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
CHD5	26038	broad.mit.edu	37	1	6214898	6214898	+	Silent	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6214898A>C	uc001amb.1	-	5	667	c.567T>G	c.(565-567)GGT>GGG	p.G189G		NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	189					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCCACTTGGCACCCAGGACGG	0.498													12	49	---	---	---	---	PASS
AADACL3	126767	broad.mit.edu	37	1	12785985	12785985	+	3'UTR	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12785985A>G	uc009vnn.1	+	4					AADACL3_uc001aug.1_3'UTR	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1								hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTGCTGGTACTGCGGTGTG	0.502													16	52	---	---	---	---	PASS
IFFO2	126917	broad.mit.edu	37	1	19246190	19246190	+	Silent	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19246190A>G	uc001bbd.2	-	3	804	c.804T>C	c.(802-804)TTT>TTC	p.F268F		NM_001136265	NP_001129737	Q5TF58	IFFO2_HUMAN	intermediate filament family orphan 2	268											0						TAAGCCCCTTAAACACCACCA	0.612													41	107	---	---	---	---	PASS
AKR7A3	22977	broad.mit.edu	37	1	19611597	19611597	+	Silent	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19611597A>G	uc001bbv.1	-	4	596	c.519T>C	c.(517-519)AAT>AAC	p.N173N		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	173					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGGTGATGGCATTGTACATGC	0.542													27	65	---	---	---	---	PASS
CDC42	998	broad.mit.edu	37	1	22408281	22408281	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22408281A>G	uc001bfq.2	+	4	464	c.172A>G	c.(172-174)ACT>GCT	p.T58A	CDC42_uc009vqg.1_Missense_Mutation_p.T58A|CDC42_uc001bfp.2_Missense_Mutation_p.T58A|CDC42_uc001bfr.2_Missense_Mutation_p.T58A|CDC42_uc010odr.1_Missense_Mutation_p.T103A|CDC42_uc010ods.1_Missense_Mutation_p.T100A|CDC42_uc009vqh.2_Intron	NM_001039802	NP_001034891	P60953	CDC42_HUMAN	cell division cycle 42 isoform 1	58	GTP (By similarity).				actin cytoskeleton organization|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|establishment or maintenance of cell polarity|macrophage differentiation|muscle cell differentiation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of protein complex assembly|positive regulation of muscle cell differentiation|positive regulation of pseudopodium assembly|regulation of filopodium assembly|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|filopodium|plasma membrane	GTP binding|GTPase activity|protein binding|thioesterase binding			haematopoietic_and_lymphoid_tissue(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		ACTTTTTGATACTGCAGGTGA	0.348													6	611	---	---	---	---	PASS
KTI12	112970	broad.mit.edu	37	1	52498994	52498994	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52498994G>A	uc001ctj.1	-	1	479	c.440C>T	c.(439-441)GCG>GTG	p.A147V	TXNDC12_uc001cti.2_Intron	NM_138417	NP_612426	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated	147							ATP binding			central_nervous_system(2)	2						GCTGCTGCCCGCCGCCTGGGC	0.652													8	9	---	---	---	---	PASS
MIER1	57708	broad.mit.edu	37	1	67412098	67412098	+	Intron	SNP	A	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67412098A>T	uc001dde.2	+						MIER1_uc001dda.3_3'UTR|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_Intron|MIER1_uc001ddi.2_Intron	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TGACTGAAAAATTTTGTGTGA	0.279													15	38	---	---	---	---	PASS
GNG12	55970	broad.mit.edu	37	1	68171068	68171068	+	3'UTR	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68171068T>C	uc001dea.1	-	4						NM_018841	NP_061329	Q9UBI6	GBG12_HUMAN	G-protein gamma-12 subunit precursor						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0						TGAAGGTAAATCTCTTCAAGG	0.383													88	219	---	---	---	---	PASS
ZZZ3	26009	broad.mit.edu	37	1	78099072	78099072	+	5'UTR	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78099072G>A	uc001dhq.2	-	5					ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_5'UTR|ZZZ3_uc001dhp.2_5'UTR	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						CGGTCATCATGATCCACTCAT	0.363													3	18	---	---	---	---	PASS
RBMXL1	494115	broad.mit.edu	37	1	89447509	89447509	+	3'UTR	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89447509A>C	uc009wcx.2	-	3					CCBL2_uc001dmp.2_Intron|CCBL2_uc001dmq.2_Intron|CCBL2_uc001dmr.2_Intron|RBMXL1_uc001dms.2_3'UTR	NM_001162536	NP_001156008	Q96E39	RBMXL_HUMAN	RNA binding motif protein, X-linked-like 1								nucleotide binding|RNA binding				0						TTTAGAAGTCATAAGCCTTTA	0.333													6	23	---	---	---	---	PASS
GBAP1	2630	broad.mit.edu	37	1	155188758	155188758	+	5'UTR	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155188758A>C	uc001fjd.2	-	1					RAG1AP1_uc010pey.1_Intron|GBAP1_uc001fjf.3_Intron|GBAP1_uc001fje.3_Intron					SubName: Full=cDNA FLJ56170, highly similar to Glucosylceramidase (EC 3.2.1.45);												0						GGATGCAGGTACCTGCCATAG	0.478													9	15	---	---	---	---	PASS
TOMM40L	84134	broad.mit.edu	37	1	161196254	161196254	+	5'UTR	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161196254G>T	uc001fzd.2	+	2					APOA2_uc001fzc.1_5'Flank|TOMM40L_uc010pkk.1_RNA|TOMM40L_uc010pkl.1_5'UTR|TOMM40L_uc009wue.2_5'UTR|TOMM40L_uc009wuf.1_RNA|TOMM40L_uc001fze.2_5'UTR	NM_032174	NP_115550	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40						protein transport	mitochondrial outer membrane|pore complex	porin activity|voltage-gated anion channel activity			large_intestine(1)	1	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GGCTAACCTCGGCTCTTCCCA	0.632													11	33	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207685001	207685001	+	Splice_Site	SNP	T	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207685001T>A	uc001hfy.2	+	4	627	c.487_splice	c.e4+2	p.R163_splice	CR1_uc009xcl.1_Splice_Site_p.R163_splice|CR1_uc001hfx.2_Splice_Site_p.R163_splice|CR1_uc009xcj.1_Splice_Site_p.R163_splice|CR1_uc009xck.1_Splice_Site_p.R163_splice	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor						complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						TTTGTGACAGtgagttgaaat	0.214													96	327	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235377281	235377281	+	Silent	SNP	C	T	T	rs113894806		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235377281C>T	uc001hwq.2	-	17	2142	c.1644G>A	c.(1642-1644)GAG>GAA	p.E548E	ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwt.3_Silent_p.E229E	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	548	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cttcttcttcctcctcctcct	0.249													5	427	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1652347	1652347	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1652347C>T	uc002qxa.2	-	17	3269	c.3205G>A	c.(3205-3207)GCC>ACC	p.A1069T		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1069					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AACCTGAAGGCCGCGGTGGCG	0.597													13	33	---	---	---	---	PASS
PDIA6	10130	broad.mit.edu	37	2	10924426	10924426	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10924426G>A	uc002rau.2	-	13	1419	c.1281C>T	c.(1279-1281)CTC>CTT	p.L427L	ATP6V1C2_uc002ras.2_3'UTR|ATP6V1C2_uc002rat.2_3'UTR|PDIA6_uc010yjg.1_Silent_p.L424L|PDIA6_uc002rav.2_Silent_p.L479L|PDIA6_uc010yjh.1_Silent_p.L432L|PDIA6_uc002raw.2_Silent_p.L475L	NM_005742	NP_005733	Q15084	PDIA6_HUMAN	protein disulfide isomerase A6 precursor	427	Asp/Glu-rich (acidic).				cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		CCACATCACTGAGGTCAATGT	0.483													59	149	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15564514	15564514	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15564514C>A	uc002rcc.1	-	23	2528	c.2502G>T	c.(2500-2502)ATG>ATT	p.M834I	NBAS_uc010exl.1_Missense_Mutation_p.M26I|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	834										ovary(2)|liver(1)|skin(1)	4						TAAGCTGGGTCATCCTGAACC	0.483													60	212	---	---	---	---	PASS
WDR43	23160	broad.mit.edu	37	2	29149359	29149359	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29149359T>C	uc002rmo.2	+	9	1144	c.1112T>C	c.(1111-1113)ATG>ACG	p.M371T	SNORD53_uc002rmq.1_5'Flank	NM_015131	NP_055946	Q15061	WDR43_HUMAN	WD repeat domain 43	371						nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					GAACCTCATATGTGTTTAGTA	0.333													6	302	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116534808	116534808	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116534808C>T	uc002tla.1	+	14	1703	c.1246C>T	c.(1246-1248)CGG>TGG	p.R416W	DPP10_uc002tlb.1_Missense_Mutation_p.R366W|DPP10_uc002tlc.1_Missense_Mutation_p.R412W|DPP10_uc002tle.2_Missense_Mutation_p.R420W|DPP10_uc002tlf.1_Missense_Mutation_p.R409W	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	416	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						AATTACCGTGCGGCATCTGAC	0.378													6	315	---	---	---	---	PASS
PKP4	8502	broad.mit.edu	37	2	159526361	159526361	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159526361C>A	uc002tzv.2	+	17	3118	c.2858C>A	c.(2857-2859)GCA>GAA	p.A953E	PKP4_uc002tzw.2_Missense_Mutation_p.A953E|PKP4_uc002tzx.2_Missense_Mutation_p.A610E|PKP4_uc002uaa.2_Missense_Mutation_p.A805E|uc002uab.1_Intron|PKP4_uc002uac.2_Missense_Mutation_p.A134E|PKP4_uc002uad.2_RNA|PKP4_uc002uae.1_Missense_Mutation_p.A40E	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	953	ARM 9.				cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						ATGGAGAACGCAAAAGCCCTG	0.592										HNSCC(62;0.18)			16	36	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179456349	179456349	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179456349G>A	uc010zfg.1	-	252	52717	c.52493C>T	c.(52492-52494)CCG>CTG	p.P17498L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.P11193L|TTN_uc010zfi.1_Missense_Mutation_p.P11126L|TTN_uc010zfj.1_Missense_Mutation_p.P11001L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18425							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACATTCTATCGGGATAGTTGT	0.333													5	269	---	---	---	---	PASS
ALS2CR11	151254	broad.mit.edu	37	2	202356571	202356571	+	Intron	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202356571T>C	uc002uye.2	-						ALS2CR11_uc002uyf.2_Missense_Mutation_p.E1498G|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3						GTCTTGAATCTCTGTTTTATG	0.353													7	373	---	---	---	---	PASS
USP37	57695	broad.mit.edu	37	2	219414549	219414549	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219414549A>G	uc002vie.2	-	6	865	c.412T>C	c.(412-414)TCT>CCT	p.S138P	USP37_uc010fvs.1_Missense_Mutation_p.S138P|USP37_uc010zkf.1_Missense_Mutation_p.S138P|USP37_uc002vif.2_Missense_Mutation_p.S138P|USP37_uc002vig.2_Missense_Mutation_p.S66P|USP37_uc010zkg.1_Missense_Mutation_p.S138P	NM_020935	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	138					ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TCTGAGTAAGAAAGCTGCCTG	0.338													6	445	---	---	---	---	PASS
OGG1	4968	broad.mit.edu	37	3	9792671	9792671	+	Silent	SNP	G	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9792671G>C	uc003bsi.2	+	2	523	c.180G>C	c.(178-180)GCG>GCC	p.A60A	OGG1_uc003bsh.2_Silent_p.A60A|OGG1_uc003bsj.2_Silent_p.A60A|OGG1_uc003bsk.2_Silent_p.A60A|OGG1_uc003bsl.2_Silent_p.A60A|OGG1_uc003bsm.2_Silent_p.A60A|OGG1_uc003bsn.2_Silent_p.A60A|OGG1_uc003bso.2_Silent_p.A60A|OGG1_uc003bsp.1_5'Flank|OGG1_uc010hcm.1_5'Flank|OGG1_uc003bsq.1_5'Flank|OGG1_uc003bsr.1_5'Flank	NM_002542	NP_002533	O15527	OGG1_HUMAN	8-oxoguanine DNA-glycosylase 1 isoform 1a	60					depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)					GTGTACTAGCGGATCAAGTAT	0.567								BER_DNA_glycosylases					56	39	---	---	---	---	PASS
C3orf19	51244	broad.mit.edu	37	3	14697079	14697079	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14697079G>A	uc003byw.2	+	3	282	c.191G>A	c.(190-192)CGA>CAA	p.R64Q	C3orf19_uc010hei.1_Missense_Mutation_p.R64Q	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	64	Potential.										0						GTTTCAAATCGAGCTGAGAAG	0.368													5	285	---	---	---	---	PASS
CADPS	8618	broad.mit.edu	37	3	62423832	62423832	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62423832C>G	uc003dll.2	-	28	4084	c.3724G>C	c.(3724-3726)GAT>CAT	p.D1242H	CADPS_uc003dlj.1_Missense_Mutation_p.D197H|CADPS_uc003dlk.1_Missense_Mutation_p.D690H|CADPS_uc003dlm.2_Missense_Mutation_p.D1203H|CADPS_uc003dln.2_Missense_Mutation_p.D1163H	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	1242	Mediates targeting and association with DCVs (By similarity).				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CGCAGGACATCCTGAGAATGG	0.468													49	58	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66436782	66436782	+	Intron	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66436782G>T	uc003dmx.2	-						SLC25A26_uc011bft.1_RNA|LRIG1_uc011bfu.1_Intron|LRIG1_uc003dmw.2_Intron|LRIG1_uc010hnz.2_Intron|LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGAGGAACCAGCTGCTGTTCA	0.537													6	50	---	---	---	---	PASS
C3orf17	25871	broad.mit.edu	37	3	112724476	112724476	+	Silent	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112724476C>T	uc003dzr.2	-	9	1672	c.1611G>A	c.(1609-1611)TCG>TCA	p.S537S	GTPBP8_uc011bhy.1_Intron|C3orf17_uc003dzq.2_Silent_p.S162S|C3orf17_uc011bhz.1_Silent_p.S162S|C3orf17_uc010hqh.2_Silent_p.S162S|C3orf17_uc003dzt.2_Silent_p.S440S|C3orf17_uc003dzs.2_Silent_p.S401S|C3orf17_uc010hqg.2_Silent_p.S362S|C3orf17_uc011bia.1_Silent_p.S334S|C3orf17_uc003dzu.2_Silent_p.S466S|C3orf17_uc011bib.1_Silent_p.S426S|C3orf17_uc011bic.1_Silent_p.S370S|C3orf17_uc011bid.1_RNA	NM_015412	NP_056227	Q6NW34	CC017_HUMAN	hypothetical protein LOC25871	537						integral to membrane					0						TCACCGTCCACGAATCAGTTT	0.358													15	520	---	---	---	---	PASS
KIAA2018	205717	broad.mit.edu	37	3	113379615	113379615	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113379615T>C	uc003eam.2	-	7	1325	c.914A>G	c.(913-915)CAC>CGC	p.H305R	KIAA2018_uc003eal.2_Missense_Mutation_p.H249R	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	305					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						TGAGGAGCTGTGGGGGATGTT	0.413													31	150	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142169063	142169063	+	Intron	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142169063C>A	uc003eux.3	-						XRN1_uc003eus.2_5'Flank|XRN1_uc003eut.2_5'Flank|XRN1_uc003euu.2_5'Flank|XRN1_uc003euw.2_5'Flank|XRN1_uc011bnh.1_5'Flank|ATR_uc003euy.1_3'UTR	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						GACTTATGTTCCAGCAGAACT	0.498								Other_conserved_DNA_damage_response_genes					7	39	---	---	---	---	PASS
EIF2A	83939	broad.mit.edu	37	3	150264590	150264590	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150264590A>G	uc003eya.2	+	1	17	c.1A>G	c.(1-3)ATG>GTG	p.M1V	SERP1_uc003exy.2_5'Flank|SERP1_uc003exz.2_RNA|EIF2A_uc003eyb.2_5'UTR|EIF2A_uc003eyc.2_5'UTR|EIF2A_uc011bnv.1_Missense_Mutation_p.M1V|EIF2A_uc011bnw.1_Missense_Mutation_p.M1V	NM_032025	NP_114414	Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A	1					regulation of translation|ribosome assembly	eukaryotic translation initiation factor 2 complex	ribosome binding|translation initiation factor activity|tRNA binding				0		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CCGGGACAACATGGCGCCGTC	0.537													33	61	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155301326	155301326	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155301326A>G	uc011bok.1	-	5	947	c.670T>C	c.(670-672)TAC>CAC	p.Y224H	PLCH1_uc011boj.1_Missense_Mutation_p.Y224H|PLCH1_uc011bol.1_Missense_Mutation_p.Y206H	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	224					lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTGTCACTGTAGCTCAAAAGT	0.358													5	285	---	---	---	---	PASS
MCCC1	56922	broad.mit.edu	37	3	182759471	182759471	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182759471G>C	uc003fle.2	-	11	1288	c.1151C>G	c.(1150-1152)GCT>GGT	p.A384G	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Missense_Mutation_p.A267G|MCCC1_uc003flg.2_Missense_Mutation_p.A275G|MCCC1_uc011bqp.1_Missense_Mutation_p.A337G	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	384	Biotin carboxylation.				biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	ATATATTCTAGCTTCGAAGGC	0.458													139	158	---	---	---	---	PASS
DLG1	1739	broad.mit.edu	37	3	196876613	196876613	+	Splice_Site	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196876613C>T	uc003fxo.3	-	7	826	c.636_splice	c.e7+1	p.Y212_splice	DLG1_uc011bub.1_Splice_Site_p.Y96_splice|DLG1_uc011buc.1_Splice_Site_p.Y96_splice|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Splice_Site_p.Y212_splice|DLG1_uc011bue.1_Splice_Site_p.Y179_splice|DLG1_uc010ial.2_Splice_Site_p.Y212_splice|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Splice_Site|DLG1_uc010iam.1_Splice_Site_p.Y179_splice|DLG1_uc010ian.2_Splice_Site_p.Y96_splice	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		ATGGAACTTACGTAAGTTGGT	0.363													6	625	---	---	---	---	PASS
LRCH3	84859	broad.mit.edu	37	3	197562605	197562605	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197562605C>T	uc011bul.1	+	9	1168	c.1163C>T	c.(1162-1164)GCC>GTC	p.A388V	LRCH3_uc003fyj.1_Missense_Mutation_p.A388V|LRCH3_uc011bum.1_Missense_Mutation_p.A388V|LRCH3_uc011bun.1_Missense_Mutation_p.A262V|LRCH3_uc003fyk.2_5'UTR	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)	388	Poly-Glu.					extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		GAAGAGGAGGCCGAGGTGAGA	0.423													4	189	---	---	---	---	PASS
ACOX3	8310	broad.mit.edu	37	4	8418179	8418179	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8418179A>G	uc010idk.2	-	2	215	c.70T>C	c.(70-72)TAC>CAC	p.Y24H	ACOX3_uc003glc.3_Missense_Mutation_p.Y24H|ACOX3_uc003gld.3_Missense_Mutation_p.Y24H|ACOX3_uc003gle.1_5'Flank	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	24					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						CTTGCTCGGTAGGCATCGAGG	0.602													18	44	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20543097	20543097	+	Silent	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20543097T>C	uc003gpr.1	+	20	2202	c.1998T>C	c.(1996-1998)TTT>TTC	p.F666F	SLIT2_uc003gps.1_Silent_p.F658F	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	666	LRRCT 3.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						CCAATCCTTTTAACTGTAACT	0.453													48	147	---	---	---	---	PASS
RBM47	54502	broad.mit.edu	37	4	40440590	40440590	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40440590G>A	uc003gvc.2	-	4	1031	c.321C>T	c.(319-321)GAC>GAT	p.D107D	RBM47_uc003gvd.2_Silent_p.D107D|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_Silent_p.D69D|RBM47_uc003gvg.1_Silent_p.D107D	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	107	RRM 1.					nucleus	nucleotide binding|RNA binding			breast(3)	3						GGTTCTTGCCGTCAAAGTCCA	0.647													3	24	---	---	---	---	PASS
ADH1B	125	broad.mit.edu	37	4	100235104	100235104	+	Silent	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100235104T>C	uc003hus.3	-	6	786	c.702A>G	c.(700-702)AAA>AAG	p.K234K	ADH1A_uc011ceg.1_Intron|ADH1B_uc003hut.3_Silent_p.K194K|ADH1B_uc011ceh.1_Silent_p.K79K|ADH1B_uc011cei.1_Silent_p.K194K	NM_000668	NP_000659	P00325	ADH1B_HUMAN	class I alcohol dehydrogenase, beta subunit	234					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|zinc ion binding			ovary(1)|breast(1)	2				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Fomepizole(DB01213)|NADH(DB00157)	CACCCAACTCTTTGGCCTTTG	0.483													7	470	---	---	---	---	PASS
TRIP13	9319	broad.mit.edu	37	5	914680	914680	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:914680A>G	uc003jbr.2	+	11	1231	c.1121A>G	c.(1120-1122)AAT>AGT	p.N374S		NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	374					double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CTTCTTTTGAATGACATTTCA	0.413													9	141	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13716685	13716685	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13716685C>T	uc003jfd.2	-	74	12862	c.12820G>A	c.(12820-12822)GAA>AAA	p.E4274K	DNAH5_uc003jfc.2_Missense_Mutation_p.E442K	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4274					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					AACATATTTTCACTGAACCAA	0.383									Kartagener_syndrome				10	502	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13719054	13719054	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13719054A>C	uc003jfd.2	-	72	12478	c.12436T>G	c.(12436-12438)TCC>GCC	p.S4146A	DNAH5_uc003jfc.2_Missense_Mutation_p.S314A	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4146	AAA 6 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					AATTTAATGGACATCTGAAGG	0.463									Kartagener_syndrome				113	170	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16673836	16673836	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16673836G>A	uc003jft.3	-	36	5595	c.5127C>T	c.(5125-5127)GGC>GGT	p.G1709G	MYO10_uc011cnb.1_Silent_p.G338G|MYO10_uc011cnc.1_Silent_p.G588G|MYO10_uc011cnd.1_Silent_p.G1066G|MYO10_uc011cne.1_Silent_p.G1066G|MYO10_uc010itx.2_Silent_p.G1331G	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1709	FERM.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						TGCAGGAGCCGCCGCCATGGC	0.527													4	199	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43656801	43656801	+	Silent	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43656801C>T	uc003joe.2	+	16	2595	c.2340C>T	c.(2338-2340)CTC>CTT	p.L780L	NNT_uc003jof.2_Silent_p.L780L	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	780	Helical; (Potential).				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	GGCACTTACTCAATGCAGGCT	0.483													5	307	---	---	---	---	PASS
BHMT	635	broad.mit.edu	37	5	78411662	78411662	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78411662A>G	uc003kfu.3	+	2	211	c.106A>G	c.(106-108)AGG>GGG	p.R36G	BHMT_uc011cti.1_Missense_Mutation_p.R36G	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	36	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ACTGGAGAAGAGGGGCTACGT	0.478													9	679	---	---	---	---	PASS
TCF7	6932	broad.mit.edu	37	5	133482273	133482273	+	3'UTR	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133482273A>G	uc003kyt.2	+	10					TCF7_uc003kyv.2_3'UTR|TCF7_uc003kyw.2_3'UTR|TCF7_uc003kyx.2_3'UTR|TCF7_uc003kyy.2_3'UTR|TCF7_uc003kyz.2_3'UTR|TCF7_uc003kza.2_3'UTR|TCF7_uc003kzb.2_3'UTR|TCF7_uc010jdu.2_RNA	NM_003202	NP_003193	P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific,						cellular response to interleukin-4|immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription regulatory region DNA binding				0		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGACCCAGATCTCATGGAA	0.572											OREG0016787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	10	---	---	---	---	PASS
PPP2R2B	5521	broad.mit.edu	37	5	146070789	146070789	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146070789G>T	uc003loe.2	-	4	874	c.349C>A	c.(349-351)CTG>ATG	p.L117M	PPP2R2B_uc010jgm.2_Missense_Mutation_p.L106M|PPP2R2B_uc003log.3_Missense_Mutation_p.L117M|PPP2R2B_uc003lof.3_Missense_Mutation_p.L117M|PPP2R2B_uc003loi.3_Missense_Mutation_p.L120M|PPP2R2B_uc003loh.3_Missense_Mutation_p.L117M|PPP2R2B_uc003loj.3_Missense_Mutation_p.L97M|PPP2R2B_uc003lok.3_Missense_Mutation_p.L106M|PPP2R2B_uc011dbu.1_Missense_Mutation_p.L123M|PPP2R2B_uc011dbv.1_Missense_Mutation_p.L175M	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein	117	WD 2.				apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTTTCCACAGCTTCACAGTT	0.512													58	250	---	---	---	---	PASS
C5orf25	375484	broad.mit.edu	37	5	175717637	175717637	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175717637G>A	uc003mds.3	+	4	1460	c.1053G>A	c.(1051-1053)AGG>AGA	p.R351R	C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc011dfk.1_Silent_p.R370R|uc003mdu.1_Silent_p.R262R			Q8NDZ2	CE025_HUMAN	RecName: Full=Uncharacterized protein C5orf25;	351	Pro-rich.										0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)		CAGGAGACAGGCCTGACTTTA	0.517													22	116	---	---	---	---	PASS
GCNT2	2651	broad.mit.edu	37	6	10621587	10621587	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10621587T>C	uc010joo.2	+	4	1480	c.929T>C	c.(928-930)GTT>GCT	p.V310A	GCNT2_uc010jol.2_Missense_Mutation_p.V24A|GCNT2_uc010jom.2_RNA|GCNT2_uc010jop.2_RNA|GCNT2_uc003mza.2_RNA|GCNT2_uc003mzc.3_Missense_Mutation_p.V309A|GCNT2_uc003mzd.2_Missense_Mutation_p.V308A|GCNT2_uc003mze.2_Missense_Mutation_p.V310A	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,	310	Lumenal (Potential).					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		ATTGCAGGTGTTCCTGGCTCT	0.468													53	201	---	---	---	---	PASS
KIAA1586	57691	broad.mit.edu	37	6	56917523	56917523	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56917523T>A	uc003pdj.2	+	4	396	c.226T>A	c.(226-228)TTG>ATG	p.L76M	KIAA1586_uc011dxm.1_Missense_Mutation_p.L49M	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	76							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GGGTGATTTTTTGCATTTTTT	0.308													33	84	---	---	---	---	PASS
SMAP1	60682	broad.mit.edu	37	6	71501445	71501445	+	Silent	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71501445A>G	uc003pfr.2	+	5	716	c.468A>G	c.(466-468)CAA>CAG	p.Q156Q	SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Silent_p.Q146Q	NM_001044305	NP_001037770	Q8IYB5	SMAP1_HUMAN	stromal membrane-associated GTPase-activating	156					regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0						CTTCTCTGCAAGCTGCTGTTG	0.393													7	604	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83872600	83872600	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83872600G>C	uc003pjs.1	+	38	7314	c.7054G>C	c.(7054-7056)GTG>CTG	p.V2352L	DOPEY1_uc011dyy.1_Missense_Mutation_p.V2343L|DOPEY1_uc010kbl.1_Missense_Mutation_p.V2343L|DOPEY1_uc003pjt.2_RNA	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	2352					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TAAACCTTACGTGGTACGACT	0.393													74	243	---	---	---	---	PASS
TRMT11	60487	broad.mit.edu	37	6	126319220	126319220	+	Silent	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126319220T>C	uc003qam.2	+	4	355	c.234T>C	c.(232-234)GGT>GGC	p.G78G	TRMT11_uc003qan.2_RNA|TRMT11_uc010kev.2_Silent_p.G78G	NM_001031712	NP_001026882	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11	78					tRNA processing		methyltransferase activity|nucleic acid binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0356)		AACTATGGGGTCATGGACAAT	0.388													8	551	---	---	---	---	PASS
PHF14	9678	broad.mit.edu	37	7	11076155	11076155	+	Silent	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11076155C>T	uc003sry.1	+	9	2148	c.1713C>T	c.(1711-1713)AGC>AGT	p.S571S	PHF14_uc011jxi.1_Silent_p.S286S|PHF14_uc003srz.2_Silent_p.S571S|PHF14_uc011jxj.1_Silent_p.S286S	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	571							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		CACTCACCAGCAGTGCTTCAG	0.493													4	148	---	---	---	---	PASS
AHR	196	broad.mit.edu	37	7	17367399	17367399	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17367399T>C	uc011jxz.1	+	4	990	c.377T>C	c.(376-378)GTA>GCA	p.V126A	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	126	PAS 1.				apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					AATGGCTTTGTATTAGTTGTC	0.289													5	593	---	---	---	---	PASS
OSBPL3	26031	broad.mit.edu	37	7	24870477	24870477	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24870477G>A	uc003sxf.2	-	16	2199	c.1794C>T	c.(1792-1794)TAC>TAT	p.Y598Y	OSBPL3_uc003sxd.2_RNA|OSBPL3_uc003sxe.2_RNA|OSBPL3_uc003sxg.2_Silent_p.Y562Y|OSBPL3_uc003sxh.2_Silent_p.Y567Y|OSBPL3_uc003sxi.2_Silent_p.Y531Y	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform	598					lipid transport		lipid binding|protein binding			skin(1)	1						TTCCAGCTCGGTAGTAGCTAG	0.428													5	139	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	65222986	65222986	+	Intron	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65222986G>T	uc003tud.1	-						CCT6P1_uc003tug.2_RNA|CCT6P1_uc003tuh.2_RNA|CCT6P1_uc003tui.2_RNA|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		GAATTCTGGCGTTTTTTACAA	0.289													3	25	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	78150751	78150751	+	Silent	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78150751T>C	uc003ugx.2	-	4	1004	c.750A>G	c.(748-750)ACA>ACG	p.T250T	MAGI2_uc003ugy.2_Silent_p.T250T|MAGI2_uc011kgr.1_Silent_p.T82T|MAGI2_uc011kgs.1_Silent_p.T87T	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	250	Guanylate kinase-like.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				ACTAACCTGGTGTTACTACTA	0.313													5	161	---	---	---	---	PASS
GPR37	2861	broad.mit.edu	37	7	124387183	124387183	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124387183C>T	uc003vli.2	-	2	1889	c.1238G>A	c.(1237-1239)CGA>CAA	p.R413Q		NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37 precursor	413	Extracellular (Potential).					endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|lung(1)|central_nervous_system(1)	3						TGCCGGAGCTCGGCCACTAAA	0.493													4	207	---	---	---	---	PASS
AKR1B15	441282	broad.mit.edu	37	7	134261166	134261166	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134261166A>G	uc011kpr.1	+	9	1108	c.809A>G	c.(808-810)AAA>AGA	p.K270R	AKR1B15_uc011kps.1_Missense_Mutation_p.K242R	NM_001080538	NP_001074007	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	270							oxidoreductase activity			ovary(1)	1						GCAAAGCACAAAAAAACCACA	0.448													37	108	---	---	---	---	PASS
UBN2	254048	broad.mit.edu	37	7	138966788	138966788	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138966788C>T	uc011kqr.1	+	14	2105	c.2105C>T	c.(2104-2106)CCC>CTC	p.P702L		NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	702										ovary(1)|skin(1)	2						CATTCTTTCCCCACTATGCTT	0.348													5	608	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131916085	131916085	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131916085C>A	uc003ytd.3	-	7	2100	c.1844G>T	c.(1843-1845)GGG>GTG	p.G615V	ADCY8_uc010mds.2_Missense_Mutation_p.G615V	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	615	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GAATGTGGCCCCACTGTTTCT	0.493										HNSCC(32;0.087)			4	98	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131916086	131916086	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131916086C>A	uc003ytd.3	-	7	2099	c.1843G>T	c.(1843-1845)GGG>TGG	p.G615W	ADCY8_uc010mds.2_Missense_Mutation_p.G615W	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	615	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AATGTGGCCCCACTGTTTCTC	0.493										HNSCC(32;0.087)			4	99	---	---	---	---	PASS
KCNV2	169522	broad.mit.edu	37	9	2729474	2729474	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2729474A>G	uc003zho.1	+	2	1599	c.1385A>G	c.(1384-1386)GAC>GGC	p.D462G		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	462	Selectivity filter (By similarity).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)		GGCTACGGAGACATGTACCCA	0.512													33	113	---	---	---	---	PASS
DAPK1	1612	broad.mit.edu	37	9	90258354	90258354	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90258354A>G	uc004apc.2	+	11	1120	c.982A>G	c.(982-984)ATG>GTG	p.M328V	DAPK1_uc004ape.2_Missense_Mutation_p.M328V|DAPK1_uc004apd.2_Missense_Mutation_p.M328V|DAPK1_uc011ltg.1_Missense_Mutation_p.M328V|DAPK1_uc011lth.1_Missense_Mutation_p.M65V	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	328	Calmodulin-binding.				apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						CAGAAGTAACATGAGTGTTGC	0.428									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				53	158	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107548824	107548824	+	Intron	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107548824G>A	uc004bcl.2	-						NIPSNAP3B_uc004bcj.1_RNA	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	gtgtagtggtgtttacaattg	0.030													11	17	---	---	---	---	PASS
PALM2	114299	broad.mit.edu	37	9	112705833	112705833	+	3'UTR	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112705833C>G	uc004beg.2	+	7					PALM2_uc004bef.2_3'UTR|PALM2_uc004beh.3_3'UTR|PALM2-AKAP2_uc004bei.2_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001037293	NP_001032370	Q8IXS6	PALM2_HUMAN	paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2						AGTTGAATTGCTTTGATCTCT	0.453													6	15	---	---	---	---	PASS
PALM2	114299	broad.mit.edu	37	9	112705834	112705834	+	3'UTR	SNP	T	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112705834T>A	uc004beg.2	+	7					PALM2_uc004bef.2_3'UTR|PALM2_uc004beh.3_3'UTR|PALM2-AKAP2_uc004bei.2_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001037293	NP_001032370	Q8IXS6	PALM2_HUMAN	paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2						GTTGAATTGCTTTGATCTCTC	0.453													6	14	---	---	---	---	PASS
FAM188A	80013	broad.mit.edu	37	10	15875681	15875681	+	Silent	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15875681C>T	uc001iod.1	-	8	899	c.678G>A	c.(676-678)ACG>ACA	p.T226T	FAM188A_uc001ioe.1_Silent_p.T53T|FAM188A_uc001iof.1_Silent_p.T226T	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97	226					apoptosis	nucleus	calcium ion binding			ovary(1)	1						CAGCATGTCCCGTCAGCAGGA	0.308													4	328	---	---	---	---	PASS
NEBL	10529	broad.mit.edu	37	10	21158725	21158725	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21158725C>G	uc001iqi.2	-	6	923	c.526G>C	c.(526-528)GAA>CAA	p.E176Q	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	176	Nebulin 5.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						CGGTCAAGTTCTGCACTGTAC	0.368													85	288	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55581961	55581961	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55581961C>A	uc001jju.1	-	33	5920	c.5525G>T	c.(5524-5526)TGT>TTT	p.C1842F	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.C1839F|PCDH15_uc010qhw.1_Missense_Mutation_p.C1802F|PCDH15_uc010qhx.1_Missense_Mutation_p.C1773F|PCDH15_uc010qhy.1_Missense_Mutation_p.C1849F|PCDH15_uc010qhz.1_Missense_Mutation_p.C1844F|PCDH15_uc010qia.1_Missense_Mutation_p.C1822F|PCDH15_uc010qib.1_Missense_Mutation_p.C1819F	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1842	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ACCTGTTATACAGACACACTC	0.279										HNSCC(58;0.16)			7	414	---	---	---	---	PASS
BICC1	80114	broad.mit.edu	37	10	60573818	60573818	+	Intron	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60573818A>G	uc001jki.1	+						BICC1_uc001jkj.1_Missense_Mutation_p.T510A	NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						TTGGAGTATCACTGACTGTGG	0.289													15	27	---	---	---	---	PASS
MYST4	23522	broad.mit.edu	37	10	76790353	76790353	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76790353C>G	uc001jwn.1	+	18	6264	c.5771C>G	c.(5770-5772)TCC>TGC	p.S1924C	MYST4_uc001jwo.1_Missense_Mutation_p.S1632C|MYST4_uc001jwp.1_Missense_Mutation_p.S1741C	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1924	Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					GGCCACATCTCCATGAGAACC	0.562			T	CREBBP	AML								25	52	---	---	---	---	PASS
CALHM3	119395	broad.mit.edu	37	10	105236264	105236264	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105236264G>A	uc001kxg.3	-	2	538	c.330C>T	c.(328-330)CCC>CCT	p.P110P		NM_001129742	NP_001123214	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	110	Helical; (Potential).					integral to membrane				large_intestine(1)	1						TCCAGACCAGGGGGGCGGCCA	0.622													17	24	---	---	---	---	PASS
TDRD1	56165	broad.mit.edu	37	10	115980406	115980406	+	Silent	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115980406A>G	uc001lbg.1	+	19	2727	c.2574A>G	c.(2572-2574)CAA>CAG	p.Q858Q	TDRD1_uc001lbf.2_Silent_p.Q735Q|TDRD1_uc001lbh.1_Silent_p.Q849Q|TDRD1_uc001lbi.1_Silent_p.Q849Q|TDRD1_uc010qsc.1_Silent_p.Q462Q|TDRD1_uc001lbj.2_Silent_p.Q567Q	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	858					DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TAAAATTGCAAGCCAGAGTGG	0.393													5	243	---	---	---	---	PASS
C10orf93	255352	broad.mit.edu	37	10	134743171	134743171	+	Missense_Mutation	SNP	G	A	A	rs149229934	byFrequency	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134743171G>A	uc001llt.1	-	9	1080	c.1004C>T	c.(1003-1005)GCG>GTG	p.A335V		NM_173572	NP_775843	Q5SR76	CJ093_HUMAN	hypothetical protein LOC255352	Error:Variant_position_missing_in_Q5SR76_after_alignment							binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)		GGTGAGCAGCGCCTCATCCCC	0.557													24	70	---	---	---	---	PASS
LOC646813	646813	broad.mit.edu	37	11	50379673	50379673	+	RNA	SNP	C	T	T	rs117065335	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50379673C>T	uc001nhe.2	+	6		c.1156C>T			LOC646813_uc001nhf.1_Intron|LOC646813_uc001nhg.1_Intron|LOC646813_uc001nhh.1_Intron|LOC646813_uc010rib.1_RNA	NR_024504				Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit09-11-09-R.												0						ATATGTACAACGGAGAGCTGT	0.348													6	16	---	---	---	---	PASS
C11orf80	79703	broad.mit.edu	37	11	66571657	66571657	+	Splice_Site	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66571657T>C	uc001ojf.2	+	9	1039	c.1032_splice	c.e9+2	p.S344_splice	C11orf80_uc001ojg.2_Splice_Site_p.S110_splice|C11orf80_uc001ojh.2_Splice_Site_p.S111_splice|C11orf80_uc001oji.2_Splice_Site_p.S111_splice	NM_024650	NP_078926	Q8N6T0	CK080_HUMAN	hypothetical protein LOC79703												0						ATTTCTTCAGTTTCCATATCC	0.418													4	76	---	---	---	---	PASS
RPS6KB2	6199	broad.mit.edu	37	11	67198840	67198840	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67198840C>T	uc001old.2	+	5	393	c.311C>T	c.(310-312)GCC>GTC	p.A104V	RPS6KB2_uc001olf.2_5'UTR|RPS6KB2_uc001olg.2_Missense_Mutation_p.A104V|RPS6KB2_uc009yrq.2_Intron|RPS6KB2_uc001ole.2_RNA|RPS6KB2_uc001olh.2_RNA|RPS6KB2_uc009yrr.2_5'UTR	NM_003952	NP_003943	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	104	Protein kinase.				nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			TATCTCCAGGCCAAAATTGTG	0.353													4	122	---	---	---	---	PASS
CHRDL2	25884	broad.mit.edu	37	11	74413875	74413875	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74413875C>T	uc001ovi.2	-	9	1337	c.1084G>A	c.(1084-1086)GAC>AAC	p.D362N	CHRDL2_uc001ovg.2_Missense_Mutation_p.D246N|CHRDL2_uc001ovh.2_Missense_Mutation_p.D362N|CHRDL2_uc001ovj.1_RNA|CHRDL2_uc001ovk.1_Missense_Mutation_p.D297N			Q6WN34	CRDL2_HUMAN	RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;	362					cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)					TCCACCAAGTCCGAGGCCTCG	0.632											OREG0021223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	34	71	---	---	---	---	PASS
TMEM135	65084	broad.mit.edu	37	11	86947689	86947689	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86947689T>C	uc001pch.2	+	6	495	c.472T>C	c.(472-474)TTT>CTT	p.F158L	TMEM135_uc010rtt.1_Missense_Mutation_p.F19L|TMEM135_uc001pci.2_Missense_Mutation_p.F136L	NM_022918	NP_075069	Q86UB9	TM135_HUMAN	transmembrane protein 135	158	Helical; (Potential).					integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGTCCTTTTGTTTTGCATCAC	0.313													8	773	---	---	---	---	PASS
AMOTL1	154810	broad.mit.edu	37	11	94592715	94592715	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94592715A>G	uc001pfb.2	+	9	2140	c.1970A>G	c.(1969-1971)AAC>AGC	p.N657S	AMOTL1_uc001pfc.2_Missense_Mutation_p.N607S	NM_130847	NP_570899	Q8IY63	AMOL1_HUMAN	angiomotin like 1	657						cytoplasm|tight junction	identical protein binding			ovary(1)|breast(1)	2		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CAGCCAGCCAACATGCCGGAA	0.517													47	145	---	---	---	---	PASS
KDM4DL	390245	broad.mit.edu	37	11	94758636	94758636	+	5'UTR	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94758636G>T	uc010ruf.1	+	1						NM_001161630	NP_001155102	B2RXH2	KD4DL_HUMAN	lysine (K)-specific demethylase 4D-like						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						AAAAACAAAGGGGAGAAAAGA	0.453													23	43	---	---	---	---	PASS
RDX	5962	broad.mit.edu	37	11	110124794	110124794	+	Missense_Mutation	SNP	C	T	T	rs150863373		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110124794C>T	uc001pku.2	-	9	1146	c.836G>A	c.(835-837)CGG>CAG	p.R279Q	RDX_uc009yxx.1_RNA|RDX_uc009yxy.2_Missense_Mutation_p.R279Q|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Missense_Mutation_p.R143Q	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin	279	FERM.				actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GGCCAAAATCCGCTTATTGAT	0.383													89	254	---	---	---	---	PASS
HYOU1	10525	broad.mit.edu	37	11	118917418	118917418	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118917418G>A	uc001puu.2	-	23	2885	c.2692C>T	c.(2692-2694)CTG>TTG	p.L898L	HYOU1_uc001put.2_Silent_p.L863L|HYOU1_uc010ryu.1_Silent_p.L856L|HYOU1_uc010ryv.1_Silent_p.L787L|HYOU1_uc001pux.3_Silent_p.L898L	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	898						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TCTCGGTCCAGGGCCATCATC	0.572													36	97	---	---	---	---	PASS
RAP1B	5908	broad.mit.edu	37	12	69042542	69042542	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69042542G>A	uc001sub.2	+	2	201	c.38G>A	c.(37-39)GGC>GAC	p.G13D	RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Missense_Mutation_p.G13D|RAP1B_uc010stf.1_Missense_Mutation_p.G13D|RAP1B_uc010stg.1_Missense_Mutation_p.G13D|RAP1B_uc010sth.1_Missense_Mutation_p.G13D|RAP1B_uc010sti.1_Missense_Mutation_p.G13D	NM_001089704	NP_001083173	P61224	RAP1B_HUMAN	SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;	13	GTP.				blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)		GGCTCAGGAGGCGTTGGAAAG	0.363													9	334	---	---	---	---	PASS
PTPRQ	374462	broad.mit.edu	37	12	80928716	80928716	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80928716C>T	uc001sze.2	+	16	2885	c.2885C>T	c.(2884-2886)TCT>TTT	p.S962F		NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						AACCTCAGTTCTTCATCAATA	0.318													4	321	---	---	---	---	PASS
PLEKHG7	440107	broad.mit.edu	37	12	93131234	93131234	+	5'UTR	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93131234C>T	uc001tcj.2	+	2						NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						AGCAAGAGGCCGTGTGGGAAC	0.398													5	585	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	103981134	103981134	+	5'UTR	SNP	A	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103981134A>T	uc001tjw.2	+	1						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						AAAGGAAAGGAAGGGATTTAA	0.408													12	37	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60212848	60212848	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60212848T>C	uc001xen.1	-	2	802	c.593A>G	c.(592-594)GAC>GGC	p.D198G		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	198					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCTGGTTATGTCAATGTATTT	0.448													118	259	---	---	---	---	PASS
MARK3	4140	broad.mit.edu	37	14	103966456	103966456	+	Intron	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103966456T>C	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron|MARK3_uc010tyb.1_Intron|MARK3_uc010awq.2_Intron|MARK3_uc001ynd.2_Missense_Mutation_p.F20S	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			CTTTTCTCTTTCCCTCTTCTC	0.423											OREG0022950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	451	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20488770	20488770	+	RNA	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20488770A>G	uc001ytf.1	+	2		c.253A>G								full-length cDNA clone CS0DI026YN18 of Placenta Cot 25-normalized of Homo sapiens (human).																		TGGGCACTCCAAGATTTTGGG	0.408													8	189	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21937204	21937204	+	RNA	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21937204C>G	uc010tzj.1	-	1		c.3536G>C				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						AGGTAACTGTCCAAGAAGTTA	0.378													45	642	---	---	---	---	PASS
ZFAND6	54469	broad.mit.edu	37	15	80429828	80429828	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80429828A>C	uc002bfe.1	+	7	796	c.485A>C	c.(484-486)GAA>GCA	p.E162A	ZFAND6_uc002bff.1_Missense_Mutation_p.E162A|ZFAND6_uc002bfg.1_Missense_Mutation_p.E150A|ZFAND6_uc002bfh.1_Missense_Mutation_p.E162A|ZFAND6_uc002bfi.1_Missense_Mutation_p.E162A	NM_019006	NP_061879	Q6FIF0	ZFAN6_HUMAN	zinc finger, AN1-type domain 6	162	AN1-type.						DNA binding|zinc ion binding				0						CCAGGGTTTGAATGCCGGTGT	0.373													6	468	---	---	---	---	PASS
TM6SF1	53346	broad.mit.edu	37	15	83805287	83805287	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83805287A>G	uc002bjp.2	+	10	1085	c.976A>G	c.(976-978)AGA>GGA	p.R326G	TM6SF1_uc010bmq.2_Missense_Mutation_p.R295G|TM6SF1_uc002bjq.2_3'UTR|TM6SF1_uc010bmr.2_RNA|TM6SF1_uc002bjr.2_Missense_Mutation_p.R178G	NM_023003	NP_075379	Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1 isoform 1	326						integral to membrane				ovary(1)	1						TTATGTCTACAGAGTCCCTGA	0.373													44	129	---	---	---	---	PASS
IGF1R	3480	broad.mit.edu	37	15	99192876	99192876	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99192876G>A	uc002bul.2	+	1	116	c.66G>A	c.(64-66)GCG>GCA	p.A22A	IGF1R_uc010urq.1_Silent_p.A22A|IGF1R_uc010bon.2_Silent_p.A22A	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor	22					anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	TCTCCGCCGCGCTCTCGCTCT	0.607													13	30	---	---	---	---	PASS
IFT140	9742	broad.mit.edu	37	16	1652468	1652468	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1652468T>A	uc002cmb.2	-	4	634	c.272A>T	c.(271-273)CAG>CTG	p.Q91L		NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140	91	WD 2.									ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)				CTCCTTGTCCTGCTTGTTAAA	0.632													32	86	---	---	---	---	PASS
NOMO1	23420	broad.mit.edu	37	16	14989981	14989981	+	3'UTR	SNP	A	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14989981A>C	uc002dcv.2	+	31						NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor							integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1						GGTAAAAATCAATAAAATGGC	0.443													61	382	---	---	---	---	PASS
GTF3C1	2975	broad.mit.edu	37	16	27509071	27509071	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27509071C>T	uc002dov.1	-	14	2277	c.2237G>A	c.(2236-2238)AGT>AAT	p.S746N	GTF3C1_uc002dou.2_Missense_Mutation_p.S746N	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	746						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						CCCTGATCCACTTGGGCCCTC	0.453													6	339	---	---	---	---	PASS
TSNAXIP1	55815	broad.mit.edu	37	16	67859889	67859889	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67859889A>T	uc002euj.2	+	9	1286	c.892A>T	c.(892-894)AGC>TGC	p.S298C	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Missense_Mutation_p.S175C|TSNAXIP1_uc002euf.3_Missense_Mutation_p.S6C|TSNAXIP1_uc010vka.1_Missense_Mutation_p.S352C|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.S283C|TSNAXIP1_uc002eug.3_Missense_Mutation_p.S6C|TSNAXIP1_uc002euh.3_Missense_Mutation_p.S6C|TSNAXIP1_uc002eui.3_Missense_Mutation_p.S6C|TSNAXIP1_uc002euk.2_Missense_Mutation_p.S6C	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	298					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)		GCTGCACATGAGCACGCTGAA	0.612													12	36	---	---	---	---	PASS
TSNAXIP1	55815	broad.mit.edu	37	16	67859890	67859890	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67859890G>A	uc002euj.2	+	9	1287	c.893G>A	c.(892-894)AGC>AAC	p.S298N	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Missense_Mutation_p.S175N|TSNAXIP1_uc002euf.3_Missense_Mutation_p.S6N|TSNAXIP1_uc010vka.1_Missense_Mutation_p.S352N|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.S283N|TSNAXIP1_uc002eug.3_Missense_Mutation_p.S6N|TSNAXIP1_uc002euh.3_Missense_Mutation_p.S6N|TSNAXIP1_uc002eui.3_Missense_Mutation_p.S6N|TSNAXIP1_uc002euk.2_Missense_Mutation_p.S6N	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	298					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)		CTGCACATGAGCACGCTGAAG	0.612													13	37	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76481948	76481948	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76481948T>C	uc002feu.1	+	7	963	c.578T>C	c.(577-579)CTC>CCC	p.L193P	CNTNAP4_uc002fev.1_Missense_Mutation_p.L105P|CNTNAP4_uc010chb.1_Missense_Mutation_p.L168P|CNTNAP4_uc002fex.1_Missense_Mutation_p.L196P|CNTNAP4_uc002few.2_Missense_Mutation_p.L168P	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	193	Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						AGTTCCCTTCTCTACAGATTT	0.353													6	269	---	---	---	---	PASS
CBFA2T3	863	broad.mit.edu	37	16	88945789	88945789	+	Silent	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88945789G>A	uc002fmm.1	-	11	1737	c.1551C>T	c.(1549-1551)CAC>CAT	p.H517H	CBFA2T3_uc002fml.1_Silent_p.H431H|CBFA2T3_uc002fmk.1_Silent_p.H16H	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16	517	Potential.				cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0275)		TGATGAGCTCGTGCGCTTTGC	0.662			T	RUNX1	AML								12	19	---	---	---	---	PASS
ETV4	2118	broad.mit.edu	37	17	41606595	41606595	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41606595G>A	uc002idw.2	-	12	1266	c.1138C>T	c.(1138-1140)CTC>TTC	p.L380F	ETV4_uc002idv.2_Missense_Mutation_p.L103F|ETV4_uc010wih.1_Missense_Mutation_p.L326F|ETV4_uc010czh.2_Missense_Mutation_p.L379F|ETV4_uc010wii.1_Missense_Mutation_p.L341F|ETV4_uc002idx.2_Missense_Mutation_p.L380F|ETV4_uc010wij.1_Missense_Mutation_p.L341F	NM_001986	NP_001977	P43268	ETV4_HUMAN	ets variant gene 4 (E1A enhancer binding	380	ETS.				positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		ATGCCCCAGAGCCTGGCGACC	0.522			T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								4	165	---	---	---	---	PASS
ZNF652	22834	broad.mit.edu	37	17	47394770	47394770	+	Silent	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47394770T>C	uc002iov.3	-	2	782	c.318A>G	c.(316-318)GAA>GAG	p.E106E	ZNF652_uc002iow.2_Silent_p.E106E|ZNF652_uc002iou.3_RNA	NM_001145365	NP_001138837	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	106	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			CTTCTTCCTCTTCCTCCTCTG	0.423													5	217	---	---	---	---	PASS
MBTD1	54799	broad.mit.edu	37	17	49279412	49279412	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49279412A>T	uc002itr.3	-	11	1434	c.1090T>A	c.(1090-1092)TTT>ATT	p.F364I	MBTD1_uc002itp.3_Missense_Mutation_p.F200I|MBTD1_uc002itq.3_Missense_Mutation_p.F364I	NM_017643	NP_060113	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	364	MBT 3.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			GGTGTATCAAAATGTCCATCC	0.343													99	365	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60072679	60072679	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60072679A>G	uc002izo.2	-	10	2092	c.2015T>C	c.(2014-2016)GTG>GCG	p.V672A		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	672					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						ATATTGCTGCACTAATTCATC	0.294													125	486	---	---	---	---	PASS
CD300C	10871	broad.mit.edu	37	17	72537855	72537855	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72537855C>G	uc002jky.1	-	4	909	c.548G>C	c.(547-549)CGC>CCC	p.R183P		NM_006678	NP_006669	Q08708	CLM6_HUMAN	CD300C antigen precursor	183	Extracellular (Potential).				cellular defense response	integral to plasma membrane	transmembrane receptor activity				0						GAGCAGGAAGCGGACATTGCT	0.632													21	59	---	---	---	---	PASS
GREB1L	80000	broad.mit.edu	37	18	19076555	19076555	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19076555G>T	uc010xam.1	+	21	3558	c.3287G>T	c.(3286-3288)GGG>GTG	p.G1096V	GREB1L_uc010dlp.1_Missense_Mutation_p.G987V|GREB1L_uc010xan.1_Missense_Mutation_p.G512V|GREB1L_uc010dlr.1_Missense_Mutation_p.G207V	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast	1096						integral to membrane					0						GACCTCAGCGGGAAGGAGCAG	0.597													20	53	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28935225	28935225	+	Silent	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28935225C>T	uc002kwp.2	+	15	3278	c.3066C>T	c.(3064-3066)CAC>CAT	p.H1022H	DSG1_uc010xbp.1_Silent_p.H381H	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	1022	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CTGACCATCACTTTAACCAAA	0.542													25	72	---	---	---	---	PASS
SERPINB3	6317	broad.mit.edu	37	18	61323112	61323112	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61323112T>C	uc002lji.2	-	8	1096	c.952A>G	c.(952-954)ACC>GCC	p.T318A	SERPINB4_uc002ljg.2_Intron|SERPINB3_uc010dqa.2_Missense_Mutation_p.T266A	NM_006919	NP_008850	P29508	SPB3_HUMAN	serine (or cysteine) proteinase inhibitor, clade	318					regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						CGGCTCCCGGTCATGCCTGAG	0.552													7	152	---	---	---	---	PASS
MUM1	84939	broad.mit.edu	37	19	1358304	1358304	+	Intron	SNP	T	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1358304T>C	uc010xgm.1	+						MUM1_uc010dsi.2_Intron|MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsc.1_5'UTR			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAAATGAAAATAATTCTTTTG	0.418													39	105	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2229711	2229711	+	Intron	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2229711C>A	uc002lvb.3	+						DOT1L_uc002lvc.1_3'UTR	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGTCCCCAGCCTGGGTGAGT	0.637													6	27	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9066157	9066157	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9066157G>A	uc002mkp.2	-	3	21493	c.21289C>T	c.(21289-21291)CCT>TCT	p.P7097S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7099	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						AGCAGGGAAGGGAGAGAGCTG	0.507													6	422	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9066178	9066178	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9066178G>C	uc002mkp.2	-	3	21472	c.21268C>G	c.(21268-21270)CTG>GTG	p.L7090V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7092	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGATTTTCCAGAGAGGGAGAG	0.498													103	291	---	---	---	---	PASS
ZNF433	163059	broad.mit.edu	37	19	12125862	12125862	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12125862A>G	uc002msy.1	-	4	1991	c.1820T>C	c.(1819-1821)ATG>ACG	p.M607T	uc002msx.1_Intron|ZNF433_uc002msz.1_Missense_Mutation_p.M572T	NM_001080411	NP_001073880	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	607	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CCTTCCATGCATTTGAAGTCG	0.473													23	87	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22952718	22952718	+	Intron	SNP	C	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22952718C>A	uc010xrh.1	-							NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ATAACATGTACATTTTTGAGT	0.289													57	244	---	---	---	---	PASS
PSG4	5672	broad.mit.edu	37	19	43699365	43699365	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43699365A>G	uc002ovy.2	-	4	872	c.770T>C	c.(769-771)GTC>GCC	p.V257A	PSG6_uc010xwk.1_Intron|PSG4_uc002owa.2_RNA|PSG4_uc002owb.2_Missense_Mutation_p.V164A|PSG4_uc002ovz.2_Intron	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	257	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)				GAAGGTTAAGACATCCTTATT	0.468													8	739	---	---	---	---	PASS
FAM182A	284800	broad.mit.edu	37	20	26063752	26063752	+	RNA	SNP	T	G	G	rs78544920	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26063752T>G	uc010gdq.2	+	5		c.1310T>G				NR_026713				Homo sapiens cDNA FLJ38374 fis, clone FEBRA2002552.												0						CACCTGGGGATTGGGTATCCA	0.537													3	24	---	---	---	---	PASS
SYCP2	10388	broad.mit.edu	37	20	58490525	58490525	+	Silent	SNP	A	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58490525A>G	uc002yaz.2	-	8	733	c.594T>C	c.(592-594)ATT>ATC	p.I198I	SYCP2_uc010gju.1_Silent_p.I99I	NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	198					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)			ATTACATGAGAATTAACATTT	0.269													7	665	---	---	---	---	PASS
SLC5A3	6526	broad.mit.edu	37	21	35467806	35467806	+	Silent	SNP	G	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35467806G>C	uc002yto.2	+	2	821	c.309G>C	c.(307-309)CGG>CGC	p.R103R	MRPS6_uc002ytp.2_Intron	NM_006933	NP_008864	P53794	SC5A3_HUMAN	solute carrier family 5 (inositol transporters),	103	Helical; (Potential).					integral to plasma membrane	myo-inositol:sodium symporter activity			ovary(2)	2						TTTACATCCGGTCAGGGGTAT	0.448													113	288	---	---	---	---	PASS
LIF	3976	broad.mit.edu	37	22	30642773	30642773	+	5'UTR	SNP	T	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30642773T>A	uc003agz.2	-	1					LIF_uc011aks.1_5'UTR|uc003aha.2_Silent_p.I94I	NM_002309	NP_002300	P15018	LIF_HUMAN	leukemia inhibitory factor (cholinergic						immune response|leukemia inhibitory factor signaling pathway|negative regulation of hormone secretion|positive regulation of cell proliferation|positive regulation of macrophage differentiation|positive regulation of MAPKKK cascade|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of peptidyl-serine phosphorylation of STAT protein|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of metanephric nephron tubule epithelial cell differentiation		cytokine activity|growth factor activity|leukemia inhibitory factor receptor binding				0			Epithelial(10;0.171)			TTTGCCTGATTTATATACTGG	0.458													13	23	---	---	---	---	PASS
FAM19A5	25817	broad.mit.edu	37	22	49145683	49145683	+	3'UTR	SNP	C	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49145683C>T	uc003bim.3	+	4					FAM19A5_uc003bio.3_3'UTR	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		TGAGGGGCCCCGGGAGTGGCC	0.657													21	53	---	---	---	---	PASS
FRMPD4	9758	broad.mit.edu	37	X	12734314	12734314	+	Missense_Mutation	SNP	C	T	T	rs149409320	byFrequency	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12734314C>T	uc004cuz.1	+	15	2242	c.1736C>T	c.(1735-1737)ACG>ATG	p.T579M	FRMPD4_uc011mij.1_Missense_Mutation_p.T571M	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	579					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						AAGCAGAAGACGGTGGAGATC	0.478													5	96	---	---	---	---	PASS
MSN	4478	broad.mit.edu	37	X	64959657	64959657	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64959657G>T	uc004dwf.2	+	13	1834	c.1636G>T	c.(1636-1638)GCT>TCT	p.A546S		NM_002444	NP_002435	P26038	MOES_HUMAN	moesin	546					leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10						CATGATCCATGCTGAGAACAT	0.527			T	ALK	ALCL								3	51	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9859	9859	+	RNA	SNP	G	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9859G>A	uc011mfi.1	+	1		c.1197G>A			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		CCTCACTATCTGCTTCATCCG	0.453													36	25	---	---	---	---	PASS
LOC643837	643837	broad.mit.edu	37	1	769139	769140	+	Intron	DEL	AT	-	-	rs59306077		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:769139_769140delAT	uc009vjn.1	+						LOC643837_uc001abp.1_Intron|LOC643837_uc001abq.1_Intron|LOC643837_uc009vjo.1_Intron|LOC643837_uc001abr.1_Intron					Homo sapiens cDNA: FLJ23220 fis, clone ADSU01957.												0						CTGGTGAGACATGTGTGAGGAG	0.510													4	2	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3238615	3238616	+	Intron	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3238615_3238616delGT	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		tttggaggtcgtgtgtgtgtgG	0.233			T	EVI1	MDS|AML								4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7525288	7525288	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7525288delC	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGGCCCTGTGCCCTCAGGAGC	0.532													4	2	---	---	---	---	
C1orf144	26099	broad.mit.edu	37	1	16722101	16722101	+	3'UTR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16722101delT	uc001aym.3	+	4					C1orf144_uc010ocb.1_3'UTR|C1orf144_uc001ayi.3_3'UTR|C1orf144_uc001ayk.3_3'UTR	NM_001114600	NP_001108072	Q7Z422	CA144_HUMAN	putative MAPK activating protein PM20,PM21												0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.12e-05)|Kidney(64;0.00018)|KIRC - Kidney renal clear cell carcinoma(64;0.00267)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		ATATCCTTTCTTTTTTTTTTC	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18932645	18932645	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18932645delA								KLHDC7A (120106 upstream) : PAX7 (24855 downstream)																							TTTGAAAGGTAAAAAAAAAAT	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18951093	18951093	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18951093delA								KLHDC7A (138554 upstream) : PAX7 (6407 downstream)																							AGATAAATACAAAAAAAAAAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19819064	19819064	+	IGR	DEL	A	-	-	rs34911159		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19819064delA								CAPZB (7072 upstream) : C1orf151 (104403 downstream)																							ctcctatcataaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33466744	33466746	+	Intron	DEL	AGA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33466744_33466746delAGA	uc001bwn.2	+											Homo sapiens cDNA clone IMAGE:4825059, with apparent retained intron.																		GTGGGTGTGGAGAAGAAGAAGAC	0.429													4	2	---	---	---	---	
PHC2	1912	broad.mit.edu	37	1	33836943	33836948	+	Intron	DEL	GCACTC	-	-	rs72427573		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33836943_33836948delGCACTC	uc001bxg.1	-						PHC2_uc001bxh.1_Intron|PHC2_uc009vuh.1_Intron|PHC2_uc001bxi.1_Intron	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a						multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				tTGCCACTGAGCACTCCAACTATTAG	0.257													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37897507	37897507	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37897507delC								GRIK3 (397663 upstream) : ZC3H12A (42612 downstream)																							GGCCTGCCCACCACACACACA	0.408													4	2	---	---	---	---	
ATPAF1	64756	broad.mit.edu	37	1	47123488	47123488	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47123488delA	uc001cqh.2	-						ATPAF1_uc001cqg.2_Intron|ATPAF1_uc009vyk.2_Intron|ATPAF1_uc010omg.1_Intron|ATPAF1_uc001cqi.2_Intron	NM_022745	NP_073582	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly						protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)					GGTGGAGTGGAAAAAAAAGGA	0.328													5	3	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49990297	49990297	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49990297delT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.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)		TATGCAGAACTTTTTTTTTTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55220031	55220032	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55220031_55220032delTG								C1orf175 (12051 upstream) : PARS2 (2541 downstream)																							gtgtgcgtgctgtgtgtgtgtg	0.426													6	3	---	---	---	---	
ST6GALNAC3	256435	broad.mit.edu	37	1	77058257	77058258	+	Intron	DEL	AG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77058257_77058258delAG	uc001dhh.2	+						ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						aggagaaaacagagaagagaag	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78239446	78239446	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78239446delA								USP33 (13909 upstream) : FAM73A (5863 downstream)																							ACACCCCCTCaaaaaaaaaat	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79788927	79788927	+	IGR	DEL	T	-	-	rs116114629	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79788927delT								ELTD1 (316432 upstream) : None (None downstream)																							atttttattctttttttttcc	0.000													4	2	---	---	---	---	
SH3GLB1	51100	broad.mit.edu	37	1	87167271	87167271	+	5'Flank	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87167271delA	uc001dlw.2	+						SH3GLB1_uc001dlx.2_5'Flank|SH3GLB1_uc001dly.2_5'Flank|SH3GLB1_uc001dlz.2_5'Flank	NM_016009	NP_057093	Q9Y371	SHLB1_HUMAN	SH3-containing protein SH3GLB1						anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		AATGAGCCATAAAAAAAAAAG	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88971661	88971662	+	IGR	INS	-	C	C	rs139288655	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88971661_88971662insC								None (None upstream) : PKN2 (178260 downstream)																							AGAGCTACTTTAAACACAATTC	0.302													2	5	---	---	---	---	
AKNAD1	254268	broad.mit.edu	37	1	109409533	109409533	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109409533delC	uc010ovb.1	-							NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268											ovary(3)	3						gccacttcctccagaaccttc	0.005													4	2	---	---	---	---	
CHIA	27159	broad.mit.edu	37	1	111860990	111860990	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111860990delA	uc001eas.2	+						CHIA_uc001ear.2_Intron|CHIA_uc001eaq.2_Intron|CHIA_uc009wgc.2_Intron|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_Intron|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c						apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		AAATGTTTTGAAAAAAATACT	0.368													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115821560	115821561	+	IGR	DEL	CG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115821560_115821561delCG								TSPAN2 (189445 upstream) : NGF (6976 downstream)																							GGTTGTCATCCGCACCACATTT	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142583243	142583243	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142583243delC								None (None upstream) : None (None downstream)																							aaatctaaaacaagagagcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142589815	142589816	+	IGR	INS	-	A	A	rs149233471		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142589815_142589816insA								None (None upstream) : None (None downstream)																							atcaggcctagaagcacgagaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143536419	143536420	+	IGR	INS	-	TT	TT	rs75386219	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143536419_143536420insTT								None (None upstream) : LOC100286793 (111219 downstream)																							GTGAATATAACTGTCATTTACA	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143984235	143984235	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143984235delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		ATTTCTTGGATTTTTTTTTTC	0.403													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144527406	144527406	+	Intron	DEL	G	-	-	rs2940061	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144527406delG	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ttgattttttgttttgtagag	0.000													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145352463	145352464	+	Intron	INS	-	GC	GC	rs1973810		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145352463_145352464insGC	uc001end.3	+						NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oyq.1_Intron|NBPF10_uc010oyr.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyp.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		tgtgtgtgtgtgtgtgtgtgtg	0.243													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146807322	146807322	+	Intron	DEL	T	-	-	rs111398167		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146807322delT	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																		CTAATAAGAGTTTTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148848389	148848391	+	IGR	DEL	TCA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148848389_148848391delTCA								NBPF16 (90078 upstream) : LOC645166 (79895 downstream)																							ttgtttcatttcatcatttcatt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149030090	149030090	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149030090delG								LOC645166 (77036 upstream) : LOC388692 (249386 downstream)																							tatttcttttgctccattatt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149225904	149225905	+	IGR	INS	-	C	C	rs142337689		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149225904_149225905insC								LOC645166 (272850 upstream) : LOC388692 (53571 downstream)																							agagttctccttggagaccata	0.054													3	3	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149979055	149979056	+	Intron	DEL	CC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149979055_149979056delCC	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CTCATATATTCCCCCCACTCAC	0.436													4	2	---	---	---	---	
ANXA9	8416	broad.mit.edu	37	1	150954702	150954702	+	5'UTR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150954702delG	uc001ewa.2	+	1						NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9						cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GACAACTGCTGGGTTCGTCCC	0.602													4	2	---	---	---	---	
PYHIN1	149628	broad.mit.edu	37	1	158910177	158910178	+	Intron	DEL	AG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158910177_158910178delAG	uc001ftb.2	+						PYHIN1_uc001ftc.2_Intron|PYHIN1_uc001ftd.2_Intron|PYHIN1_uc001fte.2_Intron	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1						cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)					GGAATAGGGAAGAGAGCTCAGG	0.376													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172647544	172647544	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172647544delT								FASLG (11534 upstream) : TNFSF18 (362816 downstream)																							acactatacctttttttttga	0.000													3	3	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180742382	180742382	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180742382delA	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						ATACTTGGGGAAAAAAAATGT	0.413													4	2	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186101783	186101783	+	Intron	DEL	T	-	-	rs66823627		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186101783delT	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						gtggcagagctttttttttta	0.119													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192372018	192372018	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192372018delT								RGS21 (35606 upstream) : RGS1 (172839 downstream)																							TAGGCTCTCATTTTTACAATG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194122688	194122691	+	IGR	DEL	TTCT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194122688_194122691delTTCT								CDC73 (898748 upstream) : None (None downstream)																							AATACTAAAATTCTTTCTGAGATG	0.221													24	14	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202173556	202173559	+	Intron	DEL	CAAA	-	-	rs139246238		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202173556_202173559delCAAA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						cacacacctccaaacacacacaca	0.000													4	2	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202577010	202577010	+	Intron	DEL	T	-	-	rs111761064		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202577010delT	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976	Q8N9I0	SYT2_HUMAN	synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	CTCTGTGACCTTTTTttttta	0.269													4	2	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208402215	208402215	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208402215delC	uc001hgz.2	-							NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTCTCCATCTCCAATCTCCTT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209716917	209716917	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209716917delT								LOC642587 (111027 upstream) : CAMK1G (40128 downstream)																							tgatatgtcctttttactttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211701716	211701717	+	IGR	INS	-	T	T	rs148624720	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211701716_211701717insT								RD3 (35457 upstream) : SLC30A1 (46664 downstream)																							ttctttttttcttttttttttg	0.267													2	4	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216222186	216222186	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216222186delA	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GACTCATGAGAAAAAATTGTG	0.388										HNSCC(13;0.011)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218742317	218742317	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218742317delT								TGFB2 (124358 upstream) : LYPLAL1 (604875 downstream)																							tttaaaaaaattttttttCAA	0.249													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230258362	230258363	+	Intron	DEL	TG	-	-	rs5781568		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230258362_230258363delTG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGGGTGGCTCtgtgtgtgtgtg	0.292													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238696152	238696152	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238696152delG								LOC339535 (46835 upstream) : CHRM3 (853713 downstream)																							gtgtgtgtgtgtggtgagtgt	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238696154	238696154	+	IGR	DEL	G	-	-	rs67032763		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238696154delG								LOC339535 (46837 upstream) : CHRM3 (853711 downstream)																							gtgtgtgtgtggtgagtgtgC	0.274													4	2	---	---	---	---	
TTC15	51112	broad.mit.edu	37	2	3481815	3481815	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3481815delC	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)		GCTTGTATTGCCCCCGTTTTC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7543592	7543592	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7543592delT								RNF144A (359285 upstream) : LOC339788 (518966 downstream)																							ATATCAGAGGTTTTAAGACTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15267988	15267989	+	IGR	INS	-	A	A	rs139830029	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15267988_15267989insA								FAM84A (477055 upstream) : NBAS (39043 downstream)																							CACCTGAGCCCCTGACCCCCAA	0.525													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18699636	18699636	+	IGR	DEL	A	-	-	rs113652737		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18699636delA								KCNS3 (585412 upstream) : NT5C1B (36355 downstream)																							TTCTGTCAGGAAAAAAAAAAA	0.353													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20291478	20291478	+	IGR	DEL	T	-	-	rs72342726		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20291478delT								LAPTM4A (39689 upstream) : SDC1 (109080 downstream)																							TACACACTGATTTTTTTTTTT	0.478													4	2	---	---	---	---	
RBKS	64080	broad.mit.edu	37	2	28061177	28061178	+	Intron	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28061177_28061178delTG	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411	Q9H477	RBSK_HUMAN	ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					tggtaactgttgaagctaaatg	0.035													4	2	---	---	---	---	
SLC8A1	6546	broad.mit.edu	37	2	40360842	40360844	+	Intron	DEL	CCC	-	-	rs71945830		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40360842_40360844delCCC	uc002rrx.2	-						uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	GGGCAAAAATCCCCCCCCCCCAC	0.483													3	3	---	---	---	---	
SIX3	6496	broad.mit.edu	37	2	45169041	45169042	+	5'UTR	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45169041_45169042delGT	uc002run.1	+	1						NM_005413	NP_005404	O95343	SIX3_HUMAN	SIX homeobox 3						visual perception	nucleus					0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ggctgcgcgggtgtgtgtgtgt	0.218													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72719733	72719733	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72719733delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						ttgttggctgaaaaaaaaata	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84610375	84610375	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84610375delT								FUNDC2P2 (91051 upstream) : SUCLG1 (40279 downstream)																							aatcaaccacttTttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90417041	90417045	+	Intron	DEL	ATGAA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417041_90417045delATGAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		aaatgatgacatgaaatgaaatgaa	0.146													7	4	---	---	---	---	
TGFBRAP1	9392	broad.mit.edu	37	2	105924979	105924980	+	Intron	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105924979_105924980delAC	uc002tcq.2	-						TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						acagacacatacacacacacac	0.406													4	3	---	---	---	---	
CKAP2L	150468	broad.mit.edu	37	2	113518554	113518554	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113518554delT	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|CKAP2L_uc010yxq.1_Intron	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome					0						GCTCCTACTCTTTTTTTTTTT	0.303													3	5	---	---	---	---	
CCDC93	54520	broad.mit.edu	37	2	118697848	118697848	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118697848delG	uc002tlj.2	-						CCDC93_uc010fld.1_Intron	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93											large_intestine(1)|ovary(1)	2						GAGAAGAGGTGGTCACTTCTT	0.473													4	2	---	---	---	---	
EPB41L5	57669	broad.mit.edu	37	2	120830505	120830506	+	Intron	INS	-	A	A	rs71977546		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120830505_120830506insA	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron	NM_020909	NP_065960	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1						ttaaagtatttaaaaaaaaaaa	0.188													5	3	---	---	---	---	
POTEE	445582	broad.mit.edu	37	2	131995605	131995608	+	Intron	DEL	TTAT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131995605_131995608delTTAT	uc002tsn.2	+						PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Intron|POTEE_uc002tsl.2_Intron	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,								ATP binding				0						attttaattattatttatttaaca	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046453	133046454	+	IGR	INS	-	GACA	GACA	rs146739177		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046453_133046454insGACA								NCRNA00164 (30911 upstream) : GPR39 (127693 downstream)																							CAAACCAATGTGACAGACAGAG	0.386													2	4	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	144945486	144945486	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144945486delA	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)		ttttccttataaaaaaggaca	0.000													4	2	---	---	---	---	
PRPF40A	55660	broad.mit.edu	37	2	153526016	153526019	+	5'UTR	DEL	AAAC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153526016_153526019delAAAC	uc002tyg.3	-	1					PRPF40A_uc002tyh.3_Intron|PRPF40A_uc010zcd.1_Intron	NM_017892	NP_060362	O75400	PR40A_HUMAN	formin binding protein 3						mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0						ccccgtctctaaacaaacaaacaa	0.098													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	160777419	160777420	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160777419_160777420delTG								LY75 (16157 upstream) : PLA2R1 (20592 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.198													4	2	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163670468	163670468	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163670468delA	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	TGTCTACAGTAAAAAAAAGTG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	165827404	165827405	+	IGR	DEL	CA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165827404_165827405delCA								SLC38A11 (15369 upstream) : SCN3A (116627 downstream)																							CGCATATGTGCACACACACACA	0.426													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171057458	171057458	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171057458delG	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002uga.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						gcgtgactttgggggagtcag	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	171616005	171616005	+	Intron	DEL	C	-	-	rs6733809	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171616005delC	uc002ugf.1	-											Homo sapiens cDNA FLJ13453 fis, clone PLACE1003205.																		caaaacaaaacaaaagactgc	0.000													4	2	---	---	---	---	
CIR1	9541	broad.mit.edu	37	2	175215130	175215131	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175215130_175215131insT	uc002uim.2	-						CIR1_uc002uin.2_Intron|CIR1_uc002uio.2_Intron|CIR1_uc002uip.2_Intron	NM_004882	NP_004873	Q86X95	CIR1_HUMAN	CBF1 interacting corepressor						mRNA processing|negative regulation of transcription, DNA-dependent|RNA splicing	nuclear speck	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			large_intestine(1)	1						AGTAAAAGCTATAAATAAGTCT	0.272													6	3	---	---	---	---	
NFE2L2	4780	broad.mit.edu	37	2	178132703	178132704	+	5'Flank	DEL	GA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178132703_178132704delGA	uc002ulh.3	-						NFE2L2_uc002uli.3_Intron	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			actctaaatggagagagagaga	0.000			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	180971717	180971717	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180971717delT								CWC22 (99877 upstream) : UBE2E3 (873395 downstream)																							tacaactaaatttttttttgc	0.040													3	3	---	---	---	---	
ALS2	57679	broad.mit.edu	37	2	202609345	202609345	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202609345delT	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.2_Intron|ALS2_uc010ftl.2_5'Flank	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						cagaCTAGGGTTTTTTTTGGG	0.209													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206122054	206122054	+	Intron	DEL	T	-	-	rs10708473		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206122054delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		AGCCAATCAGTTTTTTTTTTA	0.333													4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	213315278	213315279	+	Intron	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213315278_213315279insA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		cctagaggctcaaaaaatacag	0.000										TSP Lung(8;0.080)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217716164	217716165	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217716164_217716165delTG								IGFBP5 (155892 upstream) : TNP1 (8019 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.317													4	2	---	---	---	---	
WDFY1	57590	broad.mit.edu	37	2	224770386	224770386	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224770386delG	uc002vnq.2	-							NM_020830	NP_065881	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1							cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		tgtaTGAAGAGTAGTGTGTGT	0.144													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	227520912	227520912	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227520912delC								KIAA1486 (925441 upstream) : IRS1 (75122 downstream)																							AAAAAACTTTCAAGACATACT	0.358													4	2	---	---	---	---	
PID1	55022	broad.mit.edu	37	2	230040618	230040618	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230040618delT	uc002vpr.3	-						PID1_uc002vps.3_Intron|PID1_uc002vpt.3_Intron|PID1_uc002vpu.3_Intron	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1							cytoplasm				breast(3)|skin(1)	4		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		CTAGAAAAGGTTTTTTTACAG	0.423													4	2	---	---	---	---	
DGKD	8527	broad.mit.edu	37	2	234359852	234359852	+	Intron	DEL	T	-	-	rs3214825		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234359852delT	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TGAAAAGTGCTTTTTTTTTTT	0.418													3	3	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	237021061	237021061	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237021061delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						ttccatctcgaaaaaaaaaaa	0.179													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238188027	238188029	+	IGR	DEL	AAG	-	-	rs139802520		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238188027_238188029delAAG								COPS8 (180540 upstream) : COL6A3 (44626 downstream)																							AAAGCCCACCAAGGGTAGCTTAG	0.527													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240168242	240168243	+	Intron	INS	-	CCGGCCAC	CCGGCCAC	rs145684778	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240168242_240168243insCCGGCCAC	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GGTGATGGCCACGGCGCCGGCA	0.668													7	4	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240306471	240306471	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240306471delA	uc002vyk.3	-						HDAC4_uc010fza.2_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TCTGATCCCTAAAATGCCGAT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240741989	240741989	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240741989delC								HDAC4 (418643 upstream) : NDUFA10 (158169 downstream)																							CATGCAGCCGCCCACACACGT	0.547													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10119557	10119557	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10119557delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		cttattaattaaaaaaaaaaa	0.000			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				6	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10188287	10188287	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188287delG	uc003bvc.2	+	2	643	c.430delG	c.(430-432)GGAfs	p.G144fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	144	Involved in binding to CCT complex.				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.G144fs*14(5)|p.G144fs*15(4)|p.G144*(3)|p.Q145fs*30(1)|p.G144A(1)|p.N141fs*30(1)|p.G144fs*19(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)		CAATGTTGACGGACAGCCTAT	0.423		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				256	228	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14597622	14597622	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14597622delT								GRIP2 (14034 upstream) : C3orf19 (95631 downstream)																							TAGATAATCCTCCCCGGAGCC	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18256075	18256075	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18256075delA	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																		caggcaaaagaaaaaaaaaag	0.000													2	4	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	21575894	21575895	+	Intron	DEL	CA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21575894_21575895delCA	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						TAATCGCCACCACACACACACA	0.386													5	3	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25446380	25446381	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25446380_25446381insT	uc011awl.1	+							NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TTACTCGCTACTTTTTTTTCAG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	31417135	31417136	+	IGR	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31417135_31417136insA								GADL1 (480982 upstream) : STT3B (157355 downstream)																							AATATCCATGCTGTAGAaaatc	0.262													4	2	---	---	---	---	
FBXL2	25827	broad.mit.edu	37	3	33405866	33405868	+	Intron	DEL	TTT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33405866_33405868delTTT	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289	Q9UKC9	FBXL2_HUMAN	F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1						CAGgttttggtttttgcatttgt	0.379													2	4	---	---	---	---	
VILL	50853	broad.mit.edu	37	3	38043433	38043434	+	Intron	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38043433_38043434delTC	uc003chj.2	+						VILL_uc003chl.2_Intron|VILL_uc010hgu.2_3'UTR	NM_015873	NP_056957	O15195	VILL_HUMAN	villin-like protein						actin filament capping|cytoskeleton organization	actin cytoskeleton	actin binding|structural constituent of cytoskeleton				0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CTAAGCACCTTCTCTTTGGGCC	0.609													18	13	---	---	---	---	
DLEC1	9940	broad.mit.edu	37	3	38159800	38159800	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38159800delC	uc003cho.1	+						DLEC1_uc003chp.1_Intron|DLEC1_uc010hgv.1_Intron|DLEC1_uc003chr.1_Intron|DLEC1_uc003chs.1_Intron	NM_007335	NP_031361	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform						negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|skin(2)|breast(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCCTCTTAGTCCCCACTGCTG	0.552											OREG0015476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
BSN	8927	broad.mit.edu	37	3	49705763	49705763	+	3'UTR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49705763delG	uc003cxe.3	+	12						NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein						synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CTGTACACCTGGGGATTTCTT	0.478													4	2	---	---	---	---	
DCP1A	55802	broad.mit.edu	37	3	53321906	53321906	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53321906delT	uc003dgs.3	-						DCP1A_uc003dgt.3_Intron	NM_018403	NP_060873	Q9NPI6	DCP1A_HUMAN	DCP1 decapping enzyme homolog A						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		TCTGTTTTTGTTTTTTTtttg	0.204													4	4	---	---	---	---	
CADPS	8618	broad.mit.edu	37	3	62437283	62437283	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62437283delA	uc003dll.2	-						CADPS_uc003dlj.1_Intron|CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GATCTCTCACAAAAAAAAAGG	0.428													4	3	---	---	---	---	
LOC285401	285401	broad.mit.edu	37	3	63041720	63041720	+	Intron	DEL	T	-	-	rs72404864		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63041720delT	uc003dlo.2	+						LOC285401_uc010hnr.1_Intron					Homo sapiens, clone IMAGE:5557531, mRNA.												0						TTTTTGATTGTTTTTTTTTTC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70452346	70452346	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70452346delT								MITF (434860 upstream) : FOXP1 (552391 downstream)																							CACCCATTCCTACCCTGCCCT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73394373	73394374	+	IGR	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73394373_73394374delGT								PPP4R2 (279362 upstream) : PDZRN3 (37278 downstream)																							GGATTTGGGGGTGTGTGTGTCT	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	74014688	74014688	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74014688delA								PDZRN3 (340616 upstream) : CNTN3 (297034 downstream)																							GCCTCCTTTTAAAAGAAGTAT	0.289													4	2	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89154012	89154012	+	5'Flank	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89154012delC	uc003dqy.2	+						EPHA3_uc003dqx.1_5'Flank|EPHA3_uc010hon.1_5'Flank	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ACTGTTAATTCCTAACTTGAG	0.358										TSP Lung(6;0.00050)			4	2	---	---	---	---	
ZPLD1	131368	broad.mit.edu	37	3	102165543	102165543	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102165543delG	uc003dvs.1	+						ZPLD1_uc003dvt.1_Intron|ZPLD1_uc011bhg.1_Intron	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						CTAACCAGTTGGAACTATTTT	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105838548	105838548	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105838548delA								CBLB (250282 upstream) : LOC100302640 (717112 downstream)																							GCTGCTTTGTAAATGCCAGAT	0.393													4	2	---	---	---	---	
KIAA1524	57650	broad.mit.edu	37	3	108278419	108278419	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108278419delA	uc003dxb.3	-							NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						acaaggtagcaaaaaaaaatc	0.025													4	2	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	121126719	121126719	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121126719delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		AAAAGAATGATTTttcaatca	0.144													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136152643	136152643	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136152643delT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						TACTTTGCTATTTTTTTTTTT	0.269													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	143906498	143906498	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143906498delT								C3orf58 (195289 upstream) : None (None downstream)																							CTAAGATATCTTTTTTTTGTA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150246376	150246376	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150246376delA								TSC22D2 (68763 upstream) : SERP1 (13405 downstream)																							TTGTCACCACAAAAAAAAAAT	0.343													0	6	---	---	---	---	
PIK3CA	5290	broad.mit.edu	37	3	178939919	178939919	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178939919delA	uc003fjk.2	+							NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TAGTAAAAGGAAAAAAAAAAG	0.348		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			4	3	---	---	---	---	
GNB4	59345	broad.mit.edu	37	3	179118847	179118847	+	3'UTR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179118847delT	uc003fjv.3	-	10					GNB4_uc003fju.3_3'UTR	NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			CCACCCCCACTTTTTTTTTGG	0.358													6	3	---	---	---	---	
TACC3	10460	broad.mit.edu	37	4	1728353	1728353	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1728353delC	uc003gdo.2	+						TACC3_uc010ibz.2_Intron|TACC3_uc003gdp.2_Intron	NM_006342	NP_006333	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing							centrosome				ovary(1)|central_nervous_system(1)	2		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GTGGTGCACACCCTTCAGTGA	0.473											OREG0016037	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FAM193A	8603	broad.mit.edu	37	4	2728279	2728280	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2728279_2728280insT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603											ovary(3)	3						CCTGTGGCTTCTTTTTTTTTGG	0.431													3	3	---	---	---	---	
OTOP1	133060	broad.mit.edu	37	4	4227465	4227465	+	Intron	DEL	C	-	-	rs80279674		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4227465delC	uc003ghp.1	-							NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1						biomineral tissue development	extracellular space|integral to membrane				ovary(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACACCCACTTCGTGCCAGGCC	0.552													4	2	---	---	---	---	
JAKMIP1	152789	broad.mit.edu	37	4	6069371	6069372	+	Intron	DEL	CA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6069371_6069372delCA	uc003giu.3	-						JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_Intron|JAKMIP1_uc003giv.3_Intron|JAKMIP1_uc010ide.2_Intron	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						AGCTCTTCTGCACACACACACA	0.574													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13120094	13120095	+	IGR	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13120094_13120095insT								None (None upstream) : HSP90AB2P (214942 downstream)																							atcgggtttcatttttggcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31610975	31610975	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31610975delT								PCDH7 (462554 upstream) : None (None downstream)																							ggcagaaacattttttataca	0.000													4	2	---	---	---	---	
RELL1	768211	broad.mit.edu	37	4	37597549	37597549	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37597549delA	uc003gsz.2	-							NM_001085399	NP_001078868	Q8IUW5	RELL1_HUMAN	receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0						GAAGAGAAGGAAAAAAAGGGT	0.448													4	2	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42587705	42587705	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42587705delC	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	aggcttaaggccaggaatatt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43871070	43871070	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43871070delC								GRXCR1 (838397 upstream) : KCTD8 (304852 downstream)																							tacaaacctaccacagcccat	0.000													4	2	---	---	---	---	
ATP10D	57205	broad.mit.edu	37	4	47548354	47548355	+	Intron	INS	-	AAAG	AAAG	rs144202110	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47548354_47548355insAAAG	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron|ATP10D_uc003gxj.3_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						gtgtctgaaacagagatgcttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49220204	49220204	+	IGR	DEL	G	-	-	rs73152053	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49220204delG								CWH43 (156111 upstream) : None (None downstream)																							agaacctcttggaaaacctct	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49506430	49506430	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49506430delT								CWH43 (442337 upstream) : None (None downstream)																							TTCTTCTCTATTTTTTTGTAC	0.279													2	4	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54555024	54555025	+	Intron	INS	-	AG	AG	rs149876843	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54555024_54555025insAG	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	CTGTGCTCTACAGAGCTAATCT	0.312			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			3	3	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	55095489	55095490	+	5'UTR	DEL	AG	-	-	rs113739379		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55095489_55095490delAG	uc003han.3	+	1					PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_5'UTR|PDGFRA_uc010igq.1_5'UTR|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GGAGAGAAACAGAGGAGGAGAC	0.450			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58783488	58783488	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58783488delT								IGFBP7 (806949 upstream) : None (None downstream)																							AAATAGGTACTTTTTTTTTCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61197336	61197336	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61197336delT								None (None upstream) : LPHN3 (869638 downstream)																							ACTTGGTATCTTTTTTTGAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63072672	63072673	+	IGR	INS	-	TCT	TCT	rs137985283	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63072672_63072673insTCT								LPHN3 (134505 upstream) : None (None downstream)																							CTGCCGCCGCCtcttcttcttc	0.337													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63633267	63633268	+	IGR	INS	-	A	A	rs149002669	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63633267_63633268insA								LPHN3 (695100 upstream) : None (None downstream)																							acaactggaccaataccctgct	0.050													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84133956	84133956	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84133956delA								PLAC8 (98045 upstream) : COQ2 (48733 downstream)																							TTGGGAGGGGAAAAAAAGTGC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90449863	90449863	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90449863delA								GPRIN3 (220702 upstream) : SNCA (195388 downstream)																							GTTTATATGTAAAATGTCTGA	0.453													4	2	---	---	---	---	
MANBA	4126	broad.mit.edu	37	4	103573123	103573126	+	Intron	DEL	TTAA	-	-	rs147202824		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103573123_103573126delTTAA	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TTTAttatttttaattgacacaat	0.147													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118727529	118727529	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118727529delG								TRAM1L1 (720793 upstream) : NDST3 (227244 downstream)																							ACTCACCAGTGGGGAAGAGTT	0.393													4	2	---	---	---	---	
ANKRD50	57182	broad.mit.edu	37	4	125610388	125610391	+	Intron	DEL	GAAT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125610388_125610391delGAAT	uc003ifg.3	-						ANKRD50_uc011cgo.1_Intron|ANKRD50_uc010inw.2_Intron	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50											central_nervous_system(1)	1						aatatttatggaatgaatgaatGA	0.142													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139637496	139637496	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139637496delA								SLC7A11 (473993 upstream) : CCRN4L (299447 downstream)																							tttctgaaccaaaaaaaaagt	0.149													4	2	---	---	---	---	
ELF2	1998	broad.mit.edu	37	4	140022447	140022447	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140022447delA	uc003ihp.1	-							NM_201999	NP_973728	Q15723	ELF2_HUMAN	E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)					TAGTTCACATAAAAAAAACAC	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	159222316	159222317	+	IGR	DEL	CA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159222316_159222317delCA								TMEM144 (45878 upstream) : RXFP1 (220730 downstream)																							ACAGCCCCATCACATCCCTCAT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181033243	181033244	+	IGR	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181033243_181033244delTC								None (None upstream) : None (None downstream)																							ATCTTTGACTTCTCTCTCTCTC	0.351													5	3	---	---	---	---	
FAM92A3	403315	broad.mit.edu	37	4	183958293	183958293	+	5'Flank	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183958293delA	uc003ivi.3	+							NR_003612				Homo sapiens family with sequence similarity 92, member A3, mRNA (cDNA clone IMAGE:4822144).												0						gtcaattatgaaaactcagag	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190565934	190565934	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565934delG								None (None upstream) : FRG1 (296040 downstream)																							ACAGGTGAAAGGCGGAGCTAG	0.453													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190818144	190818144	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190818144delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		actaacaaaagggaaatgatt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190825682	190825683	+	Intron	INS	-	T	T	rs138468383		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190825682_190825683insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		AACTACTGTGATATTTTTTAGA	0.347													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3660146	3660147	+	IGR	INS	-	T	T	rs113715465	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3660146_3660147insT								IRX1 (58630 upstream) : None (None downstream)																							ATGACCTGCCCGTTATGACCTC	0.351													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11223466	11223466	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11223466delG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						AGCAGCCCaaggcaagtcacc	0.239													4	2	---	---	---	---	
MARCH11	441061	broad.mit.edu	37	5	16180839	16180839	+	5'Flank	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16180839delA	uc003jfo.2	-						uc003jfp.2_Intron	NM_001102562	NP_001096032	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0						TTCTTTCTGGAAAAAAAAAAA	0.453													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17716612	17716613	+	IGR	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17716612_17716613delAC								BASP1 (439677 upstream) : None (None downstream)																							CGTCCAGCTTACAAAGATAACC	0.500													4	2	---	---	---	---	
SUB1	10923	broad.mit.edu	37	5	32592819	32592819	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32592819delA	uc003jhs.2	+						SUB1_uc003jht.2_Intron	NM_006713	NP_006704	P53999	TCP4_HUMAN	activated RNA polymerase II transcription						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0						GATGTGATTGAAAAAAAAAAT	0.398													3	4	---	---	---	---	
C5orf42	65250	broad.mit.edu	37	5	37247469	37247469	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37247469delA	uc011cpa.1	-							NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ACATAATATGAAAAAAATAGT	0.289													4	2	---	---	---	---	
HCN1	348980	broad.mit.edu	37	5	45303479	45303479	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45303479delA	uc003jok.2	-							NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						GGTTCCAGATAAAGAGGTTGA	0.338													4	2	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53331989	53331989	+	Intron	DEL	A	-	-	rs35663217		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53331989delA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				cgtaaaaaagaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	57100803	57100803	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57100803delT								ACTBL2 (322167 upstream) : PLK2 (649009 downstream)																							AACTCTGAAGTTTTTTTTTTA	0.303													4	2	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	58018240	58018240	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58018240delA	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		AATCAATGCCAAAAAAAAAAA	0.338													3	3	---	---	---	---	
C5orf44	80006	broad.mit.edu	37	5	64951737	64951737	+	Intron	DEL	T	-	-	rs142113777		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64951737delT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2											ovary(1)	1						CTTCTTTAGATTTTTTTTTTA	0.303													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71228089	71228089	+	IGR	DEL	A	-	-	rs113516059		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71228089delA								CARTPT (211217 upstream) : MAP1B (175029 downstream)																							CTTCCTGTACAAAAAAAAAAA	0.378													3	3	---	---	---	---	
POLK	51426	broad.mit.edu	37	5	74889506	74889506	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74889506delA	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Intron|POLK_uc010izr.2_Intron|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Intron	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		ctgattctacaaaaaaataaa	0.000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	76877855	76877855	+	IGR	DEL	A	-	-	rs139015230		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76877855delA								WDR41 (89523 upstream) : OTP (46683 downstream)																							ttaattagagaaaaaatcaat	0.000													4	2	---	---	---	---	
CETN3	1070	broad.mit.edu	37	5	89705199	89705199	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89705199delA	uc003kjo.2	-							NM_004365	NP_004356	O15182	CETN3_HUMAN	centrin 3						cell division|centrosome cycle|mitosis	centriole	calcium ion binding				0		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		CCTCGCTCGCAACTAAGCCCA	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92246457	92246457	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92246457delG								None (None upstream) : FLJ42709 (498608 downstream)																							CAACACTTTTGGGGGAAAAGC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	107728672	107728672	+	IGR	DEL	T	-	-	rs34167980		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107728672delT								FBXL17 (10873 upstream) : FER (354851 downstream)																							atagaatgccttttttttttt	0.030													7	5	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108090226	108090226	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108090226delC	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		GAAGTGAATGCCCCTTTAGTT	0.274													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109202858	109202858	+	3'UTR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109202858delG	uc003kou.1	+	22						NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AGTACAGTaagaaaaaaaaaa	0.303													6	3	---	---	---	---	
PRR16	51334	broad.mit.edu	37	5	119811726	119811726	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119811726delC	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		TTTCCCGCTGCCACCTCTCTA	0.368													4	2	---	---	---	---	
ALDH7A1	501	broad.mit.edu	37	5	125919996	125919997	+	Intron	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125919996_125919997insG	uc003ktx.2	-						ALDH7A1_uc003kty.2_Intron|ALDH7A1_uc011cxa.1_Intron|ALDH7A1_uc003ktz.2_Intron	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1						cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	GGAAATAAAAAGGAAGCTGAGA	0.327													4	2	---	---	---	---	
DDX46	9879	broad.mit.edu	37	5	134160968	134160968	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134160968delT	uc003kzw.2	+							NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GACTTCGGTCTTGATTCTTCT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134980721	134980721	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134980721delA								CXCL14 (65752 upstream) : LOC340074 (3653 downstream)																							TCCCCATTCTAAAACAGCCAA	0.498													4	2	---	---	---	---	
SIL1	64374	broad.mit.edu	37	5	138414066	138414067	+	Intron	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138414066_138414067insA	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron	NM_022464	NP_071909	Q9H173	SIL1_HUMAN	SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CAAAGGAATTTAAAAAAAAAAG	0.297									Marinesco-Sj_gren_syndrome				4	3	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142200024	142200024	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142200024delA	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)			AAAAACAAACAAAAAAAACCC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147518063	147518063	+	IGR	DEL	G	-	-	rs12652896	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147518063delG								SPINK5 (1138 upstream) : SPINK14 (31233 downstream)																							AAGAAAAAAAGAAGAAGGGCC	0.299													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149032543	149032543	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149032543delT								ARHGEF37 (18016 upstream) : PPARGC1B (77321 downstream)																							catcatgcacttttTTTTGGC	0.219													3	3	---	---	---	---	
C5orf62	85027	broad.mit.edu	37	5	150170527	150170527	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150170527delA	uc003lsw.2	+							NM_032947	NP_116565	Q9BZL3	NID67_HUMAN	putative small membrane protein NID67							integral to membrane					0						AGACAAAAACAAAAAAAAAGC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152576336	152576337	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152576336_152576337delTG								NMUR2 (791496 upstream) : GRIA1 (292838 downstream)																							gggttgcacatgtgtgtgtggc	0.000													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	156182463	156182463	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156182463delA	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGAGAATGGCAAAAAAAACCA	0.423													4	2	---	---	---	---	
ATP10B	23120	broad.mit.edu	37	5	160065598	160065598	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160065598delC	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron|ATP10B_uc003lyo.2_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTGGGAACTCCAGGCCACCC	0.517													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166978617	166978618	+	Intron	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166978617_166978618delAC	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)		atacatacatacacacacacat	0.183													4	2	---	---	---	---	
KCNIP1	30820	broad.mit.edu	37	5	169956250	169956250	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169956250delG	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009	Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ctctaaccttggggttccaag	0.000													4	2	---	---	---	---	
RANBP17	64901	broad.mit.edu	37	5	170688079	170688080	+	Intron	INS	-	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170688079_170688080insC	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc010jjs.2_Intron	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CATTAGCTTCACCCCCCACCCC	0.337			T	TRD@	ALL								5	3	---	---	---	---	
RIPK1	8737	broad.mit.edu	37	6	3110842	3110842	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3110842delT	uc010jni.2	+						RIPK1_uc003muv.3_Intron|RIPK1_uc003muw.3_Intron|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Intron	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine						activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				gtgttatttcttttttttttt	0.085													4	2	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7189246	7189246	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7189246delT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				ATTTTACCCCTTCAGAAAGAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9005388	9005388	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9005388delA								HULC (351311 upstream) : None (None downstream)																							ATTCCTCATCAACCCCTGTGT	0.413													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21809540	21809540	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21809540delT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						TCTCTCCAGCTTTTTTCGTGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23835489	23835489	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23835489delA								None (None upstream) : NRSN1 (290925 downstream)																							ACTCCCAGTGAAAAAAAAAAA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28760134	28760134	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28760134delA								SCAND3 (205022 upstream) : TRIM27 (110646 downstream)																							gacactgtcgaaaaaaaaaac	0.000													4	2	---	---	---	---	
KIF6	221458	broad.mit.edu	37	6	39325730	39325730	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39325730delT	uc003oot.2	-						KIF6_uc003oos.2_Intron|KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464	Q6ZMV9	KIF6_HUMAN	kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3						catgtattcctttttaaagat	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43766547	43766548	+	IGR	INS	-	TC	TC			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43766547_43766548insTC								VEGFA (12326 upstream) : LOC100132354 (92217 downstream)																							gtgtgtgcgtgtgtgtgtgtgt	0.495													4	2	---	---	---	---	
LOC100132354	100132354	broad.mit.edu	37	6	43858933	43858934	+	RNA	INS	-	TC	TC	rs143500986	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43858933_43858934insTC	uc011dvm.1	+	1		c.169_170insTC				NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0						CCTTTTCTGCTTCTCTGCTCCT	0.446													4	8	---	---	---	---	
CAPN11	11131	broad.mit.edu	37	6	44149296	44149299	+	Intron	DEL	ACAG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44149296_44149299delACAG	uc003owt.1	+						CAPN11_uc011dvn.1_Intron	NM_007058	NP_008989	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			acactcacatacagacacaaccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44520422	44520422	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44520422delG								CDC5L (105643 upstream) : SUPT3H (256632 downstream)																							ttcctcaactgggataatcat	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44710039	44710039	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44710039delT								CDC5L (295260 upstream) : SUPT3H (67015 downstream)																							gttGGGCCACTTTTTAAGGCA	0.264													4	2	---	---	---	---	
TNFRSF21	27242	broad.mit.edu	37	6	47200300	47200300	+	3'UTR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47200300delA	uc003oyv.2	-	6						NM_014452	NP_055267	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily,						cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)			AGAGTTATTTAAAAAAAAAAG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47330853	47330854	+	IGR	DEL	CA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47330853_47330854delCA								TNFRSF21 (53173 upstream) : CD2AP (114671 downstream)																							tccccactaccacacacacaca	0.000													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51518008	51518008	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51518008delC	uc003pah.1	-							NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CTTTGTATGACAAGAATGACT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	53361898	53361898	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53361898delA								ELOVL5 (147956 upstream) : GCLC (242 downstream)																							AGTAAAAAAGAAAAAAAAAAT	0.473													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57390726	57390728	+	Intron	DEL	TTG	-	-	rs34695317		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390726_57390728delTTG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		GTTTTGAGCATTGTTGTGGCACT	0.448													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85869233	85869234	+	IGR	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85869233_85869234insT								TBX18 (395334 upstream) : NT5E (290068 downstream)																							TCTGCTGGTGCTTTTTTTTTCT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104235658	104235658	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104235658delT								None (None upstream) : HACE1 (940310 downstream)																							TGTTTTGTGATTTTTTTTTGC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	111973646	111973647	+	IGR	INS	-	A	A	rs141377044	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111973646_111973647insA								TRAF3IP2 (46172 upstream) : FYN (8840 downstream)																							TAGTATCTAATAATCTTCAGCC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	121971416	121971416	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121971416delA								GJA1 (200544 upstream) : HSF2 (749280 downstream)																							AAATAGTAATAAGGATTTGGG	0.408													4	2	---	---	---	---	
PKIB	5570	broad.mit.edu	37	6	122967117	122967117	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122967117delT	uc003pyz.2	+						PKIB_uc003pza.2_Intron|PKIB_uc003pzb.2_Intron	NM_181794	NP_861459	Q9C010	IPKB_HUMAN	cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)		CAGCCTTGCCTTTTTTTTTTG	0.368													4	2	---	---	---	---	
C6orf174	387104	broad.mit.edu	37	6	127799105	127799105	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127799105delA	uc003qbd.2	-						C6orf174_uc003qbc.2_5'Flank	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor							integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)		AGCATAAAAGAAAAAAAAATA	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134872753	134872753	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134872753delA	uc003qev.1	-											AJ606331																		agaagagaccaaaaaaagtac	0.030													4	2	---	---	---	---	
TNFAIP3	7128	broad.mit.edu	37	6	138204004	138204004	+	3'UTR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138204004delA	uc003qhr.2	+	9					TNFAIP3_uc003qhs.2_3'UTR	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3						anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GCTCTAGAAGAAAAAAAAAAA	0.403			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								4	2	---	---	---	---	
UTRN	7402	broad.mit.edu	37	6	144635353	144635353	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144635353delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAAAATCTAGAAAAAAAAAAT	0.438													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162935501	162935501	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162935501delT	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		ACTGGCTAGCTTTTAATGTAA	0.438													4	2	---	---	---	---	
LOC285796	285796	broad.mit.edu	37	6	163747518	163747518	+	5'Flank	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163747518delC	uc011egh.1	-											Homo sapiens cDNA FLJ37410 fis, clone BRAMY2028593.												0						TTCACAAACACCCCACAACTC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2357580	2357580	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2357580delT								SNX8 (3481 upstream) : EIF3B (36894 downstream)																							TGATAGCTGCTTCCTTCCTCC	0.493													4	2	---	---	---	---	
CARD11	84433	broad.mit.edu	37	7	3067979	3067980	+	Intron	INS	-	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3067979_3067980insC	uc003smv.2	-							NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		ATGGAATGGCTCGCCGGGAACG	0.545			Mis		DLBCL								4	2	---	---	---	---	
VWDE	221806	broad.mit.edu	37	7	12419977	12419977	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12419977delA	uc003ssj.2	-						VWDE_uc011jxl.1_Intron|VWDE_uc011jxm.1_Intron	NM_001135924	NP_001129396	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains							extracellular region					0						AATTGCAAGGAAAAAAAAACA	0.269													5	4	---	---	---	---	
SNX13	23161	broad.mit.edu	37	7	17836751	17836751	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17836751delA	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc010kub.2_Intron			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TTAGGGGTTCAAAAAAAACGA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25900996	25900996	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25900996delT								NPVF (632891 upstream) : MIR148A (88543 downstream)																							gctccttaactttttttttta	0.119													4	2	---	---	---	---	
SKAP2	8935	broad.mit.edu	37	7	26728379	26728379	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26728379delA	uc003syc.2	-						SKAP2_uc011jzi.1_Intron|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1						TGTTTACTTTAAAAGGGCTTT	0.338													4	2	---	---	---	---	
ADCYAP1R1	117	broad.mit.edu	37	7	31145410	31145410	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31145410delT	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron|uc003tcg.2_5'Flank	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						TGTTCAGAGCTTGCAGTGAAA	0.408													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32744756	32744756	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32744756delG	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						aaaggaaccagggctccttgg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	40155084	40155085	+	IGR	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40155084_40155085insG								CDK13 (19939 upstream) : C7orf11 (17258 downstream)																							ttgctttgactgaaacctggct	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51543574	51543574	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51543574delT								COBL (159059 upstream) : None (None downstream)																							TTTTTTCTCATTTACACTCTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54970216	54970216	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54970216delT								SEC61G (143277 upstream) : EGFR (116509 downstream)																							CACAAGCAACTGGACCTGAGA	0.428													3	3	---	---	---	---	
LANCL2	55915	broad.mit.edu	37	7	55451776	55451776	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55451776delA	uc003tqp.2	+							NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2						negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			tgcaaaacagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68418805	68418805	+	IGR	DEL	C	-	-	rs144474228		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68418805delC								None (None upstream) : AUTS2 (645100 downstream)																							CCGACCCTTGCTTTTTTTTTT	0.318													4	3	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75308419	75308420	+	Intron	INS	-	C	C	rs142092603	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75308419_75308420insC	uc003uds.1	-							NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						tccagctatgaccccccttctt	0.000			T	PDGFRB	CMML								1	6	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626477	76626478	+	Intron	INS	-	GT	GT	rs141618293	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626477_76626478insGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						AAGTGTgtggggtgtgaggtgg	0.015													6	3	---	---	---	---	
MYH16	84176	broad.mit.edu	37	7	98874400	98874401	+	Intron	DEL	GA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98874400_98874401delGA	uc003upw.2	+							NR_002147				SubName: Full=cDNA: FLJ22037 fis, clone HEP08868; Flags: Fragment;												0						TGAAAGgagtgagagagagaga	0.277													4	2	---	---	---	---	
HBP1	26959	broad.mit.edu	37	7	106826610	106826611	+	Intron	DEL	TC	-	-	rs28630031		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106826610_106826611delTC	uc003vdy.2	+						HBP1_uc011klv.1_Intron|HBP1_uc003vdz.2_Intron|HBP1_uc003vea.2_Intron|HBP1_uc003veb.1_Intron	NM_012257	NP_036389	O60381	HBP1_HUMAN	HMG-box transcription factor 1						cell cycle arrest|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	DNA binding			skin(1)	1						tctttttttttctttttttttt	0.188													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114865870	114865870	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114865870delA								MDFIC (206607 upstream) : TFEC (709332 downstream)																							ATAGTGCATTAAAAAAAGGGA	0.408													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133682149	133682149	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133682149delC	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				GTTAACCAAGCTAGTAAAAAC	0.333													11	7	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139565397	139565397	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139565397delA	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron|TBXAS1_uc011kqx.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					gaggaggaggaggaggaagag	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144082225	144082226	+	IGR	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144082225_144082226insG								ARHGEF5 (4501 upstream) : NOBOX (13815 downstream)																							CAGGGAGAAAAGGGAAATGCAG	0.480													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152109065	152109068	+	Intron	DEL	TAAA	-	-	rs66577827		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152109065_152109068delTAAA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GCaaaaaatttaaataaataaata	0.328			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154815077	154815077	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154815077delC								LOC202781 (17665 upstream) : HTR5A (47469 downstream)																							agatgccaatcccagacagac	0.000													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157940288	157940289	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157940288_157940289insT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GTCTTTCCCCCTCAATGACACC	0.589													6	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157957395	157957395	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157957395delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TGAATGGGGCTTTTTAAGCTG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	949481	949481	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:949481delT	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																		gtggtttttcttttttttttt	0.000													1	5	---	---	---	---	
INTS10	55174	broad.mit.edu	37	8	19689337	19689337	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19689337delA	uc003wzj.2	+							NM_018142	NP_060612	Q9NVR2	INT10_HUMAN	integrator complex subunit 10						snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		tagcatctaCAAAATATTGCT	0.154													7	4	---	---	---	---	
LPL	4023	broad.mit.edu	37	8	19809598	19809599	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19809598_19809599insT	uc003wzk.3	+							NM_000237	NP_000228	P06858	LIPL_HUMAN	lipoprotein lipase precursor						fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)	CAGCGTGGATATTATTTTATAT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19950088	19950088	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19950088delT								LPL (125319 upstream) : SLC18A1 (52279 downstream)																							TGACCAAATGTTTTTTTCCCT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23446984	23446984	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23446984delG								SLC25A37 (16923 upstream) : NKX3-1 (89223 downstream)																							GGTGACAGCTGGTCCTATCGA	0.378													4	2	---	---	---	---	
RBPMS	11030	broad.mit.edu	37	8	30264858	30264858	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30264858delT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858	Q93062	RBPMS_HUMAN	RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)		tttctttttgttttttttttG	0.294													3	3	---	---	---	---	
SLC20A2	6575	broad.mit.edu	37	8	42292374	42292375	+	Intron	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42292374_42292375delGT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ATGAAACATGgtgtgtgtgtga	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	56929380	56929380	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56929380delA								LYN (5444 upstream) : RPS20 (51359 downstream)																							AGATAAGGAGAAAAAAAAAAG	0.398													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64204257	64204258	+	IGR	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64204257_64204258delGT								YTHDF3 (78912 upstream) : None (None downstream)																							ggagatgttcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
CYP7B1	9420	broad.mit.edu	37	8	65612738	65612738	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65612738delA	uc003xvj.2	-							NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				AAGAGCAATCAAACATGAGCA	0.438													4	2	---	---	---	---	
STAU2	27067	broad.mit.edu	37	8	74423553	74423555	+	Intron	DEL	TCT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74423553_74423555delTCT	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			CTCCTCCTCATCTTCTTCTTCCC	0.384													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75705499	75705499	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75705499delA								MIR2052 (87517 upstream) : PI15 (31273 downstream)																							CGCTGAACTCAAAAAAATGAC	0.289													4	2	---	---	---	---	
RALYL	138046	broad.mit.edu	37	8	85095902	85095902	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85095902delT	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_5'UTR|RALYL_uc010lzy.2_5'UTR|RALYL_uc003yct.3_5'Flank	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						gttttttttctttttttCCAC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88800585	88800586	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88800585_88800586delTG								CNBD1 (405630 upstream) : DCAF4L2 (82387 downstream)																							AATCTCTTGTTGTTGATATTGT	0.347													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90533917	90533917	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90533917delC								None (None upstream) : RIPK2 (236058 downstream)																							AGTCAGTTATCCAAGAACTAG	0.363													4	2	---	---	---	---	
DECR1	1666	broad.mit.edu	37	8	91027340	91027341	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91027340_91027341insT	uc003yek.1	+						DECR1_uc011lgc.1_Intron|DECR1_uc011lgd.1_Intron	NM_001359	NP_001350	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1 precursor						fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)			aagatctaatcatacttattgg	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	99189937	99189937	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99189937delA								POP1 (17869 upstream) : NIPAL2 (14450 downstream)																							tacaatagacaaaaaaataag	0.000													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99492777	99492777	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99492777delA	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GTATGATTTCAAAAAAAACAA	0.303													4	2	---	---	---	---	
FBXO43	286151	broad.mit.edu	37	8	101146729	101146729	+	Intron	DEL	A	-	-	rs74444650		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101146729delA	uc003yjd.2	-						FBXO43_uc003yje.2_Intron	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b						meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			TCCTTTTCAGAAAAAAAAACA	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106270875	106270875	+	IGR	DEL	C	-	-	rs7010607	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106270875delC								LRP12 (669655 upstream) : ZFPM2 (60272 downstream)																							ctttgcccatcttttagtgag	0.000													4	2	---	---	---	---	
KLHL38	340359	broad.mit.edu	37	8	124667106	124667106	+	5'Flank	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124667106delT	uc003yqs.1	-							NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38												0						CTTCCATGCATTTTTTTTTCT	0.488													4	2	---	---	---	---	
SQLE	6713	broad.mit.edu	37	8	126021742	126021742	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126021742delA	uc011liq.1	+							NM_003129	NP_003120	Q14534	ERG1_HUMAN	squalene epoxidase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	CCAAATTAATAAAAAAAAGTT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129418744	129418744	+	RNA	DEL	T	-	-	rs68158962		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129418744delT	uc003ysn.2	-	6		c.826delA								Homo sapiens cDNA clone IMAGE:3877235, partial cds.																		tgtgtgtccatttttttttat	0.159													4	2	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	131992439	131992439	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131992439delT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			tgttctcttcttataaggata	0.000										HNSCC(32;0.087)			4	2	---	---	---	---	
C8orf77	286103	broad.mit.edu	37	8	146230497	146230498	+	3'UTR	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146230497_146230498insG	uc003zfb.3	+	1					ZNF252_uc003zew.3_5'Flank|ZNF252_uc011llo.1_5'Flank	NR_026974				RecName: Full=Uncharacterized protein C8orf77;												0						TGAGAGTGGCTGCTTAAATTTC	0.381													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2085651	2085651	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2085651delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ATCGAGGTAGTTTTTTTTTTG	0.388													4	2	---	---	---	---	
C9orf72	203228	broad.mit.edu	37	9	27571084	27571084	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27571084delA	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)		AATGCAGCTGAAAAAAATCAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32919948	32919948	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32919948delT								TMEM215 (130751 upstream) : APTX (52661 downstream)																							ttaatttttcttttttttttc	0.000													3	4	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37706934	37706937	+	Intron	DEL	TCCA	-	-	rs111320993		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37706934_37706937delTCCA	uc004aag.1	+						FRMPD1_uc004aah.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		TGTCAGtccgtccatccatccatc	0.245													23	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66485832	66485832	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66485832delG								FAM74A4 (991446 upstream) : LOC442421 (10638 downstream)																							gtctcaaaaagtaaaaaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67301383	67301384	+	IGR	INS	-	G	G	rs144184994		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67301383_67301384insG								AQP7P1 (11891 upstream) : FAM27B (491546 downstream)																							GGAGCATGTTTGGGCATCAGTG	0.569													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68393548	68393548	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68393548delA								FAM27B (599359 upstream) : MIR1299 (608691 downstream)																							atatccctttagcatttcttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68431705	68431705	+	IGR	DEL	T	-	-	rs76484925		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68431705delT								FAM27B (637516 upstream) : MIR1299 (570534 downstream)																							TGTAAGAAAATACCTACATTT	0.323													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	77835365	77835365	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77835365delT								OSTF1 (73252 upstream) : PCSK5 (670195 downstream)																							tatatggctatttttttcatg	0.000													4	2	---	---	---	---	
GKAP1	80318	broad.mit.edu	37	9	86357182	86357182	+	Intron	DEL	T	-	-	rs3217183		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86357182delT	uc004amy.2	-						GKAP1_uc004amz.2_Intron	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0						AGATACAGGGTTAAGTTCTAT	0.413													2	7	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94663252	94663252	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94663252delT	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						GGGCAGATTGTTTTTTAAGCT	0.438													4	2	---	---	---	---	
ZNF484	83744	broad.mit.edu	37	9	95624901	95624902	+	Intron	INS	-	A	A	rs140120101	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95624901_95624902insA	uc004asu.1	-						ANKRD19_uc004asr.3_Intron|ZNF484_uc011lub.1_Intron|ZNF484_uc010mrb.1_Intron|ZNF484_uc004asv.1_Intron	NM_031486	NP_113674	Q5JVG2	ZN484_HUMAN	zinc finger protein 484 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGTATGCAGTGAAGGAAAGGTG	0.371													4	2	---	---	---	---	
OR13C3	138803	broad.mit.edu	37	9	107299374	107299374	+	5'Flank	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107299374delC	uc004bcb.1	-							NM_001001961	NP_001001961	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1						ATTTCATCAACCCCAGCAAAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111578454	111578454	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111578454delA								None (None upstream) : ACTL7B (38417 downstream)																							GCTGCTGAAGAAAGAAGTCCG	0.498													4	2	---	---	---	---	
IKBKAP	8518	broad.mit.edu	37	9	111688584	111688584	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111688584delA	uc004bdm.3	-						IKBKAP_uc011lwc.1_Intron|IKBKAP_uc010mtq.2_Intron	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene						immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						TTTGGGTAATAACTATCTAAG	0.423													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119410854	119410854	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119410854delG	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|ASTN2_uc004bjv.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GTGTTAGTTTGGGGACCTCTG	0.284													4	2	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127288844	127288844	+	Intron	DEL	A	-	-	rs111378093		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127288844delA	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						CAGTTTGAAGAAAAAAAAAAA	0.418													4	3	---	---	---	---	
MAPKAP1	79109	broad.mit.edu	37	9	128218231	128218231	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128218231delT	uc004bpv.2	-						MAPKAP1_uc011lzt.1_Intron|MAPKAP1_uc010mwz.2_Intron|MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc004bpu.2_Intron	NM_001006617	NP_001006618	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4						aattatttcattttttttgat	0.000													4	2	---	---	---	---	
GARNL3	84253	broad.mit.edu	37	9	130091892	130091893	+	Intron	INS	-	T	T	rs150307397	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130091892_130091893insT	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc004bqt.1_5'Flank	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						CCTATAAAACCTTTTAAAAGCA	0.455													4	2	---	---	---	---	
SARDH	1757	broad.mit.edu	37	9	136567900	136567901	+	Intron	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136567900_136567901insA	uc004cep.3	-						SARDH_uc004ceo.2_Intron|SARDH_uc011mdn.1_Intron|SARDH_uc011mdo.1_Intron|SARDH_uc004cen.2_Intron	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor						glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GGAGTCAGCCGAAAAAAGCGTG	0.614													4	2	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	8019488	8019488	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8019488delT	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						ACGTAAAGGATTTTTTTTTTC	0.303													3	4	---	---	---	---	
PIP4K2A	5305	broad.mit.edu	37	10	22916018	22916018	+	Intron	DEL	A	-	-	rs71749974		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22916018delA	uc001irl.3	-							NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						TATCAACTATAAAAAAAAGAT	0.333													4	2	---	---	---	---	
ARMC4	55130	broad.mit.edu	37	10	28248313	28248313	+	Intron	DEL	C	-	-	rs12767652	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28248313delC	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_Intron	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4								binding			ovary(4)|skin(2)	6						TTCTTTTTTTCTTTCCCCCAG	0.483													4	4	---	---	---	---	
SVIL	6840	broad.mit.edu	37	10	29933917	29933917	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29933917delA	uc001iuu.1	-						SVIL_uc009xld.1_Intron	NM_003174	NP_003165	O95425	SVIL_HUMAN	supervillin isoform 1						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				GGAGGACACTAAAAAAAAAAA	0.398													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36304091	36304091	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36304091delT								FZD8 (373729 upstream) : None (None downstream)																							CTCTTTGTCATTTTTTTAACC	0.498													4	2	---	---	---	---	
BICC1	80114	broad.mit.edu	37	10	60390104	60390104	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60390104delG	uc001jki.1	+							NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						AGAAGACAGAGGGGGAAAAAG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	69982699	69982699	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69982699delC								MYPN (10928 upstream) : ATOH7 (7687 downstream)																							TCGTGGAGCACCCACAGCTGA	0.368													4	2	---	---	---	---	
HK1	3098	broad.mit.edu	37	10	71144996	71144997	+	Intron	DEL	TT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71144996_71144997delTT	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1						tcttagtgtcttttgtttctgc	0.000													4	2	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76445647	76445647	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76445647delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	GGTTAAGGAATTTTTTTTTTG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79900520	79900520	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79900520delT								RPS24 (83950 upstream) : LOC283050 (802564 downstream)																							TGCCATTTGCTTTTTTTTTTT	0.383													4	3	---	---	---	---	
GLUD1	2746	broad.mit.edu	37	10	88851618	88851618	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88851618delT	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	GCAGATGAGGTTTTTTTTTTT	0.383													3	3	---	---	---	---	
LIPA	3988	broad.mit.edu	37	10	91152229	91152229	+	Intron	DEL	C	-	-	rs113116320		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91152229delC	uc001kgc.3	-						LIPA_uc001kgb.3_Intron|IFIT1_uc001kgi.2_5'Flank|IFIT1_uc009xtt.2_5'Flank	NM_001127605	NP_001121077	P38571	LICH_HUMAN	lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		TCATTCCCCACCCCCCCCCGT	0.468													6	3	---	---	---	---	
GBF1	8729	broad.mit.edu	37	10	104040731	104040732	+	Intron	INS	-	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104040731_104040732insC	uc001kux.1	+						GBF1_uc001kuw.2_Intron|GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TTCTTTTTTTTCCCAGGGCAGA	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107662435	107662435	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107662435delT								SORCS3 (637442 upstream) : SORCS1 (670987 downstream)																							GCTTTTACTCTTAGGATTATT	0.338													4	2	---	---	---	---	
STK32C	282974	broad.mit.edu	37	10	134039768	134039769	+	Intron	INS	-	AA	AA			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134039768_134039769insAA	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron|STK32C_uc001llb.2_Intron|STK32C_uc001llc.1_Intron	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		ATACCTCACAGATATTTTCATT	0.386													4	2	---	---	---	---	
ADAM8	101	broad.mit.edu	37	10	135076463	135076463	+	3'UTR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135076463delG	uc010qva.1	-	20					ADAM8_uc010quz.1_3'UTR|ADAM8_uc009ybi.2_3'UTR			P78325	ADAM8_HUMAN	SubName: Full=cDNA FLJ50704, highly similar to ADAM 8 (EC 3.4.24.-) (A disintegrinand metalloproteinase domain 8);						integrin-mediated signaling pathway|proteolysis		metalloendopeptidase activity			large_intestine(2)|central_nervous_system(1)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		ACGTGGCCAAGGCGGGGAGAA	0.612													4	5	---	---	---	---	
TUBGCP2	10844	broad.mit.edu	37	10	135101533	135101533	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135101533delG	uc001lmg.1	-						TUBGCP2_uc001lmf.1_Intron|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		TCGCCTCACCGGGACGGGGAG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	8195599	8195602	+	IGR	DEL	ATAT	-	-	rs146054127		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8195599_8195602delATAT								RIC3 (5009 upstream) : LMO1 (50255 downstream)																							GTTCAGGTGCATATATTAATAAAA	0.466													4	2	---	---	---	---	
MICAL2	9645	broad.mit.edu	37	11	12117443	12117444	+	Intron	DEL	CC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12117443_12117444delCC	uc010rch.1	+							NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		TCTGCTTCTTCCCCCACTGTGT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17584253	17584254	+	IGR	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17584253_17584254insA								USH1C (18290 upstream) : MYOD1 (156856 downstream)																							CCTCAGTGTTTAAAAAAAAATC	0.297													4	2	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	17840074	17840074	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17840074delA	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						gagactgagtaattggatcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	19363879	19363879	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19363879delC								E2F8 (100712 upstream) : NAV2 (8392 downstream)																							AAGGTGCATTCCCCCCAGAAG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44979129	44979130	+	IGR	DEL	GG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44979129_44979130delGG								TP53I11 (6289 upstream) : LOC221122 (16323 downstream)																							ACCCTGGGATGGGGGAGAGAGA	0.589													4	2	---	---	---	---	
OR8H3	390152	broad.mit.edu	37	11	55889624	55889624	+	5'Flank	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55889624delT	uc001nii.1	+							NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					TAAACAGAAAttttttttgat	0.104													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92591716	92591716	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92591716delA	uc001pdj.3	+						FAT3_uc001pdi.3_Intron	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AAGGCAATTTAAAAAAAAGAG	0.368										TCGA Ovarian(4;0.039)			4	2	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107683420	107683420	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107683420delT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		aataaaaTAGTTTTTTTTTAA	0.184													4	2	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108804766	108804766	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108804766delT	uc001pkm.2	+							NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		tttcagatggtgtgatagaga	0.000			T	NUP98	AML*								4	2	---	---	---	---	
TEX12	56158	broad.mit.edu	37	11	112038384	112038384	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112038384delG	uc001pnc.2	+						TEX12_uc001pnd.2_Intron	NM_031275	NP_112565	Q9BXU0	TEX12_HUMAN	testis expressed sequence 12												0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.2e-06)|BRCA - Breast invasive adenocarcinoma(274;1.4e-06)|all cancers(92;1.97e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		ATGGGGCAGAGGGGACAGTGC	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114188316	114188316	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114188316delT								NNMT (5078 upstream) : C11orf71 (73854 downstream)																							AAATGCTAGATTTTTTTTTTG	0.303											OREG0021349	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116881932	116881932	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116881932delT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						TCCACACTCCTTTTTTTTTCC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127713614	127713615	+	IGR	DEL	CG	-	-	rs3083889	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127713614_127713615delCG								KIRREL3 (840259 upstream) : ETS1 (615041 downstream)																							cacacacacacGGGGACATaag	0.025											OREG0021493	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130630508	130630508	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130630508delC								ADAMTS15 (286793 upstream) : SNX19 (115259 downstream)																							GAAAGAGACACCCAGGAGGAG	0.493													4	2	---	---	---	---	
SNX19	399979	broad.mit.edu	37	11	130782544	130782545	+	Intron	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130782544_130782545insG	uc001qgk.3	-						SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Intron|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GAGTTGTGGCTGGTGCTTTACA	0.416													4	2	---	---	---	---	
GLB1L2	89944	broad.mit.edu	37	11	134236992	134236992	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134236992delC	uc001qhp.2	+						GLB1L2_uc009zdg.1_RNA	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor						carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		GCGAATTTGGCCCTCACCTAT	0.328													19	9	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7169575	7169575	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7169575delA	uc001qsj.2	+						C1S_uc001qsk.2_Intron|C1S_uc001qsl.2_Intron|C1S_uc009zfr.2_Intron|C1S_uc009zfs.2_Intron	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	aacctgtctcaaaaaaaaaaa	0.219													4	2	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18644731	18644731	+	Intron	DEL	A	-	-	rs111543133		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18644731delA	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				CAGTTCAGTGAAAAAAAAAAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19870939	19870940	+	IGR	INS	-	TG	TG	rs139105636	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19870939_19870940insTG								AEBP2 (195766 upstream) : PDE3A (651257 downstream)																							gtgtgtgtgtttgtgtgtgtgt	0.361													6	3	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26537140	26537141	+	Intron	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26537140_26537141delTC	uc001rhg.2	-							NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					TACAAAATCTTCTCTCTCTCTA	0.396													4	2	---	---	---	---	
IPO8	10526	broad.mit.edu	37	12	30801830	30801831	+	Intron	INS	-	T	T	rs143565540	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									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													3	5	---	---	---	---	
AMN1	196394	broad.mit.edu	37	12	31825530	31825530	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31825530delA	uc001rkq.3	-						AMN1_uc001rko.3_Intron|AMN1_uc010skc.1_Intron|AMN1_uc001rkp.3_Intron|AMN1_uc009zjs.2_Intron	NM_001113402	NP_001106873	Q8IY45	AMN1_HUMAN	antagonist of mitotic exit network 1 homolog												0	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			TTACTTGTTTAAAAAAAAAAA	0.219													4	4	---	---	---	---	
C12orf40	283461	broad.mit.edu	37	12	40088228	40088230	+	Intron	DEL	GTA	-	-	rs139998136		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40088228_40088230delGTA	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461											ovary(6)	6						gtgattctgtgtactggggagag	0.000													0	6	---	---	---	---	
ANO6	196527	broad.mit.edu	37	12	45781746	45781746	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45781746delT	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						tgattttaagtttcctgaggc	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46504127	46504127	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46504127delG								SFRS2IP (118224 upstream) : SLC38A1 (72716 downstream)																							cctcttggctggaggccaact	0.000													4	2	---	---	---	---	
RND1	27289	broad.mit.edu	37	12	49258209	49258210	+	Intron	INS	-	GT	GT			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49258209_49258210insGT	uc001rsn.2	-							NM_014470	NP_055285	Q92730	RND1_HUMAN	GTP-binding protein RHO6 precursor						actin filament organization|axon guidance|negative regulation of cell adhesion|neuron remodeling|small GTPase mediated signal transduction	adherens junction|cytoskeleton|cytosol	GTP binding|GTPase activity|receptor binding			ovary(1)	1						tgcgcgcgcgcgcgtgtgtgtg	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56035872	56035873	+	IGR	INS	-	A	A	rs147286625	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56035872_56035873insA								OR10P1 (4256 upstream) : METTL7B (39457 downstream)																							ACTGAAAAGATAGAGAGATACG	0.376													5	3	---	---	---	---	
TMEM194A	23306	broad.mit.edu	37	12	57472777	57472777	+	5'Flank	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57472777delC	uc001smy.2	-						TMEM194A_uc001smx.2_5'Flank|TMEM194A_uc010sra.1_5'Flank	NM_001130963	NP_001124435	O14524	T194A_HUMAN	transmembrane protein 194A isoform a							integral to membrane					0						ACAGGAAGATCCCACCCCGCT	0.488													4	2	---	---	---	---	
NXPH4	11247	broad.mit.edu	37	12	57612767	57612768	+	Intron	DEL	TG	-	-	rs138474144		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57612767_57612768delTG	uc010srf.1	+						NXPH4_uc009zpj.2_Intron	NM_007224	NP_009155	O95158	NXPH4_HUMAN	neurexophilin 4 precursor						neuropeptide signaling pathway	extracellular region					0						tctgtgtgcttgtgattgtgag	0.158													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105190044	105190059	+	IGR	DEL	GTGTGTGTGTGTGTGT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105190044_105190059delGTGTGTGTGTGTGTGT								CHST11 (38161 upstream) : SLC41A2 (7217 downstream)																							gtAGGTGAACgtgtgtgtgtgtgtgtgtgtgtgtgt	0.023													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108513322	108513323	+	IGR	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108513322_108513323delTC								ASCL4 (342902 upstream) : WSCD2 (10188 downstream)																							accatgtccttctctctctctc	0.000													4	3	---	---	---	---	
RPH3A	22895	broad.mit.edu	37	12	113238786	113238786	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113238786delT	uc010syl.1	+						RPH3A_uc001ttz.2_Intron|RPH3A_uc001tty.2_Intron|RPH3A_uc009zwe.1_Intron|RPH3A_uc010sym.1_Intron	NM_001143854	NP_001137326	Q9Y2J0	RP3A_HUMAN	rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)		GGGTTTTTTGTTTTTTTTTCT	0.488													3	3	---	---	---	---	
ULK1	8408	broad.mit.edu	37	12	132398256	132398256	+	Intron	DEL	C	-	-	rs68126752		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132398256delC	uc001uje.2	+							NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		ccaaaaaaaacaaaaaaaTGC	0.318													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20813994	20813995	+	IGR	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20813994_20813995delTG								GJB6 (7460 upstream) : CRYL1 (163814 downstream)																							ACCCAGAGGATGTGTGTGTGTG	0.391													4	2	---	---	---	---	
WASF3	10810	broad.mit.edu	37	13	27189090	27189092	+	Intron	DEL	TGT	-	-	rs147733848		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27189090_27189092delTGT	uc001uqv.2	+						WASF3_uc001uqw.2_Intron	NM_006646	NP_006637	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3						actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		GTGTTCAGACTGTTGTTGTAGGT	0.488													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31603621	31603624	+	IGR	DEL	TCTT	-	-	rs112822473		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31603621_31603624delTCTT								C13orf26 (54470 upstream) : HSPH1 (107141 downstream)																							ccttcctttctctttctttctttt	0.245													3	5	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33226360	33226360	+	Intron	DEL	T	-	-	rs113948248		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33226360delT	uc010abf.2	+						PDS5B_uc001uun.2_3'UTR|PDS5B_uc001uuo.2_Intron|PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ACAGTGTGTATTTTTTTTATA	0.274													4	2	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	35622839	35622839	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35622839delT	uc001uvb.2	+							NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATATGTTTAATTTTAGTACTT	0.259													65	29	---	---	---	---	
FREM2	341640	broad.mit.edu	37	13	39451645	39451646	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39451645_39451646insT	uc001uwv.2	+							NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTTCTCGAATGTTTTTTTTCAA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44475933	44475934	+	IGR	INS	-	T	T	rs35359880		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44475933_44475934insT								C13orf31 (7866 upstream) : LOC121838 (120537 downstream)																							GGAGATGGGGCTTTTTTTTTTT	0.332													3	4	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94419232	94419232	+	Intron	DEL	T	-	-	rs80001617		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94419232delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATGCACTTAATTTTTTTTTTT	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	98439350	98439351	+	IGR	INS	-	T	T	rs138982363	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98439350_98439351insT								RAP2A (319099 upstream) : IPO5 (166578 downstream)																							GTATTGAtttattttttttttg	0.035													4	2	---	---	---	---	
IPO5	3843	broad.mit.edu	37	13	98658181	98658181	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98658181delA	uc001vnf.1	+						IPO5_uc001vne.2_Intron|IPO5_uc010tik.1_Intron|IPO5_uc010til.1_Intron|IPO5_uc001vng.1_Intron	NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3						TAGAAGAGAGAAAAAAAAAAT	0.343													6	3	---	---	---	---	
PCCA	5095	broad.mit.edu	37	13	101137297	101137298	+	Intron	DEL	CT	-	-	rs61970534		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101137297_101137298delCT	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	CCTTCCTGCCCTCTCTCTCTCT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112679928	112679928	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112679928delG								C13orf16 (683335 upstream) : SOX1 (41985 downstream)																							caaaagtgctggggcaagggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20228122	20228122	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20228122delG								OR4Q3 (11596 upstream) : OR4M1 (20360 downstream)																							TGATCATGGTGGGAAATTTGC	0.398													4	2	---	---	---	---	
HOMEZ	57594	broad.mit.edu	37	14	23755033	23755034	+	Intron	INS	-	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23755033_23755034insC	uc001wja.2	-						HOMEZ_uc001wjb.2_Intron	NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CCTAGAATTATCCCCCCACCAG	0.599													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93244098	93244099	+	IGR	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93244098_93244099delAC								LGMN (29086 upstream) : GOLGA5 (16551 downstream)																							CTATTTATCAACACACACACAC	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95856205	95856205	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95856205delG								CLMN (69960 upstream) : C14orf139 (17401 downstream)																							GCAGGAAGCTGGTGGGTGGTG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96064338	96064339	+	IGR	INS	-	GCC	GCC	rs143243674	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96064338_96064339insGCC								GLRX5 (53283 upstream) : TCL6 (52496 downstream)																							TTATTCTCTCTGCCGACAGTGG	0.584													2	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96281630	96281631	+	IGR	INS	-	G	G	rs148376721	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96281630_96281631insG								TCL1A (101097 upstream) : C14orf132 (224031 downstream)																							tgcgatgtaaaTGGCCATTTAC	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97803585	97803585	+	IGR	DEL	G	-	-	rs35277692		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97803585delG								VRK1 (455635 upstream) : C14orf64 (588362 downstream)																							CAGTTGGGTTGGGGGGTCTTT	0.493													1	5	---	---	---	---	
KIAA0284	283638	broad.mit.edu	37	14	105356248	105356254	+	Intron	DEL	TGGATGG	-	-	rs79560126	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105356248_105356254delTGGATGG	uc010axb.2	+						INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Intron|KIAA0284_uc001yps.2_Intron|KIAA0284_uc001ypt.2_Intron	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1							cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		gacaaatggatggatggatggatggat	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20127638	20127638	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20127638delG								None (None upstream) : GOLGA6L6 (609456 downstream)																							TGCACTGGGAGTCATATGAGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20564458	20564459	+	IGR	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20564458_20564459insA								None (None upstream) : GOLGA6L6 (172635 downstream)																							GGTGTATTTCCAAAAAACACTT	0.361													7	4	---	---	---	---	
OR4N4	283694	broad.mit.edu	37	15	22315641	22315642	+	Intron	INS	-	A	A	rs148598371	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22315641_22315642insA	uc001yuc.1	+						LOC727924_uc001ytz.1_Intron|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)		gttggtttgttatactgttcgc	0.000													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	25970930	25970930	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25970930delT	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		tacaggcacattttttttgta	0.000													4	2	---	---	---	---	
CHRNA7	1139	broad.mit.edu	37	15	32358278	32358278	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32358278delG	uc001zft.2	+						CHRNA7_uc010bab.1_Intron|CHRNA7_uc010bac.1_Intron|CHRNA7_uc010bad.1_Intron|CHRNA7_uc010bae.1_Intron|CHRNA7_uc010baf.2_Intron|CHRNA7_uc010bag.1_Intron|CHRNA7_uc010bah.1_Intron	NM_000746	NP_000737	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7						activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Nicotine(DB00184)|Varenicline(DB01273)	tgccaacactggggattcatg	0.000													4	2	---	---	---	---	
ATPBD4	89978	broad.mit.edu	37	15	35719448	35719448	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35719448delG	uc001zja.2	-						ATPBD4_uc001ziz.2_Intron	NM_080650	NP_542381	Q7L8W6	ATBD4_HUMAN	ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)		GAAAAACAGTGGGGTAGTAGT	0.284													4	2	---	---	---	---	
LTK	4058	broad.mit.edu	37	15	41806269	41806269	+	5'Flank	DEL	A	-	-	rs3217533		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41806269delA	uc001zoa.3	-						LTK_uc001zob.3_5'Flank|LTK_uc010ucx.1_5'Flank|LTK_uc010bcg.2_5'Flank	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1						apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		AGTGGGAGCCACACCTCGGAC	0.612										TSP Lung(18;0.14)			5	3	---	---	---	---	
MAPKBP1	23005	broad.mit.edu	37	15	42097791	42097791	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42097791delA	uc001zok.3	+						MAPKBP1_uc001zoj.3_Intron|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Intron|MAPKBP1_uc010udb.1_Intron|MAPKBP1_uc010bck.2_Intron|uc001zol.2_5'Flank	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein											central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TTAAGTGGGGAGGAGAAGAGG	0.542													4	2	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49291785	49291785	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49291785delA	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						AGCCTGGAAGAAAAAAACCAC	0.308													4	2	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	54000889	54000891	+	Intron	DEL	CAT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54000889_54000891delCAT	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		tcatcatcaccatcatcatcatc	0.310													4	2	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54530202	54530202	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54530202delT	uc002ack.2	+							NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ttttacgaggttttcccCAAA	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55193883	55193883	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55193883delA								UNC13C (273078 upstream) : RSL24D1 (279638 downstream)																							CTCATTATCCAAATCAGTTTC	0.423													4	2	---	---	---	---	
PIGB	9488	broad.mit.edu	37	15	55612211	55612211	+	Intron	DEL	T	-	-	rs77286116		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55612211delT	uc002act.2	+						uc002acs.2_5'Flank|PIGB_uc010ugg.1_Intron	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)		TAACCCACTCttttttttttg	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61669547	61669548	+	IGR	DEL	GA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61669547_61669548delGA								RORA (148045 upstream) : VPS13C (475044 downstream)																							GGCCGGGAAGGAGAGAGAGAGC	0.436													4	2	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66405054	66405057	+	Intron	DEL	GGCA	-	-	rs77862698		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66405054_66405057delGGCA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						gaaactgcagggcaggcagtgcaa	0.000													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	66866446	66866446	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66866446delT								LCTL (8129 upstream) : SMAD6 (128228 downstream)																							CAAATCCTTCTTTTTTTTGGA	0.393													4	2	---	---	---	---	
LOC145837	145837	broad.mit.edu	37	15	69790202	69790203	+	Intron	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69790202_69790203delTC	uc002asf.1	+						LOC145837_uc002asg.1_Intron|LOC145837_uc010bij.1_Intron					Homo sapiens cDNA clone IMAGE:5189446.												0						actcagactttctctctctcAC	0.327													4	2	---	---	---	---	
UACA	55075	broad.mit.edu	37	15	70963643	70963643	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70963643delT	uc002asr.2	-						UACA_uc010uke.1_Intron|UACA_uc002asq.2_Intron|UACA_uc010bin.1_Intron	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						ACTAGGTTGGTTTTTTTTTTT	0.303													9	5	---	---	---	---	
GOLGA6B	55889	broad.mit.edu	37	15	72954513	72954514	+	Intron	INS	-	TG	TG			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72954513_72954514insTG	uc010uks.1	+							NM_018652	NP_061122	A6NDN3	GOG6B_HUMAN	golgi autoantigen, golgin subfamily a, 6B												0						AGGAGGtttttttttttttttt	0.500													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74058154	74058154	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74058154delT								C15orf59 (14338 upstream) : TBC1D21 (107814 downstream)																							tttaccaaagttttttttttt	0.224													2	5	---	---	---	---	
IL16	3603	broad.mit.edu	37	15	81595688	81595688	+	Intron	DEL	T	-	-	rs113855862		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81595688delT	uc002bgh.3	+						IL16_uc010blq.1_Intron|IL16_uc002bge.3_Intron|IL16_uc010unp.1_Intron|IL16_uc002bgg.2_Intron|IL16_uc002bgi.1_Intron|IL16_uc002bgj.2_Intron|IL16_uc002bgk.2_Intron|IL16_uc002bgl.1_Intron|IL16_uc010unq.1_Intron	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2						immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						tttacatacattttttttttc	0.194													4	5	---	---	---	---	
SH3GL3	6457	broad.mit.edu	37	15	84242374	84242375	+	Intron	DEL	TG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84242374_84242375delTG	uc002bjw.2	+						SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3						GTCTAGCCTATGTGACAGAGAT	0.470													4	2	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84574649	84574649	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84574649delT	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			ggagattatcttttttttTTT	0.114													6	4	---	---	---	---	
ZSCAN2	54993	broad.mit.edu	37	15	85160662	85160662	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85160662delA	uc002bkr.2	+						ZSCAN2_uc010bmz.1_Intron|ZSCAN2_uc010bna.2_Intron|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		gtgagactccaaaaaaaaaaa	0.229													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86418745	86418746	+	IGR	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86418745_86418746insA								KLHL25 (80556 upstream) : AGBL1 (266496 downstream)																							aatcataaaataaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88845911	88845911	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88845911delA								NTRK3 (46250 upstream) : MRPL46 (156797 downstream)																							GGTGCCTGGCAAAAGCAGGAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89000708	89000709	+	IGR	INS	-	AC	AC	rs150894906	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89000708_89000709insAC								NTRK3 (201047 upstream) : MRPL46 (1999 downstream)																							TTGTACATGTTacacacacaca	0.347													4	3	---	---	---	---	
C16orf91	283951	broad.mit.edu	37	16	1479062	1479064	+	Intron	DEL	GCA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1479062_1479064delGCA	uc010uvd.1	-							NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951							integral to membrane					0						CTCACCTGGGGCATGGGCTCCCT	0.665													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9455387	9455387	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9455387delA								C16orf72 (241842 upstream) : GRIN2A (391880 downstream)																							ggggctgaggaaaaaaaagct	0.095													4	2	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12093271	12093272	+	Intron	INS	-	T	T			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12093271_12093272insT	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						CAGATAATTAATGTAGGTCATT	0.401			T	CIITA	PMBL|Hodgkin Lymphona|								77	39	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12296611	12296611	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12296611delT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						CATGCTTTCATTTTGGGCTTA	0.483													4	2	---	---	---	---	
ABCC6	368	broad.mit.edu	37	16	16272482	16272482	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16272482delG	uc002den.3	-						ABCC6_uc010bvo.2_Intron	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		gtaagctgctgggatctgggg	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33979535	33979536	+	IGR	INS	-	T	T	rs147143292		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33979535_33979536insT								MIR1826 (13943 upstream) : UBE2MP1 (424266 downstream)																							tgagaaacttcttttttaggtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49156337	49156338	+	IGR	DEL	GC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49156337_49156338delGC								N4BP1 (512217 upstream) : CBLN1 (155873 downstream)																							ACCTGTTCTTGCAGCATGTCCA	0.455													4	2	---	---	---	---	
CBFB	865	broad.mit.edu	37	16	67132960	67132960	+	3'UTR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67132960delC	uc002era.2	+	6					CBFB_uc002erb.2_3'UTR|CBFB_uc010vja.1_3'UTR	NM_001755	NP_001746	Q13951	PEBB_HUMAN	core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		TTGAAACTATCAACTGTAAAG	0.289			T	MYH11	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86498226	86498228	+	IGR	DEL	TGA	-	-	rs141606079		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86498226_86498228delTGA								LOC732275 (118941 upstream) : FOXF1 (45905 downstream)																							gtagtgatggtgatgatgatgtt	0.064													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87210230	87210232	+	Intron	DEL	ATT	-	-	rs149095477		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87210230_87210232delATT	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		attctttttcattattgagttga	0.039													4	3	---	---	---	---	
VPS53	55275	broad.mit.edu	37	17	558855	558855	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:558855delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		AGTCGTCCTGAAAGGCTTCTG	0.507													4	2	---	---	---	---	
ALOX12	239	broad.mit.edu	37	17	6900357	6900357	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6900357delG	uc002gdx.3	+							NM_000697	NP_000688	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1						GTGAGCAGGCGGCGTCGGGGA	0.682													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9825514	9825516	+	Intron	DEL	GAT	-	-	rs35713235		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9825514_9825516delGAT	uc002gmg.1	-						GAS7_uc010vvc.1_Intron|GAS7_uc002gmh.1_Intron|GAS7_uc010vvd.1_Intron|GAS7_uc002gmi.2_Intron|GAS7_uc002gmj.1_Intron|GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						tggtgatgaagatgatgatgatg	0.197			T	MLL	AML*								4	3	---	---	---	---	
TRIM16	10626	broad.mit.edu	37	17	15475193	15475193	+	3'UTR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15475193delA	uc002gor.1	-	17								O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		gacaaaagacagcatgtcgta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15597938	15597938	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15597938delT								TRIM16 (10325 upstream) : ZNF286A (4953 downstream)																							AGCAAAACTATTTTTTTTCtt	0.219													4	2	---	---	---	---	
MPRIP	23164	broad.mit.edu	37	17	17006334	17006334	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17006334delG	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0						TGAGAGTGCTGGGGGTTGGAA	0.473													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21202528	21202528	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21202528delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CCTAGCCCTAGGGGAGAGTAT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21229525	21229526	+	IGR	INS	-	T	T	rs138391409		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21229525_21229526insT								MAP2K3 (10976 upstream) : KCNJ12 (50173 downstream)																							gtttaaaatgattttttctttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21714529	21714529	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21714529delA								C17orf51 (236798 upstream) : FAM27L (110841 downstream)																							agttttttttaaaaaacctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25333174	25333175	+	IGR	INS	-	T	T	rs66926562		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25333174_25333175insT								None (None upstream) : WSB1 (287931 downstream)																							CCCTTCCCATGCCTGTACCCAC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25333175	25333176	+	IGR	INS	-	CA	CA	rs66926562		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25333175_25333176insCA								None (None upstream) : WSB1 (287930 downstream)																							CCTTCCCATGCCTGTACCCACC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33058569	33058569	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33058569delG								TMEM132E (92233 upstream) : CCT6B (196371 downstream)																							tgtcatcactggagagataag	0.030													4	2	---	---	---	---	
CDK12	51755	broad.mit.edu	37	17	37660037	37660038	+	Intron	INS	-	G	G			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37660037_37660038insG	uc010cvv.2	+						CDK12_uc010wef.1_Intron|CDK12_uc002hrw.3_Intron	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich						mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						TGAGATGGCCTGGAGAAAATGG	0.510										TCGA Ovarian(9;0.13)			2	4	---	---	---	---	
FAM117A	81558	broad.mit.edu	37	17	47793182	47793183	+	Intron	DEL	CT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47793182_47793183delCT	uc002ipk.2	-						FAM117A_uc010wlz.1_Intron	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A											ovary(1)	1						CTCGCTCTCGCTCTCTCTCTCT	0.446													4	2	---	---	---	---	
UTP18	51096	broad.mit.edu	37	17	49353502	49353503	+	Intron	DEL	AG	-	-	rs146867897		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49353502_49353503delAG	uc002its.2	+							NM_016001	NP_057085	Q9Y5J1	UTP18_HUMAN	UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			CAGAAGTGACAGAGTTCATTTA	0.406													11	9	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50212364	50212364	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50212364delA	uc002itw.3	-						CA10_uc002itv.3_5'UTR|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			ctgcatctccaacccagactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61067566	61067566	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61067566delG								MIR633 (45893 upstream) : TANC2 (19332 downstream)																							TGAGAGGCCTGGAGTGAAATT	0.368													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78660783	78660787	+	Intron	DEL	TTCAG	-	-	rs66898204		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78660783_78660787delTTCAG	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						CTCTTGTTCTTTCAGTTCAGTAACC	0.444													4	5	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78826855	78826855	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78826855delA	uc002jyt.1	+						RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						CACCCTGGTCAAACCCACCCC	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	78556	78556	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:78556delG								None (None upstream) : USP14 (79927 downstream)																							tcaacctttaggggcataaga	0.000													5	3	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13370053	13370053	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13370053delA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		ATCCTCAGCCAACGCACTAAT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19663481	19663481	+	IGR	DEL	T	-	-	rs34465557		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19663481delT								MIB1 (212571 upstream) : GATA6 (85935 downstream)																							tctttctttcttttttttttg	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19812675	19812675	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19812675delC								GATA6 (30448 upstream) : CTAGE1 (180889 downstream)																							atacatctatccatacatacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24998974	24998974	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24998974delG	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																		CCCAAATACTGGGGGTGGAGG	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32471875	32471876	+	IGR	DEL	GT	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32471875_32471876delGT								DTNA (67 upstream) : MAPRE2 (85016 downstream)																							AGTCAATGTGGTGACAGCAACA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	36323074	36323075	+	IGR	DEL	GA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36323074_36323075delGA								None (None upstream) : LOC647946 (463813 downstream)																							caaaggagaggagagagagaga	0.000													4	2	---	---	---	---	
WDR7	23335	broad.mit.edu	37	18	54517231	54517231	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54517231delT	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		cacatttgccttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58923891	58923891	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58923891delA								MC4R (883890 upstream) : CDH20 (77097 downstream)																							TCAGAAAGTGAAAAAAAAAAA	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69040856	69040856	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69040856delA								None (None upstream) : None (None downstream)																							CAACAGAGATAATGGGATGTA	0.403													4	2	---	---	---	---	
LOC284276	284276	broad.mit.edu	37	18	74258456	74258456	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74258456delG	uc002lmg.2	+							NR_015417				Homo sapiens cDNA FLJ36617 fis, clone TRACH2016481.												0						TGAGGAGGCAGGAAGAGTTGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76384300	76384301	+	IGR	DEL	AG	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76384300_76384301delAG								None (None upstream) : SALL3 (355974 downstream)																							CACAAAAAGTAGAGAGAGAGAG	0.401													4	2	---	---	---	---	
PTPRS	5802	broad.mit.edu	37	19	5239175	5239176	+	Intron	INS	-	GA	GA	rs79455606		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5239175_5239176insGA	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		ggggggagggggagagagagag	0.124													4	2	---	---	---	---	
WIZ	58525	broad.mit.edu	37	19	15541563	15541564	+	Intron	INS	-	T	T	rs147128691	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15541563_15541564insT	uc002nbc.2	-						WIZ_uc002nba.3_Intron|WIZ_uc002nbb.3_Intron	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs							nucleus	zinc ion binding				0						CTGGGTCTGAGTATGAGCTCTG	0.535													3	5	---	---	---	---	
CYP4F3	4051	broad.mit.edu	37	19	15757710	15757711	+	Intron	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15757710_15757711insA	uc002nbj.2	+						CYP4F3_uc010xok.1_Intron|CYP4F3_uc010xol.1_Intron|CYP4F3_uc010xom.1_Intron|CYP4F3_uc002nbk.2_Intron	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,						leukotriene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3						TCCCCTCCCCCATCCTGCCTTC	0.599													20	10	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17101063	17101063	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17101063delA	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						actctgactcaaaaaaaaaag	0.080													2	4	---	---	---	---	
ZNF493	284443	broad.mit.edu	37	19	21589149	21589149	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21589149delT	uc002npx.2	+						ZNF493_uc002npu.2_Intron|ZNF493_uc002npw.2_Intron|ZNF493_uc002npy.2_Intron	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CATTTTTTTGTTTTTTTTTTG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30631685	30631685	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30631685delT								C19orf2 (125074 upstream) : ZNF536 (231643 downstream)																							TGAGACGGAGttttctctctt	0.174													4	2	---	---	---	---	
DPY19L3	147991	broad.mit.edu	37	19	32911350	32911350	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32911350delT	uc002ntg.2	+						DPY19L3_uc002nth.1_Intron	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3							integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)					AGTAGttttgtttttttttgt	0.204													3	3	---	---	---	---	
ARHGEF1	9138	broad.mit.edu	37	19	42411029	42411029	+	Intron	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42411029delC	uc002orx.2	+						ARHGEF1_uc002ory.2_Intron|ARHGEF1_uc002orz.2_Intron|ARHGEF1_uc002osa.2_Intron|ARHGEF1_uc002osb.2_Intron|ARHGEF1_uc002osc.2_Intron|ARHGEF1_uc002osd.2_Intron|ARHGEF1_uc002ose.2_Intron	NM_004706	NP_004697	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor 1 isoform						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		ATCCCTACAGCCCCTTCTGTC	0.567													4	2	---	---	---	---	
LRRC4B	94030	broad.mit.edu	37	19	51024567	51024567	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51024567delG	uc002pss.2	-							NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor							cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)|skin(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		agagctttctggggtgattga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6480695	6480697	+	IGR	DEL	GGA	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6480695_6480697delGGA								FERMT1 (376504 upstream) : BMP2 (268048 downstream)																							ttatggaaggggaggaggaggag	0.020													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9079856	9079856	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9079856delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						GAACATGGGGAAGGTATCTGA	0.328													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9227210	9227210	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9227210delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						CATATAGCACTTTTTTTTTTT	0.353													2	4	---	---	---	---	
PLK1S1	55857	broad.mit.edu	37	20	21215001	21215001	+	Intron	DEL	C	-	-	rs2424352	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21215001delC	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|PLK1S1_uc002wsd.2_Intron	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0						AAAAAAAAAACCACACAAAAA	0.368													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24375699	24375705	+	IGR	DEL	CAGGATG	-	-	rs141965574		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24375699_24375705delCAGGATG								GGTLC1 (406283 upstream) : TMEM90B (74130 downstream)																							gagacaggaccaggatgcaggatgcag	0.203													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29618862	29618863	+	Intron	DEL	CT	-	-	rs112384226		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29618862_29618863delCT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						aggtctctacctctctctgtgt	0.000													2	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29652356	29652356	+	3'UTR	DEL	T	-	-	rs111401906		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29652356delT	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GGACCTCTCCTCAACACAGTA	0.303													6	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29653060	29653060	+	3'UTR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29653060delC	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						cataagtagtccatgggcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40278067	40278068	+	IGR	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40278067_40278068delAC								CHD6 (30934 upstream) : PTPRT (423325 downstream)																							gagaggggagacacacacacac	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	43482166	43482166	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43482166delT								RIMS4 (43254 upstream) : YWHAB (32178 downstream)																							TTATAAAGGATTTTTTTCCCG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46429882	46429883	+	IGR	DEL	TG	-	-	rs74178769		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46429882_46429883delTG								SULF2 (14522 upstream) : LOC284749 (558771 downstream)																							tatgtgtgtatgtgagtgtatg	0.000													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47354083	47354083	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47354083delA	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)			CGGAGAGGCTAAAGGGCCCTC	0.179													4	2	---	---	---	---	
BMP7	655	broad.mit.edu	37	20	55793491	55793492	+	Intron	INS	-	TGTT	TGTT	rs149581669	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55793491_55793492insTGTT	uc010gip.1	-						BMP7_uc010giq.1_Intron|BMP7_uc002xyc.2_Intron	NM_001719	NP_001710	P18075	BMP7_HUMAN	bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			GTGGTAGCTGGTGTTTGGTGGT	0.535													4	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60363217	60363217	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60363217delA	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)			CCCGCCCAGTAAAACAGCTGG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9852426	9852426	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9852426delT								None (None upstream) : None (None downstream)																							GGGATGTGCATTCTGAAAAAT	0.303													2	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11062343	11062344	+	Intron	INS	-	AG	AG	rs148978863		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11062343_11062344insAG	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAGTAAAAGACAGCAACTTTCA	0.208													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11144766	11144767	+	IGR	INS	-	TG	TG			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11144766_11144767insTG								BAGE (45829 upstream) : None (None downstream)																							AGTGGGGTGGAtgtgtctgtgt	0.366													4	2	---	---	---	---	
C21orf99	149992	broad.mit.edu	37	21	14425970	14425972	+	Intron	DEL	CTC	-	-	rs113465228		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14425970_14425972delCTC	uc002yja.3	+							NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						cacgctgttactcctccttacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18715836	18715837	+	IGR	DEL	AC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18715836_18715837delAC								C21orf34 (733742 upstream) : CXADR (169493 downstream)																							ACACAAACATACACACACACAC	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21167367	21167367	+	IGR	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21167367delT								None (None upstream) : C21orf131 (947547 downstream)																							AATGACCATCTTTTTGATATt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	22013621	22013622	+	IGR	INS	-	T	T	rs142910076	by1000genomes	TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22013621_22013622insT								None (None upstream) : C21orf131 (101292 downstream)																							TACAATCTTTCTTTTTTTCTTT	0.337													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24817551	24817551	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24817551delC								None (None upstream) : None (None downstream)																							TTTATGAATACGGACCAAAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34876177	34876177	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34876177delA								DNAJC28 (12154 upstream) : GART (62 downstream)																							AGGCAATACCAAAAAAAAAAA	0.269													3	4	---	---	---	---	
DONSON	29980	broad.mit.edu	37	21	34958102	34958102	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34958102delA	uc002ysk.2	-						DONSON_uc002ysn.1_Intron|DONSON_uc002ysi.1_Intron|DONSON_uc002ysj.2_Intron|DONSON_uc002ysl.2_Intron|DONSON_uc010gme.2_Intron|DONSON_uc002ysm.2_Intron	NM_017613	NP_060083	Q9NYP3	DONS_HUMAN	downstream neighbor of SON						multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2						AATCTGACTTAAAAAAAAAAA	0.318													5	4	---	---	---	---	
MORC3	23515	broad.mit.edu	37	21	37741235	37741235	+	Intron	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37741235delA	uc002yvi.2	+							NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2						AAGGTCATCTATTTTGTCCAT	0.209													31	14	---	---	---	---	
KRTAP10-6	386674	broad.mit.edu	37	21	46012219	46012220	+	In_Frame_Ins	INS	-	GGGGCGCAGCAGCTG	GGGGCGCAGCAGCTG			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46012219_46012220insGGGGCGCAGCAGCTG	uc002zfm.2	-	1	167_168	c.146_147insCAGCTGCTGCGCCCC	c.(145-147)CCG>CCCAGCTGCTGCGCCCCG	p.49_49P>PSCCAP	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6	49	2.|29 X 5 AA repeats of C-C-X(3).					keratin filament					0						GGCAGGGGGCCGGGGCGCAGCA	0.688													7	7	---	---	---	---	
IL17RA	23765	broad.mit.edu	37	22	17584678	17584679	+	Intron	DEL	GT	-	-	rs72290119		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17584678_17584679delGT	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		caggtggagagtggtgtggacg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27541475	27541476	+	IGR	INS	-	C	C			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27541475_27541476insC								MIAT (426526 upstream) : MN1 (602790 downstream)																							cggaaatgtttccccatgatct	0.000													4	2	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31012013	31012016	+	Intron	DEL	TGGA	-	-	rs145631512		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31012013_31012016delTGGA	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGAAATGTTtggatggatggatg	0.333													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36128972	36128972	+	IGR	DEL	A	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36128972delA								APOL5 (3445 upstream) : RBM9 (5812 downstream)																							gtgaggtcagaaaagggaaaa	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37739524	37739525	+	IGR	DEL	TC	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37739524_37739525delTC								CYTH4 (28136 upstream) : ELFN2 (24454 downstream)																							GAGGTTTCTGTCTCTCTCTCAG	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37941625	37941626	+	IGR	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37941625_37941626insA								CARD10 (26247 upstream) : CDC42EP1 (14845 downstream)																							GCCTCTGGGGGATGACTGCCCC	0.619											OREG0026539	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37990734	37990734	+	IGR	DEL	C	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37990734delC								LGALS2 (14710 upstream) : GGA1 (13769 downstream)																							agagaaaaggcccacaggctg	0.214													4	2	---	---	---	---	
TRIOBP	11078	broad.mit.edu	37	22	38115394	38115394	+	Intron	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38115394delG	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atq.1_Intron|TRIOBP_uc003ats.1_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GCAGGTGGCTGGGGAGCGGAT	0.592													4	2	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46894553	46894554	+	Intron	INS	-	A	A			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46894553_46894554insA	uc003bhw.1	-							NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CCGGTGGTATGGGATAGAAATA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47817841	47817841	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47817841delG								TBC1D22A (248119 upstream) : None (None downstream)																							GGATCAAAGAGGGCTATCGCT	0.532													4	2	---	---	---	---	
WWC3	55841	broad.mit.edu	37	X	10046746	10046746	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10046746delT	uc004csx.3	+						WWC3_uc010nds.2_Intron|WWC3_uc010ndt.2_5'Flank	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3											ovary(4)	4						AAATCAGAGATTTAGAGTCCT	0.313													9	4	---	---	---	---	
COL4A6	1288	broad.mit.edu	37	X	107464328	107464328	+	Intron	DEL	A	-	-	rs76891094		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107464328delA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						actctgtctcaaaaaaaaaaa	0.189									Alport_syndrome_with_Diffuse_Leiomyomatosis				9	4	---	---	---	---	
GPC3	2719	broad.mit.edu	37	X	132796078	132796078	+	Intron	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132796078delT	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					tacaacatgctttttttcccc	0.124			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	146036771	146036771	+	IGR	DEL	G	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146036771delG								CXorf51 (144847 upstream) : MIR513C (234451 downstream)																							AGCGGTATAAGGTGCTTCCTG	0.393													14	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155260434	155260434	+	5'Flank	DEL	T	-	-			TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155260434delT	uc011nad.1	-											Homo sapiens partial mRNA for DEAD/H box polypeptide 11 like (DDX11L1 gene).																		gggttaggggttaggggttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59003621	59003622	+	IGR	DEL	TT	-	-	rs10547049		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59003621_59003622delTT								None (None upstream) : None (None downstream)																							TTATGAAGTCTTTATTTCTCAA	0.188													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59014683	59014684	+	IGR	DEL	AT	-	-	rs10534960		TCGA-B2-5635-01A-01D-1534-10	TCGA-B2-5635-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59014683_59014684delAT								None (None upstream) : None (None downstream)																							acaaaacagaatgagagttccc	0.035													7	4	---	---	---	---	
