd.2	+						TAF15_uc010ctw.1_Intron|TAF15_uc002hkc.2_Intron	NM_139215	NP_631961	Q92804	RBP56_HUMAN	TBP-associated factor 15 isoform 1						positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		TAF15/NR4A3(33)	bone(33)|lung(1)|skin(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TTGTTCTTATAAAGGTAGCTG	0.368			T	TEC|CHN1|ZNF384	extraskeletal myxoid chondrosarcomas|ALL								4	2	---	---	---	---	
G6PC	2538	broad.mit.edu	37	17	41050755	41050755	+	5'Flank	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41050755delG	uc002icb.1	+						LOC388387_uc002ibz.2_5'Flank|LOC388387_uc002iby.2_5'Flank|LOC388387_uc002ica.2_5'Flank|LOC388387_uc010whe.1_5'Flank|G6PC_uc010whf.1_5'Flank	NM_000151	NP_000142	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit						gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGCCCTTGGTGGGGTGGGGAG	0.527									Glycogen_Storage_Disease_type_Ia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	44486655	44486655	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44486655delT								ARL17A (47492 upstream) : LRRC37A2 (103421 downstream)																							TACAGTCttcttttttttttt	0.134													4	3	---	---	---	---	
WNT9B	7484	broad.mit.edu	37	17	44948673	44948673	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44948673delG	uc002ikw.1	+						WNT9B_uc002ikx.1_Intron	NM_003396	NP_003387	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CACCCACACTGGGGGCACCAG	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55844861	55844862	+	IGR	DEL	GA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55844861_55844862delGA								MSI2 (87562 upstream) : MRPS23 (71982 downstream)																							GGTGTGGGCTGAGCAGCTCAAA	0.500													4	2	---	---	---	---	
RGS9	8787	broad.mit.edu	37	17	63154038	63154039	+	Intron	DEL	TG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63154038_63154039delTG	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron	NM_003835	NP_003826	O75916	RGS9_HUMAN	regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4						tgtgtgtgtatgtgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63284770	63284770	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63284770delC								RGS9 (60951 upstream) : AXIN2 (239915 downstream)																							TATCGTGTCTCCCATCCTCGC	0.493													4	2	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80151419	80151419	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80151419delA	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			agaccctgtcaaaaaaaaaaa	0.080													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2418715	2418715	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2418715delC								None (None upstream) : METTL4 (118810 downstream)																							AAACCATTCTCCAGCTTTTCC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5062127	5062128	+	IGR	INS	-	C	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5062127_5062128insC								DLGAP1 (606861 upstream) : LOC642597 (81544 downstream)																							tgtccaagtttccccctttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15168233	15168233	+	IGR	DEL	C	-	-	rs8089674	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15168233delC								ANKRD30B (315496 upstream) : LOC644669 (145322 downstream)																							TGCCCCCAATCCCTAACTACA	0.333													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22914170	22914171	+	Intron	INS	-	C	C	rs72531236	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22914170_22914171insC	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ATGCTACCATATTTTTCTTGGA	0.366			T	PAX5	ALL								1	5	---	---	---	---	
C18orf16	147429	broad.mit.edu	37	18	24459136	24459136	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24459136delA	uc002kwb.2	+						C18orf16_uc010xbm.1_Intron	NR_026908				Homo sapiens cDNA FLJ30507 fis, clone BRAWH2000554.												0						TTTGTATGTGAAAAAAAATAC	0.388													4	2	---	---	---	---	
RIT2	6014	broad.mit.edu	37	18	40381118	40381118	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40381118delA	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						GATGGTGAAGAAAAAAAAGAA	0.358													4	2	---	---	---	---	
RIT2	6014	broad.mit.edu	37	18	40618865	40618865	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40618865delT	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						aactgcaggattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58608453	58608453	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58608453delA								MC4R (568452 upstream) : CDH20 (392535 downstream)																							TTGTACTTCTAAAAAAAAAAG	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58923891	58923891	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58923891delA								MC4R (883890 upstream) : CDH20 (77097 downstream)																							TCAGAAAGTGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77473332	77473332	+	Intron	DEL	A	-	-	rs142956492	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77473332delA	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TTTGGGCTTTAAAAAAAATGG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3951066	3951068	+	IGR	DEL	TCC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3951066_3951068delTCC								ITGB1BP3 (8654 upstream) : DAPK3 (7384 downstream)																							ctcctcctcttcctcctcctccC	0.586													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13977703	13977704	+	IGR	DEL	AC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13977703_13977704delAC								MIR23A (30230 upstream) : MIR181C (7809 downstream)																							acacacacatacacacacacac	0.356													4	2	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15648967	15648967	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15648967delT	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						tgagcttcactttttttttta	0.000													7	4	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17777717	17777717	+	Intron	DEL	G	-	-	rs9797868		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17777717delG	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						gagagagagagagaaagacag	0.184													6	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17777719	17777727	+	Intron	DEL	GAAAGACAG	-	-	rs61595485		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17777719_17777727delGAAAGACAG	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						gagagagagagaaagacagagacagagac	0.167													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40309834	40309834	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40309834delT								LEUTX (33061 upstream) : DYRK1B (6157 downstream)																							taagctcctgtttggccagtg	0.000													4	2	---	---	---	---	
ZNF780B	163131	broad.mit.edu	37	19	40551250	40551250	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40551250delA	uc002omu.2	-						ZNF780B_uc002omv.2_Intron	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					aggatgagggaaaaagggaac	0.015													4	2	---	---	---	---	
ARHGEF1	9138	broad.mit.edu	37	19	42420570	42420571	+	Intron	DEL	CA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42420570_42420571delCA	uc002osc.2	+									Q92888	ARHG1_HUMAN	SubName: Full=ARHGEF1 protein; SubName: Full=Rho guanine nucleotide exchange factor (GEF) 1, isoform CRA_g;						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		ctgtcacagtcacacacacaca	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45598160	45598160	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45598160delT	uc002pas.2	+											Homo sapiens leucine rich repeat containing 68, mRNA (cDNA clone IMAGE:5573062), partial cds.																		GTTGGAGCCATAGGGCTGGGA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46699368	46699368	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46699368delC	uc002pec.2	-											Homo sapiens cDNA clone IMAGE:5478640, partial cds.																		CGCTCCAGGGCCCAGCATGTC	0.587													4	2	---	---	---	---	
PPP5C	5536	broad.mit.edu	37	19	46853181	46853181	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46853181delG	uc002pem.2	+						PPP5C_uc010xya.1_Intron|PPP5C_uc002pen.2_Intron	NM_006247	NP_006238	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit						mitosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein dephosphorylation|transcription, DNA-dependent	Golgi apparatus|nucleus	metal ion binding|protein binding|protein serine/threonine phosphatase activity|signal transducer activity			lung(1)|pancreas(1)	2		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		GGCCATAAGTGGGGCCACAGC	0.572													4	2	---	---	---	---	
TMC4	147798	broad.mit.edu	37	19	54667042	54667043	+	Intron	DEL	TT	-	-	rs71813752		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54667042_54667043delTT	uc010erf.2	-						TMC4_uc002qdn.2_Intron|TMC4_uc002qdo.2_Intron	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1							integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					tctttctttctttttttttttt	0.233													3	3	---	---	---	---	
PTPRA	5786	broad.mit.edu	37	20	2998848	2998848	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2998848delT	uc010zqd.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron|PTPRA_uc002who.2_Intron	NM_002836	NP_002827	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1						CACAGAGGGgttttttttgtt	0.244													4	2	---	---	---	---	
ESF1	51575	broad.mit.edu	37	20	13717501	13717501	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13717501delT	uc002woj.2	-							NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						CAGTCTGTAATTTTTTTTTGC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	17058033	17058033	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17058033delG								OTOR (325225 upstream) : PCSK2 (148719 downstream)																							CCTGGTAGCTGGTGGCCTCAC	0.498													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20046031	20046031	+	Intron	DEL	A	-	-	rs113741131		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20046031delA	uc002wru.2	+						C20orf26_uc010gcw.1_Intron|C20orf26_uc010zse.1_Intron|C20orf26_uc010zsf.1_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		ccaaacattTAAAAAAAAAAA	0.129													4	2	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20414401	20414401	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20414401delG	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GGATGTTTTTGTGAGATGAAG	0.398													4	2	---	---	---	---	
CST5	1473	broad.mit.edu	37	20	23860523	23860526	+	5'Flank	DEL	CCTC	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23860523_23860526delCCTC	uc002wtr.1	-							NM_001900	NP_001891	P28325	CYTD_HUMAN	cystatin D precursor							extracellular region	cysteine-type endopeptidase inhibitor activity|protein binding				0						cccccaaccacctccctccctccc	0.098													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26112118	26112118	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26112118delT								C20orf191 (17441 upstream) : MIR663 (76704 downstream)																							atttctttccttcataacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36305139	36305139	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36305139delC								BLCAP (148836 upstream) : CTNNBL1 (17295 downstream)																							GGCTGCCTGGCCCTTTCTAGC	0.483													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47373006	47373007	+	Intron	INS	-	T	T	rs11390512		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47373006_47373007insT	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GAAGAGATAGCTTTTTTTTTTT	0.381													2	5	---	---	---	---	
ZFP64	55734	broad.mit.edu	37	20	50803054	50803054	+	Intron	DEL	T	-	-	rs11479878		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50803054delT	uc002xwl.2	-						ZFP64_uc002xwk.2_Intron|ZFP64_uc002xwm.2_Intron|ZFP64_uc002xwn.2_Intron	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						AAACAACCACTTTTTTTTTTA	0.299													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57293124	57293125	+	IGR	INS	-	G	G	rs148458711	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57293124_57293125insG								NPEPL1 (1757 upstream) : MIR296 (99545 downstream)																							CTGATGGAAAATCTCTCCCCAG	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58018747	58018747	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58018747delA								EDN3 (117701 upstream) : PHACTR3 (133817 downstream)																							AAGATGTGACAAAAAAAAAAT	0.363													4	2	---	---	---	---	
SYCP2	10388	broad.mit.edu	37	20	58456722	58456722	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58456722delT	uc002yaz.2	-							NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			AATAGAATAGTTTTTTTTTTC	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59739515	59739515	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59739515delA								MIR646 (855890 upstream) : CDH4 (88044 downstream)																							ATGATTCTGGAAAAAAAAAAA	0.418													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60458416	60458416	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60458416delG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ttccaacctagggcgacgtct	0.224													4	2	---	---	---	---	
C20orf166	128826	broad.mit.edu	37	20	61161934	61161935	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61161934_61161935delGT	uc011aaj.1	+						C20orf166_uc011aal.1_5'Flank|MIR133A2_hsa-mir-133a-2|MI0000451_5'Flank	NM_178463	NP_848558	Q9H1L0	CT166_HUMAN	hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			gtatgtctgagtgtgtgtgtgt	0.530													4	3	---	---	---	---	
PPDPF	79144	broad.mit.edu	37	20	62149657	62149657	+	5'Flank	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62149657delC	uc002yff.2	+							NM_024299	NP_077275	Q9H3Y8	PPDPF_HUMAN	pancreatic progenitor cell differentiation and						cell differentiation|multicellular organismal development						0						AGCTTTTCTGCCCCCATTTCC	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9735164	9735165	+	Intron	DEL	AA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9735164_9735165delAA	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																		ACTATTCTGGAAGAAAAAAGAA	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10896106	10896106	+	IGR	DEL	G	-	-	rs112369967		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10896106delG								None (None upstream) : TPTE (10637 downstream)																							GGCTGAGGCAGAGGTGGAATG	0.547													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11053060	11053061	+	Intron	DEL	AA	-	-	rs77480017		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11053060_11053061delAA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCTCATTATTAAGAGAGTACTA	0.277													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14358885	14358886	+	IGR	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14358885_14358886insA								None (None upstream) : C21orf99 (51601 downstream)																							gcagattctacaaaaagagtgt	0.000													4	3	---	---	---	---	
TMPRSS15	5651	broad.mit.edu	37	21	19647280	19647280	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19647280delT	uc002ykw.2	-							NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor						proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						CATTCAAGTATTATGTCTAGT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29998455	29998455	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29998455delA								NCRNA00161 (85779 upstream) : N6AMT1 (246058 downstream)																							ctatttaaagaaaaaaaaaag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	31482915	31482915	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31482915delA								GRIK1 (170633 upstream) : CLDN17 (55348 downstream)																							ATTCTTACGTAGTGTGTGATG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32145268	32145268	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32145268delT								KRTAP21-1 (17572 upstream) : KRTAP8-1 (39748 downstream)																							CTCATATATCTTTTTTTTTTC	0.358													4	3	---	---	---	---	
C21orf63	59271	broad.mit.edu	37	21	33867092	33867092	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33867092delA	uc002ypr.1	+						C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron|C21orf63_uc002ypu.1_Intron|C21orf63_uc011adq.1_5'Flank	NM_058187	NP_478067	P58658	CU063_HUMAN	hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3						aatcagtttcaaaaaaaaaaa	0.080													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36577360	36577360	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36577360delA	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						agaaagaaagaaaaaaaaaag	0.343			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40493885	40493885	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40493885delA								ETS2 (297009 upstream) : PSMG1 (53505 downstream)																							cctaggggccaaagaacctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46795011	46795012	+	IGR	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46795011_46795012insG								LOC642852 (77743 upstream) : COL18A1 (30085 downstream)																							GGGTGTCAGGCGGGGGGTGGGA	0.619													4	2	---	---	---	---	
RANBP1	5902	broad.mit.edu	37	22	20106302	20106302	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20106302delG	uc002zro.1	+						TRMT2A_uc002zrk.1_5'Flank|TRMT2A_uc002zrl.1_5'Flank|TRMT2A_uc002zrm.1_5'Flank|TRMT2A_uc002zrn.1_5'Flank|TRMT2A_uc011ahk.1_5'Flank|RANBP1_uc011ahl.1_Intron|RANBP1_uc002zrp.2_Intron	NM_002882	NP_002873	P43487	RANG_HUMAN	RAN binding protein 1						intracellular transport|signal transduction|viral reproduction	nuclear envelope	GDP-dissociation inhibitor activity|GTPase activator activity|Ran GTPase binding			breast(1)	1	Colorectal(54;0.0993)					CTGTGAATCTGGGGGAGGGGC	0.463													4	2	---	---	---	---	
RGL4	266747	broad.mit.edu	37	22	24038567	24038568	+	Intron	INS	-	A	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24038567_24038568insA	uc002zxn.2	+						LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron|RGL4_uc002zxo.2_Intron|RGL4_uc002zxp.1_Intron|RGL4_uc002zxq.2_Intron	NM_153615	NP_705843	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation						small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle	guanyl-nucleotide exchange factor activity			ovary(1)	1						AGCCCTCAGAGGccctgtgagg	0.332													5	3	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26402277	26402277	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26402277delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ATTCCAATTCTTTTTTTTTTT	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	26543036	26543037	+	IGR	INS	-	TGGA	TGGA	rs71960820		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26543036_26543037insTGGA								MYO18B (116029 upstream) : SEZ6L (22443 downstream)																							ggatgggtgagtggatggatgg	0.030													3	3	---	---	---	---	
BPIL2	254240	broad.mit.edu	37	22	32827106	32827106	+	Intron	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32827106delT	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN	bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2						TTAACGTCCCttttttttttt	0.194													3	3	---	---	---	---	
TOM1	10043	broad.mit.edu	37	22	35702741	35702742	+	Intron	INS	-	C	C	rs142013402	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35702741_35702742insC	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						CATTCCTGGGACCCAGTCTAAG	0.317													2	4	---	---	---	---	
TOM1	10043	broad.mit.edu	37	22	35719379	35719379	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35719379delA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						AGATGTAGTTAAAAAAAAAAA	0.547													6	4	---	---	---	---	
CACNA1I	8911	broad.mit.edu	37	22	39994293	39994294	+	Intron	INS	-	GCCCT	GCCCT	rs148307297	by1000genomes	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39994293_39994294insGCCCT	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,						axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	cgccccgccccgccctgcccTC	0.327													5	3	---	---	---	---	
ADSL	158	broad.mit.edu	37	22	40760081	40760081	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40760081delA	uc003ayp.3	+						ADSL_uc003ays.3_Intron|ADSL_uc003ayq.3_Intron|ADSL_uc003ayr.3_Intron|ADSL_uc003ayt.3_Intron	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a						AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1						actctgtctcaaaaaaaaaag	0.124													4	2	---	---	---	---	
TTLL12	23170	broad.mit.edu	37	22	43585500	43585500	+	5'Flank	DEL	A	-	-	rs66783446		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43585500delA	uc003bdq.2	-						TTLL12_uc003bdr.1_5'Flank	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12						protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)				AGAAACAGGGAAAAAAAAAAG	0.259													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48721866	48721866	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48721866delA								None (None upstream) : FAM19A5 (163422 downstream)																							CATATTCTGCAAGGAATCAGA	0.254													4	2	---	---	---	---	
ZBED4	9889	broad.mit.edu	37	22	50245322	50245322	+	5'Flank	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50245322delG	uc003bix.2	+							NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4							cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		tctcggcactgggcatgctcc	0.214													4	2	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536640	1536641	+	Intron	DEL	CG	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536640_1536641delCG	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				gacatgctcacgcacagacatg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5321618	5321618	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5321618delG								None (None upstream) : NLGN4X (486466 downstream)																							AATCCAACATGGCACCCAATG	0.433													4	2	---	---	---	---	
NLGN4X	57502	broad.mit.edu	37	X	6144365	6144365	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6144365delA	uc010ndh.2	-						NLGN4X_uc004crq.2_Intron|NLGN4X_uc010ndi.2_Intron|NLGN4X_uc004crr.2_Intron|NLGN4X_uc010ndj.2_Intron	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor						brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4						CGCAGTCCGGAAAAAAAAAAA	0.572													2	4	---	---	---	---	
MID1	4281	broad.mit.edu	37	X	10560187	10560188	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10560187_10560188delGT	uc004ctg.3	-						MID1_uc004cth.3_Intron|MID1_uc004ctk.3_Intron|MID1_uc004cti.3_Intron|MID1_uc004ctj.3_Intron|MID1_uc011mie.1_Intron|MID1_uc004cug.1_5'Flank	NM_000381	NP_000372	O15344	TRI18_HUMAN	midline 1						microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3						ATGGCTtgtggtgtgtgtgtgt	0.257													4	2	---	---	---	---	
PHEX	5251	broad.mit.edu	37	X	22051522	22051522	+	Intron	DEL	T	-	-	rs36019507		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22051522delT	uc004dah.2	+						PHEX_uc011mjr.1_Intron	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3						GGGTGGAAAATTTTTTATGTG	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	24106995	24106995	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24106995delT								EIF2S3 (10070 upstream) : ZFX (60767 downstream)																							cagctttgtcttctttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	35041277	35041277	+	IGR	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35041277delA								FAM47B (78243 upstream) : MAGEB16 (775182 downstream)																							atatagggttaaaaaaaaaaa	0.000													7	5	---	---	---	---	
EFHC2	80258	broad.mit.edu	37	X	44086884	44086885	+	Intron	DEL	GA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44086884_44086885delGA	uc004dgb.3	-							NM_025184	NP_079460	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2								calcium ion binding			breast(3)|ovary(2)|central_nervous_system(1)	6						attcgaataggagaagacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	44653322	44653322	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44653322delG								FUNDC1 (251101 upstream) : DUSP21 (49927 downstream)																							tttgctttttgtttgttttgt	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	44999151	44999151	+	IGR	DEL	T	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44999151delT								KDM6A (27308 upstream) : CXorf36 (8467 downstream)																							AATTCTGTAATTTTTTTTTTC	0.303													2	4	---	---	---	---	
STARD8	9754	broad.mit.edu	37	X	67910403	67910403	+	Intron	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67910403delC	uc004dxa.2	+						STARD8_uc004dxb.2_Intron	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						GCTGATAGGTCCCCCAAAGGT	0.313													4	2	---	---	---	---	
NHSL2	340527	broad.mit.edu	37	X	71156583	71156584	+	Intron	DEL	GT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71156583_71156584delGT	uc011mqa.1	+							NM_001013627	NP_001013649	Q5HYW2	NHSL2_HUMAN	NHS-like 2												0	Renal(35;0.156)					GATGATGGTGGTGTGTGTGTGT	0.426													4	2	---	---	---	---	
PCDH11X	27328	broad.mit.edu	37	X	91715097	91715097	+	Intron	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91715097delG	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CAAATACTGTGGACAATGCCT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	95724202	95724203	+	IGR	INS	-	T	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95724202_95724203insT								LOC643486 (131301 upstream) : DIAPH2 (215459 downstream)																							ccctccattcctttttttttct	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	100964292	100964292	+	IGR	DEL	G	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100964292delG								ARMCX2 (49429 upstream) : NXF5 (122793 downstream)																							GAACATCACAGAGCAGGAATG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	107064127	107064128	+	IGR	DEL	TT	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107064127_107064128delTT								TSC22D3 (44925 upstream) : MID2 (4956 downstream)																							GTCGAATGTCTTTTTTTTTTTT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	116543250	116543250	+	IGR	DEL	C	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116543250delC								CXorf61 (949113 upstream) : KLHL13 (488527 downstream)																							gccatgaccaccccccacatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	137367302	137367306	+	IGR	DEL	TTTTT	-	-	rs2087225		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137367302_137367306delTTTTT								ZIC3 (713045 upstream) : LOC158696 (329586 downstream)																							agatggccactttttttttgttttg	0.000													0	6	---	---	---	---	
FGF13	2258	broad.mit.edu	37	X	137975802	137975802	+	Intron	DEL	A	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137975802delA	uc004faq.2	-						FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					AAGGGTAAGGAAAAAAAAACA	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142567709	142567710	+	IGR	INS	-	CA	CA	rs80354505		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142567709_142567710insCA								SPANXN4 (445644 upstream) : SPANXN3 (28855 downstream)																							cctttcatagccacacacacct	0.000													4	2	---	---	---	---	
AFF2	2334	broad.mit.edu	37	X	147606700	147606701	+	Intron	DEL	GA	-	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147606700_147606701delGA	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					GCATGTGCAGGAGAGAGAGAGA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	151822479	151822480	+	IGR	INS	-	G	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151822479_151822480insG								GABRQ (654 upstream) : MAGEA6 (44765 downstream)																							TGGCAGAGGGTGGGGGGTGATG	0.525													4	2	---	---	---	---	
