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
DVL1	1855	broad.mit.edu	37	1	1275504	1275504	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1275504C>G	uc001aer.3	-	8	870	c.823G>C	c.(823-825)GAC>CAC	p.D275H	DVL1_uc002quu.2_5'UTR|DVL1_uc009vka.2_5'UTR|DVL1_uc001aeu.1_5'UTR	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	275	PDZ.				canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ATGCCGCCGTCTCCACGGTCG	0.652													3	23	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7725174	7725174	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7725174C>T	uc001aoi.2	+	9	2774	c.2567C>T	c.(2566-2568)TCG>TTG	p.S856L		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	856					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)		TCGGCCGCCTCGGCCCAGGGC	0.677													7	27	---	---	---	---	PASS
PADI4	23569	broad.mit.edu	37	1	17690223	17690223	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17690223C>A	uc001baj.2	+	16	1993	c.1965C>A	c.(1963-1965)TCC>TCA	p.S655S		NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	655					chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	AGCCCTTCTCCTTCAAGTGGT	0.602													4	31	---	---	---	---	PASS
USP48	84196	broad.mit.edu	37	1	22033294	22033294	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22033294C>A	uc001bfb.2	-	16	2269	c.2031G>T	c.(2029-2031)CAG>CAT	p.Q677H	USP48_uc001bfa.2_Missense_Mutation_p.Q215H|USP48_uc010odq.1_Missense_Mutation_p.Q689H|USP48_uc009vqc.2_Missense_Mutation_p.Q611H|USP48_uc001bfc.2_Missense_Mutation_p.Q677H|USP48_uc001bfd.1_5'Flank	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	677	DUSP 2.				ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		TTGGAAAGTACTGCTGCAGTT	0.403													18	65	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35351124	35351124	+	Silent	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35351124C>G	uc001byc.2	-	5	1869	c.1869G>C	c.(1867-1869)CGG>CGC	p.R623R		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	623					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				GCGCCAGGCTCCGCAGCTCCT	0.721													4	9	---	---	---	---	PASS
ZMYM1	79830	broad.mit.edu	37	1	35579229	35579229	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35579229G>A	uc001bym.2	+	11	1946	c.1798G>A	c.(1798-1800)GAA>AAA	p.E600K	ZMYM1_uc001byn.2_Missense_Mutation_p.E600K|ZMYM1_uc010ohu.1_Missense_Mutation_p.E581K|ZMYM1_uc001byo.2_Missense_Mutation_p.E240K|ZMYM1_uc009vut.2_Missense_Mutation_p.E525K	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	600						nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TAAAGGAGAAGAAACATTTCG	0.318													6	27	---	---	---	---	PASS
CLSPN	63967	broad.mit.edu	37	1	36202137	36202137	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36202137G>A	uc001bzi.2	-	25	4060	c.3980C>T	c.(3979-3981)TCA>TTA	p.S1327L	CLSPN_uc009vux.2_Missense_Mutation_p.S1263L	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	1327					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CGTCAATCCTGAAGTGCTATC	0.443													9	64	---	---	---	---	PASS
EIF2C3	192669	broad.mit.edu	37	1	36479647	36479647	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36479647G>C	uc001bzp.2	+	11	1660	c.1404G>C	c.(1402-1404)TTG>TTC	p.L468F	EIF2C3_uc001bzq.2_Missense_Mutation_p.L234F	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	468					mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGAAATATTGAAGTAAGACA	0.378													6	91	---	---	---	---	PASS
FAM176B	55194	broad.mit.edu	37	1	36788602	36788602	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36788602T>G	uc001cai.1	-	1	248	c.37A>C	c.(37-39)AAC>CAC	p.N13H	C1orf113_uc010oic.1_Intron|FAM176B_uc001caj.1_Missense_Mutation_p.N13H	NM_018166	NP_060636	Q9NVM1	F176B_HUMAN	hypothetical protein LOC55194	13						integral to membrane				pancreas(1)	1						GCCAGGCTGTTGCTGAGCAAC	0.667													9	21	---	---	---	---	PASS
ZSWIM5	57643	broad.mit.edu	37	1	45484503	45484503	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45484503T>G	uc001cnd.2	-	14	3409	c.3181A>C	c.(3181-3183)ATC>CTC	p.I1061L		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	1061							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					ACCAGGGGGATGAGAGCTGCC	0.582											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	28	---	---	---	---	PASS
SPATA6	54558	broad.mit.edu	37	1	48771547	48771547	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48771547C>A	uc001crr.1	-	12	1363	c.1198G>T	c.(1198-1200)GAG>TAG	p.E400*	SPATA6_uc001crs.1_Nonsense_Mutation_p.E384*|SPATA6_uc010omv.1_Nonsense_Mutation_p.E386*	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor	400					cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1						AGGTCTCTCTCATCCTGAAAA	0.368													19	53	---	---	---	---	PASS
NRD1	4898	broad.mit.edu	37	1	52266248	52266248	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52266248G>C	uc001ctc.3	-	23	2947	c.2625C>G	c.(2623-2625)ATC>ATG	p.I875M	NRD1_uc009vzb.2_Missense_Mutation_p.I570M|NRD1_uc001ctd.3_Missense_Mutation_p.I807M|NRD1_uc001cte.2_Missense_Mutation_p.I743M|NRD1_uc001ctf.2_Missense_Mutation_p.I807M|NRD1_uc010ong.1_RNA	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	806					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0						TCTCGGGCTTGATGAGGATGT	0.428													5	114	---	---	---	---	PASS
ZFYVE9	9372	broad.mit.edu	37	1	52811902	52811902	+	3'UTR	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52811902G>C	uc001cto.2	+	19					ZFYVE9_uc001ctp.2_3'UTR	NM_004799	NP_004790	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8						AAACAGAGAAGACTTCATTTT	0.408													8	30	---	---	---	---	PASS
CPT2	1376	broad.mit.edu	37	1	53676146	53676146	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53676146C>G	uc001cvb.3	+	4	1315	c.800C>G	c.(799-801)TCG>TGG	p.S267W		NM_000098	NP_000089	P23786	CPT2_HUMAN	carnitine O-palmitoyltransferase precursor	267	Mitochondrial matrix (By similarity).				carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	mitochondrial inner membrane	carnitine O-palmitoyltransferase activity				0					L-Carnitine(DB00583)|Perhexiline(DB01074)	GTGAGCCCCTCGGAAATCCAG	0.512													6	83	---	---	---	---	PASS
C1orf168	199920	broad.mit.edu	37	1	57221609	57221609	+	Intron	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57221609A>G	uc001cym.3	-						C1orf168_uc009vzu.1_Intron|C1orf168_uc001cyl.2_Intron	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920											ovary(3)|skin(2)	5						GGCTGAAAGTAAAGTGGAAAA	0.403													11	51	---	---	---	---	PASS
ALG6	29929	broad.mit.edu	37	1	63876833	63876833	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63876833C>G	uc010oow.1	+	8	816	c.511C>G	c.(511-513)CTT>GTT	p.L171V	ALG6_uc001daz.2_RNA|ALG6_uc009waj.2_RNA|ALG6_uc010oox.1_5'UTR	NM_013339	NP_037471	Q9Y672	ALG6_HUMAN	dolichyl pyrophosphate Man9GlcNAc2	171					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity				0						TTCTGTGAGTCTTGGCTTTGC	0.358													4	116	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70504896	70504896	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70504896C>T	uc001dep.2	+	19	3305	c.3275C>T	c.(3274-3276)TCT>TTT	p.S1092F	LRRC7_uc009wbg.2_Missense_Mutation_p.S376F|LRRC7_uc001deq.2_Missense_Mutation_p.S333F	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1092						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TCTCAGCCATCTGTGAATGAG	0.532													17	37	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70518754	70518754	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70518754G>T	uc001dep.2	+	21	4072	c.4042G>T	c.(4042-4044)GTA>TTA	p.V1348L	LRRC7_uc009wbg.2_Missense_Mutation_p.V632L|LRRC7_uc001deq.2_Missense_Mutation_p.V542L	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1348						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ACAAGAAGATGTATCTCCTAG	0.408													11	45	---	---	---	---	PASS
ASB17	127247	broad.mit.edu	37	1	76387905	76387905	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76387905T>G	uc001dhe.1	-	2	681	c.541A>C	c.(541-543)ATT>CTT	p.I181L	ASB17_uc001dhf.1_RNA	NM_080868	NP_543144	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box-containing 17	181					intracellular signal transduction					ovary(1)	1						GTTAAGACAATGTTGATAGGG	0.363													10	36	---	---	---	---	PASS
AK5	26289	broad.mit.edu	37	1	77779471	77779471	+	Intron	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77779471C>G	uc001dhn.2	+						AK5_uc001dho.2_Intron|AK5_uc001dhm.1_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						TCTTTTACTTCTTTTTCAGTA	0.522													11	26	---	---	---	---	PASS
LPHN2	23266	broad.mit.edu	37	1	82436211	82436211	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82436211G>C	uc001dit.3	+	15	3077	c.2896G>C	c.(2896-2898)GAA>CAA	p.E966Q	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.E966Q|LPHN2_uc001div.2_Missense_Mutation_p.E966Q|LPHN2_uc009wcd.2_Missense_Mutation_p.E966Q|LPHN2_uc001diw.2_Missense_Mutation_p.E550Q|LPHN2_uc009wce.1_Missense_Mutation_p.E52Q	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	979	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTATGGAACAGAAAAAGCGTA	0.373													9	27	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86590590	86590590	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86590590C>A	uc001dlj.2	-	3	1471	c.1429G>T	c.(1429-1431)GAT>TAT	p.D477Y	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Missense_Mutation_p.D477Y	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	477					cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		GTATTTAGATCCTCATAATAA	0.338													9	27	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103461545	103461545	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103461545C>G	uc001dul.2	-	27	2613	c.2295G>C	c.(2293-2295)AAG>AAC	p.K765N	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Missense_Mutation_p.K777N|COL11A1_uc001dun.2_Missense_Mutation_p.K726N|COL11A1_uc009weh.2_Missense_Mutation_p.K649N	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	765	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTAACGTTACCTTTACTCCCC	0.398													3	33	---	---	---	---	PASS
CSDE1	7812	broad.mit.edu	37	1	115269613	115269613	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115269613T>C	uc001efk.2	-	13	1921	c.1455A>G	c.(1453-1455)ATA>ATG	p.I485M	CSDE1_uc001efi.2_Missense_Mutation_p.I531M|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_Missense_Mutation_p.I454M|CSDE1_uc001efm.2_Missense_Mutation_p.I500M|CSDE1_uc009wgv.2_Missense_Mutation_p.I485M|CSDE1_uc001efn.2_Missense_Mutation_p.I454M	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	485	CSD 6.				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTTATCTCCTATTTGAGGAG	0.403													8	18	---	---	---	---	PASS
UBAP2L	9898	broad.mit.edu	37	1	154227733	154227733	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154227733A>C	uc001fep.3	+	17	2182	c.2015A>C	c.(2014-2016)CAT>CCT	p.H672P	UBAP2L_uc009wot.2_Missense_Mutation_p.H672P|UBAP2L_uc010pek.1_Missense_Mutation_p.H664P|UBAP2L_uc010pel.1_Missense_Mutation_p.H682P|UBAP2L_uc010pen.1_Missense_Mutation_p.H586P|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	672					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			ACCAATCAGCATTCATCCTCC	0.502													10	68	---	---	---	---	PASS
UBAP2L	9898	broad.mit.edu	37	1	154227736	154227736	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154227736C>T	uc001fep.3	+	17	2185	c.2018C>T	c.(2017-2019)TCA>TTA	p.S673L	UBAP2L_uc009wot.2_Missense_Mutation_p.S673L|UBAP2L_uc010pek.1_Missense_Mutation_p.S665L|UBAP2L_uc010pel.1_Missense_Mutation_p.S683L|UBAP2L_uc010pen.1_Missense_Mutation_p.S587L|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	673					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AATCAGCATTCATCCTCCTTG	0.507													9	71	---	---	---	---	PASS
CD5L	922	broad.mit.edu	37	1	157805709	157805709	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157805709C>A	uc001frk.3	-	3	435	c.292G>T	c.(292-294)GGA>TGA	p.G98*		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like precursor	98	SRCR 1.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TCTTCTGTTCCTGTGCAACTG	0.493													52	104	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158644424	158644424	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158644424C>A	uc001fst.1	-	9	1353	c.1154G>T	c.(1153-1155)TGG>TTG	p.W385L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	385	Spectrin 5.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CTCGTTCATCCAGCCTGAGAG	0.468													6	124	---	---	---	---	PASS
FCER1G	2207	broad.mit.edu	37	1	161185114	161185114	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161185114G>A	uc001fyz.1	+	1	28	c.3G>A	c.(1-3)ATG>ATA	p.M1I	FCER1G_uc001fza.1_Missense_Mutation_p.M1I	NM_004106	NP_004097	P30273	FCERG_HUMAN	Fc fragment of IgE, high affinity I, receptor	1					platelet activation	integral to plasma membrane					0	all_cancers(52;1.35e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Benzylpenicilloyl Polylysine(DB00895)	AGCCCAAGATGATTCCAGCAG	0.572													20	58	---	---	---	---	PASS
UHMK1	127933	broad.mit.edu	37	1	162468041	162468041	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162468041A>T	uc001gcc.1	+	1	387	c.251A>T	c.(250-252)CAG>CTG	p.Q84L	UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Missense_Mutation_p.Q84L	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin	84	Protein kinase.				cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GAACAGTTGCAGGGTCACAGA	0.602													5	21	---	---	---	---	PASS
DDR2	4921	broad.mit.edu	37	1	162725039	162725039	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162725039G>T	uc001gcf.2	+	7	976	c.511G>T	c.(511-513)GAC>TAC	p.D171Y	DDR2_uc001gcg.2_Missense_Mutation_p.D171Y	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	171	Extracellular (Potential).|F5/8 type C.				cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			TCCAGTCACCGACCACTCCAT	0.478													12	48	---	---	---	---	PASS
TBX19	9095	broad.mit.edu	37	1	168260586	168260586	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168260586T>G	uc001gfl.2	+	2	443	c.392T>G	c.(391-393)TTT>TGT	p.F131C	TBX19_uc001gfj.3_Missense_Mutation_p.F62C	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19	131	T-box.				anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)					TCCCCCAACTTTGGGGCCCAC	0.602													30	107	---	---	---	---	PASS
SERPINC1	462	broad.mit.edu	37	1	173873178	173873178	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173873178G>T	uc001gjt.2	-	7	1363	c.1244C>A	c.(1243-1245)GCT>GAT	p.A415D		NM_000488	NP_000479	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C, member 1	415					blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)	GGTACTTGCAGCTGCTTCACT	0.463													7	42	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175362941	175362941	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175362941C>A	uc001gkp.1	-	4	1412	c.1331G>T	c.(1330-1332)GGG>GTG	p.G444V	TNR_uc009wwu.1_Missense_Mutation_p.G444V|TNR_uc010pmz.1_3'UTR	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	444	Fibronectin type-III 2.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GATTTCCCACCCATCGAAGGA	0.473													38	195	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	179966134	179966134	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179966134A>G	uc001gnt.2	+	6	1225	c.842A>G	c.(841-843)AAA>AGA	p.K281R	CEP350_uc001gnr.1_Missense_Mutation_p.K255R|CEP350_uc009wxl.2_Missense_Mutation_p.K280R|CEP350_uc001gnu.2_Missense_Mutation_p.K115R	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	281						centrosome|nucleus|spindle				ovary(4)	4						CATGATGTCAAACTGGAAAAA	0.423													30	97	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186017921	186017921	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186017921C>T	uc001grq.1	+	42	6756	c.6527C>T	c.(6526-6528)GCA>GTA	p.A2176V		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	2176	Ig-like C2-type 19.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						ACTTGTGAAGCAACAAATGTT	0.358													17	28	---	---	---	---	PASS
TROVE2	6738	broad.mit.edu	37	1	193038725	193038725	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193038725G>C	uc001gss.2	+	2	716	c.541G>C	c.(541-543)GAT>CAT	p.D181H	TROVE2_uc001gst.1_Intron|TROVE2_uc001gsu.1_Intron|TROVE2_uc001gsv.1_Missense_Mutation_p.D181H|TROVE2_uc001gsw.2_Missense_Mutation_p.D181H|TROVE2_uc009wyp.2_Missense_Mutation_p.D181H|TROVE2_uc009wyq.2_Missense_Mutation_p.D181H|TROVE2_uc001gsx.1_Missense_Mutation_p.D181H	NM_004600	NP_004591	P10155	RO60_HUMAN	TROVE domain family, member 2 isoform 2	181	TROVE.				transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0						GTCTCACAAAGATCTATTAAG	0.418													11	61	---	---	---	---	PASS
FAM58B	339521	broad.mit.edu	37	1	200183337	200183337	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200183337G>C	uc009wzi.1	+	1	682	c.646G>C	c.(646-648)GAG>CAG	p.E216Q		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	216					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent		protein kinase binding				0	Prostate(682;0.19)					CGCCGAGGTCGAGGCTGAGAA	0.562													16	42	---	---	---	---	PASS
IKBKE	9641	broad.mit.edu	37	1	206664179	206664179	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206664179A>G	uc001hdz.1	+	17	2089	c.1721A>G	c.(1720-1722)CAC>CGC	p.H574R	IKBKE_uc009xbv.1_Missense_Mutation_p.H574R|IKBKE_uc001hea.1_Missense_Mutation_p.H489R	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon	574					DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)					GAGCAGATTCACAAGCTGGAT	0.557											OREG0014171	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	33	---	---	---	---	PASS
CD34	947	broad.mit.edu	37	1	208072428	208072428	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208072428G>A	uc001hgw.1	-	3	664	c.406C>T	c.(406-408)CCT>TCT	p.P136S	CD34_uc001hgx.1_Missense_Mutation_p.P136S|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	136	Extracellular (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GACAGGCTAGGCTTCAAGGTT	0.463													5	177	---	---	---	---	PASS
ANGEL2	90806	broad.mit.edu	37	1	213186487	213186487	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213186487G>A	uc001hjz.2	-	2	488	c.333C>T	c.(331-333)TAC>TAT	p.Y111Y	ANGEL2_uc010pto.1_Intron|ANGEL2_uc010ptp.1_Intron|ANGEL2_uc001hka.2_Intron|ANGEL2_uc010ptq.1_Intron|ANGEL2_uc001hkb.2_Silent_p.Y89Y	NM_144567	NP_653168	Q5VTE6	ANGE2_HUMAN	LOC90806 protein	111											0				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CGTTCATGACGTAACTAGAGA	0.428													22	68	---	---	---	---	PASS
ESRRG	2104	broad.mit.edu	37	1	216850613	216850613	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216850613C>A	uc001hkw.1	-	2	443	c.277G>T	c.(277-279)GGT>TGT	p.G93C	ESRRG_uc001hky.1_Missense_Mutation_p.G70C|ESRRG_uc009xdp.1_Missense_Mutation_p.G70C|ESRRG_uc001hkz.1_Missense_Mutation_p.G70C|ESRRG_uc010puc.1_Missense_Mutation_p.G70C|ESRRG_uc001hla.1_Missense_Mutation_p.G70C|ESRRG_uc001hlb.1_Missense_Mutation_p.G70C|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Missense_Mutation_p.G70C|ESRRG_uc001hld.1_Missense_Mutation_p.G70C|ESRRG_uc001hkx.1_Missense_Mutation_p.G98C|ESRRG_uc009xdo.1_Missense_Mutation_p.G70C|ESRRG_uc001hle.1_Missense_Mutation_p.G70C	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1	93					positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	GGCCCACTACCTCCCAGGATA	0.527													16	62	---	---	---	---	PASS
RRP15	51018	broad.mit.edu	37	1	218480911	218480911	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218480911G>T	uc001hlj.2	+	4	672	c.642G>T	c.(640-642)TTG>TTT	p.L214F		NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog	214						mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		TCAGTGTTTTGAGAGGGATGG	0.368													13	36	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229568773	229568773	+	Missense_Mutation	SNP	C	A	A	rs113546590		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568773C>A	uc001htm.2	-	2	195	c.90G>T	c.(88-90)AGG>AGT	p.R30S		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	30					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)	GGAACACGGCCCTAGGGGCGT	0.692													7	29	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229568774	229568774	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568774C>A	uc001htm.2	-	2	194	c.89G>T	c.(88-90)AGG>ATG	p.R30M		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	30					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)	GAACACGGCCCTAGGGGCGTC	0.687													7	30	---	---	---	---	PASS
COG2	22796	broad.mit.edu	37	1	230827305	230827305	+	Nonsense_Mutation	SNP	G	T	T	rs140155560		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230827305G>T	uc001htw.2	+	17	2261	c.2110G>T	c.(2110-2112)GAG>TAG	p.E704*	COG2_uc001htx.2_Nonsense_Mutation_p.E703*|COG2_uc010pwc.1_Nonsense_Mutation_p.E577*	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	704					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GTACTTGGGAGAGCAGGTAAC	0.587													10	42	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237674978	237674978	+	Intron	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237674978C>T	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AATTTCCTGTCCTGTTTCAGG	0.463													7	13	---	---	---	---	PASS
PLD5	200150	broad.mit.edu	37	1	242253414	242253414	+	Intron	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253414T>A	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CAAAATTTCCTGCAAACAAAC	0.388													13	47	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525700	248525700	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525700G>T	uc001ieh.1	+	1	818	c.818G>T	c.(817-819)TGC>TTC	p.C273F		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	273	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTTGCCACCTGCTCCTCCCAC	0.542													15	98	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685656	248685656	+	Missense_Mutation	SNP	G	A	A	rs147303796		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248685656G>A	uc001ien.1	+	1	709	c.709G>A	c.(709-711)GCC>ACC	p.A237T		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCGCCAAAAGGCCTTTGGGAC	0.453													10	50	---	---	---	---	PASS
ACP1	52	broad.mit.edu	37	2	277020	277020	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:277020G>C	uc002qwg.2	+	5	430	c.334G>C	c.(334-336)GCT>CCT	p.A112P	ACP1_uc002qwh.2_RNA|ACP1_uc002qwf.2_Missense_Mutation_p.A112P	NM_007099	NP_009030	P24666	PPAC_HUMAN	acid phosphatase 1, soluble isoform b	112						cytoplasm|internal side of plasma membrane|nucleus|soluble fraction	acid phosphatase activity|identical protein binding|non-membrane spanning protein tyrosine phosphatase activity			skin(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)		AACCTGCAAAGCTAAAATTGA	0.308													17	33	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15519752	15519752	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15519752G>C	uc002rcc.1	-	30	3590	c.3564C>G	c.(3562-3564)CTC>CTG	p.L1188L	NBAS_uc010exl.1_Silent_p.L260L|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1188										ovary(2)|liver(1)|skin(1)	4						AGCTATCAGTGAGGTTGGTAG	0.428													9	71	---	---	---	---	PASS
FAM179A	165186	broad.mit.edu	37	2	29240096	29240096	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29240096G>T	uc010ezl.2	+	9	1472	c.1121G>T	c.(1120-1122)AGG>ATG	p.R374M	FAM179A_uc010ymm.1_Missense_Mutation_p.R374M|FAM179A_uc002rmr.3_Intron	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	374							binding			ovary(3)|skin(1)	4						CTGCTTCGGAGGCTGGAGGAG	0.582													11	82	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50280591	50280591	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50280591C>T	uc010fbp.2	-	4	1558	c.751G>A	c.(751-753)GCC>ACC	p.A251T	NRXN1_uc002rxb.3_Missense_Mutation_p.A988T|NRXN1_uc010fbq.2_Missense_Mutation_p.A1356T|NRXN1_uc002rxe.3_Missense_Mutation_p.A1286T	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor	251	Extracellular (Potential).|Laminin G-like.				angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCGATGTTGGCATCGTTTTCG	0.512													5	33	---	---	---	---	PASS
EFEMP1	2202	broad.mit.edu	37	2	56097912	56097912	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56097912G>A	uc002rzh.2	-	10	1593	c.1263C>T	c.(1261-1263)AAC>AAT	p.N421N	EFEMP1_uc002rzi.2_Silent_p.N421N|EFEMP1_uc002rzj.2_Silent_p.N421N|EFEMP1_uc010ypc.1_Silent_p.N283N	NM_004105	NP_004096	Q12805	FBLN3_HUMAN	EGF-containing fibulin-like extracellular matrix	421	Mediates interaction with TIMP3.				negative regulation of chondrocyte differentiation|peptidyl-tyrosine phosphorylation|regulation of transcription, DNA-dependent|visual perception	extracellular space|proteinaceous extracellular matrix	calcium ion binding|epidermal growth factor receptor activity|epidermal growth factor receptor binding|growth factor activity			ovary(4)|pancreas(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TATTGATGGTGTTGGCATAAA	0.413													7	62	---	---	---	---	PASS
COMMD1	150684	broad.mit.edu	37	2	62228088	62228088	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62228088A>G	uc002sbp.2	+	2	444	c.433A>G	c.(433-435)ATA>GTA	p.I145V	COMMD1_uc002sbq.1_RNA	NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1	145	COMM.				copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			TGTTGCCATTATAGAGCTGGA	0.448													19	50	---	---	---	---	PASS
EDAR	10913	broad.mit.edu	37	2	109513383	109513383	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109513383G>A	uc002teq.3	-	12	1758	c.1327C>T	c.(1327-1329)CAG>TAG	p.Q443*	EDAR_uc010fjn.2_Nonsense_Mutation_p.Q475*|EDAR_uc010yws.1_Nonsense_Mutation_p.Q475*	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	443	Cytoplasmic (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GCATGTGGCTGGGAGGCAGGT	0.582													6	6	---	---	---	---	PASS
CBWD2	150472	broad.mit.edu	37	2	114195465	114195465	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114195465C>G	uc002tju.2	+	1	198	c.20C>G	c.(19-21)TCT>TGT	p.S7C	CBWD2_uc002tjt.2_Missense_Mutation_p.S7C|CBWD2_uc010yxw.1_Translation_Start_Site|CBWD2_uc002tjv.2_Translation_Start_Site|CBWD2_uc010fkv.2_RNA	NM_172003	NP_742000	Q8IUF1	CBWD2_HUMAN	COBW domain-containing protein 2	7							ATP binding|protein binding				0						GCTGTTGGATCTGCGGATGAG	0.632													6	22	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	115200401	115200401	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115200401T>A	uc002tla.1	+	1	503	c.46T>A	c.(46-48)TCA>ACA	p.S16T		NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	16	Mediates effects on KCND2.|Cytoplasmic (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						GTGTCAACCCTCAAAAACAAT	0.468													11	46	---	---	---	---	PASS
CCDC93	54520	broad.mit.edu	37	2	118715998	118715998	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118715998G>C	uc002tlj.2	-	12	1074	c.948C>G	c.(946-948)CGC>CGG	p.R316R	CCDC93_uc010fld.1_Silent_p.R316R	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	316	Potential.									large_intestine(1)|ovary(1)	2						TGACTTTCCGGCGATGTAGCT	0.403													7	30	---	---	---	---	PASS
PCDP1	200373	broad.mit.edu	37	2	120383210	120383210	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120383210G>T	uc002tmb.2	+	16	1696	c.604G>T	c.(604-606)GAC>TAC	p.D202Y	PCDP1_uc010yyq.1_Missense_Mutation_p.D332Y	NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	488						cilium	calmodulin binding				0	Colorectal(110;0.196)					TCGTGAAATGGACAAAGAGAG	0.413													5	38	---	---	---	---	PASS
MKI67IP	84365	broad.mit.edu	37	2	122485356	122485356	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122485356C>G	uc002tnk.2	-	7	903	c.826G>C	c.(826-828)GAG>CAG	p.E276Q	uc002tnj.1_Intron	NM_032390	NP_115766	Q9BYG3	MK67I_HUMAN	MKI67 interacting nucleolar phosphoprotein	276					protein complex assembly|rRNA metabolic process|rRNA transcription	condensed nuclear chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GTTTGAGTCTCTTGTATTTCT	0.308													5	55	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125547543	125547543	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125547543G>A	uc002tno.2	+	18	3178	c.2814G>A	c.(2812-2814)CAG>CAA	p.Q938Q	CNTNAP5_uc010flu.2_Silent_p.Q939Q	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	938	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGAATGGACAGAAAATGGACC	0.522													15	63	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128775348	128775348	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128775348T>A	uc002tpp.2	-	3	464	c.332A>T	c.(331-333)CAT>CTT	p.H111L	SAP130_uc002tpo.2_5'Flank|SAP130_uc010fmd.2_Missense_Mutation_p.H111L|SAP130_uc002tpq.1_Missense_Mutation_p.H85L	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	111					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TGCGACAGCATGGTGTGTCGA	0.567													18	41	---	---	---	---	PASS
HS6ST1	9394	broad.mit.edu	37	2	129026380	129026380	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129026380C>A	uc002tpt.3	-	2	626	c.592G>T	c.(592-594)GTG>TTG	p.V198L		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	198	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CCCCTCTGCACATGCCGCCAC	0.637													4	23	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141110606	141110606	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141110606G>A	uc002tvj.1	-	76	12538	c.11566C>T	c.(11566-11568)CAT>TAT	p.H3856Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3856	Extracellular (Potential).|EGF-like 9.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATACATTGATGGGAACATGTG	0.363										TSP Lung(27;0.18)			12	52	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141113992	141113992	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141113992A>G	uc002tvj.1	-	75	12421	c.11449T>C	c.(11449-11451)TAT>CAT	p.Y3817H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3817	Extracellular (Potential).|EGF-like 8.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGATTACAATATGCATCATCT	0.323										TSP Lung(27;0.18)			3	17	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141274583	141274583	+	Intron	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141274583G>T	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTTTTGAACTGTGATAAAATA	0.299										TSP Lung(27;0.18)			4	21	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141294240	141294240	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141294240A>T	uc002tvj.1	-	46	8524	c.7552T>A	c.(7552-7554)TGT>AGT	p.C2518S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2518	Extracellular (Potential).|LDL-receptor class A 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCATTTCCACATTCAAACTCC	0.383										TSP Lung(27;0.18)			8	32	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145158874	145158874	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145158874G>T	uc002tvu.2	-	7	1288	c.808C>A	c.(808-810)CAC>AAC	p.H270N	ZEB2_uc002tvv.2_Missense_Mutation_p.H264N|ZEB2_uc010zbm.1_Missense_Mutation_p.H241N|ZEB2_uc010fnp.2_Missense_Mutation_p.H178N|ZEB2_uc010fnq.1_Missense_Mutation_p.H299N	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	270						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		AGCATTTGGTGCTATAAAAGG	0.393													9	53	---	---	---	---	PASS
GPD2	2820	broad.mit.edu	37	2	157436286	157436286	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157436286A>C	uc002tzf.3	+	16	2404	c.2044A>C	c.(2044-2046)AAT>CAT	p.N682H	GPD2_uc010zch.1_Missense_Mutation_p.N455H|GPD2_uc002tzd.3_Missense_Mutation_p.N682H|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	682	EF-hand 2.|Potential.				cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						GGTTGAACTCAATGAATTTTT	0.303													9	20	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166856244	166856244	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166856244C>G	uc010zcz.1	-	22	4312	c.4294G>C	c.(4294-4296)GAT>CAT	p.D1432H	SCN1A_uc002udo.3_Missense_Mutation_p.D1312H|SCN1A_uc010fpk.2_Missense_Mutation_p.D1284H	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1443	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	TTTCTGGAATCAACTGCTGCA	0.313													4	54	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168105057	168105057	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168105057G>A	uc002udx.2	+	8	7173	c.7155G>A	c.(7153-7155)CCG>CCA	p.P2385P	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.P2210P|XIRP2_uc010fpq.2_Silent_p.P2163P|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2210					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CCTCTGCTCCGGAAAAGCACA	0.453													15	51	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170177289	170177289	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170177289C>A	uc002ues.2	-	2	398	c.185G>T	c.(184-186)TGC>TTC	p.C62F	LRP2_uc010zdf.1_Missense_Mutation_p.C62F	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	62	LDL-receptor class A 1.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TCACTTACCGCAGCCAATTTC	0.493													4	39	---	---	---	---	PASS
KLHL23	151230	broad.mit.edu	37	2	170592730	170592730	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170592730G>C	uc002ufh.1	+	4	1544	c.1206G>C	c.(1204-1206)ATG>ATC	p.M402I	KLHL23_uc002ufi.1_Missense_Mutation_p.M402I	NM_144711	NP_653312	Q8NBE8	KLH23_HUMAN	kelch-like 23	402	Kelch 3.										0						TTGCAAACATGATTAAAGGTA	0.388													23	66	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179396364	179396364	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179396364G>A	uc010zfg.1	-	307	97498	c.97274C>T	c.(97273-97275)ACG>ATG	p.T32425M	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T26120M|TTN_uc010zfi.1_Missense_Mutation_p.T26053M|TTN_uc010zfj.1_Missense_Mutation_p.T25928M|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33352							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)			GACTCCACTCGTGTTGGTGTA	0.453													12	47	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179396750	179396750	+	Silent	SNP	C	T	T	rs144094650	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179396750C>T	uc010zfg.1	-	307	97112	c.96888G>A	c.(96886-96888)CCG>CCA	p.P32296P	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.P25991P|TTN_uc010zfi.1_Silent_p.P25924P|TTN_uc010zfj.1_Silent_p.P25799P|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33223							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)			ATTCCTCAGCCGGTTGTGGAC	0.532													9	29	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179611100	179611100	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179611100T>C	uc002unb.2	-	46	16251	c.16027A>G	c.(16027-16029)ATG>GTG	p.M5343V	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							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)			CTCACAATCATACTTTTATGG	0.328													5	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179640092	179640092	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179640092G>T	uc010zfg.1	-	28	6723	c.6499C>A	c.(6499-6501)CTT>ATT	p.L2167I	TTN_uc010zfh.1_Missense_Mutation_p.L2121I|TTN_uc010zfi.1_Missense_Mutation_p.L2121I|TTN_uc010zfj.1_Missense_Mutation_p.L2121I|TTN_uc002unb.2_Missense_Mutation_p.L2167I|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2167							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)			CCTTGGACAAGTAAGAATGCG	0.408													9	48	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179664420	179664420	+	Silent	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179664420T>A	uc002und.2	-	6	933	c.708A>T	c.(706-708)ACA>ACT	p.T236T	TTN_uc010zfg.1_Silent_p.T236T|TTN_uc010zfh.1_Silent_p.T236T|TTN_uc010zfi.1_Silent_p.T236T|TTN_uc010zfj.1_Silent_p.T236T|TTN_uc002unb.2_Silent_p.T236T			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	236							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)			CCATCTCAACTGTTGCAATTG	0.493													9	30	---	---	---	---	PASS
OBSL1	23363	broad.mit.edu	37	2	220420739	220420739	+	Intron	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220420739C>G	uc010fwk.2	-						OBSL1_uc002vmh.1_Missense_Mutation_p.E437Q|OBSL1_uc010zli.1_Missense_Mutation_p.E345Q|OBSL1_uc010fwl.1_Missense_Mutation_p.E1013Q	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1						cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACGGGGCACTCACGCCTCACG	0.627													8	39	---	---	---	---	PASS
KIAA1486	57624	broad.mit.edu	37	2	226516290	226516290	+	3'UTR	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226516290G>C	uc002voe.2	+	6					KIAA1486_uc010fxa.1_3'UTR|KIAA1486_uc002vof.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		GACTTCCTGTGATACAACTTG	0.483													6	198	---	---	---	---	PASS
COL4A3	1285	broad.mit.edu	37	2	228109562	228109562	+	Intron	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228109562T>C	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron|uc002voq.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CCAGTTATAGTGGAGGAAAAA	0.289													10	31	---	---	---	---	PASS
NEU2	4759	broad.mit.edu	37	2	233899557	233899557	+	Silent	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233899557C>G	uc010zmn.1	+	2	933	c.933C>G	c.(931-933)CTC>CTG	p.L311L		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	311							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)		GTGCCTACCTCAACCCGCGAC	0.697													3	32	---	---	---	---	PASS
OXNAD1	92106	broad.mit.edu	37	3	16327951	16327951	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16327951C>T	uc003caw.2	+	5	743	c.286C>T	c.(286-288)CAG>TAG	p.Q96*	OXNAD1_uc010her.1_RNA|OXNAD1_uc003cax.2_Nonsense_Mutation_p.Q96*|OXNAD1_uc011awb.1_Nonsense_Mutation_p.Q114*	NM_138381	NP_612390	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	96	FAD-binding FR-type.						oxidoreductase activity			skin(1)	1						TAAAGCTGGCCAGTGGTAAGT	0.463													12	31	---	---	---	---	PASS
EOMES	8320	broad.mit.edu	37	3	27758626	27758626	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27758626C>T	uc003cdx.2	-	6	1996	c.1996G>A	c.(1996-1998)GAA>AAA	p.E666K	EOMES_uc003cdy.3_Missense_Mutation_p.E685K|EOMES_uc010hfn.2_3'UTR|EOMES_uc011axc.1_Missense_Mutation_p.E390K	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	666	Required for transcription activation (By similarity).				CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4						CTATACTCTTCAGCATTAATG	0.393													5	101	---	---	---	---	PASS
IFT57	55081	broad.mit.edu	37	3	107885739	107885739	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107885739C>A	uc003dwx.3	-	8	1191	c.943G>T	c.(943-945)GTT>TTT	p.V315F		NM_018010	NP_060480	Q9NWB7	IFT57_HUMAN	estrogen-related receptor beta like 1	315	Potential.				activation of caspase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cilium|microtubule basal body	DNA binding|protein binding			ovary(1)|skin(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			TATTCTTGAACCAAATTCTCA	0.373													13	31	---	---	---	---	PASS
ARHGAP31	57514	broad.mit.edu	37	3	119134765	119134765	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119134765C>T	uc003ecj.3	+	12	4521	c.3989C>T	c.(3988-3990)TCT>TTT	p.S1330F		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	1330					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						GAGCGACCATCTGGGGGTTCT	0.522													7	105	---	---	---	---	PASS
GTF2E1	2960	broad.mit.edu	37	3	120500143	120500143	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120500143G>T	uc003edz.3	+	5	1260	c.1146G>T	c.(1144-1146)GAG>GAT	p.E382D		NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	382	Asp/Glu-rich (acidic).				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)		AGGATGAAGAGGAAGATGACG	0.537													5	108	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121208732	121208732	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121208732C>A	uc003eee.3	-	16	3175	c.3046G>T	c.(3046-3048)GTT>TTT	p.V1016F	POLQ_uc003eed.2_Missense_Mutation_p.V188F	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1016					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		AAAGTCTGAACAACTTTCTTA	0.363								DNA_polymerases_(catalytic_subunits)					11	73	---	---	---	---	PASS
NEK11	79858	broad.mit.edu	37	3	130871272	130871272	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130871272C>G	uc003eny.2	+	8	1014	c.688C>G	c.(688-690)CAT>GAT	p.H230D	NEK11_uc003enx.2_Missense_Mutation_p.H230D|NEK11_uc003eoa.2_Missense_Mutation_p.H230D|NEK11_uc003enz.2_Missense_Mutation_p.H48D|NEK11_uc010htn.2_RNA|NEK11_uc011blk.1_Missense_Mutation_p.H82D|NEK11_uc011bll.1_Intron|NEK11_uc011blm.1_Missense_Mutation_p.H230D|NEK11_uc010hto.1_Missense_Mutation_p.H82D	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1	230	Protein kinase.				cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						CTGCATGAATCATGCATTCGC	0.343													18	80	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142178212	142178212	+	Silent	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142178212T>A	uc003eux.3	-	43	7328	c.7206A>T	c.(7204-7206)ACA>ACT	p.T2402T	ATR_uc003euy.1_Silent_p.T288T	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2402	PI3K/PI4K.				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						GTTCTTTTCCTGTCATATACA	0.383								Other_conserved_DNA_damage_response_genes					9	21	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164756916	164756916	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164756916C>A	uc003fei.2	-	20	2313	c.2251G>T	c.(2251-2253)GAT>TAT	p.D751Y		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	751	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CTCACAGTATCTGCTCCCTAA	0.294										HNSCC(35;0.089)			4	6	---	---	---	---	PASS
BCHE	590	broad.mit.edu	37	3	165548739	165548739	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165548739G>T	uc003fem.3	-	2	243	c.83C>A	c.(82-84)ACT>AAT	p.T28N	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	28					choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)	GTCATCTTCAGTATGTGACTT	0.378													5	25	---	---	---	---	PASS
NDUFB5	4711	broad.mit.edu	37	3	179334808	179334808	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179334808C>T	uc003fkc.2	+	4	347	c.318C>T	c.(316-318)GTC>GTT	p.V106V	NDUFB5_uc003fkd.2_RNA|NDUFB5_uc003fke.2_Silent_p.V54V	NM_002492	NP_002483	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta	106					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			skin(1)	1	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)		NADH(DB00157)	AAGGCTATGTCCCAGAACACT	0.328													17	22	---	---	---	---	PASS
HTR3C	170572	broad.mit.edu	37	3	183770895	183770895	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183770895G>A	uc003fmk.2	+	1	61	c.27G>A	c.(25-27)CAG>CAA	p.Q9Q		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	9						integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CTGCAAGGCAGAGTGCCCTCC	0.557													4	72	---	---	---	---	PASS
HTR3C	170572	broad.mit.edu	37	3	183777395	183777395	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183777395G>A	uc003fmk.2	+	7	926	c.892G>A	c.(892-894)GAC>AAC	p.D298N		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	298	Helical; Name=2; (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CATGATGAATGACTTGCTCCC	0.572													8	136	---	---	---	---	PASS
ECE2	9718	broad.mit.edu	37	3	183976098	183976098	+	Intron	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183976098G>C	uc003fni.3	+						ECE2_uc003fnh.3_Missense_Mutation_p.G168A	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A						brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTTGTCCCTGGAGGCCGGTTT	0.547													10	160	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196612846	196612846	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196612846G>A	uc003fwz.3	+	2	1043	c.794G>A	c.(793-795)CGA>CAA	p.R265Q	SENP5_uc011bty.1_Missense_Mutation_p.R265Q	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	265					cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AAAGCCCAGCGAAGCTGGGTA	0.483													13	46	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196654687	196654687	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196654687G>A	uc003fwz.3	+	8	2292	c.2043G>A	c.(2041-2043)CTG>CTA	p.L681L	SENP5_uc011bty.1_Silent_p.L635L	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	681	Protease.				cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AGTATTTGCTGACTGAAGCCA	0.403													9	39	---	---	---	---	PASS
TADA2B	93624	broad.mit.edu	37	4	7056395	7056395	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7056395C>T	uc003gjw.3	+	2	1028	c.877C>T	c.(877-879)CGG>TGG	p.R293W	TADA2B_uc010idi.2_Missense_Mutation_p.R218W	NM_152293	NP_689506	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2 (ADA2 homolog,	293					regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|zinc ion binding				0						AGAACTGCAGCGGTACCGGCG	0.522													4	32	---	---	---	---	PASS
SRP72	6731	broad.mit.edu	37	4	57361544	57361544	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57361544G>A	uc003hbv.2	+	17	1702	c.1662G>A	c.(1660-1662)AAG>AAA	p.K554K	SRP72_uc010ihe.2_Silent_p.K493K	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa	554	Poly-Lys.				response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					TGAAAAAGAAGAAAAAGAAAA	0.254													3	14	---	---	---	---	PASS
UGT2B15	7366	broad.mit.edu	37	4	69512834	69512834	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69512834C>T	uc011cal.1	-	6	1619	c.1581G>A	c.(1579-1581)AAG>AAA	p.K527K		NM_001076	NP_001067	P54855	UDB15_HUMAN	UDP glycosyltransferase 2B15 precursor	527					steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0						AATCTCTTTTCTTCTTCTTTC	0.388													19	80	---	---	---	---	PASS
SMR3A	26952	broad.mit.edu	37	4	71232643	71232643	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71232643C>G	uc003hfg.1	+	3	418	c.337C>G	c.(337-339)CCA>GCA	p.P113A	SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3	113	Pro-rich.					extracellular region					0		all_hematologic(202;0.196)				AAGACCCTATCCACCTGGACC	0.532													12	52	---	---	---	---	PASS
GK2	2712	broad.mit.edu	37	4	80328533	80328533	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80328533T>A	uc003hlu.2	-	1	840	c.822A>T	c.(820-822)CAA>CAT	p.Q274H		NM_033214	NP_149991	Q14410	GLPK2_HUMAN	glycerol kinase 2	274					glycerol-3-phosphate metabolic process	mitochondrial outer membrane	ATP binding|glycerol kinase activity			ovary(2)|skin(2)	4						TGTTTTTGGCTTGTCCCTCCT	0.458													15	70	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	99064295	99064295	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99064295C>T	uc003htt.1	-	1	97	c.7G>A	c.(7-9)GAT>AAT	p.D3N		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	3											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		GGAGCCCGATCATACATAGTG	0.577											OREG0016268	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	14	---	---	---	---	PASS
LRIT3	345193	broad.mit.edu	37	4	110791573	110791573	+	Silent	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110791573A>T	uc003hzx.3	+	3	1726	c.1533A>T	c.(1531-1533)CCA>CCT	p.P511P	LRIT3_uc003hzw.3_Silent_p.P373P	NM_198506	NP_940908	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and	511	Fibronectin type-III.					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GTGTCTGTCCAAAAGGAGTGC	0.498													8	42	---	---	---	---	PASS
EGF	1950	broad.mit.edu	37	4	110865119	110865119	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110865119G>C	uc003hzy.3	+	4	1083	c.631G>C	c.(631-633)GAT>CAT	p.D211H	EGF_uc011cfu.1_Missense_Mutation_p.D211H|EGF_uc011cfv.1_Missense_Mutation_p.D211H	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	211	LDL-receptor class B 3.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)	GGATGTGCTTGATAAGCGGCT	0.443													10	22	---	---	---	---	PASS
TMEM155	132332	broad.mit.edu	37	4	122682747	122682747	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122682747G>T	uc003idx.1	-	5	717	c.158C>A	c.(157-159)GCA>GAA	p.A53E	TMEM155_uc003idy.1_Missense_Mutation_p.A53E	NM_152399	NP_689612	Q4W5P6	TM155_HUMAN	transmembrane protein 155 precursor	53						extracellular region					0						CTGGCACCTTGCCATTCCCAG	0.413													4	42	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126328188	126328188	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126328188C>T	uc003ifj.3	+	3	5461	c.5461C>T	c.(5461-5463)CAG>TAG	p.Q1821*	FAT4_uc011cgp.1_Nonsense_Mutation_p.Q119*	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1821	Cadherin 17.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TGATGGTCTTCAGTCCTCGGA	0.478													7	83	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186545038	186545038	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186545038G>A	uc003iyl.2	-	13	2391	c.1533C>T	c.(1531-1533)TCC>TCT	p.S511S	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Silent_p.S611S|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Silent_p.S415S|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Silent_p.S625S|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	511						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTTCGAATTCGGAGATGCGTG	0.572													5	61	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187171402	187171402	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187171402C>T	uc003iyy.2	+	7	675	c.604C>T	c.(604-606)CAC>TAC	p.H202Y	KLKB1_uc011clc.1_5'UTR|KLKB1_uc011cld.1_Missense_Mutation_p.H164Y	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	202	Apple 3.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		CACAGGTTGCCACATGAACAT	0.438													15	61	---	---	---	---	PASS
CLPTM1L	81037	broad.mit.edu	37	5	1341845	1341845	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1341845T>C	uc003jch.2	-	3	440	c.394A>G	c.(394-396)ACC>GCC	p.T132A	CLPTM1L_uc003jcg.2_5'UTR	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	132	Extracellular (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		ACCATGTAGGTGGTCAGAGGA	0.562													12	66	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10410379	10410379	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10410379G>C	uc003jet.1	+	18	1865	c.1682G>C	c.(1681-1683)GGA>GCA	p.G561A	MARCH6_uc011cmu.1_Missense_Mutation_p.G513A|MARCH6_uc003jeu.1_Missense_Mutation_p.G259A|MARCH6_uc011cmv.1_Missense_Mutation_p.G456A	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	561	Cytoplasmic (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						GTGACCGCCGGATACTTGCTG	0.527													3	35	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16694532	16694532	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16694532C>G	uc003jft.3	-	27	4216	c.3748G>C	c.(3748-3750)GAA>CAA	p.E1250Q	MYO10_uc011cnc.1_Missense_Mutation_p.E129Q|MYO10_uc011cnd.1_Missense_Mutation_p.E607Q|MYO10_uc011cne.1_Missense_Mutation_p.E607Q|MYO10_uc010itx.2_Missense_Mutation_p.E873Q	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1250	PH 1.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CTGTCGTTTTCAAAGTACATC	0.552													9	145	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35644570	35644570	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35644570G>A	uc003jjo.2	+	4	639	c.528G>A	c.(526-528)GAG>GAA	p.E176E	SPEF2_uc003jjn.1_Silent_p.E176E|SPEF2_uc003jjq.3_Silent_p.E176E	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	176					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity	p.E176G(1)		skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCATTTTGAGAAACTTGAAA	0.313													6	19	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45645292	45645292	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45645292C>T	uc003jok.2	-	2	869	c.844G>A	c.(844-846)GAA>AAA	p.E282K		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	282	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CTTACCTCTTCCCATTGATGT	0.333													3	8	---	---	---	---	PASS
PCSK1	5122	broad.mit.edu	37	5	95728693	95728693	+	3'UTR	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95728693C>T	uc003kls.1	-	14					PCSK1_uc010jbi.1_3'UTR	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1						cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AACTTGGGACCACACACTTAT	0.383													24	98	---	---	---	---	PASS
PCSK1	5122	broad.mit.edu	37	5	95728791	95728791	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95728791C>T	uc003kls.1	-	14	2382	c.2176G>A	c.(2176-2178)GAT>AAT	p.D726N	PCSK1_uc010jbi.1_Missense_Mutation_p.D416N	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	726					cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TAAAAAACATCAACATAGTCA	0.403													28	78	---	---	---	---	PASS
CHD1	1105	broad.mit.edu	37	5	98228350	98228350	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98228350G>T	uc003knf.2	-	14	2207	c.2059C>A	c.(2059-2061)CAC>AAC	p.H687N		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	687					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AGCTCCTTGTGAAGGCTTGCA	0.383													13	32	---	---	---	---	PASS
SRFBP1	153443	broad.mit.edu	37	5	121356289	121356289	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121356289A>G	uc003kst.1	+	6	931	c.859A>G	c.(859-861)ATT>GTT	p.I287V		NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1	287					regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		CGACTTCTTCATTGGGAAAGT	0.383													17	43	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128862084	128862084	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128862084C>A	uc003kvb.1	+	4	1003	c.1003C>A	c.(1003-1005)CCA>ACA	p.P335T	ADAMTS19_uc003kvc.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	335	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GGTTGCAGACCCAGCAATGGT	0.393													10	33	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140208830	140208830	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140208830T>C	uc003lho.2	+	1	1181	c.1154T>C	c.(1153-1155)GTG>GCG	p.V385A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Missense_Mutation_p.V385A|PCDHA6_uc011dab.1_Missense_Mutation_p.V385A	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	385	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGGGCAGGTGAACTGCTCG	0.547													31	97	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209110	140209110	+	Silent	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209110T>C	uc003lho.2	+	1	1461	c.1434T>C	c.(1432-1434)TCT>TCC	p.S478S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Silent_p.S478S|PCDHA6_uc011dab.1_Silent_p.S478S	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	478	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACGGTGTCTGCGCGAGACG	0.647													8	21	---	---	---	---	PASS
CAMK2A	815	broad.mit.edu	37	5	149631622	149631622	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149631622G>T	uc003lru.2	-	8	736	c.521C>A	c.(520-522)GCA>GAA	p.A174E	CAMK2A_uc003lrt.2_Missense_Mutation_p.A174E|CAMK2A_uc010jhe.2_Missense_Mutation_p.A154E|CAMK2A_uc010jhf.1_Missense_Mutation_p.Q12K	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II	174	Protein kinase.				interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGAGTCCCTGCAAACCCTGC	0.552													7	20	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160059368	160059368	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160059368C>T	uc003lym.1	-	13	2235	c.1388G>A	c.(1387-1389)CGA>CAA	p.R463Q	ATP10B_uc003lyn.2_Missense_Mutation_p.R21Q	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	463	Cytoplasmic (Potential).				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)			GGTCTCCAGTCGCTTAGCTGC	0.527													17	40	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169683582	169683582	+	Intron	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169683582G>A	uc003man.1	-						LCP2_uc011des.1_Intron|LCP2_uc011det.1_Intron	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2						immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGCTGTTACTGAGGAGACAGA	0.483													17	41	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12163563	12163563	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12163563C>T	uc003nac.2	+	9	7205	c.7026C>T	c.(7024-7026)CCC>CCT	p.P2342P	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	2342					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AGCACAGCCCCCAGACAGCAG	0.512													6	144	---	---	---	---	PASS
HLA-F	3134	broad.mit.edu	37	6	29695871	29695871	+	Silent	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29695871T>C	uc011dlx.1	+	8	1420	c.1296T>C	c.(1294-1296)TCT>TCC	p.S432S	HLA-F_uc011dly.1_Intron|LOC285830_uc003nnp.2_Intron|LOC285830_uc011dlz.1_Intron	NM_018950	NP_061823	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	Error:Variant_position_missing_in_P30511_after_alignment					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						taccagcatcttgtggggaat	0.000													7	17	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33154404	33154404	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33154404C>A	uc003ocx.1	-	5	1026	c.798G>T	c.(796-798)CAG>CAT	p.Q266H	COL11A2_uc003ocy.1_Missense_Mutation_p.Q266H|COL11A2_uc003ocz.1_Missense_Mutation_p.Q266H|COL11A2_uc003oda.2_Missense_Mutation_p.Q266H	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	266	Nonhelical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						GCTCCCTCACCTGGCTCTGGG	0.577													17	45	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66205243	66205243	+	Nonsense_Mutation	SNP	C	A	A	rs148294551		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66205243C>A	uc011dxu.1	-	4	599	c.61G>T	c.(61-63)GGA>TGA	p.G21*	EYS_uc003peq.2_Nonsense_Mutation_p.G21*|EYS_uc003per.1_Nonsense_Mutation_p.G21*|EYS_uc010kaj.1_RNA	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	21					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CATGTTTTTCCATTTATGAAA	0.373													7	22	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70866115	70866115	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70866115G>T	uc003pfc.1	+	32	2293	c.2176G>T	c.(2176-2178)GCC>TCC	p.A726S	COL19A1_uc010kam.1_Missense_Mutation_p.A622S	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	726	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TGATTCCATGGCCCGGAAGGT	0.493													16	26	---	---	---	---	PASS
FILIP1	27145	broad.mit.edu	37	6	76022993	76022993	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76022993A>G	uc003pia.2	-	5	2928	c.2555T>C	c.(2554-2556)GTT>GCT	p.V852A	FILIP1_uc003phy.1_Missense_Mutation_p.V852A|FILIP1_uc003phz.2_Missense_Mutation_p.V753A|FILIP1_uc010kbe.2_Missense_Mutation_p.V855A|FILIP1_uc003pib.1_Missense_Mutation_p.V604A	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	852										skin(3)|ovary(1)	4						CCTGTCTAGAACAGAAGATCT	0.458													20	60	---	---	---	---	PASS
MRAP2	112609	broad.mit.edu	37	6	84772654	84772654	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84772654T>C	uc003pkg.3	+	3	360	c.170T>C	c.(169-171)GTG>GCG	p.V57A	MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	57					positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2						GCAGTCTTCGTGATTTTTATG	0.403													5	32	---	---	---	---	PASS
FHL5	9457	broad.mit.edu	37	6	97058603	97058603	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97058603C>T	uc003pos.1	+	6	1065	c.660C>T	c.(658-660)AAC>AAT	p.N220N	FHL5_uc003pot.1_Silent_p.N220N	NM_020482	NP_065228	Q5TD97	FHL5_HUMAN	activator of cAMP-responsive element modulator	220	LIM zinc-binding 3.					nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TTTATGCCAACAAGTGTGTAG	0.413													13	46	---	---	---	---	PASS
HACE1	57531	broad.mit.edu	37	6	105224980	105224980	+	Missense_Mutation	SNP	T	G	G	rs145211482	byFrequency	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105224980T>G	uc003pqu.1	-	16	1961	c.1684A>C	c.(1684-1686)ATT>CTT	p.I562L	HACE1_uc010kcy.1_Missense_Mutation_p.I44L|HACE1_uc010kcz.1_Intron|HACE1_uc010kcx.1_Intron|HACE1_uc003pqt.1_Missense_Mutation_p.I215L	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	562					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CTCCTAAAAATAGAATCTAAA	0.328													8	22	---	---	---	---	PASS
RTN4IP1	84816	broad.mit.edu	37	6	107050751	107050751	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107050751G>C	uc003prj.2	-	5	1144	c.667C>G	c.(667-669)CAG>GAG	p.Q223E	RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Missense_Mutation_p.Q123E	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	223						mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		GGTTTTACCTGTATAGCAAAA	0.328													13	44	---	---	---	---	PASS
FYN	2534	broad.mit.edu	37	6	112017519	112017519	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112017519C>G	uc003pvj.2	-	9	1343	c.1003G>C	c.(1003-1005)GAG>CAG	p.E335Q	FYN_uc003pvi.2_Missense_Mutation_p.E280Q|FYN_uc003pvk.2_Missense_Mutation_p.E335Q|FYN_uc003pvh.2_Missense_Mutation_p.E332Q|FYN_uc010kdy.1_Intron	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a	335	Protein kinase.				axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	ATGGGCTCCTCAGACACCACT	0.517													4	81	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117700284	117700284	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117700284C>A	uc003pxp.1	-	17	2734	c.2535G>T	c.(2533-2535)CTG>CTT	p.L845L	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	845	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CCAACCAATACAGGAGCCCAT	0.393			T	GOPC|ROS1	glioblastoma|NSCLC								4	29	---	---	---	---	PASS
SLC35F1	222553	broad.mit.edu	37	6	118635205	118635205	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118635205T>A	uc003pxx.3	+	8	1218	c.1017T>A	c.(1015-1017)TAT>TAA	p.Y339*	SLC35F1_uc003pxy.1_Nonsense_Mutation_p.Y144*	NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	339	Helical; (Potential).				transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		CAGGACTTTATCTCCTGTCTT	0.478													13	72	---	---	---	---	PASS
TNFAIP3	7128	broad.mit.edu	37	6	138202416	138202416	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138202416A>G	uc003qhr.2	+	9	2399	c.2333A>G	c.(2332-2334)TAC>TGC	p.Y778C	TNFAIP3_uc003qhs.2_Missense_Mutation_p.Y778C	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	778	A20-type 7.				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	p.0?(22)		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)		TGCAACGGCTACTGCAACGAA	0.607			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								24	74	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144809979	144809979	+	Intron	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144809979G>C	uc003qkt.2	+							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)		AGGTATTGCCGTGCATTTGAG	0.483													4	21	---	---	---	---	PASS
ESR1	2099	broad.mit.edu	37	6	152163866	152163866	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152163866A>G	uc003qom.3	+	4	957	c.587A>G	c.(586-588)CAT>CGT	p.H196R	ESR1_uc010kin.2_Missense_Mutation_p.H196R|ESR1_uc010kio.2_Missense_Mutation_p.H196R|ESR1_uc010kip.2_Missense_Mutation_p.H196R|ESR1_uc003qon.3_Missense_Mutation_p.H196R|ESR1_uc003qoo.3_Missense_Mutation_p.H196R|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_RNA|ESR1_uc011eeu.1_RNA|ESR1_uc011eev.1_Missense_Mutation_p.H23R|ESR1_uc011eew.1_Missense_Mutation_p.I28V	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4	196	NR C4-type.|Nuclear receptor.|Mediates interaction with DNTTIP2.				positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	TCAGGCTACCATTATGGAGTC	0.453													11	37	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152466691	152466691	+	Intron	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152466691C>A	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Splice_Site_p.D8255_splice|SYNE1_uc003qou.3_Intron|SYNE1_uc003qop.3_Splice_Site_p.D488_splice|SYNE1_uc011eez.1_Intron|SYNE1_uc003qoq.3_Intron|SYNE1_uc003qor.3_Splice_Site_p.D1226_splice	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATCATTACATCTGCAAAAAAA	0.448										HNSCC(10;0.0054)			9	27	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152725365	152725365	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152725365T>C	uc010kiw.2	-	46	7410	c.6808A>G	c.(6808-6810)ACA>GCA	p.T2270A	SYNE1_uc003qot.3_Missense_Mutation_p.T2277A|SYNE1_uc003qou.3_Missense_Mutation_p.T2270A|SYNE1_uc010kjb.1_Missense_Mutation_p.T2253A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2270	Potential.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTGGCGGTGTTTCTAGATTT	0.333										HNSCC(10;0.0054)			10	52	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154360761	154360761	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154360761C>T	uc003qpr.2	+	1	319	c.82C>T	c.(82-84)CCC>TCC	p.P28S	OPRM1_uc011efb.1_Missense_Mutation_p.P76S|OPRM1_uc011efc.1_Intron|OPRM1_uc011efd.1_Intron|OPRM1_uc011efe.1_Missense_Mutation_p.P121S|OPRM1_uc003qpn.2_Missense_Mutation_p.P28S|OPRM1_uc003qpo.1_Missense_Mutation_p.P28S|OPRM1_uc011eff.1_Missense_Mutation_p.P28S|OPRM1_uc011efg.1_Missense_Mutation_p.P28S|OPRM1_uc011efh.1_Missense_Mutation_p.P28S|OPRM1_uc003qpq.1_Missense_Mutation_p.P28S|OPRM1_uc003qpt.1_Missense_Mutation_p.P28S|OPRM1_uc011efi.1_Missense_Mutation_p.P28S|OPRM1_uc003qpp.2_RNA|OPRM1_uc003qps.2_RNA	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1	28	Extracellular (Potential).				behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	AGCACCCAGCCCCGGTTCCTG	0.652													5	12	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158358489	158358489	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158358489G>C	uc003qqv.1	+	15	1640	c.1467G>C	c.(1465-1467)CTG>CTC	p.L489L		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	489	BAR.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TCCATTTCCTGATGGAATGTA	0.373													4	75	---	---	---	---	PASS
MRPL18	29074	broad.mit.edu	37	6	160212095	160212095	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160212095T>C	uc003qsw.3	+	2	304	c.176T>C	c.(175-177)TTA>TCA	p.L59S	TCP1_uc003qsr.2_5'Flank|TCP1_uc003qss.2_5'Flank|TCP1_uc010kjz.2_5'Flank|TCP1_uc003qst.2_5'Flank|TCP1_uc010kka.1_5'Flank|MRPL18_uc010kkb.2_RNA	NM_014161	NP_054880	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18 precursor	59					rRNA transport|translation	mitochondrial ribosome	5S rRNA binding|structural constituent of ribosome				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		CTGGAGCTTTTATCTGTAGCC	0.562													4	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	2517296	2517296	+	IGR	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2517296G>A								CHST12 (43082 upstream) : LFNG (42183 downstream)																							TGGGACTGCTGAGGCCGGGAG	0.716											OREG0017835	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	9	---	---	---	---	PASS
ELMO1	9844	broad.mit.edu	37	7	37136261	37136261	+	Silent	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37136261G>T	uc003tfk.1	-	15	1570	c.1263C>A	c.(1261-1263)ACC>ACA	p.T421T	ELMO1_uc011kbc.1_Silent_p.T325T|ELMO1_uc010kxg.1_Silent_p.T421T	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	421	ELMO.				actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						ATAGCATCTTGGTCAGCTCTA	0.468													10	43	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	38402587	38402587	+	Intron	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38402587C>G	uc003tgp.1	+						uc003tgs.1_Missense_Mutation_p.E78Q					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																		ACTCCTGATTCCAACACAACC	0.458													13	39	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65429349	65429349	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65429349C>A	uc003tun.2	-	11	1826	c.1750G>T	c.(1750-1752)GAG>TAG	p.E584*	GUSB_uc011kdt.1_Nonsense_Mutation_p.E438*	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	584					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						CAAATGAGCTCTCCAACCACG	0.453													27	104	---	---	---	---	PASS
RABGEF1	27342	broad.mit.edu	37	7	66270167	66270167	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66270167G>A	uc011kee.1	+	8	1067	c.903G>A	c.(901-903)AAG>AAA	p.K301K	RABGEF1_uc003tvf.2_Silent_p.K160K|RABGEF1_uc003tvg.2_Silent_p.K95K|RABGEF1_uc010lag.2_Silent_p.K287K|RABGEF1_uc003tvh.2_Silent_p.K287K|RABGEF1_uc003tvi.2_Silent_p.K121K	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	504	VPS9.				endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						CTCGAGACAAGCTGGCCTGCA	0.463													15	34	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79846672	79846672	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79846672C>G	uc003uhb.1	+	8	1265	c.928C>G	c.(928-930)CTC>GTC	p.L310V	GNAI1_uc011kgt.1_Missense_Mutation_p.L258V	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	310					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GTTTGAAGACCTCAATAAAAG	0.343													7	26	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88963668	88963668	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88963668C>A	uc011khi.1	+	4	1910	c.1372C>A	c.(1372-1374)CCT>ACT	p.P458T		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	458						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TCTTCAATGGCCTACGGAACT	0.418										HNSCC(36;0.09)			14	57	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107572753	107572753	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107572753C>T	uc003vew.2	-	28	4593	c.4258G>A	c.(4258-4260)GAA>AAA	p.E1420K	LAMB1_uc003vev.2_Missense_Mutation_p.E1444K|LAMB1_uc003veu.2_5'Flank	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1420	Domain alpha.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTCTCTCCTTCGTCAGTTCTG	0.572													9	54	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107743501	107743501	+	Missense_Mutation	SNP	A	T	T	rs140607116	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107743501A>T	uc010ljo.1	-	10	1252	c.1168T>A	c.(1168-1170)TAC>AAC	p.Y390N	LAMB4_uc003vey.2_Missense_Mutation_p.Y390N	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	390	Laminin EGF-like 2.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						ATGCACGCGTAGGGATCTGAG	0.587													7	27	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107743502	107743502	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107743502G>A	uc010ljo.1	-	10	1251	c.1167C>T	c.(1165-1167)CCC>CCT	p.P389P	LAMB4_uc003vey.2_Silent_p.P389P	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	389	Laminin EGF-like 2.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TGCACGCGTAGGGATCTGAGA	0.592													7	27	---	---	---	---	PASS
C7orf60	154743	broad.mit.edu	37	7	112472715	112472715	+	Silent	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112472715T>G	uc003vgo.1	-	4	616	c.489A>C	c.(487-489)TCA>TCC	p.S163S	C7orf60_uc011kms.1_Silent_p.S189S	NM_152556	NP_689769	Q1RMZ1	CG060_HUMAN	hypothetical protein LOC154743	163										ovary(2)|skin(1)	3						TGATTTTTCCTGAGGCTTGTA	0.294													16	44	---	---	---	---	PASS
ZNF777	27153	broad.mit.edu	37	7	149129570	149129570	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149129570A>T	uc003wfv.2	-	6	1956	c.1793T>A	c.(1792-1794)GTG>GAG	p.V598E		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	598					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			GCCTCCGCGCACGCGGTGGAT	0.672													10	35	---	---	---	---	PASS
GIMAP7	168537	broad.mit.edu	37	7	150217426	150217426	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150217426T>A	uc003whk.2	+	2	494	c.364T>A	c.(364-366)TCA>ACA	p.S122T		NM_153236	NP_694968	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	122							GTP binding			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTTTGGGAAGTCAGCCATGAA	0.527													5	43	---	---	---	---	PASS
GIMAP4	55303	broad.mit.edu	37	7	150269977	150269977	+	Silent	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150269977A>G	uc003whl.2	+	3	901	c.819A>G	c.(817-819)GAA>GAG	p.E273E	GIMAP4_uc011kuu.1_Silent_p.E134E|GIMAP4_uc011kuv.1_Silent_p.E287E	NM_018326	NP_060796	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	273	Potential.						GTP binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGAGCAGGAAAAGAGAAAGA	0.468													8	44	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25317909	25317909	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25317909C>G	uc003xep.1	+	3	550	c.71C>G	c.(70-72)TCT>TGT	p.S24C	PPP2R2A_uc003xek.2_Intron|KCTD9_uc003xeo.2_5'Flank|CDCA2_uc011lae.1_Missense_Mutation_p.S24C|CDCA2_uc003xeq.1_Missense_Mutation_p.S9C	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	24					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		GGAAATGCCTCTTTCATTTTG	0.428													28	116	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39466640	39466640	+	Splice_Site	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39466640G>T	uc003xni.2	+	4	267	c.267_splice	c.e4+1	p.M89_splice	ADAM18_uc003xnh.2_Splice_Site_p.M89_splice|ADAM18_uc010lww.2_Splice_Site|ADAM18_uc010lwx.2_Splice_Site_p.M89_splice	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18						cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			ATATTTTATGGTAAAGTAAGA	0.269													4	7	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55542146	55542146	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55542146C>T	uc003xsd.1	+	4	5852	c.5704C>T	c.(5704-5706)CAG>TAG	p.Q1902*	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1902					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TGGTACACTTCAGGAAGCTGA	0.398													6	52	---	---	---	---	PASS
FAM110B	90362	broad.mit.edu	37	8	59058961	59058961	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59058961A>T	uc003xtj.1	+	5	1052	c.172A>T	c.(172-174)AAG>TAG	p.K58*		NM_147189	NP_671722	Q8TC76	F110B_HUMAN	hypothetical protein LOC90362	58						microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				GGAGGCCGACAAGGCCAAGTA	0.677													8	15	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72951230	72951230	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72951230T>C	uc003xza.2	-	19	2340	c.2165A>G	c.(2164-2166)AAT>AGT	p.N722S	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	722	Helical; Name=1; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	AGATCCTAAATTCATCATATG	0.348													9	45	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72963055	72963055	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72963055A>T	uc003xza.2	-	15	2038	c.1863T>A	c.(1861-1863)TGT>TGA	p.C621*	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	621	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	CTGTAATTGGACATTTATTGC	0.328													5	32	---	---	---	---	PASS
GDAP1	54332	broad.mit.edu	37	8	75275277	75275277	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275277A>G	uc003yah.2	+	5	762	c.683A>G	c.(682-684)GAA>GGA	p.E228G	GDAP1_uc011lfj.1_Missense_Mutation_p.E113G|GDAP1_uc003yai.2_Missense_Mutation_p.E160G	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated	228	GST C-terminal.					cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			AGAAGAAATGAAGAAACCCCA	0.348													15	63	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77761266	77761266	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77761266G>T	uc003yav.2	+	7	3799	c.3412G>T	c.(3412-3414)GTG>TTG	p.V1138L	ZFHX4_uc003yau.1_Missense_Mutation_p.V1183L|ZFHX4_uc003yaw.1_Missense_Mutation_p.V1138L	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1138						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAGTTAGTGTGGCAGGGGG	0.388										HNSCC(33;0.089)			4	10	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77765710	77765710	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77765710C>A	uc003yav.2	+	10	6805	c.6418C>A	c.(6418-6420)CGA>AGA	p.R2140R	ZFHX4_uc003yau.1_Silent_p.R2185R|ZFHX4_uc003yaw.1_Silent_p.R2140R	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2140	Homeobox 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTTAAGGAACGACAGAGAAA	0.378										HNSCC(33;0.089)			8	107	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87679237	87679237	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87679237C>T	uc003ydx.2	-	6	814	c.768G>A	c.(766-768)GCG>GCA	p.A256A	CNGB3_uc010maj.2_Silent_p.A118A	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	256	Helical; Name=H2; (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						ATATGATGTCCGCAATAAGCC	0.438													7	42	---	---	---	---	PASS
TM7SF4	81501	broad.mit.edu	37	8	105361034	105361034	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105361034T>C	uc003ylx.1	+	2	303	c.254T>C	c.(253-255)GTC>GCC	p.V85A		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	85					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			ATTCTTCTTGTCTTTCTCTCT	0.473													12	28	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113246625	113246625	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113246625A>G	uc003ynu.2	-	68	10868	c.10709T>C	c.(10708-10710)ATG>ACG	p.M3570T	CSMD3_uc003yns.2_Missense_Mutation_p.M2772T|CSMD3_uc003ynt.2_Missense_Mutation_p.M3530T|CSMD3_uc011lhx.1_Missense_Mutation_p.M3401T	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3570	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TTCTTCCTTCATTTTCTTCAC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			16	53	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125113330	125113330	+	Intron	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125113330A>G	uc003yqw.2	+						uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTTTGAATCTATTTTTAGGTG	0.398													13	58	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131812807	131812807	+	Silent	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131812807A>T	uc003ytd.3	-	15	3181	c.2925T>A	c.(2923-2925)TCT>TCA	p.S975S	ADCY8_uc010mds.2_Silent_p.S844S	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	975	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)			CATAGGATTGAGAATACAGCT	0.502										HNSCC(32;0.087)			12	48	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	134042191	134042191	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134042191G>C	uc003ytw.2	+	41	7203	c.7162G>C	c.(7162-7164)GGG>CGG	p.G2388R	TG_uc010mdw.2_Missense_Mutation_p.G1147R|TG_uc011ljb.1_Missense_Mutation_p.G757R|TG_uc011ljc.1_Missense_Mutation_p.G521R	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2388					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGACCGTGGCGGGGCTGATGT	0.642													7	9	---	---	---	---	PASS
CYP11B2	1585	broad.mit.edu	37	8	143996220	143996220	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143996220T>G	uc003yxk.1	-	4	703	c.700A>C	c.(700-702)ACC>CCC	p.T234P		NM_000498	NP_000489	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B,	234					aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|potassium ion homeostasis|regulation of blood volume by renal aldosterone|sodium ion homeostasis|xenobiotic metabolic process		corticosterone 18-monooxygenase activity|electron carrier activity|steroid 11-beta-monooxygenase activity				0	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Candesartan(DB00796)|Metyrapone(DB01011)	AGCTGGACGGTGGATTTGAAC	0.582									Familial_Hyperaldosteronism_type_I				10	10	---	---	---	---	PASS
OPLAH	26873	broad.mit.edu	37	8	145109735	145109735	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145109735C>G	uc003zar.3	-	18	2573	c.2491G>C	c.(2491-2493)GAC>CAC	p.D831H	OPLAH_uc003zas.1_Missense_Mutation_p.D80H	NM_017570	NP_060040	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	831							5-oxoprolinase (ATP-hydrolyzing) activity|ATP binding				0	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		L-Glutamic Acid(DB00142)	ACAGTCAGGTCTGGCAGGTGG	0.652													3	12	---	---	---	---	PASS
ZNF251	90987	broad.mit.edu	37	8	145947489	145947489	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145947489C>T	uc003zdv.3	-	5	1812	c.1556G>A	c.(1555-1557)AGA>AAA	p.R519K		NM_138367	NP_612376	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	519					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		ACCATGTTTTCTGCACTTACG	0.527													5	93	---	---	---	---	PASS
JAK2	3717	broad.mit.edu	37	9	5066761	5066761	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5066761A>G	uc010mhm.2	+	9	1411	c.1298A>G	c.(1297-1299)AAT>AGT	p.N433S	JAK2_uc003ziw.2_Missense_Mutation_p.N433S	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	433	SH2; atypical.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)		AAGGACTTTAATAAATATTTT	0.328		1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				5	9	---	---	---	---	PASS
NFIB	4781	broad.mit.edu	37	9	14307382	14307382	+	Silent	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14307382T>A	uc003zle.2	-	2	603	c.168A>T	c.(166-168)GCA>GCT	p.A56A	NFIB_uc003zlf.2_Silent_p.A56A|NFIB_uc011lmo.1_Silent_p.A56A	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B	56	CTF/NF-I.				anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		CATCTTTGACTGCTCTTTCTT	0.453			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								10	28	---	---	---	---	PASS
TEK	7010	broad.mit.edu	37	9	27206656	27206656	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27206656C>A	uc003zqi.3	+	15	2883	c.2441C>A	c.(2440-2442)ACA>AAA	p.T814K	TEK_uc011lno.1_Missense_Mutation_p.T771K|TEK_uc011lnp.1_Missense_Mutation_p.T666K|TEK_uc003zqj.1_Missense_Mutation_p.T748K	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	814	Cytoplasmic (Potential).				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)		CCAGATCCTACAATTTATCCA	0.438													15	11	---	---	---	---	PASS
PAX5	5079	broad.mit.edu	37	9	36846882	36846882	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36846882A>T	uc003zzo.1	-	9	1505	c.1057T>A	c.(1057-1059)TCG>ACG	p.S353T	PAX5_uc011lpt.1_Missense_Mutation_p.S149T|PAX5_uc011lpu.1_RNA|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Missense_Mutation_p.S253T|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Missense_Mutation_p.S310T|PAX5_uc011lqa.1_Missense_Mutation_p.S245T|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Missense_Mutation_p.S319T|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Silent_p.P275P	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	353					cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(11)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		TCGTTGTACGAGGAATACTGA	0.592			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								10	19	---	---	---	---	PASS
FOXB2	442425	broad.mit.edu	37	9	79635629	79635629	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79635629C>T	uc004ako.1	+	1	1059	c.1059C>T	c.(1057-1059)CAC>CAT	p.H353H		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	353					brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						CCCTGTGCCACTCGGCAAGCC	0.602													3	3	---	---	---	---	PASS
NCBP1	4686	broad.mit.edu	37	9	100433431	100433431	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100433431G>C	uc004axq.2	+	23	2782	c.2323G>C	c.(2323-2325)GAC>CAC	p.D775H		NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	775					gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				TGCTGAATTAGACCCTCATAT	0.438													13	50	---	---	---	---	PASS
TMEFF1	8577	broad.mit.edu	37	9	103261052	103261052	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103261052A>G	uc004baz.1	+	2	312	c.202A>G	c.(202-204)AAT>GAT	p.N68D	TMEFF1_uc004bay.1_Missense_Mutation_p.N142D	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two	68	Extracellular (Potential).				multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				TGCAGAATTAAATGTGAGGGA	0.269													3	41	---	---	---	---	PASS
OR13C9	286362	broad.mit.edu	37	9	107380010	107380010	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107380010T>C	uc011lvr.1	-	1	476	c.476A>G	c.(475-477)CAA>CGA	p.Q159R		NM_001001956	NP_001001956	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C,	159	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AAATGTAGTTTGTACTGCAGA	0.438													22	47	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16893354	16893354	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16893354C>A	uc001ioo.2	-	60	9595	c.9543G>T	c.(9541-9543)AAG>AAT	p.K3181N	CUBN_uc009xjq.1_RNA	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3181	CUB 24.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGTTTAAATTCTTGTCATACA	0.408													21	22	---	---	---	---	PASS
ST8SIA6	338596	broad.mit.edu	37	10	17363099	17363099	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17363099C>T	uc001ipd.2	-	8	975	c.975G>A	c.(973-975)TTG>TTA	p.L325L	ST8SIA6_uc010qce.1_RNA	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	325	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TTGTGATCATCAAGCCGGTGG	0.443													47	71	---	---	---	---	PASS
PLXDC2	84898	broad.mit.edu	37	10	20508041	20508041	+	Intron	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20508041G>C	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						GGTAGGAATTGATACTTTTCT	0.303													6	8	---	---	---	---	PASS
MTPAP	55149	broad.mit.edu	37	10	30602551	30602551	+	Missense_Mutation	SNP	C	G	G	rs148562969	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30602551C>G	uc001iva.3	-	9	1799	c.1736G>C	c.(1735-1737)AGT>ACT	p.S579T	MTPAP_uc001ivb.3_Missense_Mutation_p.S709T	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	579					cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						TGTCTGAGTACTAATTGTTCT	0.358													35	61	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38344864	38344864	+	Silent	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38344864A>T	uc001izh.2	+	5	1987	c.1809A>T	c.(1807-1809)ACA>ACT	p.T603T	ZNF33A_uc001izg.2_Silent_p.T604T|ZNF33A_uc010qev.1_Silent_p.T610T|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	603						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						GAACACATACAGGGGAGAAAC	0.373													14	25	---	---	---	---	PASS
SLC18A3	6572	broad.mit.edu	37	10	50819812	50819812	+	Silent	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50819812C>G	uc001jhw.2	+	1	1466	c.1026C>G	c.(1024-1026)GTC>GTG	p.V342V	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	342	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2						TGCTGGGCGTCTACCTCACCG	0.672													16	30	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106983002	106983002	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106983002A>G	uc001kyi.1	+	20	3090	c.2863A>G	c.(2863-2865)ACA>GCA	p.T955A	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	955	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CGGCAATAGCACAAAGGTTTG	0.453													41	77	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118451864	118451864	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118451864G>T	uc001lct.2	-	6	766	c.661C>A	c.(661-663)CAG>AAG	p.Q221K	HSPA12A_uc001lcu.2_Missense_Mutation_p.Q138K	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	221							ATP binding			ovary(1)	1				all cancers(201;0.0158)		ACCCTCACCTGGTAGGCAGCT	0.597													5	122	---	---	---	---	PASS
PRLHR	2834	broad.mit.edu	37	10	120354611	120354611	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120354611G>T	uc001ldp.1	-	2	285	c.146C>A	c.(145-147)CCC>CAC	p.P49H		NM_004248	NP_004239	P49683	PRLHR_HUMAN	G protein-coupled receptor 10	49	Extracellular (Potential).				female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		GCTCTGGAAGGGCGTGACGGC	0.697													4	15	---	---	---	---	PASS
C10orf90	118611	broad.mit.edu	37	10	128153547	128153547	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128153547T>C	uc001ljq.2	-	4	1373	c.1252A>G	c.(1252-1254)AAA>GAA	p.K418E	C10orf90_uc001ljp.2_Intron|C10orf90_uc010qum.1_Missense_Mutation_p.K515E|C10orf90_uc009yao.2_3'UTR|C10orf90_uc001ljo.2_5'Flank	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611	418										ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GAAAATACTTTTGTGTGTACT	0.423													15	21	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093094	1093094	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093094T>G	uc001lsx.1	+	31	12026	c.11999T>G	c.(11998-12000)GTG>GGG	p.V4000G		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4000						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accactacggtgaccccaacc	0.000													3	8	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1272059	1272059	+	Intron	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1272059G>C	uc009ycr.1	+						MUC5B_uc001ltb.2_Missense_Mutation_p.R4653T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		cacaccgccagagtgctgacc	0.169													4	6	---	---	---	---	PASS
OR52A4	390053	broad.mit.edu	37	11	5142713	5142713	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142713C>T	uc001lzz.1	-	1	96	c.96G>A	c.(94-96)GGG>GGA	p.G32G	OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		AGAATGGAATCCCAATCCAGC	0.423													6	145	---	---	---	---	PASS
ZNF214	7761	broad.mit.edu	37	11	7021527	7021527	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7021527C>A	uc001mfa.2	-	3	1690	c.1387G>T	c.(1387-1389)GTC>TTC	p.V463F	ZNF214_uc010ray.1_Missense_Mutation_p.V463F|ZNF214_uc009yfh.1_Missense_Mutation_p.V463F	NM_013249	NP_037381	Q9UL59	ZN214_HUMAN	zinc finger protein 214	463	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		CCTGTATGGACTCTCTGATGA	0.423													12	43	---	---	---	---	PASS
RIC3	79608	broad.mit.edu	37	11	8132433	8132433	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8132433G>A	uc001mgd.2	-	6	976	c.922C>T	c.(922-924)CAT>TAT	p.H308Y	RIC3_uc001mgb.2_Missense_Mutation_p.H146Y|RIC3_uc001mgc.2_Missense_Mutation_p.H307Y|RIC3_uc001mge.2_Missense_Mutation_p.H126Y|RIC3_uc010rbl.1_Missense_Mutation_p.H258Y|RIC3_uc010rbm.1_Missense_Mutation_p.H336Y|RIC3_uc009yfm.2_Missense_Mutation_p.H227Y|RIC3_uc009yfn.2_Missense_Mutation_p.H111Y	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	308	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCGTCTTCATGAAAACAGCAG	0.493													5	68	---	---	---	---	PASS
INSC	387755	broad.mit.edu	37	11	15243165	15243165	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15243165G>A	uc001mly.2	+	8	1149	c.1103G>A	c.(1102-1104)AGC>AAC	p.S368N	INSC_uc001mlz.2_Missense_Mutation_p.S321N|INSC_uc001mma.2_Missense_Mutation_p.S321N|INSC_uc010rcs.1_Missense_Mutation_p.S356N|INSC_uc001mmb.2_Missense_Mutation_p.S321N|INSC_uc001mmc.2_Missense_Mutation_p.S279N	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	368					cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						TTCCTGGAGAGCATGGAGGAG	0.632													6	21	---	---	---	---	PASS
OR4X2	119764	broad.mit.edu	37	11	48266676	48266676	+	Silent	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48266676G>T	uc001ngs.1	+	1	21	c.21G>T	c.(19-21)CTG>CTT	p.L7L		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	7	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TCATTTTTCTGGTACTTTCTC	0.418													5	68	---	---	---	---	PASS
APLNR	187	broad.mit.edu	37	11	57004291	57004291	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57004291G>A	uc001njo.2	-	1	637	c.188C>T	c.(187-189)TCA>TTA	p.S63L	APLNR_uc001njn.3_RNA	NM_005161	NP_005152	P35414	APJ_HUMAN	apelin receptor	63	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			lung(5)|ovary(1)	6						GATATCAGCTGAGCGCCTCTT	0.612													10	38	---	---	---	---	PASS
CCDC86	79080	broad.mit.edu	37	11	60609992	60609992	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60609992G>A	uc001nqa.2	+	1	564	c.395G>A	c.(394-396)GGA>GAA	p.G132E	CCDC86_uc001nqb.2_Intron	NM_024098	NP_077003	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	132	Pro-rich.				interspecies interaction between organisms	nucleus					0						CAGGACCAGGGAGTACTGGCC	0.617													13	58	---	---	---	---	PASS
DDB1	1642	broad.mit.edu	37	11	61070589	61070589	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61070589C>A	uc001nrc.3	-	23	3097	c.2871G>T	c.(2869-2871)GTG>GTT	p.V957V	DDB1_uc010rle.1_Silent_p.V268V|DDB1_uc010rlf.1_Silent_p.V957V	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	957	Interaction with CDT1 and CUL4A.				cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						CCAAGATTTCCACAGCACTCA	0.438								NER					6	106	---	---	---	---	PASS
POLD4	57804	broad.mit.edu	37	11	67120556	67120556	+	Intron	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67120556G>A	uc001okm.2	-						LOC100130987_uc010rpo.1_Intron|POLD4_uc001okn.2_Intron|POLD4_uc001oko.2_Intron|POLD4_uc001okp.1_Intron	NM_021173	NP_066996	Q9HCU8	DPOD4_HUMAN	DNA-directed DNA polymerase delta 4						base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA-directed DNA polymerase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(15;3.08e-06)			CCCCTGCAATGACAGCTGCTC	0.657													3	9	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68191058	68191058	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68191058G>A	uc001ont.2	+	14	3204	c.3129G>A	c.(3127-3129)GAG>GAA	p.E1043E	LRP5_uc009ysg.2_Silent_p.E453E	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1043	LDL-receptor class B 17.|Beta-propeller 4.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						GGACGTGCGAGGCCACCAATA	0.622													9	37	---	---	---	---	PASS
NUMA1	4926	broad.mit.edu	37	11	71740319	71740319	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71740319C>A	uc001orl.1	-	4	232	c.60G>T	c.(58-60)GTG>GTT	p.V20V	NUMA1_uc001ork.1_Silent_p.V20V|NUMA1_uc001orm.1_Silent_p.V20V|NUMA1_uc009ysx.1_Silent_p.V20V|NUMA1_uc001oro.1_Silent_p.V20V|NUMA1_uc009ysy.1_Silent_p.V20V|NUMA1_uc001orp.2_Silent_p.V20V|NUMA1_uc001orq.2_Silent_p.V20V	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	20					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						CAGGGTCAGCCACGTGTAGAC	0.498			T	RARA	APL								3	14	---	---	---	---	PASS
ELMOD1	55531	broad.mit.edu	37	11	107524922	107524922	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107524922G>T	uc010rvs.1	+	10	1076	c.672G>T	c.(670-672)GAG>GAT	p.E224D	ELMOD1_uc001pjm.2_Missense_Mutation_p.E216D|ELMOD1_uc010rvt.1_Missense_Mutation_p.E218D	NM_018712	NP_061182	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1 isoform 1	224	ELMO.				phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		CAGAATGGGAGAAGAAAAGGA	0.373													4	23	---	---	---	---	PASS
FAM55A	120400	broad.mit.edu	37	11	114393009	114393009	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114393009A>C	uc001ppa.2	-	6	1316	c.899T>G	c.(898-900)TTT>TGT	p.F300C	FAM55A_uc010rxd.1_Missense_Mutation_p.F149C	NM_152315	NP_689528	Q8N323	FA55A_HUMAN	hypothetical protein LOC120400	442						extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)		AAATGGTCTAAAGTGCTGGCC	0.438													13	44	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	121028813	121028813	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121028813C>T	uc010rzo.1	+	13	4569	c.4569C>T	c.(4567-4569)ATC>ATT	p.I1523I		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1523	VWFD 4.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGCCCGACATCTCCTTCCAGC	0.577													12	38	---	---	---	---	PASS
OR8A1	390275	broad.mit.edu	37	11	124440189	124440189	+	Silent	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124440189C>G	uc010san.1	+	1	225	c.225C>G	c.(223-225)CCC>CCG	p.P75P		NM_001005194	NP_001005194	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A,	75	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TGCACACCCCCATGTACTACT	0.488													9	68	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4736450	4736450	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4736450C>A	uc001qnb.3	-	4	1847	c.1618G>T	c.(1618-1620)GCC>TCC	p.A540S		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	540					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						CCTCCCTGGGCCAGGTGATAT	0.517													6	26	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4736451	4736451	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4736451C>A	uc001qnb.3	-	4	1846	c.1617G>T	c.(1615-1617)CTG>CTT	p.L539L		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	539					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						CTCCCTGGGCCAGGTGATATT	0.522													6	26	---	---	---	---	PASS
GNB3	2784	broad.mit.edu	37	12	6952169	6952169	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6952169G>A	uc001qrd.2	+	5	537	c.132G>A	c.(130-132)CAG>CAA	p.Q44Q	GNB3_uc001qrc.2_5'UTR|GNB3_uc009zfe.2_Silent_p.Q44Q	NM_002075	NP_002066	P16520	GBB3_HUMAN	guanine nucleotide-binding protein, beta-3	44					cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|GTPase binding|signal transducer activity				0						GACGAGTCCAGATGCGGACGC	0.597													7	24	---	---	---	---	PASS
C1R	715	broad.mit.edu	37	12	7187907	7187907	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7187907C>A	uc010sfy.1	-	10	2106	c.2047G>T	c.(2047-2049)GGC>TGC	p.G683C		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	683	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AAGCCATAGCCCCTGCTGCAC	0.572													6	41	---	---	---	---	PASS
CD163L1	283316	broad.mit.edu	37	12	7528090	7528090	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7528090C>A	uc001qsy.2	-	11	2814	c.2788G>T	c.(2788-2790)GAC>TAC	p.D930Y	CD163L1_uc010sge.1_Missense_Mutation_p.D940Y	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	930	SRCR 9.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11						TCTTCTGGGTCCCAGTGGGTG	0.512													6	24	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9243921	9243921	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9243921G>C	uc001qvk.1	-	19	2458	c.2345C>G	c.(2344-2346)TCC>TGC	p.S782C	A2M_uc009zgk.1_Missense_Mutation_p.S632C	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	782					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	AGAGGCAGTGGAAGAGATACC	0.562													21	99	---	---	---	---	PASS
RAPGEF3	10411	broad.mit.edu	37	12	48142237	48142237	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48142237C>A	uc009zkp.2	-	11	1557	c.1117G>T	c.(1117-1119)GAG>TAG	p.E373*	RAPGEF3_uc010sln.1_5'Flank|RAPGEF3_uc001rpy.2_5'Flank|RAPGEF3_uc009zkq.2_Nonsense_Mutation_p.E373*|RAPGEF3_uc001rpz.3_Nonsense_Mutation_p.E415*|RAPGEF3_uc001rqa.2_5'Flank|RAPGEF3_uc009zkr.2_RNA|RAPGEF3_uc009zks.2_Nonsense_Mutation_p.E427*	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	373					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TTGCCCTTACCTGTTGGGTCA	0.532													4	31	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53038841	53038841	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53038841C>G	uc001sat.2	-	9	1915	c.1882G>C	c.(1882-1884)GAA>CAA	p.E628Q		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	628	Tail.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		CCAAAAGCTTCACCTGAGCTA	0.537													6	88	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57594585	57594585	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57594585C>T	uc001snd.2	+	64	10678	c.10212C>T	c.(10210-10212)GAC>GAT	p.D3404D		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3404	Extracellular (Potential).|LDL-receptor class A 22.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACAACAGTGACGAGGCCAACT	0.597													5	53	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62887715	62887715	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62887715G>T	uc001sre.2	+	3	587	c.196G>T	c.(196-198)GAG>TAG	p.E66*	MON2_uc009zqj.2_Nonsense_Mutation_p.E66*|MON2_uc010ssl.1_5'UTR|MON2_uc010ssm.1_Nonsense_Mutation_p.E66*|MON2_uc010ssn.1_Nonsense_Mutation_p.E66*|MON2_uc001srd.1_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	66					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAACAGCTCAGAGGTTGTACA	0.328													3	11	---	---	---	---	PASS
TMPO	7112	broad.mit.edu	37	12	98927852	98927852	+	Intron	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98927852C>T	uc001tfj.2	+						TMPO_uc001tfi.1_Intron|TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron|TMPO_uc001tfh.1_Missense_Mutation_p.S606L	NM_001032283	NP_001027454	P42167	LAP2B_HUMAN	thymopoietin isoform beta							integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2						ATTCTTAGCTCAGATCCTAGT	0.453													5	47	---	---	---	---	PASS
UTP20	27340	broad.mit.edu	37	12	101680199	101680199	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101680199G>C	uc001tia.1	+	5	583	c.427G>C	c.(427-429)GAG>CAG	p.E143Q	UTP20_uc009ztz.1_Missense_Mutation_p.E143Q	NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	143					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						TCAGGACACAGAGTTGTTAGA	0.433													6	113	---	---	---	---	PASS
IGF1	3479	broad.mit.edu	37	12	102811758	102811758	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102811758C>G	uc001tjp.3	-	4	645	c.426G>C	c.(424-426)AAG>AAC	p.K142N	IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Missense_Mutation_p.K142N|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3	142					anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						ACTTCGTGTTCTTGTTGGTAG	0.468													10	115	---	---	---	---	PASS
RPH3A	22895	broad.mit.edu	37	12	113307828	113307828	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113307828C>T	uc010syl.1	+	10	1142	c.780C>T	c.(778-780)TCC>TCT	p.S260S	RPH3A_uc001ttz.2_Silent_p.S260S|RPH3A_uc001tty.2_Silent_p.S256S|RPH3A_uc009zwe.1_Silent_p.S256S|RPH3A_uc010sym.1_Silent_p.S211S|RPH3A_uc001tua.2_Silent_p.S20S	NM_001143854	NP_001137326	Q9Y2J0	RP3A_HUMAN	rabphilin 3A homolog isoform 1	260	Pro-rich.				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)		CTGGAGACTCCAGCCGGAGCC	0.542													4	16	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117669887	117669887	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117669887G>A	uc001twm.1	-	22	3971	c.3285C>T	c.(3283-3285)ATC>ATT	p.I1095I		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1095	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	AGGCCTGGAAGATGGTGCAGG	0.597													5	20	---	---	---	---	PASS
B3GNT4	79369	broad.mit.edu	37	12	122691663	122691663	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122691663C>T	uc001ubx.2	+	3	1083	c.865C>T	c.(865-867)CGG>TGG	p.R289W	B3GNT4_uc001uby.2_Missense_Mutation_p.R264W	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	289	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		AGCCACAGTGCGGCGCCTCCA	0.557													8	35	---	---	---	---	PASS
ATP6V0A2	23545	broad.mit.edu	37	12	124220151	124220151	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124220151C>G	uc001ufr.2	+	8	1053	c.805C>G	c.(805-807)CGC>GGC	p.R269G	ATP6V0A2_uc001ufq.1_Missense_Mutation_p.R269G	NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	269	Cytoplasmic (Potential).				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GCTGAACACCCGCATCCAGGA	0.493													5	12	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133312095	133312095	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133312095C>T	uc001ukx.2	-	9	1664	c.1597G>A	c.(1597-1599)GAA>AAA	p.E533K	ANKLE2_uc009zyw.1_5'Flank|ANKLE2_uc001uky.3_Missense_Mutation_p.E471K	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	533						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CGAAAATCTTCTGCCTATGAA	0.527													11	39	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111134895	111134895	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111134895C>A	uc001vqx.2	+	32	3080	c.2791C>A	c.(2791-2793)CAA>AAA	p.Q931K		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	931	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGATGGTTTCCAAGGCATGCC	0.522													5	140	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20216239	20216239	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20216239C>T	uc010tkt.1	+	1	653	c.653C>T	c.(652-654)TCT>TTT	p.S218F		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	218	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTACTATTCTCTTATGCTATC	0.507													11	63	---	---	---	---	PASS
FLJ10357	55701	broad.mit.edu	37	14	21548879	21548879	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21548879G>T	uc001vzp.2	+	12	2463	c.2434G>T	c.(2434-2436)GAC>TAC	p.D812Y	FLJ10357_uc001vzo.1_5'UTR|FLJ10357_uc010aij.2_RNA|FLJ10357_uc010tln.1_Missense_Mutation_p.D98Y	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701	812					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)		TATGCCTGGGGACACCTTGTC	0.647													10	34	---	---	---	---	PASS
MYH7	4625	broad.mit.edu	37	14	23889431	23889431	+	Nonsense_Mutation	SNP	C	A	A	rs141735183		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23889431C>A	uc001wjx.2	-	27	3455	c.3349G>T	c.(3349-3351)GAG>TAG	p.E1117*	MIR208B_hsa-mir-208b|MI0005570_5'Flank	NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1117	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		tcctccagctcctcGATGCGT	0.562													9	22	---	---	---	---	PASS
FOXG1	2290	broad.mit.edu	37	14	29237714	29237714	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29237714T>G	uc001wqe.2	+	1	1428	c.1229T>G	c.(1228-1230)CTC>CGC	p.L410R		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	410					axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GTCAACCTGCTCGCGGGCCAG	0.687													4	27	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	32902696	32902696	+	5'UTR	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32902696C>T	uc001wrq.2	+	2					AKAP6_uc010aml.2_5'UTR	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTTTAGACTTCTCCATGTTAA	0.458													11	28	---	---	---	---	PASS
EGLN3	112399	broad.mit.edu	37	14	34400377	34400377	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34400377G>C	uc001wsa.3	-	2	728	c.402C>G	c.(400-402)CGC>CGG	p.R134R	EGLN3_uc001wry.2_Silent_p.R40R|EGLN3_uc001wrz.2_Silent_p.R134R	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3	134	Fe2OG dioxygenase.				apoptosis	cytoplasm|nucleus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding				0	Breast(36;0.0303)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.000246)|Lung(238;0.000959)|Epithelial(34;0.155)	GBM - Glioblastoma multiforme(112;0.0118)	Vitamin C(DB00126)	TGTCCACGTGGCGAACATAAC	0.473													14	43	---	---	---	---	PASS
FOXA1	3169	broad.mit.edu	37	14	38061517	38061517	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38061517C>T	uc001wuf.2	-	2	784	c.472G>A	c.(472-474)GAC>AAC	p.D158N	FOXA1_uc010tpz.1_Missense_Mutation_p.D125N	NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	158					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GTCTTGGCGTcgccgccgccg	0.557													13	31	---	---	---	---	PASS
RPL10L	140801	broad.mit.edu	37	14	47120615	47120615	+	Missense_Mutation	SNP	C	G	G	rs11557561		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47120615C>G	uc001wwg.2	-	1	414	c.325G>C	c.(325-327)GAC>CAC	p.D109H		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	109					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1						TGGAGCCTGTCAGCCCCAGCA	0.547													9	45	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72190544	72190544	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72190544G>C	uc001xms.2	+	16	4800	c.4452G>C	c.(4450-4452)CTG>CTC	p.L1484L	SIPA1L1_uc001xmt.2_Silent_p.L1463L|SIPA1L1_uc001xmu.2_Silent_p.L1463L|SIPA1L1_uc001xmv.2_Silent_p.L1484L|SIPA1L1_uc010ttm.1_Silent_p.L938L|SIPA1L1_uc001xmw.2_Silent_p.L249L	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1484	Ser-rich.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GCAAGTACCTGATTGGATGGA	0.428													10	131	---	---	---	---	PASS
ANGEL1	23357	broad.mit.edu	37	14	77272759	77272759	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77272759C>T	uc001xsv.2	-	5	1493	c.1380G>A	c.(1378-1380)AAG>AAA	p.K460K	ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120	Q9UNK9	ANGE1_HUMAN	angel homolog 1	460										ovary(2)|central_nervous_system(1)|skin(1)	4			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCCATTTCACCTTCCAGGCTG	0.532													5	37	---	---	---	---	PASS
CPSF2	53981	broad.mit.edu	37	14	92622903	92622903	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92622903A>G	uc001yah.1	+	12	1760	c.1523A>G	c.(1522-1524)GAT>GGT	p.D508G		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2	508					histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		ACAAATGGAGATGAACCTATG	0.323													15	74	---	---	---	---	PASS
C14orf177	283598	broad.mit.edu	37	14	99183521	99183521	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99183521A>G	uc001yfz.1	+	4	707	c.288A>G	c.(286-288)ATA>ATG	p.I96M		NM_182560	NP_872366	Q52M58	CN177_HUMAN	hypothetical protein LOC283598	96											0		Melanoma(154;0.128)				ATCACCAAATAATGTCTGCTT	0.423													17	68	---	---	---	---	PASS
ASPG	374569	broad.mit.edu	37	14	104559906	104559906	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104559906C>T	uc001yoq.1	+	3	330	c.270C>T	c.(268-270)ATC>ATT	p.I90I	ASPG_uc001yoo.1_Silent_p.I118I|ASPG_uc001yop.1_Silent_p.I90I|ASPG_uc001yor.1_Silent_p.I90I	NM_001080464	NP_001073933	Q86U10	LPP60_HUMAN	60 kDa lysophospholipase	90	Asparaginase.				lipid catabolic process		1-alkyl-2-acetylglycerophosphocholine esterase activity|asparaginase activity|lysophospholipase activity				0						ACATGACCATCGCTGAGTGGG	0.408													20	79	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105411849	105411849	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105411849G>A	uc010axc.1	-	7	10059	c.9939C>T	c.(9937-9939)TTC>TTT	p.F3313F	AHNAK2_uc001ypx.2_Silent_p.F3213F	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3313						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACGGCATCTTGAATTTGGGCA	0.622													14	352	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106209343	106209343	+	RNA	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106209343T>A	uc010tyt.1	-	3625		c.58380A>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_5'UTR|uc001ysf.2_5'UTR|uc001ysg.1_RNA					Parts of antibodies, mostly variable regions.												0						CCAGGGCTGCTGTGCCCCCAG	0.672													5	19	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22382701	22382701	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22382701G>T	uc001yuc.1	+	7	1210	c.229G>T	c.(229-231)GTG>TTG	p.V77L	LOC727924_uc001yub.1_RNA|OR4N4_uc010tzv.1_Missense_Mutation_p.V77L	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	77	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTCCTTCATTGTGGCTCCCAG	0.493													18	190	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41280040	41280040	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41280040G>A	uc001zni.2	-	30	3916	c.3703C>T	c.(3703-3705)CTG>TTG	p.L1235L	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	1235	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						GCTCTTTGCAGAATGCGTTCT	0.502													12	214	---	---	---	---	PASS
MGA	23269	broad.mit.edu	37	15	42042356	42042356	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42042356G>T	uc010ucy.1	+	17	6732	c.6551G>T	c.(6550-6552)AGG>ATG	p.R2184M	MGA_uc010ucz.1_Missense_Mutation_p.R1975M|MGA_uc010uda.1_Missense_Mutation_p.R800M|MGA_uc001zoi.2_Missense_Mutation_p.R398M	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2145	Basic motif.					MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		CCCTTAACCAGGAAATGTGTT	0.428													22	75	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54685268	54685268	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54685268G>C	uc002ack.2	+	16	4736	c.4736G>C	c.(4735-4737)CGT>CCT	p.R1579P	UNC13C_uc002acl.2_Missense_Mutation_p.R409P	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1579					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)		GATATTCCTCGTGAAGATCAG	0.388													12	54	---	---	---	---	PASS
SIN3A	25942	broad.mit.edu	37	15	75684849	75684849	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75684849G>C	uc002bai.2	-	15	2844	c.2585C>G	c.(2584-2586)CCT>CGT	p.P862R	SIN3A_uc002baj.2_Missense_Mutation_p.P862R|SIN3A_uc010uml.1_Missense_Mutation_p.P862R	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	862					blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						CTTGGACTTAGGGGGACTGCC	0.428													5	87	---	---	---	---	PASS
ST20	400410	broad.mit.edu	37	15	80191279	80191279	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80191279G>C	uc002bez.3	-	3	914	c.234C>G	c.(232-234)TAC>TAG	p.Y78*	ST20_uc002bfa.3_Nonsense_Mutation_p.Y78*|MTHFS_uc002bex.3_5'Flank	NM_001100879	NP_001094349	Q9HBF5	ST20_HUMAN	cervical cancer suppressor-1	78											0						TTATTTAAAAGTAGAAGTATG	0.338													3	62	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100341295	100341295	+	RNA	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100341295C>A	uc010urx.1	-	3		c.352G>T			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|C15orf51_uc010bow.2_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						AGGAGTCCACCAGGTTCTGGG	0.547													4	50	---	---	---	---	PASS
E4F1	1877	broad.mit.edu	37	16	2282275	2282275	+	Silent	SNP	C	G	G	rs149258624		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2282275C>G	uc002cpm.2	+	4	567	c.519C>G	c.(517-519)CTC>CTG	p.L173L	E4F1_uc010bsi.2_Silent_p.L173L|E4F1_uc010bsj.2_Silent_p.L173L	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	173					cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						GGCTGGGGCTCGCAGGGGAGG	0.667													9	28	---	---	---	---	PASS
ZNF434	54925	broad.mit.edu	37	16	3434852	3434852	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3434852G>C	uc002cuz.2	-	5	1007	c.205C>G	c.(205-207)CAG>GAG	p.Q69E	ZNF434_uc002cux.3_Missense_Mutation_p.Q280E|ZNF434_uc010uwx.1_5'UTR|ZNF434_uc002cuy.3_5'UTR|ZNF434_uc010uwy.1_5'UTR|ZNF434_uc010uwz.1_Missense_Mutation_p.Q280E|ZNF434_uc010uxa.1_Missense_Mutation_p.Q69E	NM_017810	NP_060280	Q9NX65	ZN434_HUMAN	zinc finger protein 434	69					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CTGTTCTGCTGACAGGTCTGG	0.527													4	112	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9862740	9862740	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9862740C>G	uc002czo.3	-	12	3111	c.2563G>C	c.(2563-2565)GAC>CAC	p.D855H	GRIN2A_uc010uym.1_Missense_Mutation_p.D855H|GRIN2A_uc010uyn.1_Missense_Mutation_p.D698H|GRIN2A_uc002czr.3_Missense_Mutation_p.D855H	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	855	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	CCAGGCCGGTCGGAGCACACG	0.567													15	79	---	---	---	---	PASS
ACSM5	54988	broad.mit.edu	37	16	20422839	20422839	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20422839G>A	uc002dhe.2	+	2	180	c.33G>A	c.(31-33)CAG>CAA	p.Q11Q	ACSM5_uc002dhd.1_Silent_p.Q11Q	NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	11					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2						TAGTCCTCCAGGCACTGAGGA	0.557													7	21	---	---	---	---	PASS
ACSM1	116285	broad.mit.edu	37	16	20702312	20702312	+	Intron	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20702312C>G	uc002dhm.1	-						ACSM1_uc002dhn.1_Intron|ACSM1_uc010bwg.1_Intron	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member						benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2						CACGGCAGATCTCTTACCTTC	0.443													14	44	---	---	---	---	PASS
TBX6	6911	broad.mit.edu	37	16	30100411	30100411	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30100411C>T	uc010veh.1	-	4	534	c.474G>A	c.(472-474)TGG>TGA	p.W158*	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Nonsense_Mutation_p.W158*	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	158	T-box.				anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						CGCTGGGCTCCCAGCGCCGGC	0.647													4	27	---	---	---	---	PASS
TBX6	6911	broad.mit.edu	37	16	30102165	30102165	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30102165C>T	uc010veh.1	-	3	327	c.267G>A	c.(265-267)CCG>CCA	p.P89P	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Silent_p.P89P	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	89					anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						GGCTGACCCCCGGGAGGGAAT	0.662													5	17	---	---	---	---	PASS
PHKB	5257	broad.mit.edu	37	16	47732355	47732355	+	Intron	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47732355C>G	uc002eev.3	+						PHKB_uc002eeu.3_Intron|PHKB_uc002eew.3_Intron	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TCTGTCTCTTCTAGTTACTTA	0.368													3	46	---	---	---	---	PASS
SLC12A3	6559	broad.mit.edu	37	16	56906359	56906359	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56906359T>A	uc010ccm.2	+	7	978	c.949T>A	c.(949-951)TTC>ATC	p.F317I	SLC12A3_uc002ekd.3_Missense_Mutation_p.F317I|SLC12A3_uc010ccn.2_Missense_Mutation_p.F316I	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3	317					sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CTCCAAAGGCTTCTTCAGCTA	0.567													6	32	---	---	---	---	PASS
MIR328	442901	broad.mit.edu	37	16	67236282	67236282	+	RNA	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67236282C>G	hsa-mir-328|MI0000804	-			c.17C>G			ELMO3_uc002esa.2_Intron|ELMO3_uc002esb.2_Intron|ELMO3_uc002esc.2_Intron|uc010vjf.1_RNA																	0						CTGAGCCCCTCCTGCCCCCCC	0.632													4	59	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72821790	72821790	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72821790T>C	uc002fck.2	-	10	11058	c.10385A>G	c.(10384-10386)CAG>CGG	p.Q3462R	ZFHX3_uc002fcl.2_Missense_Mutation_p.Q2548R	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	3462					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				CAACTTGTACTGCACCTTTGG	0.597													13	50	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74497334	74497334	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74497334A>C	uc002fcy.3	-	20	2761	c.2711T>G	c.(2710-2712)TTG>TGG	p.L904W	GLG1_uc002fcx.2_Missense_Mutation_p.L904W|GLG1_uc002fcw.3_Missense_Mutation_p.L893W|GLG1_uc002fcz.3_Missense_Mutation_p.L321W	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	904	Cys-rich GLG1 13.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						ATTTTGCTTCAAGCACTGCAA	0.413													12	33	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76555068	76555068	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76555068C>A	uc002feu.1	+	18	2782	c.2397C>A	c.(2395-2397)ACC>ACA	p.T799T	CNTNAP4_uc002fev.1_Silent_p.T663T|CNTNAP4_uc010chb.1_Silent_p.T726T|CNTNAP4_uc002fex.1_Silent_p.T802T	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	799	Extracellular (Potential).|Laminin G-like 3.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						CCTTTGATACCGAGGCTTCAT	0.323													19	81	---	---	---	---	PASS
DEF8	54849	broad.mit.edu	37	16	90015915	90015915	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90015915G>A	uc002fpn.1	+	2	131	c.42G>A	c.(40-42)GCG>GCA	p.A14A	DEF8_uc002fpl.2_5'UTR|DEF8_uc002fpm.2_Intron|DEF8_uc002fpo.1_5'UTR|DEF8_uc002fpp.1_5'UTR|DEF8_uc010vpq.1_5'UTR|DEF8_uc010vpr.1_5'UTR	NM_207514	NP_997397	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 isoform 1	14					intracellular signal transduction		zinc ion binding			central_nervous_system(1)	1		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CCTGGCAGGCGATGCAGGTAT	0.662													10	44	---	---	---	---	PASS
AMAC1L3	643664	broad.mit.edu	37	17	7386197	7386197	+	Silent	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7386197T>C	uc010cmj.1	+	2	1009	c.894T>C	c.(892-894)TAT>TAC	p.Y298Y	ZBTB4_uc002ghd.3_Intron|POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.3_5'Flank	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3	298	DUF6 2.|Helical; (Potential).					integral to membrane					0		Prostate(122;0.173)				TACTGCAGTATTATATGCTCC	0.572													7	89	---	---	---	---	PASS
UBB	7314	broad.mit.edu	37	17	16285361	16285361	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16285361G>T	uc002gpx.2	+	2	278	c.140G>T	c.(139-141)GGC>GTC	p.G47V	UBB_uc010vwe.1_Missense_Mutation_p.G47V	NM_018955	NP_061828	P0CG47	UBB_HUMAN	ubiquitin B precursor	47	Ubiquitin-like 1.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			skin(3)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		ATCTTTGCAGGCAAGCAGCTG	0.547													11	72	---	---	---	---	PASS
FLJ40504	284085	broad.mit.edu	37	17	26603835	26603835	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26603835C>T	uc002has.3	-	3	736	c.640G>A	c.(640-642)GAG>AAG	p.E214K		NM_173624	NP_775895			SubName: Full=Putative uncharacterized protein FLJ40504; SubName: Full=cDNA FLJ40504 fis, clone TESTI2045509, highly similar to KERATIN, TYPE I CYTOSKELETAL 18;												0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		ATGTCACTCTCCACAGACTGG	0.517													12	29	---	---	---	---	PASS
COASY	80347	broad.mit.edu	37	17	40717709	40717709	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40717709C>T	uc002hzz.2	+	9	1675	c.1518C>T	c.(1516-1518)CTC>CTT	p.L506L	COASY_uc010cyj.2_Silent_p.L535L|COASY_uc002iab.2_Silent_p.L211L|COASY_uc002iad.2_Silent_p.L506L|COASY_uc002iac.2_Silent_p.L506L|COASY_uc002iae.2_Silent_p.L301L|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042529	NP_001035994	Q13057	COASY_HUMAN	coenzyme A synthase isoform a	506	DPCK.				coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GGGATGGCCTCAGTGAAGCCG	0.577													4	29	---	---	---	---	PASS
PPP1R9B	84687	broad.mit.edu	37	17	48212999	48212999	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48212999C>T	uc002iqh.3	-	11	2322	c.2319G>A	c.(2317-2319)CTG>CTA	p.L773L		NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	771	Potential.|Interacts with TGN38 (By similarity).				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0						TCTCCTTTTTCAGGAACTCGA	0.602													4	12	---	---	---	---	PASS
RSAD1	55316	broad.mit.edu	37	17	48559474	48559474	+	Missense_Mutation	SNP	G	A	A	rs138384713		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48559474G>A	uc002iqw.1	+	4	553	c.497G>A	c.(496-498)CGG>CAG	p.R166Q	RSAD1_uc010wmq.1_RNA	NM_018346	NP_060816	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing	166					porphyrin biosynthetic process	mitochondrion	4 iron, 4 sulfur cluster binding|coproporphyrinogen oxidase activity|metal ion binding				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			ACTGAGCTCCGGCTGTTGGGA	0.612											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	27	83	---	---	---	---	PASS
CSNK1D	1453	broad.mit.edu	37	17	80211007	80211007	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80211007G>T	uc002kej.2	-	4	766	c.450C>A	c.(448-450)TTC>TTA	p.F150L	SLC16A3_uc002kee.2_Intron|CSNK1D_uc002kef.2_Missense_Mutation_p.F150L|CSNK1D_uc002kei.2_Missense_Mutation_p.F150L|CSNK1D_uc010wvj.1_Intron|CSNK1D_uc010dil.2_5'Flank|CSNK1D_uc002keh.2_Missense_Mutation_p.F15L|CSNK1D_uc010dim.1_5'Flank	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1	150	Protein kinase.				circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	centrosome|cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			TGGCCAGCCCGAAGTCGATGA	0.552													4	88	---	---	---	---	PASS
TMEM200C	645369	broad.mit.edu	37	18	5891854	5891854	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5891854G>A	uc002kmx.1	-	1	250	c.209C>T	c.(208-210)GCG>GTG	p.A70V		NM_001080209	NP_001073678	A6NKL6	T200C_HUMAN	transmembrane protein 200C	70	Helical; (Potential).					integral to membrane					0						GCCCACCACCGCCATGGCTAT	0.662													11	12	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	7014032	7014032	+	Missense_Mutation	SNP	C	A	A	rs138476816		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7014032C>A	uc002knm.2	-	23	3239	c.3145G>T	c.(3145-3147)GTG>TTG	p.V1049L	LAMA1_uc010wzj.1_Missense_Mutation_p.V525L	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1049	Laminin EGF-like 12.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTCGACCCCACGAGACTGCAA	0.483													5	14	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21494522	21494522	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21494522A>T	uc002kuq.2	+	57	7564	c.7478A>T	c.(7477-7479)CAG>CTG	p.Q2493L	LAMA3_uc002kur.2_Missense_Mutation_p.Q2437L|LAMA3_uc002kus.3_Missense_Mutation_p.Q884L|LAMA3_uc002kut.3_Missense_Mutation_p.Q828L	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	2493	Laminin G-like 1.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTGAAATTTCAGAGGTACAAG	0.458													6	26	---	---	---	---	PASS
OSBPL1A	114876	broad.mit.edu	37	18	21921529	21921529	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21921529T>A	uc002kve.2	-	5	550	c.376A>T	c.(376-378)ATC>TTC	p.I126F		NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	126					cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ATGCTTCTGATTTCTTCAGCA	0.343													6	43	---	---	---	---	PASS
MEX3C	51320	broad.mit.edu	37	18	48703809	48703809	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48703809C>T	uc002lfc.3	-	2	892	c.892G>A	c.(892-894)GAG>AAG	p.E298K		NM_016626	NP_057710	Q5U5Q3	MEX3C_HUMAN	ring finger and KH domain containing 2	298						cytoplasm|nucleus	RNA binding|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		GAGAAGTGCTCTGCAGCTGAG	0.483													4	45	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56202164	56202164	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56202164G>C	uc002lhj.3	-	5	5469	c.5255C>G	c.(5254-5256)TCA>TGA	p.S1752*	ALPK2_uc002lhk.1_Nonsense_Mutation_p.S1083*	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1752							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						AAGAAAGGCTGAGTTCTTTCT	0.413													6	47	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76754570	76754570	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76754570C>G	uc002lmt.2	+	2	2579	c.2579C>G	c.(2578-2580)ACC>AGC	p.T860S	SALL3_uc010dra.2_Missense_Mutation_p.T467S	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	860					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CAGCAGCTGACCGGCCTCAAG	0.682													9	17	---	---	---	---	PASS
ELAVL1	1994	broad.mit.edu	37	19	8032655	8032655	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8032655C>A	uc002mjb.2	-	5	617	c.450G>T	c.(448-450)GCG>GCT	p.A150A		NM_001419	NP_001410	Q15717	ELAV1_HUMAN	ELAV-like 1	150	RRM 2.				3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding				0						ACCGGATAAACGCAACCCCTC	0.453													5	45	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8181625	8181625	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8181625C>T	uc002mjf.2	-	28	3666	c.3645G>A	c.(3643-3645)ATG>ATA	p.M1215I		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1215	EGF-like 17.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GACCCCCTGGCATGTTGGTGC	0.632													9	37	---	---	---	---	PASS
MARCH2	51257	broad.mit.edu	37	19	8491686	8491686	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8491686G>A	uc002mjv.2	+	4	811	c.370G>A	c.(370-372)GAG>AAG	p.E124K	MARCH2_uc002mjw.2_Missense_Mutation_p.E124K|MARCH2_uc002mjx.2_Missense_Mutation_p.E124K	NM_016496	NP_057580	Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2	124					endocytosis	cytoplasmic vesicle|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						ACCCCTCACAGAGGTACCCTT	0.592													6	18	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9072126	9072126	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9072126G>T	uc002mkp.2	-	3	15524	c.15320C>A	c.(15319-15321)ACT>AAT	p.T5107N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5109	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						GTCTTTAGAAGTGGCCAGTAT	0.423													11	86	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9087486	9087486	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9087486C>A	uc002mkp.2	-	1	4533	c.4329G>T	c.(4327-4329)CTG>CTT	p.L1443L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1443	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						GAGCAAGGACCAGGGGTTCCC	0.512													5	96	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9088466	9088466	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9088466C>G	uc002mkp.2	-	1	3553	c.3349G>C	c.(3349-3351)GAA>CAA	p.E1117Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1117	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						ATTGTAATTTCTCTGGATGTT	0.468													5	70	---	---	---	---	PASS
ZNF559	84527	broad.mit.edu	37	19	9453519	9453519	+	Silent	SNP	A	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9453519A>C	uc002mlg.2	+	7	2039	c.1392A>C	c.(1390-1392)CCA>CCC	p.P464P	ZNF559_uc002mlf.2_Silent_p.P233P|ZNF559_uc010dwl.1_Silent_p.P233P|ZNF559_uc010xkn.1_Silent_p.P456P|ZNF559_uc010dwm.1_3'UTR|ZNF559_uc002mle.3_Silent_p.P528P|ZNF559_uc010dwk.1_Silent_p.P233P|ZNF559_uc002mld.2_3'UTR|ZNF559_uc010dwo.1_Intron|ZNF177_uc002mli.2_Intron|ZNF177_uc002mlj.2_Intron	NM_032497	NP_115886	Q9BR84	ZN559_HUMAN	zinc finger protein 559	464					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GGGAGAGGCCATATAAATGTC	0.443													11	32	---	---	---	---	PASS
FBXW9	84261	broad.mit.edu	37	19	12807343	12807343	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12807343G>C	uc010dyx.2	-	1	53	c.53C>G	c.(52-54)TCG>TGG	p.S18W	FBXW9_uc010xmp.1_RNA|FBXW9_uc002mum.1_Missense_Mutation_p.S18W|FBXW9_uc002mun.1_5'UTR	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	18							protein binding			ovary(1)	1						CTCTGGGTCCGAGTCATCGTC	0.677													3	38	---	---	---	---	PASS
KCNN1	3780	broad.mit.edu	37	19	18092701	18092701	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18092701G>T	uc002nht.2	+	5	992	c.682G>T	c.(682-684)GTG>TTG	p.V228L	KCNN1_uc010xqa.1_Missense_Mutation_p.V228L	NM_002248	NP_002239	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance	228	Helical; Name=Segment S4; (Potential).				synaptic transmission	voltage-gated potassium channel complex	calmodulin binding|small conductance calcium-activated potassium channel activity				0						CGACGTGGACGTGCTGCTGTC	0.672													4	15	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31038893	31038893	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31038893G>A	uc002nsu.1	+	4	2505	c.2367G>A	c.(2365-2367)ACG>ACA	p.T789T	ZNF536_uc010edd.1_Silent_p.T789T	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	789	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					ATGCCGGCACGCAGTCAGCAT	0.507													6	58	---	---	---	---	PASS
DPY19L3	147991	broad.mit.edu	37	19	32971362	32971362	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32971362T>A	uc002ntg.2	+	18	2064	c.1888T>A	c.(1888-1890)TTC>ATC	p.F630I	DPY19L3_uc002nth.1_Missense_Mutation_p.F630I|DPY19L3_uc002nti.1_RNA|DPY19L3_uc002ntj.1_Missense_Mutation_p.F52I	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3	630						integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)					CCTAAGGTCCTTCGGCACTGA	0.532													8	19	---	---	---	---	PASS
TMEM147	10430	broad.mit.edu	37	19	36037609	36037609	+	Silent	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36037609G>C	uc002oaj.1	+	4	340	c.243G>C	c.(241-243)CTG>CTC	p.L81L	uc010eec.1_5'Flank|uc002oag.2_5'Flank|TMEM147_uc002oai.1_Silent_p.L32L|TMEM147_uc002oak.1_5'UTR	NM_032635	NP_116024	Q9BVK8	TM147_HUMAN	transmembrane protein 147	81						endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TGGCAGACCTGATAGGTCTAA	0.562													12	44	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36210823	36210823	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36210823G>T	uc010eei.2	+	3	574	c.574G>T	c.(574-576)GCA>TCA	p.A192S		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	192					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GATGGTGCAGGCACTGACTGA	0.701													4	33	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40363021	40363021	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40363021C>A	uc002omp.3	-	32	15057	c.15049G>T	c.(15049-15051)GCG>TCG	p.A5017S		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	5017	VWFD 12.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GAGCCGGGCGCCCGCCATGCA	0.647													6	6	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43585368	43585368	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43585368G>A	uc002ovi.2	-	2	188	c.95C>T	c.(94-96)ACC>ATC	p.T32I	PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Missense_Mutation_p.T32I|PSG2_uc002ovq.3_Missense_Mutation_p.T32I|PSG2_uc010eiq.1_Missense_Mutation_p.T32I|PSG2_uc002ovs.3_Missense_Mutation_p.T32I|PSG2_uc002ovt.3_Missense_Mutation_p.T32I			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	32					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				TTGGGCAGTGGTGGGCAGGTT	0.493													13	111	---	---	---	---	PASS
SIGLEC6	946	broad.mit.edu	37	19	52034461	52034461	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52034461C>T	uc002pwy.2	-	2	542	c.380G>A	c.(379-381)TGG>TAG	p.W127*	SIGLEC6_uc002pwz.2_Nonsense_Mutation_p.W127*|SIGLEC6_uc002pxa.2_Nonsense_Mutation_p.W127*|SIGLEC6_uc010ydb.1_Nonsense_Mutation_p.W80*|SIGLEC6_uc010ydc.1_Nonsense_Mutation_p.W116*|SIGLEC6_uc010eoz.1_Nonsense_Mutation_p.W116*|SIGLEC6_uc010epb.1_Nonsense_Mutation_p.W80*|SIGLEC6_uc010epa.1_Nonsense_Mutation_p.W116*	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	127	Extracellular (Potential).				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GTATTTCATCCATTTGGACTT	0.537													14	74	---	---	---	---	PASS
ZNF761	388561	broad.mit.edu	37	19	53959080	53959080	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53959080G>C	uc010eqp.2	+	7	1777	c.1319G>C	c.(1318-1320)TGT>TCT	p.C440S	ZNF761_uc010ydy.1_Missense_Mutation_p.C386S|ZNF761_uc002qbt.1_Missense_Mutation_p.C386S	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761	440	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		GCTTACAAGTGTAATGAGTGT	0.378													23	87	---	---	---	---	PASS
ZNF813	126017	broad.mit.edu	37	19	53994939	53994939	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53994939C>G	uc002qbu.2	+	4	1581	c.1453C>G	c.(1453-1455)CAT>GAT	p.H485D	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	485	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		CCTCGTAATTCATACGGCAAT	0.398													7	41	---	---	---	---	PASS
CNOT3	4849	broad.mit.edu	37	19	54657541	54657541	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54657541C>G	uc002qdj.1	+	17	2438	c.2127C>G	c.(2125-2127)CAC>CAG	p.H709Q	CNOT3_uc010yel.1_3'UTR|CNOT3_uc002qdi.2_3'UTR|CNOT3_uc002qdk.1_Missense_Mutation_p.H709Q|CNOT3_uc010ere.1_RNA|CNOT3_uc002qdl.2_Missense_Mutation_p.H164Q	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	709					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCCAGAGGCACGAGGAGCCCA	0.602													4	77	---	---	---	---	PASS
ZFP28	140612	broad.mit.edu	37	19	57065985	57065985	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57065985C>T	uc002qnj.2	+	8	1902	c.1831C>T	c.(1831-1833)CAT>TAT	p.H611Y	uc002qnk.1_Intron	NM_020828	NP_065879	Q8NHY6	ZFP28_HUMAN	zinc finger protein 28	611	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		TTTAAGGATTCATACTGGGGA	0.428													5	94	---	---	---	---	PASS
ZIM2	23619	broad.mit.edu	37	19	57293432	57293432	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57293432C>G	uc002qnr.2	-	9	917	c.535G>C	c.(535-537)GAG>CAG	p.E179Q	uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_5'UTR|ZIM2_uc002qnq.2_Missense_Mutation_p.E179Q|ZIM2_uc010etp.2_Missense_Mutation_p.E179Q|ZIM2_uc010ygs.1_Missense_Mutation_p.E179Q	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	179	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		AGCACATCCTCGAAGGTCACC	0.498													7	159	---	---	---	---	PASS
VN1R1	57191	broad.mit.edu	37	19	57967431	57967431	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57967431G>T	uc002qos.1	-	1	424	c.424C>A	c.(424-426)CTC>ATC	p.L142I	ZNF547_uc002qpm.3_Intron	NM_020633	NP_065684	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	142	Helical; Name=3; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		AATCCATTGAGAAGGCAGATG	0.428													9	48	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2591070	2591070	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2591070G>C	uc002wgf.1	+	12	1434	c.1419G>C	c.(1417-1419)GAG>GAC	p.E473D	TMC2_uc002wgg.1_Missense_Mutation_p.E457D|TMC2_uc010zpw.1_Missense_Mutation_p.E305D|TMC2_uc010zpx.1_Missense_Mutation_p.E304D	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	473	Extracellular (Potential).					integral to membrane				ovary(3)	3						CTCAGGTAGAGATCGTGATGT	0.512													4	101	---	---	---	---	PASS
CDH26	60437	broad.mit.edu	37	20	58545157	58545157	+	Silent	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58545157A>T	uc002ybe.2	+	3	447	c.147A>T	c.(145-147)CTA>CTT	p.L49L	CDH26_uc010zzy.1_RNA	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	49	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			ACCAGCCTCTACGGCGATCCA	0.502													22	60	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16337633	16337633	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16337633T>C	uc002yjx.2	-	4	3479	c.2881A>G	c.(2881-2883)AAA>GAA	p.K961E		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	961					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CCTTTCTTTTTACTGTCAGCC	0.418													12	43	---	---	---	---	PASS
KRTAP27-1	643812	broad.mit.edu	37	21	31709628	31709628	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31709628C>G	uc002ynx.1	-	1	385	c.359G>C	c.(358-360)AGC>ACC	p.S120T		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	120						intermediate filament				ovary(2)	2						CTGCTGAGTGCTTTCTGATTG	0.493													9	129	---	---	---	---	PASS
KCNJ6	3763	broad.mit.edu	37	21	39086590	39086590	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39086590C>A	uc011aej.1	-	3	923	c.870G>T	c.(868-870)TGG>TGT	p.W290C	KCNJ6_uc002ywo.2_Missense_Mutation_p.W290C	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6	290	Cytoplasmic (By similarity).				synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	TGGAGATCTCCCAGAAAGGAC	0.483													5	99	---	---	---	---	PASS
POFUT2	23275	broad.mit.edu	37	21	46702293	46702293	+	Silent	SNP	C	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46702293C>G	uc002zhc.2	-	4	634	c.609G>C	c.(607-609)GCG>GCC	p.A203A	POFUT2_uc002zhb.2_RNA|POFUT2_uc002zhd.2_Silent_p.A203A|POFUT2_uc011afp.1_Silent_p.A203A	NM_133635	NP_598368	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2 isoform C	203					fucose metabolic process	endoplasmic reticulum	peptide-O-fucosyltransferase activity				0				Colorectal(79;0.243)		GCAGCAGGGGCGCCACGATGG	0.632													8	17	---	---	---	---	PASS
SFI1	9814	broad.mit.edu	37	22	31927072	31927072	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31927072T>C	uc003ale.2	+	4	688	c.295T>C	c.(295-297)TGG>CGG	p.W99R	SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Missense_Mutation_p.W99R|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	99					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						CTTATATTTATGGATTCGAAT	0.338													15	35	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45768156	45768156	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45768156A>T	uc003bgc.2	-	13	2127	c.2075T>A	c.(2074-2076)CTC>CAC	p.L692H	SMC1B_uc003bgd.2_Missense_Mutation_p.L692H|SMC1B_uc003bge.1_Missense_Mutation_p.L475H	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	692	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTCTTTGCGGAGTGTCTTCAT	0.318													6	17	---	---	---	---	PASS
SHOX	6473	broad.mit.edu	37	X	601623	601623	+	Intron	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:601623G>A	uc004cph.1	+						SHOX_uc004cpi.2_Intron	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa						skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGTGGGTGTCGGGACTGGGGG	0.592													14	47	---	---	---	---	PASS
BMX	660	broad.mit.edu	37	X	15565027	15565027	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15565027C>T	uc004cww.2	+	17	1966	c.1778C>T	c.(1777-1779)TCA>TTA	p.S593L	BMX_uc004cwx.3_Missense_Mutation_p.S593L|BMX_uc004cwy.3_Missense_Mutation_p.S593L	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	593	Protein kinase.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					AGCAGCAAGTCAGACGTATGG	0.448													10	45	---	---	---	---	PASS
ZFX	7543	broad.mit.edu	37	X	24197618	24197618	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24197618C>A	uc004dbf.2	+	4	635	c.377C>A	c.(376-378)TCA>TAA	p.S126*	ZFX_uc004dbd.1_Nonsense_Mutation_p.S126*|ZFX_uc010nfx.1_Intron|ZFX_uc004dbe.2_Nonsense_Mutation_p.S126*|ZFX_uc011mjv.1_Nonsense_Mutation_p.S165*|ZFX_uc010nfy.1_Nonsense_Mutation_p.S126*	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	126					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2						ACTTCAGCCTCAATGTCTATG	0.348													15	88	---	---	---	---	PASS
FTSJ1	24140	broad.mit.edu	37	X	48340063	48340063	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48340063C>T	uc004djo.1	+	9	938	c.615C>T	c.(613-615)TTC>TTT	p.F205F	FTSJ1_uc004djl.2_Silent_p.F205F|FTSJ1_uc004djm.2_Silent_p.F205F|FTSJ1_uc004djn.1_Silent_p.F205F|FTSJ1_uc004djp.1_Silent_p.F205F|FTSJ1_uc011mlw.1_Silent_p.F68F	NM_012280	NP_036412	Q9UET6	RRMJ1_HUMAN	FtsJ homolog 1 isoform a	205					RNA methylation|rRNA processing		methyltransferase activity|nucleic acid binding				0						CCGAGGGCTTCATCCCGGACC	0.622													6	4	---	---	---	---	PASS
TRO	7216	broad.mit.edu	37	X	54957228	54957228	+	Silent	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54957228C>T	uc004dtq.2	+	12	4178	c.4071C>T	c.(4069-4071)TTC>TTT	p.F1357F	TRO_uc004dts.2_Intron|TRO_uc004dtr.2_Intron|TRO_uc004dtt.2_RNA|TRO_uc004dtu.2_RNA|TRO_uc004dtv.2_Intron|TRO_uc011mok.1_Silent_p.F888F|TRO_uc004dtw.2_Silent_p.F960F|TRO_uc004dtx.2_Silent_p.F740F	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	1357	55; approximate.|62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1						GCACGGGCTTCAGTAGTGGAC	0.567													18	24	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65417698	65417698	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65417698G>A	uc011moz.1	+	10	1744	c.1684G>A	c.(1684-1686)GTG>ATG	p.V562M	HEPH_uc004dwn.2_Missense_Mutation_p.V562M|HEPH_uc004dwo.2_Missense_Mutation_p.V292M|HEPH_uc010nkr.2_Intron|HEPH_uc011mpa.1_Missense_Mutation_p.V562M	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	559	Extracellular (Potential).|Plastocyanin-like 3.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						CCCGCTGCTGGTGTGCAGGGC	0.567													6	4	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69561758	69561758	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69561758C>T	uc004dyg.2	+	11	1370	c.1243C>T	c.(1243-1245)CAG>TAG	p.Q415*	KIF4A_uc010nkw.2_Nonsense_Mutation_p.Q415*|KIF4A_uc004dyf.1_Nonsense_Mutation_p.Q415*	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	415	Potential.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						TCAGACAGCCCAGATGTTGGA	0.418													5	56	---	---	---	---	PASS
ZCCHC13	389874	broad.mit.edu	37	X	73524496	73524496	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524496G>A	uc004ebs.3	+	1	472	c.395G>A	c.(394-396)CGA>CAA	p.R132Q		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	132	CCHC-type 6.						nucleic acid binding|zinc ion binding				0						AAGTGTTACCGATGCGGCGAG	0.552													13	16	---	---	---	---	PASS
TBX22	50945	broad.mit.edu	37	X	79286003	79286003	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79286003G>A	uc010nmg.1	+	9	1090	c.956G>A	c.(955-957)AGC>AAC	p.S319N	TBX22_uc004edi.1_Missense_Mutation_p.S199N|TBX22_uc004edj.1_Missense_Mutation_p.S319N	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	319					multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1)	15						ACAGGTGGAAGCAGTGGCTCA	0.423													9	22	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128709224	128709224	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128709224G>A	uc004euq.2	+	16	1875	c.1710G>A	c.(1708-1710)AGG>AGA	p.R570R	OCRL_uc004eur.2_Silent_p.R570R	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	570					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						TCAGCAGGAGGGAGGTGAGCA	0.403													12	11	---	---	---	---	PASS
ELF4	2000	broad.mit.edu	37	X	129203604	129203604	+	Silent	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129203604C>A	uc004evd.3	-	8	1243	c.858G>T	c.(856-858)CTG>CTT	p.L286L	ELF4_uc004eve.3_Silent_p.L286L	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	286	ETS.				natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						ACTGGTACACCAGCCTCTGCC	0.577			T	ERG	AML								4	31	---	---	---	---	PASS
ENOX2	10495	broad.mit.edu	37	X	129790626	129790626	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129790626C>A	uc004evw.2	-	11	1563	c.1145G>T	c.(1144-1146)CGA>CTA	p.R382L	ENOX2_uc004evx.2_Missense_Mutation_p.R353L|ENOX2_uc004evy.2_Missense_Mutation_p.R353L|ENOX2_uc004evv.2_Missense_Mutation_p.R209L	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b	382	Potential.				cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						TTCTTCTTCTCGCCTGATTCC	0.313													3	40	---	---	---	---	PASS
SLC9A6	10479	broad.mit.edu	37	X	135122230	135122230	+	Intron	SNP	C	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135122230C>T	uc004ezj.2	+						SLC9A6_uc004ezk.2_Intron	NM_006359	NP_006350	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					CCTTAACCACCGCAGCTATCT	0.438													3	7	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140996085	140996085	+	Silent	SNP	G	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140996085G>A	uc004fbt.2	+	4	3181	c.2895G>A	c.(2893-2895)CTG>CTA	p.L965L	MAGEC1_uc010nsl.1_Silent_p.L32L	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	965	MAGE.						protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					GCATTTCCCTGAGAGAAGTGG	0.498										HNSCC(15;0.026)			7	81	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	721105	721105	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:721105delA								LOC100133331 (41369 upstream) : NCRNA00115 (40482 downstream)																							aaagtataataaaaaaaaatc	0.149													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	724240	724244	+	IGR	DEL	CGCAC	-	-	rs141681507	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:724240_724244delCGCAC								LOC100133331 (44504 upstream) : NCRNA00115 (37343 downstream)																							tggaatggaacgcactcgaatggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	747754	747755	+	IGR	DEL	GC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:747754_747755delGC								LOC100133331 (68018 upstream) : NCRNA00115 (13832 downstream)																							gatccttcgtgcaatgttggtg	0.000													3	3	---	---	---	---	
CDK11B	984	broad.mit.edu	37	1	1644426	1644426	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1644426delT	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_Intron|CDK11A_uc009vks.2_Intron|CDK11A_uc010nys.1_Intron|CDK11A_uc010nyt.1_Intron|CDK11A_uc010nyu.1_Intron|CDK11A_uc009vkt.1_Intron|CDK11A_uc009vku.1_Intron|CDK11A_uc009vkv.1_Intron|CDK11A_uc001aht.1_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						tgtttctagcttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4931708	4931709	+	IGR	DEL	CA	-	-	rs34042090		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4931708_4931709delCA								AJAP1 (87858 upstream) : NPHP4 (991161 downstream)																							ATGCATACCCCACACACACTCC	0.322													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4976118	4976119	+	IGR	INS	-	GTGT	GTGT	rs149735850	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4976118_4976119insGTGT								AJAP1 (132268 upstream) : NPHP4 (946751 downstream)																							tttgtgtgttcgtgtgtgtgtg	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5406138	5406138	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5406138delG								AJAP1 (562288 upstream) : NPHP4 (516732 downstream)																							ccccaactctggaaatgaaag	0.144													4	2	---	---	---	---	
GPR153	387509	broad.mit.edu	37	1	6315079	6315079	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6315079delG	uc001amp.1	-							NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		GAGCATCTGTGGGGGGGTGGC	0.587													4	2	---	---	---	---	
PRDM2	7799	broad.mit.edu	37	1	14101034	14101035	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14101034_14101035insT	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron|PRDM2_uc009vod.1_Intron|PRDM2_uc001avk.2_Intron|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger							Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGTGCCGAGAGTTTTTTTTGAA	0.376													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15085404	15085405	+	Intron	INS	-	A	A	rs141864368		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15085404_15085405insA	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						TTTGAATCCagaaaaaaaaaaa	0.272													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17006351	17006352	+	IGR	INS	-	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17006351_17006352insG								MST1P2 (29437 upstream) : ESPNP (11361 downstream)																							TGGAAATTGTACCTGGTCAACA	0.386													4	2	---	---	---	---	
ARHGEF10L	55160	broad.mit.edu	37	1	17911353	17911356	+	Intron	DEL	CACA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17911353_17911356delCACA	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CGTGTGCGTGcacacacacacaca	0.225													4	3	---	---	---	---	
KLHDC7A	127707	broad.mit.edu	37	1	18805165	18805180	+	5'Flank	DEL	AGGCAGGCAGGCAGGC	-	-	rs11269542	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18805165_18805180delAGGCAGGCAGGCAGGC	uc001bax.2	+						KLHDC7A_uc009vpg.2_5'Flank	NM_152375	NP_689588	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A							integral to membrane				ovary(2)|upper_aerodigestive_tract(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		gaaggaaggaaggcaggcaggcaggcaggcaggcag	0.134													4	2	---	---	---	---	
ECE1	1889	broad.mit.edu	37	1	21599840	21599841	+	Intron	DEL	GT	-	-	rs71569826		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21599840_21599841delGT	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron|ECE1_uc009vqa.1_Intron	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		gcgtgtgtgcgtgtgtgtgtgt	0.238													4	2	---	---	---	---	
LUZP1	7798	broad.mit.edu	37	1	23434588	23434588	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23434588delG	uc001bgk.2	-						LUZP1_uc010odv.1_Intron|LUZP1_uc001bgl.2_Intron|LUZP1_uc001bgm.1_Intron	NM_033631	NP_361013	Q86V48	LUZP1_HUMAN	leucine zipper protein 1							nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		GCCACTGACCGTTCAAGTTCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	23971171	23971171	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23971171delA								MDS2 (4115 upstream) : RPL11 (47123 downstream)																							agctgtctacaagccaggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	24538420	24538421	+	IGR	INS	-	GGT	GGT	rs138026943	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24538420_24538421insGGT								LOC284632 (240 upstream) : GRHL3 (107460 downstream)																							agggtgatagaggtgatggagg	0.040													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	24803621	24803622	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24803621_24803622insA								NIPAL3 (4149 upstream) : RCAN3 (25765 downstream)																							acataggaaggaaaaaaaaata	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25356759	25356759	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25356759delT								RUNX3 (65147 upstream) : SYF2 (192008 downstream)																							tcttcttttattttttttttt	0.025													4	2	---	---	---	---	
MAN1C1	57134	broad.mit.edu	37	1	26002080	26002081	+	Intron	INS	-	GT	GT	rs140676885	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26002080_26002081insGT	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		ttttgcggggggggggggaggt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30521203	30521206	+	IGR	DEL	ACAC	-	-	rs144328189		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30521203_30521206delACAC								PTPRU (867888 upstream) : MATN1 (662920 downstream)																							ACCTTcacatacacacacacacac	0.402													4	2	---	---	---	---	
LAPTM5	7805	broad.mit.edu	37	1	31225667	31225667	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31225667delT	uc001bsc.2	-							NM_006762	NP_006753	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5						transport	integral to plasma membrane|lysosomal membrane					0		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCTTTACCttttttttttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31258428	31258428	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31258428delG								LAPTM5 (27745 upstream) : SDC3 (83885 downstream)																							CTATGGCTCCGGGGGGTACTC	0.582													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33657744	33657744	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33657744delG								TRIM62 (10073 upstream) : ZNF362 (64430 downstream)																							cccctgggctggtaattgact	0.060													4	2	---	---	---	---	
PHC2	1912	broad.mit.edu	37	1	33862788	33862788	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33862788delC	uc009vuh.1	-						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)				AGCACCATCACCAGGCACCAG	0.269													4	2	---	---	---	---	
ZMYM1	79830	broad.mit.edu	37	1	35575348	35575348	+	Intron	DEL	T	-	-	rs76975638		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35575348delT	uc001bym.2	+						ZMYM1_uc001byn.2_Intron|ZMYM1_uc010ohu.1_Intron|ZMYM1_uc001byo.2_Intron|ZMYM1_uc009vut.2_Intron	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1							nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTTCATTGCttttttttttt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40110528	40110528	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40110528delA								HEYL (5180 upstream) : NT5C1A (14265 downstream)																							ccatctctagaaaaaaaaaaa	0.239													4	2	---	---	---	---	
C1orf210	149466	broad.mit.edu	37	1	43752636	43752637	+	5'Flank	INS	-	T	T	rs144469622		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43752636_43752637insT	uc001cit.3	-							NM_182517	NP_872323	Q8IVY1	CA210_HUMAN	hypothetical protein LOC149466							integral to membrane					0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TAttttctttcttttttttttt	0.223													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	47858804	47858804	+	IGR	DEL	T	-	-	rs68058860		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47858804delT								CMPK1 (14294 upstream) : FOXE3 (22940 downstream)																							ccttccttccttttttttttT	0.045													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	50928551	50928551	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50928551delC	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		GCAGTAAACTCCAGAAGTGAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53960679	53960680	+	IGR	DEL	TG	-	-	rs61768450		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53960679_53960680delTG								DMRTB1 (27521 upstream) : GLIS1 (11226 downstream)																							tttgtgtgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	54165977	54165979	+	Intron	DEL	CTT	-	-	rs66648376		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54165977_54165979delCTT	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						TCTCCTCCTCCTTTTCTCCCTGT	0.596													4	2	---	---	---	---	
TMEM48	55706	broad.mit.edu	37	1	54250632	54250632	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54250632delA	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557	Q9BTX1	NDC1_HUMAN	transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2						actcaatctcaaaaaaaaaaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56252986	56252987	+	IGR	DEL	CG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56252986_56252987delCG								USP24 (572224 upstream) : PPAP2B (707446 downstream)																							AGTATGTTGTCGTAGACATAGT	0.450													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58634413	58634413	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58634413delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						aagtgaggacaaaaggtgtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59685295	59685296	+	IGR	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59685295_59685296delTC								LOC729467 (72816 upstream) : FGGY (77329 downstream)																							AGACCCAGCTTCTCTCTCTCTC	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61055346	61055347	+	IGR	INS	-	CTT	CTT	rs139296934		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61055346_61055347insCTT								C1orf87 (515920 upstream) : NFIA (487599 downstream)																							tcaaatgtcacctcattgaggc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62029030	62029031	+	IGR	INS	-	AA	AA	rs148071528		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62029030_62029031insAA								NFIA (100571 upstream) : TM2D1 (117688 downstream)																							acaacaacaacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	63620570	63620570	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63620570delA								ATG4C (290521 upstream) : FOXD3 (168160 downstream)																							aaggaaacggaaaaaaaaaaa	0.000													6	3	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70157398	70157398	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70157398delT	uc001deo.1	+									Q96NW7	LRRC7_HUMAN	SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ggaggattgcttgagcctggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	75258935	75258936	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75258935_75258936insA								TYW3 (26577 upstream) : LHX8 (335183 downstream)																							GAGACTTCTAGAAAAAAAAAAG	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	82617156	82617163	+	IGR	DEL	AAGAAAGA	-	-	rs36191171	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82617156_82617163delAAGAAAGA								LPHN2 (159050 upstream) : None (None downstream)																							ggaaggaaggaagaaagaaagaaagaaa	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84315943	84315948	+	Intron	DEL	CGCGCA	-	-	rs71097826		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84315943_84315948delCGCGCA	uc001diz.3	-						uc001dja.1_Intron					Homo sapiens cDNA clone IMAGE:4815396.																		cgcgcgcgcgcgcgcacacacacaca	0.228													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89768046	89768046	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89768046delG								GBP5 (29502 upstream) : GBP6 (61390 downstream)																							ggtgctgattggtgcatttac	0.000													4	4	---	---	---	---	
BCAR3	8412	broad.mit.edu	37	1	94083683	94083684	+	Intron	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94083683_94083684delTC	uc001dpz.2	-						BCAR3_uc001dqa.2_Intron|BCAR3_uc001dqb.2_Intron	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		CAAAGACAGTTCTACACATTTC	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111932852	111932853	+	IGR	INS	-	ACAC	ACAC	rs72100830		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111932852_111932853insACAC								C1orf88 (37213 upstream) : OVGP1 (24085 downstream)																							CTGGTGTCCAGacacacacaca	0.272													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120560007	120560008	+	Intron	INS	-	A	A	rs138352700	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560007_120560008insA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		cctctgttcttataaccctgag	0.035			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142653213	142653213	+	Intron	DEL	T	-	-	rs111227773		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142653213delT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		gactgagtaattcataaacaa	0.005													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144009132	144009132	+	Intron	DEL	G	-	-	rs11364742		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144009132delG	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		tttttaatctgtttttttcag	0.204													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144045995	144045996	+	Intron	INS	-	CC	CC	rs147099033	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144045995_144045996insCC	uc010oxm.1	+						uc001eju.1_5'Flank					SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		AAAGGGAAGGTCCCAGGTCTAC	0.455													3	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145209324	145209332	+	5'UTR	DEL	GGCGGCGGC	-	-	rs72083240	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145209324_145209332delGGCGGCGGC	uc001emp.3	+	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_5'UTR|NOTCH2NL_uc001emm.3_5'UTR|NOTCH2NL_uc001emo.2_5'UTR|NOTCH2NL_uc010oyh.1_RNA	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GATCTGCCCAggcggcggcggcggcggcg	0.589													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146471954	146471954	+	IGR	DEL	A	-	-	rs67168403		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146471954delA								NBPF10 (47859 upstream) : LOC728989 (18941 downstream)																							gattttcagtagagatgaggg	0.010													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148857756	148857756	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148857756delA								NBPF16 (99445 upstream) : LOC645166 (70530 downstream)																							CCTGTCTTCGAAACTAACTAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148924072	148924072	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148924072delA								NBPF16 (165761 upstream) : LOC645166 (4214 downstream)																							aaaaaaaaacaaagtatagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149081386	149081387	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149081386_149081387insT								LOC645166 (128332 upstream) : LOC388692 (198089 downstream)																							TTTGTTTTTTGTTTTTTTTTGG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149298620	149298620	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149298620delA								LOC388692 (6878 upstream) : FCGR1C (70674 downstream)																							ccactacactacggaaacCAC	0.164													4	2	---	---	---	---	
CTSK	1513	broad.mit.edu	37	1	150779482	150779483	+	Intron	DEL	TC	-	-	rs71659432		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150779482_150779483delTC	uc001evp.1	-						CTSK_uc001evq.1_Intron|CTSK_uc009wma.1_Intron	NM_000396	NP_000387	P43235	CATK_HUMAN	cathepsin K preproprotein						proteolysis	lysosome	cysteine-type endopeptidase activity|protein binding			skin(1)	1	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTtctctctttctctctctctc	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153577826	153577827	+	IGR	DEL	AG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153577826_153577827delAG								S100A2 (39520 upstream) : S100A16 (1540 downstream)																							gaggacccttagattgacccca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165039724	165039725	+	IGR	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165039724_165039725delAC								PBX1 (185424 upstream) : LMX1A (131380 downstream)																							TTAACATCAAacacacacacac	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166257268	166257281	+	IGR	DEL	TCTCTCTCTCTCTC	-	-	rs72101459		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166257268_166257281delTCTCTCTCTCTCTC								FAM78B (121062 upstream) : FMO9P (315872 downstream)																							tttctctatttctctctctctctctctctctctc	0.294													2	4	---	---	---	---	
FMO9P	116123	broad.mit.edu	37	1	166580725	166580726	+	Intron	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166580725_166580726delTC	uc010pld.1	+							NR_002925				Homo sapiens flavin containing monooxygenase 9 pseudogene, mRNA (cDNA clone IMAGE:3997249).												0						cactgaaacttctctCTCTCTC	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170823998	170823999	+	IGR	INS	-	A	A	rs140195328	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170823998_170823999insA								PRRX1 (115458 upstream) : C1orf129 (80613 downstream)																							GCAAGGGCCAGAAAAAAAAAAG	0.446													4	2	---	---	---	---	
C1orf9	51430	broad.mit.edu	37	1	172569836	172569837	+	Intron	INS	-	TG	TG	rs139396658	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172569836_172569837insTG	uc001giq.3	+						C1orf9_uc010pmm.1_Intron|C1orf9_uc009wwd.2_Intron|C1orf9_uc010pmn.1_Intron|C1orf9_uc010pmo.1_Intron	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein						multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		agaaaattaaatgtgtgtgtgt	0.000													4	4	---	---	---	---	
TNFSF4	7292	broad.mit.edu	37	1	173172096	173172102	+	Intron	DEL	CCTCCCT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173172096_173172102delCCTCCCT	uc001giw.2	-						TNFSF4_uc001giv.2_Intron	NM_003326	NP_003317	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily,						acute inflammatory response|cellular response to lipopolysaccharide|cellular response to prostaglandin E stimulus|chemokine (C-C motif) ligand 11 production|defense response to nematode|interleukin-4-dependent isotype switching to IgE isotypes|memory T cell activation|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of regulatory T cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T-helper 1 cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of alpha-beta T cell proliferation|positive regulation of B cell activation|positive regulation of immunoglobulin mediated immune response|positive regulation of immunoglobulin secretion|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-6 production|positive regulation of memory T cell differentiation|positive regulation of T cell cytokine production|positive regulation of T-helper 2 cell differentiation|positive regulation of type 2 immune response|response to virus|signal transduction|T-helper 2 cell activation	cell surface|extracellular space|integral to plasma membrane	cytokine activity			central_nervous_system(1)	1						ctgaggcagccctccctcctccctcct	0.000													4	2	---	---	---	---	
KIAA0040	9674	broad.mit.edu	37	1	175129491	175129492	+	3'UTR	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175129491_175129492delTG	uc009wws.2	-	4					KIAA0040_uc001gkn.3_3'UTR|KIAA0040_uc010pmy.1_3'UTR|KIAA0040_uc001gko.3_3'UTR	NM_014656	NP_055471	Q15053	K0040_HUMAN	hypothetical protein LOC9674												0						TACCTGAATTTGTGTGTGTGTG	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175242546	175242546	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175242546delG								KIAA0040 (80317 upstream) : TNR (49389 downstream)																							cctggcacctgggcaatagcc	0.000													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175448855	175448855	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175448855delC	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GCAACTGAATCCTCAATCTGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181026257	181026257	+	IGR	DEL	A	-	-	rs34244742		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181026257delA								MR1 (1624 upstream) : IER5 (31381 downstream)																							ctctgtctccaaaaaaaaaaa	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185373681	185373682	+	IGR	INS	-	CA	CA	rs142580453	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185373681_185373682insCA								IVNS1ABP (87220 upstream) : HMCN1 (330001 downstream)																							TACAAAAAAACcacacacacac	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200414838	200414838	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200414838delT	uc010ppi.1	+											Homo sapiens clone HA_003012 unknown mRNA.																		ttcttttttcttttttttttt	0.000													4	2	---	---	---	---	
CACNA1S	779	broad.mit.edu	37	1	201081109	201081117	+	Intron	DEL	TCCTCGTCT	-	-	rs114284997	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201081109_201081117delTCCTCGTCT	uc001gvv.2	-							NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	tcccccaccctcctcgtcttcctcctctt	0.273													4	2	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202593965	202593966	+	Intron	INS	-	GT	GT	rs145023801		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202593965_202593966insGT	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)	tctgtagtagggtgtgtgtggt	0.000													4	2	---	---	---	---	
SNRPE	6635	broad.mit.edu	37	1	203829385	203829389	+	5'Flank	DEL	TCAAC	-	-	rs10597270		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203829385_203829389delTCAAC	uc001hai.2	+						SNRPE_uc010pqn.1_5'Flank	NM_003094	NP_003085	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AAAATCACTTTCAACTCAACCCCTT	0.166													3	3	---	---	---	---	
TMEM81	388730	broad.mit.edu	37	1	205052553	205052553	+	3'UTR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205052553delT	uc001hbt.2	-	1						NM_203376	NP_976310	Q6P7N7	TMM81_HUMAN	transmembrane protein 81 precursor							integral to membrane					0	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			CCACTCATTCTTTTGGCTGTG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209303952	209303953	+	IGR	INS	-	ACACACACACAC	ACACACACACAC	rs140311915	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209303952_209303953insACACACACACAC								PLXNA2 (886287 upstream) : LOC642587 (298215 downstream)																							TTTCCTTTcatacacacacaca	0.371													4	2	---	---	---	---	
KCNH1	3756	broad.mit.edu	37	1	211233465	211233465	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211233465delC	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		aaaatatgctcctaaatgatc	0.000													4	2	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214667418	214667418	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214667418delT	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		tttctttctctttttttttct	0.214													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229196291	229196294	+	IGR	DEL	TGTG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229196291_229196294delTGTG								RHOU (313882 upstream) : RAB4A (210585 downstream)																							tgtgtgtttctgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229360270	229360271	+	IGR	DEL	TG	-	-	rs113411142		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229360270_229360271delTG								RHOU (477861 upstream) : RAB4A (46608 downstream)																							tgtgagattctgtgtgtgtgtg	0.218													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230748260	230748261	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230748260_230748261delGT								PGBD5 (234893 upstream) : COG2 (29941 downstream)																							CACTGACCTAgtgtgtgtgtgt	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235124476	235124476	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235124476delA								IRF2BP2 (379205 upstream) : TOMM20 (148184 downstream)																							attaaaaaggaaggacattct	0.000													4	2	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241850607	241850607	+	Intron	DEL	A	-	-	rs67963688		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241850607delA	uc001hze.1	+						WDR64_uc001hzf.1_Intron			B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			gactccatctaaaaaaaaaaa	0.139													4	2	---	---	---	---	
PLD5	200150	broad.mit.edu	37	1	242681727	242681728	+	Intron	INS	-	A	A	rs142107831	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242681727_242681728insA	uc001hzn.1	-						PLD5_uc001hzo.1_Intron			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GTTTAAGCAACATTTCTGGTGT	0.371													3	3	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245446118	245446118	+	Intron	DEL	A	-	-	rs34770861		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245446118delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ccgctcctttaaaAAAAAAGA	0.179													4	2	---	---	---	---	
ZNF124	7678	broad.mit.edu	37	1	247323280	247323281	+	Intron	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247323280_247323281delTC	uc001ick.2	-						ZNF124_uc001ici.2_Intron|ZNF124_uc001icj.1_Intron	NM_003431	NP_003422	Q15973	ZN124_HUMAN	zinc finger protein 124						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			ACATAGCAGttctttttttttt	0.183													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247554579	247554579	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247554579delG								ZNF496 (59417 upstream) : NLRP3 (24879 downstream)																							agaccagcctggggcaatatg	0.000													4	2	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1133189	1133190	+	Intron	DEL	CA	-	-	rs71960569		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1133189_1133190delCA	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		tggacacatgcacacacacaca	0.218													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2456771	2456771	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2456771delT								MYT1L (121726 upstream) : TSSC1 (735970 downstream)																							GGAAGGCCCATTACCAAAGTC	0.408													4	2	---	---	---	---	
ADI1	55256	broad.mit.edu	37	2	3504893	3504894	+	Intron	INS	-	A	A	rs144556875	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3504893_3504894insA	uc002qxp.3	-						ADI1_uc010yiq.1_Intron	NM_018269	NP_060739	Q9BV57	MTND_HUMAN	acireductone dioxygenase 1						L-methionine salvage from methylthioadenosine	cytoplasm|nucleus|plasma membrane	acireductone dioxygenase (Ni2+-requiring) activity|metal ion binding|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		CCATAAAAATGAAACTACACTT	0.455													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4009236	4009236	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4009236delT	uc002qyg.3	-						uc002qyh.1_Intron					Homo sapiens cDNA clone IMAGE:5297607.																		gagatcacccttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6886666	6886666	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6886666delG	uc002qym.1	-											Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987.																		GGTGATGGCTGGGAGAGAAGA	0.328													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15663588	15663590	+	Intron	DEL	GAT	-	-	rs144574634		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15663588_15663590delGAT	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						gtaatctagagatgatgtgaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21496241	21496242	+	IGR	DEL	TT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21496241_21496242delTT								APOB (229296 upstream) : None (None downstream)																							CTGACTGACATTTTTTTTTTCT	0.490													4	2	---	---	---	---	
LOC375190	375190	broad.mit.edu	37	2	24327858	24327859	+	Intron	INS	-	CTT	CTT	rs149084474	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24327858_24327859insCTT	uc002rew.2	+											SubName: Full=Putative uncharacterized protein C2orf84;												0						acctgccagagctggcccagtg	0.000													3	4	---	---	---	---	
FOSL2	2355	broad.mit.edu	37	2	28634924	28634928	+	Frame_Shift_Del	DEL	AGCGC	-	-	rs145499484	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28634924_28634928delAGCGC	uc002rma.2	+	4	1399_1403	c.590_594delAGCGC	c.(589-594)GAGCGCfs	p.E197fs	FOSL2_uc010ymi.1_Frame_Shift_Del_p.E158fs	NM_005253	NP_005244	P15408	FOSL2_HUMAN	FOS-like antigen 2	197_198					cell death|regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(172;0.155)					AGCCCCGAGGAGCGCCGATCGCCCC	0.639													33	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30350251	30350252	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30350251_30350252insA								ALK (205819 upstream) : YPEL5 (19498 downstream)																							tcctctcaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31353601	31353602	+	Intron	DEL	TG	-	-	rs10525734		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31353601_31353602delTG	uc002rnr.2	-						GALNT14_uc002rnq.2_5'Flank|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					AGGGTACCTCtgtgtgtgtgtg	0.257													4	4	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32372414	32372415	+	Intron	INS	-	T	T	rs71407417		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32372414_32372415insT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TGTGTGTGTGGttttttttttt	0.153													6	6	---	---	---	---	
TMEM178	130733	broad.mit.edu	37	2	39941289	39941289	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39941289delT	uc002rrt.2	+						TMEM178_uc010fam.1_Intron	NM_152390	NP_689603	Q8NBL3	TM178_HUMAN	transmembrane protein 178 precursor							integral to membrane					0		all_hematologic(82;0.248)				TTCCTCTTACTTACTAAGAAC	0.443													4	2	---	---	---	---	
SLC8A1	6546	broad.mit.edu	37	2	40474575	40474576	+	Intron	DEL	TG	-	-	rs140400905		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40474575_40474576delTG	uc002rrx.2	-						uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_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)	AGCATATATAtgtgtgtgtgtg	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47008298	47008298	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47008298delT								SOCS5 (18372 upstream) : LOC100134259 (46705 downstream)																							CCAAGTCCTGTTTTTTTCCAT	0.572											OREG0014604	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	2	47986002	47986003	+	IGR	INS	-	A	A	rs146059010	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47986002_47986003insA								MSH2 (79494 upstream) : MSH6 (24218 downstream)																							tacaaaaagtgaaaaaaaaaga	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49122319	49122320	+	IGR	INS	-	AATTACTG	AATTACTG	rs142842745	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49122319_49122320insAATTACTG								LHCGR (139439 upstream) : FSHR (67333 downstream)																							TGCTGGAGTGAAATTACTGACC	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53110204	53110221	+	IGR	DEL	GATGTGGATGGGGATGTT	-	-	rs146081927		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53110204_53110221delGATGTGGATGGGGATGTT								None (None upstream) : ASB3 (786897 downstream)																							tgtgactgtggatgtggatggggatgttgatgtggctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66385453	66385453	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66385453delT								SPRED2 (725797 upstream) : MEIS1 (277079 downstream)																							GCCATATTCAttttttttttt	0.085													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67213634	67213635	+	IGR	INS	-	TG	TG	rs141136532		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67213634_67213635insTG								MEIS1 (413744 upstream) : ETAA1 (410807 downstream)																							TGACTATACCTtgtgtgtgtgt	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	68629905	68629905	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68629905delC								PLEK (5321 upstream) : FBXO48 (59602 downstream)																							caatttttttccccttgctgg	0.000													2	4	---	---	---	---	
ANTXR1	84168	broad.mit.edu	37	2	69399113	69399113	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69399113delT	uc002sfg.2	+						ANTXR1_uc002sff.2_Intron	NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor						actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						CTTAAAGGAGTTTTTGGGCTG	0.433									Familial_Infantile_Hemangioma				4	2	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75907759	75907760	+	Intron	DEL	CT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75907759_75907760delCT	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						ttgagtgagcctctctctctct	0.000													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87644152	87644152	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87644152delG	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						cagccagccagccaagccagc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89879235	89879235	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89879235delG								FLJ40330 (773110 upstream) : None (None downstream)																							cgaatggaatgcaatggaatt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90403394	90403395	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90403394_90403395insA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		aaatagtcttgaaaaaagaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91634445	91634448	+	IGR	DEL	TTTG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91634445_91634448delTTTG								None (None upstream) : LOC654342 (170744 downstream)																							AACTTACATCTTTGTTTGTCTTCC	0.392													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91976244	91976246	+	IGR	DEL	GAG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91976244_91976246delGAG								GGT8P (6091 upstream) : FKSG73 (152913 downstream)																							GTGGATGGAAGAGAAAAAAAGAA	0.310													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92265940	92265940	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92265940delC								FKSG73 (135446 upstream) : None (None downstream)																							aatcagctttcttgagttatg	0.055													4	2	---	---	---	---	
TMEM182	130827	broad.mit.edu	37	2	103417257	103417258	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103417257_103417258delTG	uc010fjb.2	+						TMEM182_uc002tcc.3_Intron|TMEM182_uc002tcd.3_Intron|TMEM182_uc010ywe.1_Intron	NM_144632	NP_653233	Q6ZP80	TM182_HUMAN	transmembrane protein 182 precursor							integral to membrane					0						TTGGACAGTTtgtgtgtgtgtg	0.257													4	2	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111550979	111550979	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111550979delG	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						GGGGGGATCTGGGAGGCCTGA	0.502													4	2	---	---	---	---	
WASH2P	375260	broad.mit.edu	37	2	114342703	114342703	+	Intron	DEL	A	-	-	rs77359205		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114342703delA	uc002tka.2	+						MIR1302-3_hsa-mir-1302-3|MI0006364_5'Flank|WASH2P_uc002tkb.2_Intron	NR_024077				Homo sapiens cDNA FLJ75027 complete cds, highly similar to Homo sapiens CXYorf1-related protein (MGC52000), mRNA.												0						TCAGATGAGCAACTACAGGCT	0.234													4	3	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	115380268	115380268	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115380268delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						GTGttgagagaaaagggcctt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131188675	131188677	+	IGR	DEL	AGA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131188675_131188677delAGA								PTPN18 (55694 upstream) : CFC1B (90159 downstream)																							AATCCTGAGGAGAAGAAGAAGAA	0.404													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132764031	132764031	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132764031delT								C2orf27B (204797 upstream) : NCRNA00164 (141133 downstream)																							tctccaggccttcatgttccc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133027208	133027209	+	IGR	INS	-	AGAC	AGAC			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133027208_133027209insAGAC								NCRNA00164 (11666 upstream) : GPR39 (146938 downstream)																							gggagggagagagacagagaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133027339	133027340	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133027339_133027340insA								NCRNA00164 (11797 upstream) : GPR39 (146807 downstream)																							gagagagaaagcagagatggag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133055010	133055011	+	IGR	INS	-	T	T	rs139949484	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133055010_133055011insT								NCRNA00164 (39468 upstream) : GPR39 (119136 downstream)																							TAATGGATGCAATTGCTGAAGG	0.267													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	165101653	165101660	+	IGR	DEL	TCTTTACA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165101653_165101660delTCTTTACA								FIGN (509140 upstream) : GRB14 (247673 downstream)																							ctttcttccttctttacatccttcctct	0.029													4	2	---	---	---	---	
DCAF17	80067	broad.mit.edu	37	2	172330592	172330619	+	Intron	DEL	AGCTTGTTGTTGGGTGCTTCCTCAGAGA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172330592_172330619delAGCTTGTTGTTGGGTGCTTCCTCAGAGA	uc002ugx.2	+						DCAF17_uc010zdq.1_Intron|DCAF17_uc010fqf.1_Intron|DCAF17_uc010zdr.1_Intron|DCAF17_uc010fqg.2_Intron	NM_025000	NP_079276	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17 isoform 1							CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0						GGAAATAATTAGCTTGTTGTTGGGTGCTTCCTCAGAGACTGGCATACA	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176730598	176730599	+	IGR	DEL	AG	-	-	rs138620508		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176730598_176730599delAG								ATP5G3 (684108 upstream) : KIAA1715 (59811 downstream)																							caggaacatcagagttggaagt	0.000													2	5	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182983486	182983486	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182983486delC	uc010frm.1	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			AATGACTATTCTAGATTCctc	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203126902	203126902	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203126902delA								SUMO1 (23580 upstream) : NOP58 (3613 downstream)																							actctgtctcaaaaaaaaaaa	0.159													4	3	---	---	---	---	
LANCL1	10314	broad.mit.edu	37	2	211336013	211336013	+	Intron	DEL	C	-	-	rs141192706		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211336013delC	uc010zjh.1	-						LANCL1_uc002ved.2_Intron|LANCL1_uc010fuq.2_Intron	NM_001136574	NP_001130046	O43813	LANC1_HUMAN	lanthionine synthetase C-like protein 1							cytoplasm|integral to plasma membrane|microtubule cytoskeleton|nucleus	catalytic activity|G-protein coupled receptor activity|glutathione binding|low-density lipoprotein particle receptor binding|SH3 domain binding|zinc ion binding				0				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)		tcgtgatccacccgcctcggc	0.070													4	3	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214787927	214787927	+	Intron	DEL	A	-	-	rs34808886		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214787927delA	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		gttggtggggatgcttgtcct	0.000													3	4	---	---	---	---	
XRCC5	7520	broad.mit.edu	37	2	217000522	217000522	+	Intron	DEL	A	-	-	rs34520726		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217000522delA	uc002vfy.2	+						XRCC5_uc002vfz.2_Intron	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II						double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		actctgtctcaaaaaaaaaaa	0.199								Direct_reversal_of_damage|NHEJ					3	3	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218789408	218789408	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218789408delA	uc002vgt.2	-						TNS1_uc010zjv.1_Intron|TNS1_uc010fvk.1_Intron|TNS1_uc002vgv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		gagaccctccaagcccgcaga	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221913845	221913848	+	IGR	DEL	TTTG	-	-	rs72195395		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221913845_221913848delTTTG								None (None upstream) : EPHA4 (368901 downstream)																							AAAGTCCACATTTGTTTGTTCTTA	0.157													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	223273401	223273401	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223273401delA								CCDC140 (103465 upstream) : SGPP2 (15921 downstream)																							GGTTGGAAACAAAAAAAAAAT	0.423													4	2	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225668717	225668718	+	Intron	INS	-	TG	TG	rs141021252	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225668717_225668718insTG	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002voa.2_Intron|DOCK10_uc002voc.2_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AAATAGAAATAtgtgtgtgtgt	0.277													6	3	---	---	---	---	
COL4A3	1285	broad.mit.edu	37	2	228058652	228058654	+	Intron	DEL	AAG	-	-	rs71036161		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228058652_228058654delAAG	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		gaagggaaataaggagagaggga	0.000													3	4	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230781253	230781253	+	Intron	DEL	A	-	-	rs78565048		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230781253delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		cctgggtgacaaaagtgagac	0.164													3	5	---	---	---	---	
SPATA3	130560	broad.mit.edu	37	2	231870293	231870295	+	Intron	DEL	CAT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231870293_231870295delCAT	uc010zmd.1	+						SPATA3_uc002vri.3_Intron|SPATA3_uc002vrk.2_Intron	NM_139073	NP_620712	Q8NHX4	SPTA3_HUMAN	testis and spermatogenesis cell apoptosis						apoptosis|spermatogenesis						0						tcatcatcaccatcatcatcctc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232439929	232439929	+	IGR	DEL	T	-	-	rs34465062		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232439929delT								NMUR1 (44747 upstream) : C2orf57 (17683 downstream)																							Ctttctcctcttttttttttt	0.015													4	2	---	---	---	---	
PTMA	5757	broad.mit.edu	37	2	232573304	232573319	+	5'UTR	DEL	CCTCCGCCGCGCGCCT	-	-	rs11558928		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232573304_232573319delCCTCCGCCGCGCGCCT	uc002vsc.3	+	1					uc002vsa.2_5'Flank|PTMA_uc002vsb.3_5'UTR|PTMA_uc010zmf.1_5'Flank	NM_001099285	NP_001092755	P06454	PTMA_HUMAN	prothymosin, alpha isoform 1						transcription, DNA-dependent	nucleus					0		Renal(207;0.0112)|all_hematologic(139;0.0315)|Acute lymphoblastic leukemia(138;0.0921)|all_lung(227;0.142)		Epithelial(121;1.75e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00221)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		gccgcagccgcctccgccgcgcgcctcctccgccgc	0.449													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	233921914	233921914	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233921914delT								NEU2 (22148 upstream) : INPP5D (3122 downstream)																							ccagaaattgttcaagtcccc	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234768381	234768382	+	IGR	DEL	TG	-	-	rs34258762		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234768381_234768382delTG								HJURP (5169 upstream) : MSL3L2 (5710 downstream)																							TGCTGCTTGCtgtgtgtgtgtg	0.287													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239444342	239444342	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239444342delA	uc002vyi.1	-											Homo sapiens cDNA FLJ32814 fis, clone TESTI2002806.																		GGGATGATCCAAAAAAACCAC	0.498													4	2	---	---	---	---	
KIF1A	547	broad.mit.edu	37	2	241752071	241752072	+	Intron	INS	-	G	G	rs148599867	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241752071_241752072insG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTTCACCTCAAGATCCACCTTC	0.584													3	3	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2540194	2540194	+	Intron	DEL	T	-	-	rs5846186		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2540194delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		aggatctcgctttgtcaccca	0.025													3	5	---	---	---	---	
SRGAP3	9901	broad.mit.edu	37	3	9048738	9048738	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9048738delT	uc003brf.1	-						SRGAP3_uc003brg.1_Intron	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		tcaacctccctgggcttaagt	0.005			T	RAF1	pilocytic astrocytoma								4	2	---	---	---	---	
ATP2B2	491	broad.mit.edu	37	3	10665239	10665239	+	Intron	DEL	G	-	-	rs35076690		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10665239delG	uc003bvw.2	-							NM_001683	NP_001674	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 2						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						CTTCATTGAAGATGAAAATAC	0.453													2	4	---	---	---	---	
VGLL4	9686	broad.mit.edu	37	3	11676064	11676064	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11676064delC	uc003bwf.2	-						VGLL4_uc010hdx.1_Intron|VGLL4_uc003bwg.2_Intron	NM_014667	NP_055482	Q14135	VGLL4_HUMAN	vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		CGCCTACTCACCCCGAGGAGC	0.363													4	2	---	---	---	---	
MKRN2	23609	broad.mit.edu	37	3	12610668	12610668	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12610668delT	uc003bxd.2	+						MKRN2_uc003bxe.2_Intron|MKRN2_uc011aus.1_Intron	NM_014160	NP_054879	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2							intracellular	ligase activity|nucleic acid binding|zinc ion binding				0						ttttcttttcttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	41197670	41197670	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41197670delC								ZNF621 (616627 upstream) : CTNNB1 (38731 downstream)																							GGCCCACTTACCATTTTTAAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	62296170	62296170	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62296170delA	uc010hno.2	-						uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron					Homo sapiens cDNA FLJ12839 fis, clone NT2RP2003237.																		TAAATGAGCTAAAAAATGAGA	0.144													4	2	---	---	---	---	
ATXN7	6314	broad.mit.edu	37	3	63988175	63988176	+	3'UTR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63988175_63988176delGT	uc003dlw.3	+	13					ATXN7_uc010hnv.2_3'UTR|ATXN7_uc011bfn.1_3'UTR|uc003dly.1_5'Flank	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		atgtgactgcgtgtgtgtgtgc	0.277													4	2	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65633965	65633966	+	Intron	INS	-	GT	GT	rs141908394	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65633965_65633966insGT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		tactacaggccgtgtgtgtgtg	0.000													4	3	---	---	---	---	
PPP4R2	151987	broad.mit.edu	37	3	73053996	73053997	+	Intron	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73053996_73053997delGT	uc003dph.1	+						PPP4R2_uc003dpi.1_Intron	NM_174907	NP_777567	Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2						mRNA processing|protein modification process|regulation of double-strand break repair via homologous recombination|RNA splicing	centrosome|nucleus|protein phosphatase 4 complex	protein binding, bridging|protein phosphatase type 4 regulator activity			lung(1)	1		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		acagtGTGGGgtgtgtgtgtgt	0.020													4	2	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	97212468	97212469	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97212468_97212469delTG	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						tttagtccTCTGTGTGTGTGTG	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99934081	99934081	+	IGR	DEL	T	-	-	rs66834185		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99934081delT								TMEM30C (21055 upstream) : TBC1D23 (45605 downstream)																							TTCCTCCACAttttttttttt	0.100													3	3	---	---	---	---	
KIAA2018	205717	broad.mit.edu	37	3	113406077	113406078	+	Intron	DEL	CA	-	-	rs111363190		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113406077_113406078delCA	uc003eam.2	-							NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717						regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						cacacacagtcacacacacaca	0.000													5	3	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114434200	114434200	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114434200delT	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		TTGTCATACCTTTTTCCCCTC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117197374	117197374	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117197374delT								LOC285194 (761489 upstream) : None (None downstream)																							cctcatctggtgcattctcca	0.075													4	2	---	---	---	---	
CD80	941	broad.mit.edu	37	3	119266836	119266836	+	Intron	DEL	T	-	-	rs11342226		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119266836delT	uc003ecq.2	-						CD80_uc010hqt.1_Intron|CD80_uc010hqu.1_Intron|CD80_uc003ecr.1_Intron	NM_005191	NP_005182	P33681	CD80_HUMAN	CD80 antigen precursor						interspecies interaction between organisms|intracellular signal transduction|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of signal transduction|positive regulation of T-helper 1 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation	intracellular	coreceptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2					Abatacept(DB01281)	tttctttttcttttttttttt	0.174													4	2	---	---	---	---	
FSTL1	11167	broad.mit.edu	37	3	120143903	120143903	+	Intron	DEL	G	-	-	rs144579564		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120143903delG	uc003eds.2	-						FSTL1_uc011bjh.1_Intron|FSTL1_uc010hrb.2_Intron	NM_007085	NP_009016	Q12841	FSTL1_HUMAN	follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)		ACAGACAGCAGGAAGAGCagc	0.303													4	3	---	---	---	---	
HGD	3081	broad.mit.edu	37	3	120402070	120402070	+	5'Flank	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120402070delT	uc003edw.2	-							NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)		caattcctcctatccttgtat	0.189													4	2	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	120900258	120900258	+	Intron	DEL	A	-	-	rs80346827		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120900258delA	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)		ggccccacttaaaagatacaa	0.005													5	3	---	---	---	---	
CASR	846	broad.mit.edu	37	3	121933952	121933953	+	Intron	DEL	TT	-	-	rs34283090		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121933952_121933953delTT	uc003eev.3	+						CASR_uc003eew.3_Intron	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor						anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GGAGAAAGTCTTTGCCTATGCA	0.500													4	3	---	---	---	---	
MUC13	56667	broad.mit.edu	37	3	124625848	124625848	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124625848delT	uc003ehq.1	-							NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0						CTAAAGTCTCTTACAGGCTTC	0.219													4	2	---	---	---	---	
MRPL3	11222	broad.mit.edu	37	3	131209544	131209544	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131209544delC	uc003eoh.2	-						MRPL3_uc011blo.1_Intron|MRPL3_uc011blp.1_Intron	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3						translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						ATTGTCTATACCAGCACTAAT	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133813137	133813137	+	IGR	DEL	G	-	-	rs137886272		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133813137delG								SLCO2A1 (64217 upstream) : RYK (62841 downstream)																							AAACTTTTTAGGGGGGGGGGT	0.234													4	2	---	---	---	---	
SLC25A36	55186	broad.mit.edu	37	3	140670862	140670862	+	Intron	DEL	T	-	-	rs78544531		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140670862delT	uc003etr.2	+						SLC25A36_uc003etp.2_Intron|SLC25A36_uc003ets.2_Intron|SLC25A36_uc003etq.2_Intron|SLC25A36_uc011bmz.1_Intron	NM_001104647	NP_001098117	Q96CQ1	S2536_HUMAN	solute carrier family 25, member 36 isoform a						response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						tctttctctcttttttttttt	0.000													4	2	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143395576	143395577	+	Intron	INS	-	CAAA	CAAA	rs111553158		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143395576_143395577insCAAA	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						agactccttctcaaacaaacaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144267006	144267007	+	IGR	INS	-	T	T	rs36150117		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144267006_144267007insT								C3orf58 (555797 upstream) : None (None downstream)																							AATGTGAAttcttttttttttt	0.158													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149939940	149939941	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149939940_149939941delGT								PFN2 (251199 upstream) : TSC22D2 (186847 downstream)																							tgtgtgtgtagtgtgtgtgtgt	0.153													4	2	---	---	---	---	
CLRN1OS	116933	broad.mit.edu	37	3	150741187	150741188	+	Intron	INS	-	AGG	AGG			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150741187_150741188insAGG	uc011bny.1	+						CLRN1OS_uc003eyl.2_Intron					Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0						AAAGAAaaggaaggaaagaagg	0.153													4	2	---	---	---	---	
SSR3	6747	broad.mit.edu	37	3	156266564	156266566	+	Intron	DEL	TAC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156266564_156266566delTAC	uc003fau.2	-						SSR3_uc011bop.1_Intron	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	signal sequence receptor gamma subunit						cotranslational protein targeting to membrane	integral to endoplasmic reticulum membrane|microsome|Sec61 translocon complex	protein binding|signal sequence binding				0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ctATTTCCATTACTACTACTACT	0.158													4	2	---	---	---	---	
GOLIM4	27333	broad.mit.edu	37	3	167814038	167814039	+	5'Flank	DEL	GT	-	-	rs142093164		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167814038_167814039delGT	uc003ffe.2	-						GOLIM4_uc011bpe.1_5'Flank|GOLIM4_uc011bpf.1_5'Flank|GOLIM4_uc011bpg.1_5'Flank	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						CGGTGAACACgtgtgtgtgtgt	0.505													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172220956	172220957	+	IGR	DEL	TT	-	-	rs3055926		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172220956_172220957delTT								GHSR (54753 upstream) : TNFSF10 (2508 downstream)																							tgtgtgtgtgtttgtatgtgtg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172555400	172555401	+	IGR	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172555400_172555401delTC								ECT2 (16137 upstream) : SPATA16 (51747 downstream)																							tctttctctgtctctctctctc	0.000													4	2	---	---	---	---	
TBL1XR1	79718	broad.mit.edu	37	3	176912203	176912204	+	Intron	DEL	CT	-	-	rs76003814	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176912203_176912204delCT	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TGCCTCTCCCCTGACTTCCTAC	0.322													3	3	---	---	---	---	
LIPH	200879	broad.mit.edu	37	3	185266349	185266349	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185266349delC	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341	Q8WWY8	LIPH_HUMAN	lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			aaccccatctccactaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	185669879	185669880	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185669879_185669880insT								TRA2B (13955 upstream) : ETV5 (94228 downstream)																							TAGAATTGTGAttttttttttt	0.074													4	3	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189546039	189546039	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189546039delA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_Intron|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Intron|MIR944_hsa-mir-944|MI0005769_5'Flank	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		caaaacaagcaaaaaaaaaaa	0.209									Hay-Wells_syndrome	HNSCC(45;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190438459	190438460	+	IGR	DEL	GT	-	-	rs72301556		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190438459_190438460delGT								IL1RAP (62616 upstream) : LOC647309 (132066 downstream)																							GAAAAGTAGGgtgtgtgtgtgt	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190717516	190717517	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190717516_190717517insA								SNAR-I (121677 upstream) : OSTN (212805 downstream)																							aggaaggaaggaaggaaggaag	0.114													4	2	---	---	---	---	
UTS2D	257313	broad.mit.edu	37	3	191014056	191014065	+	Intron	DEL	ACACACACAT	-	-	rs151319783		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191014056_191014065delACACACACAT	uc003fsu.2	-							NM_198152	NP_937795	Q765I0	UTS2B_HUMAN	urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)		acacactcacacacacacatacacacacat	0.000													5	3	---	---	---	---	
SDHAP2	727956	broad.mit.edu	37	3	195402221	195402221	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195402221delC	uc003fuw.2	+						SDHAP2_uc011btc.1_Intron|SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						ACAGGTTGTGCTTGTCTCACT	0.547													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195430023	195430023	+	Intron	DEL	A	-	-	rs76190791		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195430023delA	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		ccatctcaggaaaaaaaaaaa	0.030													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	48512	48513	+	IGR	INS	-	T	T	rs113306625		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48512_48513insT								None (None upstream) : ZNF595 (4714 downstream)																							ATTTGGCAAAGTTTTTTTTTTT	0.183													3	3	---	---	---	---	
FGFRL1	53834	broad.mit.edu	37	4	1020269	1020269	+	3'UTR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1020269delG	uc003gce.2	+	7					FGFRL1_uc003gcf.2_3'UTR|FGFRL1_uc003gcg.2_3'UTR|FGFRL1_uc010ibo.2_3'UTR	NM_021923	NP_068742	Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1						regulation of cell growth	integral to membrane|plasma membrane	fibroblast growth factor receptor activity|heparin binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			cccTGGCCTTGGCGGCTATTT	0.483													4	2	---	---	---	---	
KIAA1530	57654	broad.mit.edu	37	4	1365044	1365045	+	Intron	INS	-	TGTG	TGTG	rs147640870	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1365044_1365045insTGTG	uc003gde.3	+						KIAA1530_uc010ibv.2_Intron	NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			GTGGGTGGACCtgtgtgtgtgt	0.431													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2355365	2355365	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2355365delC	uc003gex.1	-						ZFYVE28_uc011bvk.1_Intron|ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gey.3_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						GCCCACCCCTCCCACACTGGC	0.632													4	2	---	---	---	---	
CLNK	116449	broad.mit.edu	37	4	10594023	10594023	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10594023delC	uc003gmo.3	-						CLNK_uc003gmp.2_Intron	NM_052964	NP_443196	Q7Z7G1	CLNK_HUMAN	mast cell immunoreceptor signal transducer						immune response|intracellular signal transduction	intracellular	SH3/SH2 adaptor activity			ovary(1)	1						CTCAGACATTCCTCTAGCGGG	0.463													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21513786	21513797	+	Intron	DEL	AGGGAGGGAGGA	-	-	rs141006136	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21513786_21513797delAGGGAGGGAGGA	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				ggagggagggagggagggaggaaggaaggaac	0.080													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25060205	25060205	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25060205delA								LGI2 (27791 upstream) : SEPSECS (61423 downstream)																							aggtgtccacaaggccgtgat	0.020													4	2	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	27019136	27019137	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27019136_27019137insT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TTTTAAACCTGTTTTTTTTTTG	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42252236	42252237	+	IGR	INS	-	T	T	rs138393488		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42252236_42252237insT								BEND4 (97341 upstream) : SHISA3 (147619 downstream)																							atcagaggaacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49160615	49160616	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160615_49160616insT								CWH43 (96522 upstream) : None (None downstream)																							cgcccggctaattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49640070	49640074	+	IGR	DEL	AGGGT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49640070_49640074delAGGGT								CWH43 (575977 upstream) : None (None downstream)																							atcaacccgaagggtatggaatgga	0.000													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55810089	55810090	+	IGR	INS	-	TACTT	TACTT	rs144593359	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55810089_55810090insTACTT								KIT (203210 upstream) : KDR (134337 downstream)																							aatactgtacataaagagtggt	0.129													4	3	---	---	---	---	
NMU	10874	broad.mit.edu	37	4	56483674	56483675	+	Intron	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56483674_56483675delAC	uc003hbc.2	-						NMU_uc003hbd.1_Intron|NMU_uc010igv.1_Intron|NMU_uc010igw.1_Intron|NMU_uc010igx.1_Intron	NM_006681	NP_006672	P48645	NMU_HUMAN	neuromedin U precursor						neuropeptide signaling pathway	extracellular region					0	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		GAAATCATGGacacacacacac	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57595050	57595060	+	IGR	DEL	TTTTTTTTTTT	-	-	rs67488191		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57595050_57595060delTTTTTTTTTTT								HOPX (47178 upstream) : SPINK2 (80974 downstream)																							CTTTCTTTCCttttttttttttttttttttt	0.275													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83150679	83150680	+	IGR	DEL	TT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83150679_83150680delTT								RASGEF1B (757618 upstream) : HNRNPD (123787 downstream)																							TCCATATTCCTTTTTTTTTTTT	0.302													4	2	---	---	---	---	
IBSP	3381	broad.mit.edu	37	4	88731545	88731545	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88731545delG	uc003hqx.3	+							NM_004967	NP_004958	P21815	SIAL_HUMAN	integrin-binding sialoprotein precursor						biomineral tissue development|cell adhesion|ossification						0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		AACATATAGTGTGGAGTAAGG	0.373													4	2	---	---	---	---	
EIF4E	1977	broad.mit.edu	37	4	99849192	99849192	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99849192delA	uc003hue.2	-						EIF4E_uc011cea.1_Intron|EIF4E_uc011ceb.1_Intron|EIF4E_uc011cec.1_Intron	NM_001968	NP_001959	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			lung(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		AGATAAAGAGAAAAAAAAAGT	0.343													4	2	---	---	---	---	
LOC285456	285456	broad.mit.edu	37	4	109533315	109533316	+	Intron	DEL	AA	-	-	rs149101336		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109533315_109533316delAA	uc011cfl.1	-						LOC285456_uc003hyy.2_Intron					SubName: Full=cDNA FLJ57077;												0						ACGTTTTGGGAAAAAAAAAAAA	0.371													5	3	---	---	---	---	
EXOSC9	5393	broad.mit.edu	37	4	122727916	122727916	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122727916delT	uc003iea.2	+						EXOSC9_uc003idz.2_Intron|EXOSC9_uc003ieb.2_Intron|EXOSC9_uc010inp.1_Intron	NM_005033	NP_005024	Q06265	EXOS9_HUMAN	exosome component 9 isoform 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0						acattacaacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129652679	129652680	+	IGR	INS	-	T	T	rs78559112		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129652679_129652680insT								PGRMC2 (443731 upstream) : PHF17 (78099 downstream)																							tgattcattcatttttttTTTT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153218686	153218687	+	IGR	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153218686_153218687delTC								PET112L (536540 upstream) : FBXW7 (23724 downstream)																							tttctttctttctctctctctc	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160340632	160340632	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160340632delC								RAPGEF2 (59333 upstream) : None (None downstream)																							tcagttttggccagtcacagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185156520	185156520	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185156520delA								ENPP6 (17406 upstream) : IRF2 (152358 downstream)																							gtggatgcctaaaaccacaga	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	187756007	187756008	+	IGR	INS	-	GA	GA	rs145005405	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187756007_187756008insGA								FAT1 (108157 upstream) : None (None downstream)																							TGAGGGGTGGGgagagagagag	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188606419	188606420	+	IGR	DEL	AA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188606419_188606420delAA								FAT1 (958569 upstream) : ZFP42 (310505 downstream)																							cttccttTGGAAAAAAAAAAAA	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190301673	190301674	+	IGR	DEL	CA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190301673_190301674delCA								None (None upstream) : FRG1 (560300 downstream)																							cagcagcaagcacacacacctg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190614284	190614285	+	IGR	INS	-	A	A	rs113246865		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190614284_190614285insA								None (None upstream) : FRG1 (247689 downstream)																							AGAAGAGGTAGAAAAAAAAAAG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190858143	190858144	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190858143_190858144insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		aaaggacatgattttgttattt	0.000													4	2	---	---	---	---	
CEP72	55722	broad.mit.edu	37	5	648804	648805	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:648804_648805delTG	uc003jbf.2	+							NM_018140	NP_060610	Q9P209	CEP72_HUMAN	centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			GAGGCGTGACTGTGAGGCGTGA	0.584													4	2	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	796026	796027	+	3'UTR	INS	-	TG	TG	rs146509358	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:796026_796027insTG	uc011cma.1	-	13					ZDHHC11_uc010itc.2_RNA|ZDHHC11_uc003jbj.2_RNA	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TTTCCCAGTACTGTGCTCCCAT	0.495													2	4	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	842413	842414	+	Intron	INS	-	G	G	rs143640098	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:842413_842414insG	uc011cma.1	-						ZDHHC11_uc003jbj.2_Intron|ZDHHC11_uc010itd.1_RNA|ZDHHC11_uc003jbk.2_Intron	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GACTTGCTACTGGGGGAGAAGA	0.624													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1867509	1867509	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1867509delG								NDUFS6 (51346 upstream) : IRX4 (10032 downstream)																							gagggtgtgtggggagagggt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4311496	4311496	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4311496delA								IRX1 (709980 upstream) : LOC340094 (722976 downstream)																							AAAGGTTCCTAAAAGATTGGA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4912875	4912882	+	IGR	DEL	GAAGGAAG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4912875_4912882delGAAGGAAG								None (None upstream) : LOC340094 (121590 downstream)																							ggaaagaaatgaaggaaggaaggaagga	0.111													9	5	---	---	---	---	
UBE2QL1	134111	broad.mit.edu	37	5	6454005	6454005	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6454005delT	uc003jdp.3	+							NM_001145161	NP_001138633	A1L167	U2QL1_HUMAN	ubiquitin-conjugating enzyme E2Q family-like 1								ATP binding|ubiquitin-protein ligase activity				0						AACACAGAGAttttttttgag	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6985416	6985416	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6985416delA								PAPD7 (228255 upstream) : ADCY2 (410927 downstream)																							cattattgtcaaggtcaccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7288883	7288884	+	IGR	INS	-	CTC	CTC	rs143810233	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7288883_7288884insCTC								PAPD7 (531722 upstream) : ADCY2 (107459 downstream)																							ctcttcttcttctcctcctcct	0.000													5	4	---	---	---	---	
LOC285692	285692	broad.mit.edu	37	5	9894517	9894518	+	Intron	INS	-	AAAACAAAAAC	AAAACAAAAAC	rs113490412		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9894517_9894518insAAAACAAAAAC	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0						aaacaaaaacaaaaaaaaacag	0.000													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13921859	13921860	+	Intron	INS	-	C	C	rs146846325	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13921859_13921860insC	uc003jfd.2	-						DNAH5_uc003jfe.1_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						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)					GCCCACACACACCCCCCCACAC	0.480									Kartagener_syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20263058	20263060	+	IGR	DEL	AAG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20263058_20263060delAAG								CDH18 (274751 upstream) : None (None downstream)																							agaaaaagaaaagaaggaagaat	0.054													0	6	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33787127	33787128	+	Intron	INS	-	CTG	CTG	rs142397400		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33787127_33787128insCTG	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						CATGAAATAACCTAAGTGGATG	0.401										HNSCC(64;0.19)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36577998	36577998	+	IGR	DEL	T	-	-	rs148314705		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36577998delT								RANBP3L (275987 upstream) : SLC1A3 (28459 downstream)																							cttcttcttcttttttttttt	0.005													4	2	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	37036542	37036542	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37036542delT	uc003jkl.3	+	33	6423	c.5924delT	c.(5923-5925)GTTfs	p.V1975fs	NIPBL_uc003jkk.3_Frame_Shift_Del_p.V1975fs	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1975	HEAT 3.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ACTCAACTTGTTGATAACCTA	0.249													4	2	---	---	---	---	
LIFR	3977	broad.mit.edu	37	5	38565689	38565689	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38565689delT	uc003jli.2	-						uc003jlj.2_Intron	NM_002310	NP_002301	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor						positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					TGATTGTTGAttttttttttt	0.179			T	PLAG1	salivary adenoma								2	4	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	58318185	58318185	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58318185delA	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jrt.2_Intron|PDE4D_uc003jru.2_Intron|PDE4D_uc003jrv.2_Intron|PDE4D_uc003jrw.2_Intron|PDE4D_uc010iwi.1_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	CACACTGCCTAATACGTCTTT	0.478													4	2	---	---	---	---	
KIF2A	3796	broad.mit.edu	37	5	61662223	61662224	+	Intron	INS	-	T	T	rs148411444		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61662223_61662224insT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		TTACCTTTGCATTTTTTTTTTC	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67697308	67697308	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67697308delG								PIK3R1 (99661 upstream) : SLC30A5 (692510 downstream)																							attcattattgtgaggacagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	74427615	74427616	+	IGR	INS	-	G	G	rs150995408	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74427615_74427616insG								GCNT4 (100891 upstream) : ANKRD31 (15446 downstream)																							tcatactgccaggtgtccctct	0.000													4	2	---	---	---	---	
TBCA	6902	broad.mit.edu	37	5	77070522	77070522	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77070522delG	uc003kfh.1	-						TBCA_uc003kfi.1_Intron	NM_004607	NP_004598	O75347	TBCA_HUMAN	tubulin-specific chaperone a						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway|tubulin complex assembly	cytoplasm|microtubule	chaperone binding|unfolded protein binding			ovary(1)	1		all_lung(232;0.000511)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.02e-49)|Epithelial(54;1.05e-44)|all cancers(79;4.08e-40)		gctgtagcctgaccacctcgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82886087	82886087	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82886087delG								VCAN (7965 upstream) : HAPLN1 (47931 downstream)																							TAGAAAATAAGGTCAATGTGA	0.164													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	89989390	89989390	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89989390delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_5'Flank	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTTATCATTGTTACTTTGTTT	0.189													4	2	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108125937	108125938	+	Intron	DEL	CA	-	-	rs35511156		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108125937_108125938delCA	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)		Gcatacacaccacacacacaca	0.079													4	3	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112498197	112498198	+	Intron	INS	-	T	T	rs75534784		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112498197_112498198insT	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TTGCAATCttcttttttttttc	0.050													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122238532	122238532	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122238532delA	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		TAGCCAGTTCAATTCCCCTCC	0.204													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122252951	122252951	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122252951delA	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		acttcatctcaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	136870718	136870721	+	IGR	DEL	TGAA	-	-	rs150480081		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136870718_136870721delTGAA								SPOCK1 (35700 upstream) : KLHL3 (82469 downstream)																							caatacacattgaatgaatgaatg	0.098													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152388425	152388425	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152388425delT								NMUR2 (603585 upstream) : GRIA1 (480750 downstream)																							TATTAATTTCTTTTTTTTTTT	0.413													4	2	---	---	---	---	
ATP10B	23120	broad.mit.edu	37	5	160072370	160072370	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160072370delG	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)			TTTTCATACAGGGGACAGGGG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162309906	162309906	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162309906delG								GABRG2 (727362 upstream) : CCNG1 (554671 downstream)																							ccgcagccctggcacgggatc	0.000													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168212143	168212144	+	Intron	DEL	CA	-	-	rs111405079		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168212143_168212144delCA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|SLIT3_uc003mac.1_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			cacatgcatgcacacacacaca	0.248													4	3	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168506820	168506822	+	Intron	DEL	GAG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168506820_168506822delGAG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ggaaggggaagaggaggagggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173545051	173545051	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173545051delT								HMP19 (8870 upstream) : MSX2 (606524 downstream)																							ccctccttccttccttccttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173985817	173985819	+	IGR	DEL	CCT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173985817_173985819delCCT								HMP19 (449636 upstream) : MSX2 (165756 downstream)																							tccttccttccctccttccttcc	0.000													4	2	---	---	---	---	
SLC34A1	6569	broad.mit.edu	37	5	176809097	176809098	+	5'Flank	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176809097_176809098insT	uc003mgk.3	+							NM_003052	NP_003043	Q06495	NPT2A_HUMAN	solute carrier family 34 (sodium phosphate),						phosphate ion homeostasis|response to cadmium ion|response to lead ion|response to mercury ion|sodium ion transport	brush border membrane|integral to plasma membrane	protein binding|sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ttaacttggccttttttttttt	0.000													4	2	---	---	---	---	
TBC1D9B	23061	broad.mit.edu	37	5	179329267	179329267	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179329267delC	uc003mlh.2	-						TBC1D9B_uc003mli.2_Intron|TBC1D9B_uc003mlj.2_Intron	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)							integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTAGGCACAGCAGCCAGGAGG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2505169	2505170	+	IGR	INS	-	CCT	CCT	rs140066299	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2505169_2505170insCCT								GMDS (259323 upstream) : C6orf195 (117802 downstream)																							tcctcctcacccatctcctcct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7271624	7271625	+	IGR	INS	-	G	G	rs141112495	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7271624_7271625insG								RREB1 (19932 upstream) : SSR1 (9665 downstream)																							AAAAGTGGTTTGGggctgggcg	0.262													3	3	---	---	---	---	
ATXN1	6310	broad.mit.edu	37	6	16679604	16679615	+	Intron	DEL	TGGATGGATGGA	-	-	rs72460917		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16679604_16679615delTGGATGGATGGA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				ggtgggtgggtggatggatggatggatggatg	0.009													4	3	---	---	---	---	
KDM1B	221656	broad.mit.edu	37	6	18185536	18185536	+	5'Flank	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18185536delT	uc003nco.1	+						KDM1B_uc003ncn.1_Intron	NM_153042	NP_694587	Q8NB78	KDM1B_HUMAN	amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1						ACACTCTCACttttttttttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19781907	19781907	+	IGR	DEL	T	-	-	rs36012908		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19781907delT								None (None upstream) : ID4 (55710 downstream)																							AGCGAGAATGTTCGCCTTTTT	0.537													1	5	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25313799	25313800	+	Intron	INS	-	CAGGGC	CAGGGC	rs145914530	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25313799_25313800insCAGGGC	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AGGATGAGGGGCAGGGCCAGGG	0.495													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26689006	26689006	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26689006delT								ZNF322A (29043 upstream) : GUSBL1 (150260 downstream)																							AATCTTTTCATTTTTTTCAGC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30429073	30429073	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30429073delC								TRIM39 (114441 upstream) : HLA-E (28198 downstream)																							TGAAGGATAACAAAACTGAAG	0.299													4	2	---	---	---	---	
KCTD20	222658	broad.mit.edu	37	6	36423296	36423296	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36423296delA	uc003ome.2	+						KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2						tctggaggagaaaagtggtac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41599136	41599136	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41599136delC								FOXP4 (29015 upstream) : MDFI (5794 downstream)																							gtaaccaactccctaaattaa	0.050													4	2	---	---	---	---	
TMEM63B	55362	broad.mit.edu	37	6	44102220	44102220	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44102220delC	uc003owr.2	+						TMEM63B_uc003owq.1_5'UTR|TMEM63B_uc010jyy.1_Intron|TMEM63B_uc003ows.2_5'Flank	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B							integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			GTCCTCACTGCCCCCTCCCCA	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50208710	50208711	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50208710_50208711delGT								DEFB112 (192346 upstream) : TFAP2D (472546 downstream)																							cagggccctggtgtgtcaatgc	0.000													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57422066	57422067	+	Intron	INS	-	T	T	rs141911261		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57422066_57422067insT	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)		ccttgaaaaacttttttttgca	0.000													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57488800	57488800	+	Intron	DEL	G	-	-	rs111409818		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57488800delG	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)		ttggttGACAGtttttttttt	0.015													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57509525	57509525	+	Intron	DEL	T	-	-	rs11307740		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57509525delT	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)		gacttccacctttttttttaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	62084903	62084903	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62084903delT								None (None upstream) : KHDRBS2 (304962 downstream)																							tcataattacttttttttttt	0.025													4	2	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73730644	73730645	+	Intron	DEL	CA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73730644_73730645delCA	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CCCACACATGCACACACACACA	0.272													4	2	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74445154	74445154	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74445154delT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						AGGGGGAAGATTAGTTGCATT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87846811	87846815	+	IGR	DEL	CTTCA	-	-	rs60061676		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87846811_87846815delCTTCA								CGA (41987 upstream) : ZNF292 (15736 downstream)																							tctgctccttcttcatcttcatctt	0.176													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100932184	100932184	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100932184delC								SIM1 (19379 upstream) : ASCC3 (24425 downstream)																							TCTGTCTTTTCCCCTGGCTCT	0.493													4	2	---	---	---	---	
PDSS2	57107	broad.mit.edu	37	6	107475638	107475638	+	3'UTR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107475638delT	uc003prt.2	-	8					PDSS2_uc011eak.1_3'UTR|PDSS2_uc011eal.1_3'UTR	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		CTGCTTGACCTTTTTTTCTTC	0.378													4	2	---	---	---	---	
AKD1	221264	broad.mit.edu	37	6	109932857	109932857	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109932857delT	uc003ptn.2	-							NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						TTTcctttccttttcctttcc	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	132285699	132285700	+	IGR	INS	-	T	T	rs113086815		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132285699_132285700insT								CTGF (13181 upstream) : MOXD1 (331495 downstream)																							CACATAAACTAttttttttttt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138155801	138155802	+	Intron	INS	-	AC	AC	rs148366794	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138155801_138155802insAC	uc003qhq.1	-											Homo sapiens cDNA FLJ42179 fis, clone THYMU2030796.																		CAAACAAAACAacacacacaca	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	144601451	144601453	+	IGR	DEL	ATA	-	-	rs140763		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144601451_144601453delATA								STX11 (88376 upstream) : UTRN (6037 downstream)																							cttcaatatcataatgagtactt	0.108													2	4	---	---	---	---	
GRM1	2911	broad.mit.edu	37	6	146348736	146348737	+	5'Flank	INS	-	T	T	rs112586640		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146348736_146348737insT	uc010khw.1	+						GRM1_uc010khu.1_5'Flank|GRM1_uc010khv.1_5'Flank|GRM1_uc003qll.2_5'Flank|GRM1_uc011edz.1_5'Flank|GRM1_uc011eea.1_5'Flank	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	TGGGTGACCTGTTTTTTTTTTT	0.446													4	3	---	---	---	---	
PPP1R14C	81706	broad.mit.edu	37	6	150489124	150489125	+	Intron	DEL	CT	-	-	rs75354918		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150489124_150489125delCT	uc003qnt.2	+							NM_030949	NP_112211	Q8TAE6	PP14C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of phosphorylation	cytoplasm|membrane					0		Ovarian(120;0.0284)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;9.14e-12)		ctctcctcccctcttcctctcc	0.163													5	3	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155490959	155490959	+	Intron	DEL	T	-	-	rs112991074		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155490959delT	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CACCAAATAAttttttttttt	0.209													2	4	---	---	---	---	
NOX3	50508	broad.mit.edu	37	6	155749023	155749025	+	Intron	DEL	TCC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155749023_155749025delTCC	uc003qqm.2	-							NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TCTTTTTCTTTCCTCCTCCTCCT	0.276													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160084076	160084076	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160084076delC								FNDC1 (390937 upstream) : SOD2 (16075 downstream)																							aggtgatccacccggctaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	163771079	163771079	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163771079delT								LOC285796 (25585 upstream) : QKI (64596 downstream)																							acatttcttctttctatagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164171343	164171344	+	Intron	INS	-	CTC	CTC	rs138012412	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164171343_164171344insCTC	uc003quk.1	+											Homo sapiens cDNA FLJ35795 fis, clone TESTI2005827.																		GGATGCTAATTCTCGCAACTCC	0.490													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165294162	165294163	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165294162_165294163insT								None (None upstream) : C6orf118 (398992 downstream)																							TTTTTTGTGGGTTTTTTTTTCA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170530188	170530188	+	IGR	DEL	C	-	-	rs66522185		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170530188delC								C6orf208 (327219 upstream) : LOC154449 (33234 downstream)																							AGACTCCACACCGGGAGTCAG	0.637													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	390543	390543	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:390543delC								FAM20C (89832 upstream) : PDGFA (146356 downstream)																							CACACACACACACAAGACACG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	390544	390545	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:390544_390545insT								FAM20C (89833 upstream) : PDGFA (146354 downstream)																							ACACACACACACAAGACACGAC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	506976	506977	+	IGR	INS	-	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:506976_506977insC								FAM20C (206265 upstream) : PDGFA (29922 downstream)																							aaccatcacctctcacggccat	0.050													5	3	---	---	---	---	
TTYH3	80727	broad.mit.edu	37	7	2683445	2683446	+	Intron	INS	-	AGCGGGGT	AGCGGGGT	rs139768688	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2683445_2683446insAGCGGGGT	uc003smp.2	+							NM_025250	NP_079526	Q9C0H2	TTYH3_HUMAN	tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GCGGAGGTCACACCTGTTTAGG	0.619													4	2	---	---	---	---	
RPA3	6119	broad.mit.edu	37	7	7683985	7683986	+	Intron	INS	-	TT	TT	rs35141799		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7683985_7683986insTT	uc003sri.2	-							NM_002947	NP_002938	P35244	RFA3_HUMAN	replication protein A3, 14kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	cytoplasm|DNA replication factor A complex|nucleoplasm	protein binding|single-stranded DNA binding			large_intestine(1)	1		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)		TCATTCCATCCTTTTTTTTTTT	0.282								Direct_reversal_of_damage|NER					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12998966	12998966	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12998966delT								ARL4A (268410 upstream) : ETV1 (931892 downstream)																							gataagattattttttttttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13894519	13894519	+	IGR	DEL	T	-	-	rs34475612		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13894519delT								None (None upstream) : ETV1 (36339 downstream)																							agcgattctcttgtcttagcc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17507386	17507387	+	IGR	INS	-	GTCAA	GTCAA	rs148732932	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17507386_17507387insGTCAA								AHR (121611 upstream) : SNX13 (322999 downstream)																							atttctacgttgtcaagtccaa	0.064													0	6	---	---	---	---	
HOXA5	3202	broad.mit.edu	37	7	27185066	27185075	+	5'Flank	DEL	GTTTTGTTTT	-	-	rs70994631		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27185066_27185075delGTTTTGTTTT	uc003syn.1	-						uc003syp.1_5'Flank	NM_019102	NP_061975	P20719	HXA5_HUMAN	homeobox A5						negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TGTGTGTGAGgttttgttttgttttgtttt	0.467													4	2	---	---	---	---	
C7orf16	10842	broad.mit.edu	37	7	31735444	31735444	+	Intron	DEL	T	-	-	rs68028809		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31735444delT	uc003tcl.2	+						C7orf16_uc011kaf.1_Intron	NM_006658	NP_006649	O96001	GSUB_HUMAN	G-substrate isoform 1						behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction				ovary(2)|central_nervous_system(1)	3			GBM - Glioblastoma multiforme(11;0.216)			taaaagtttattttttttacc	0.065													3	5	---	---	---	---	
AOAH	313	broad.mit.edu	37	7	36675089	36675091	+	Intron	DEL	GTC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36675089_36675091delGTC	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1						TTCAACCCTTGTCGTGTATTATA	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37527008	37527009	+	IGR	DEL	CA	-	-	rs71554513		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37527008_37527009delCA								ELMO1 (38478 upstream) : GPR141 (252987 downstream)																							CTTTGGGCATcacacacacaca	0.347													4	2	---	---	---	---	
CDK13	8621	broad.mit.edu	37	7	39999070	39999070	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39999070delT	uc003thh.3	+						CDK13_uc003thi.3_Intron	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5						tttttctttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41064973	41064973	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41064973delT								C7orf10 (164616 upstream) : INHBA (663630 downstream)																							CAATGTATGAttttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	44849073	44849073	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44849073delA								PPIA (6358 upstream) : H2AFV (17415 downstream)																							AGTGAAAATGAtttttttttt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	44894762	44894763	+	IGR	DEL	GC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44894762_44894763delGC								H2AFV (7037 upstream) : PURB (21131 downstream)																							cagtgcaatggcgcaatctcag	0.000													2	4	---	---	---	---	
ADCY1	107	broad.mit.edu	37	7	45650576	45650577	+	Intron	INS	-	GC	GC	rs10668553		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45650576_45650577insGC	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1						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|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	atggtggaggtggggggtgata	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45830641	45830641	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45830641delG								SEPT7P2 (22024 upstream) : IGFBP1 (97318 downstream)																							catattttgtggacatttgtg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46307127	46307127	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46307127delC								IGFBP3 (346256 upstream) : None (None downstream)																							tggcacattaccaaggacttc	0.000													4	2	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55607341	55607342	+	Intron	INS	-	CCC	CCC	rs137904740	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55607341_55607342insCCC	uc003tqs.2	-						VOPP1_uc003tqq.2_5'Flank|VOPP1_uc010kzh.2_5'Flank|VOPP1_uc010kzi.2_Intron|VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						TGGATCATCAGCCCCGCTGTGA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57948279	57948279	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57948279delC								ZNF716 (415014 upstream) : None (None downstream)																							tccttttctaccataggccgc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61085205	61085205	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61085205delT								None (None upstream) : None (None downstream)																							ggctgaaacattctcagaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61845608	61845609	+	IGR	INS	-	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61845608_61845609insG								None (None upstream) : LOC643955 (906063 downstream)																							ggagggagggaggaagggagaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63304170	63304170	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63304170delA								LOC100287704 (492019 upstream) : ZNF727 (201651 downstream)																							catctgtcctaaaaaaaaaaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64961321	64961321	+	IGR	DEL	T	-	-	rs35970258		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64961321delT								ZNF92 (95324 upstream) : INTS4L2 (151456 downstream)																							GTTTTACACCTGTCAAAATGT	0.284													3	3	---	---	---	---	
WBSCR26	171022	broad.mit.edu	37	7	73147993	73147994	+	5'Flank	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73147993_73147994delAC	uc011kez.1	+							NR_026690				Homo sapiens Williams Beuren syndrome chromosome region 26 (non-protein coding) (WBSCR26), non-coding RNA.												0						ccatctcaaaacacacacacac	0.005													4	2	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75242404	75242405	+	Intron	DEL	CA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75242404_75242405delCA	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						caacttgggtcacacacacaca	0.089			T	PDGFRB	CMML								4	3	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75311745	75311746	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75311745_75311746insT	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						tagccagctagttttttttttt	0.000			T	PDGFRB	CMML								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75918253	75918254	+	IGR	INS	-	AA	AA			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75918253_75918254insAA								SRRM3 (1648 upstream) : HSPB1 (13621 downstream)																							gactctgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
SEMA3E	9723	broad.mit.edu	37	7	83025864	83025865	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83025864_83025865insA	uc003uhy.1	-							NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				ACCTGTTAGGGAAAAAAAAATG	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	85590337	85590338	+	IGR	INS	-	TT	TT	rs146683302	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85590337_85590338insTT								SEMA3D (774166 upstream) : GRM3 (682892 downstream)																							ATCTCTCTCTCACCgtgtgtgt	0.337													4	2	---	---	---	---	
KIAA1324L	222223	broad.mit.edu	37	7	86680592	86680592	+	Intron	DEL	T	-	-	rs146228261		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86680592delT	uc011kha.1	-							NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					accaggagagtttggggtgct	0.055													2	5	---	---	---	---	
STEAP4	79689	broad.mit.edu	37	7	87935098	87935099	+	Intron	INS	-	TAGA	TAGA	rs143157615	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87935098_87935099insTAGA	uc003ujs.2	-						STEAP4_uc010lek.2_Intron|STEAP4_uc003ujt.2_Intron	NM_024636	NP_078912	Q687X5	STEA4_HUMAN	tumor necrosis factor, alpha-induced protein 9						fat cell differentiation|ion transport|iron ion homeostasis	Golgi membrane|integral to membrane|plasma membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	Esophageal squamous(14;0.00802)					TTTCACCTtgttagagttgaac	0.178													5	3	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98563930	98563931	+	Intron	INS	-	A	A	rs75329540		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98563930_98563931insA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ctctgtcttggaaaaaaaaaaa	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100613385	100613385	+	5'Flank	DEL	G	-	-	rs113139186		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100613385delG	uc003uxn.1	-											Homo sapiens cDNA FLJ39484 fis, clone PROST2014925.																		AGCCCTGGTCGGGAGAGAGGG	0.582													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101208178	101208178	+	IGR	DEL	G	-	-	rs140731889		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101208178delG								EMID2 (5874 upstream) : MYL10 (48428 downstream)																							CATTCACGGTGGGGGCGTGGC	0.592													3	7	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101594791	101594791	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101594791delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						gtctttttccttttttttttt	0.000													4	5	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101745527	101745528	+	Intron	INS	-	CTCTT	CTCTT	rs143037518	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101745527_101745528insCTCTT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						AAAAGGCCAACCTCTTAACAAA	0.317													4	2	---	---	---	---	
SLC26A5	375611	broad.mit.edu	37	7	103015123	103015124	+	Intron	INS	-	T	T	rs72245175		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103015123_103015124insT	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1						TCCATATAGTGTTTTTTTTTTT	0.158													4	3	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122511238	122511239	+	Intron	INS	-	A	A	rs112112751		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122511238_122511239insA	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						ACAGTGCTGGGAAAAAAAAAAA	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125991356	125991357	+	IGR	INS	-	T	T	rs144850888		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125991356_125991357insT								None (None upstream) : GRM8 (87295 downstream)																							ATACAAATAACttttttttttt	0.178													6	3	---	---	---	---	
FAM71F1	84691	broad.mit.edu	37	7	128351988	128351989	+	Intron	DEL	GG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128351988_128351989delGG	uc003vnn.1	+						FAM71F1_uc010llo.1_Intron|FAM71F1_uc011koq.1_Intron|FAM71F1_uc003vnm.1_Intron			Q96KD3	F71F1_HUMAN	SubName: Full=HCG2039358, isoform CRA_b; SubName: Full=cDNA FLJ35842 fis, clone TESTI2006735;											skin(1)	1						ccagctactcgggaggctgagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129599474	129599475	+	IGR	INS	-	AC	AC	rs61347377		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129599474_129599475insAC								UBE2H (6685 upstream) : ZC3HC1 (58652 downstream)																							cacacacacagacacacacaca	0.233													2	4	---	---	---	---	
MEST	4232	broad.mit.edu	37	7	130141836	130141841	+	Intron	DEL	AAAAAG	-	-	rs146250493	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130141836_130141841delAAAAAG	uc003vqg.2	+						MEST_uc003vqc.2_Intron|MEST_uc003vqd.2_Intron|MEST_uc003vqf.2_Intron|MEST_uc011kph.1_Intron|MEST_uc010lmg.2_Intron	NM_002402	NP_002393	Q5EB52	MEST_HUMAN	mesoderm specific transcript isoform a						mesoderm development	endoplasmic reticulum membrane|integral to membrane	hydrolase activity|protein binding			ovary(2)	2	Melanoma(18;0.0435)					tcaaaaaaaaaaaaagaaaaaaaaaa	0.034													2	4	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132247853	132247854	+	Intron	INS	-	TCC	TCC	rs144617247	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132247853_132247854insTCC	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						cctcctcttcttcctcctcctc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	132871406	132871407	+	IGR	INS	-	AGAGGAAGATGA	AGAGGAAGATGA	rs150007146	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132871406_132871407insAGAGGAAGATGA								CHCHD3 (104578 upstream) : EXOC4 (66416 downstream)																							ggaggaggaggagaggaagagt	0.332													4	3	---	---	---	---	
AGBL3	340351	broad.mit.edu	37	7	134813072	134813073	+	Intron	DEL	CG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134813072_134813073delCG	uc011kpw.1	+						uc003vsg.2_Intron|C7orf49_uc003vsh.2_Intron	NM_178563	NP_848658	Q8NEM8	CBPC3_HUMAN	carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0						aaaaaaaaaacgaaaaaaaaaa	0.005													3	3	---	---	---	---	
CHRM2	1129	broad.mit.edu	37	7	136556367	136556368	+	Intron	INS	-	A	A	rs140137379	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136556367_136556368insA	uc003vtf.1	+						CHRM2_uc003vtg.1_Intron|CHRM2_uc003vtj.1_Intron|CHRM2_uc003vtk.1_Intron|CHRM2_uc003vtl.1_Intron|CHRM2_uc003vtm.1_Intron|CHRM2_uc003vti.1_Intron|CHRM2_uc003vto.1_Intron|CHRM2_uc003vtn.1_Intron|CHRM2_uc003vth.1_RNA	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2						activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	TCATTGATAAGAAAAAAAGAGA	0.406													4	4	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138660035	138660036	+	Intron	INS	-	TT	TT			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138660035_138660036insTT	uc011kql.1	-						KIAA1549_uc011kqj.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						TTGAGTGTGTGGATGCAAGAGG	0.416			O	BRAF	pilocytic astrocytoma								4	2	---	---	---	---	
AGK	55750	broad.mit.edu	37	7	141332340	141332340	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141332340delC	uc003vwi.2	+						AGK_uc011krg.1_Intron	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					tggagagcatccaggcttggc	0.000													4	2	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	144049976	144049977	+	Intron	DEL	AG	-	-	rs5888130		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144049976_144049977delAG	uc003wec.1	-						ARHGEF5_uc003wek.2_5'Flank|ARHGEF5_uc003wel.2_5'Flank					SubName: Full=Seven transmembrane helix receptor;												0						TGATGAGAAAagagagagagag	0.406													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144655334	144655334	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144655334delC								TPK1 (122188 upstream) : None (None downstream)																							TTAAAACTCTCCCTGTCTGCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148698722	148698723	+	IGR	INS	-	CT	CT	rs142597827	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148698722_148698723insCT								MIR1975 (60068 upstream) : PDIA4 (1431 downstream)																							GGGACAGTCCCCTCTTGGGTTC	0.614													2	4	---	---	---	---	
NOS3	4846	broad.mit.edu	37	7	150706436	150706437	+	Intron	INS	-	C	C	rs142498418	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150706436_150706437insC	uc003wif.2	+						NOS3_uc011kuy.1_Intron	NM_000603	NP_000594	P29474	NOS3_HUMAN	nitric oxide synthase 3 isoform 1						anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia	caveola|cytoskeleton|cytosol|Golgi membrane	actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			central_nervous_system(5)|large_intestine(2)|skin(1)	8	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360)	ACATTCTCCCGCCCCCACCCCT	0.678													7	4	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151367016	151367017	+	Intron	INS	-	CA	CA			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151367016_151367017insCA	uc003wkk.2	-						PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		acacacacctgtgcacacactt	0.000													5	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151877690	151877691	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151877690_151877691insA	uc003wla.2	-						MLL3_uc003wkz.2_Intron|MLL3_uc003wky.2_5'Flank	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)		CTCTACAGAATAAAAAAAATAA	0.272			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152588596	152588596	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152588596delC								ACTR3B (36133 upstream) : DPP6 (995823 downstream)																							CACAGCGTGTCCCCACAGTGT	0.657													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153962233	153962235	+	Intron	DEL	ATG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153962233_153962235delATG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			gatggtgataatgatggtgatgg	0.000													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154114405	154114405	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154114405delG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			tgtagtttttgttgcagtagg	0.259													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154964405	154964405	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154964405delC								HTR5A (86946 upstream) : INSIG1 (125081 downstream)																							TATTTTCCCACCcaggacagc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156897758	156897758	+	IGR	DEL	T	-	-	rs35471917		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156897758delT								MNX1 (94411 upstream) : UBE3C (33897 downstream)																							CTGAGGCTGCTTTGCTGCAGG	0.498													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	729467	729468	+	Intron	INS	-	T	T	rs35954348		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:729467_729468insT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																		ttctttctttcttttttttttt	0.193													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1060342	1060343	+	Intron	DEL	AT	-	-	rs10532083		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1060342_1060343delAT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																		GGTCTGTGACATGTGCTGGGTC	0.564													3	4	---	---	---	---	
MSRA	4482	broad.mit.edu	37	8	10116615	10116616	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10116615_10116616insA	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc011kwy.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	tctgtcaaaggaaaaaaaaaaa	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	11868669	11868669	+	5'Flank	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11868669delT	uc003wuy.1	+											Homo sapiens cDNA FLJ33940 fis, clone CTONG2018069.																		attttatagatgagaaaactg	0.040													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13441741	13441741	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13441741delT								C8orf48 (15945 upstream) : SGCZ (505633 downstream)																							AACCTGCAGCTTCCCTGTTTG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19660077	19660077	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19660077delG								CSGALNACT1 (44695 upstream) : INTS10 (14841 downstream)																							cataccctctggggttttggg	0.000													4	2	---	---	---	---	
GSR	2936	broad.mit.edu	37	8	30581301	30581310	+	Intron	DEL	ACACACACAC	-	-	rs111543890		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30581301_30581310delACACACACAC	uc003xih.1	-							NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor						cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)	agagcAacaaacacacacacacacacacac	0.033													4	2	---	---	---	---	
PPP2CB	5516	broad.mit.edu	37	8	30643835	30643835	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30643835delA	uc003xik.2	-							NM_004156	NP_004147	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta						protein dephosphorylation	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	TGTAAATGGCAAAAAAGGAAG	0.443													4	2	---	---	---	---	
RAB11FIP1	80223	broad.mit.edu	37	8	37731433	37731434	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37731433_37731434insA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			GCAGAATCTCTAAAAAAAAAAA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	46898317	46898318	+	IGR	INS	-	G	G	rs139224318		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46898317_46898318insG								None (None upstream) : BEYLA (854190 downstream)																							ctttgtgatgttgcattcatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58248978	58248979	+	IGR	INS	-	T	T	rs113377449		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58248978_58248979insT								C8orf71 (51690 upstream) : FAM110B (658134 downstream)																							TACCAGtttccttttttttttt	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65097865	65097865	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65097865delA								YTHDF3 (972520 upstream) : MIR124-2 (193841 downstream)																							ccaaagacataaggataaggg	0.000													4	2	---	---	---	---	
JPH1	56704	broad.mit.edu	37	8	75191188	75191189	+	Intron	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75191188_75191189delAC	uc003yae.2	-						JPH1_uc003yaf.2_Intron|JPH1_uc003yag.1_Intron	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			AGCAAGacagacacacacacac	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78294859	78294859	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78294859delA								PEX2 (382335 upstream) : None (None downstream)																							aacaacaaataaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92532127	92532128	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92532127_92532128insT								SLC26A7 (121747 upstream) : RUNX1T1 (439024 downstream)																							CCAGTTTTTTGTTTTTTTTTTA	0.386													4	2	---	---	---	---	
FAM92A1	137392	broad.mit.edu	37	8	94725261	94725261	+	Intron	DEL	C	-	-	rs28838616		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94725261delC	uc010maq.2	+						FAM92A1_uc003yfv.3_Intron|FAM92A1_uc003yfx.3_Intron|FAM92A1_uc003yfw.3_Intron|FAM92A1_uc010mar.2_Intron	NM_145269	NP_660312	A1XBS5	F92A1_HUMAN	hypothetical protein LOC137392												0	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			ccttttttttctttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94875269	94875271	+	IGR	DEL	AAC	-	-	rs113356049		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94875269_94875271delAAC								TMEM67 (44923 upstream) : PDP1 (53812 downstream)																							gcaaaacaataacaacaacaaca	0.020													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100042690	100042693	+	Intron	DEL	GTGT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100042690_100042693delGTGT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yis.2_Intron|VPS13B_uc011lgy.1_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			gagtgagtgagtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	105666618	105666619	+	IGR	INS	-	TG	TG	rs149151033	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105666618_105666619insTG								LRP12 (65398 upstream) : ZFPM2 (664528 downstream)																							TATGTATTCTAtgtgtgtgtgt	0.203													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109955223	109955223	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109955223delC								TMEM74 (155453 upstream) : TRHR (144516 downstream)																							aaagaacctacgttgaaatac	0.085													2	4	---	---	---	---	
EIF3H	8667	broad.mit.edu	37	8	117712042	117712043	+	Intron	INS	-	T	T	rs142650308	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117712042_117712043insT	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747	O15372	EIF3H_HUMAN	eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					AGGTTTTTTGGTtttttttgtt	0.163													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118515583	118515584	+	IGR	INS	-	GAG	GAG	rs140411631		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118515583_118515584insGAG								SLC30A8 (326631 upstream) : MED30 (17381 downstream)																							gaaaaaaagaagaggaggagga	0.094													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124682446	124682446	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124682446delC								KLHL38 (17256 upstream) : ANXA13 (10589 downstream)																							tcctcctcctcctccccacct	0.154													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125882259	125882259	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125882259delC								MTSS1 (141529 upstream) : LOC157381 (69625 downstream)																							tggcccacttccaatctctcc	0.000													4	2	---	---	---	---	
WISP1	8840	broad.mit.edu	37	8	134232438	134232438	+	Intron	DEL	T	-	-	rs33995880		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134232438delT	uc003yub.2	+						WISP1_uc003yuc.2_Intron|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_Intron	NM_003882	NP_003873	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1						cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GTGTTCTGGCTTTTTTTTTAC	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135767652	135767653	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135767652_135767653insA								ZFAT (42371 upstream) : MIR30B (45110 downstream)																							gactctgtctcaaaaaaaaaaa	0.025													3	4	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139681463	139681463	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139681463delG	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CCAGGCACCTGGGGAGACCAG	0.627										HNSCC(7;0.00092)			4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139770287	139770287	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139770287delC	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			atctcagactccctcctttcc	0.000										HNSCC(7;0.00092)			4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140863308	140863308	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140863308delC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						CAGCTCAGCTCCCAAGCAGCA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142625900	142625900	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142625900delC								FLJ43860 (108570 upstream) : MIR1302-7 (241703 downstream)																							cccactctctccttcccttcc	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144505207	144505209	+	IGR	DEL	CCT	-	-	rs7387268		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144505207_144505209delCCT								RHPN1 (38818 upstream) : MAFA (6306 downstream)																							CCATCCCCCACCTCCTCCGCCTC	0.675													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	18919621	18919622	+	IGR	DEL	AC	-	-	rs72039683		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18919621_18919622delAC								ADAMTSL1 (8676 upstream) : FAM154A (8271 downstream)																							Tcatacacaaacacacacacac	0.277													4	3	---	---	---	---	
MLLT3	4300	broad.mit.edu	37	9	20550529	20550529	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20550529delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tcccagactcaagtgatcctc	0.015			T	MLL	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43851404	43851405	+	Intron	INS	-	T	T	rs66540067		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43851404_43851405insT	uc004acz.1	+											Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.																		GACACATTTTCttttttttgtt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481963	66481964	+	IGR	INS	-	T	T	rs139236774		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481963_66481964insT								FAM74A4 (987577 upstream) : LOC442421 (14506 downstream)																							gcaacccctgcttttttttaat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66491022	66491022	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66491022delA								FAM74A4 (996636 upstream) : LOC442421 (5448 downstream)																							agaaagacacaaactaccaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68388344	68388344	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68388344delT								FAM27B (594155 upstream) : MIR1299 (613895 downstream)																							agttccaccattgtggaagac	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68397980	68397980	+	IGR	DEL	A	-	-	rs111363805		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68397980delA								FAM27B (603791 upstream) : MIR1299 (604259 downstream)																							GGGCTACAAGAAGGCAATTAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68425242	68425242	+	IGR	DEL	A	-	-	rs66621105		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68425242delA								FAM27B (631053 upstream) : MIR1299 (576997 downstream)																							TTTTGTGGCTACTCAAATTTT	0.184													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68458977	68458977	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68458977delC								FAM27B (664788 upstream) : MIR1299 (543262 downstream)																							acggcatctgcctggcgcctg	0.000													4	2	---	---	---	---	
RORB	6096	broad.mit.edu	37	9	77112484	77112486	+	5'UTR	DEL	TCC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77112484_77112486delTCC	uc004ajh.2	+	1						NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						ctgctgcccttcctcctcctcct	0.320													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92904054	92904054	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92904054delT								LOC100129066 (569380 upstream) : DIRAS2 (468060 downstream)																							TTTTGTTCCCTTCCCCTCTCC	0.328													4	2	---	---	---	---	
OGN	4969	broad.mit.edu	37	9	95161337	95161337	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95161337delA	uc004asa.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|OGN_uc004asb.2_Intron|OGN_uc011ltx.1_Intron	NM_014057	NP_054776	P20774	MIME_HUMAN	osteoglycin preproprotein							extracellular space|proteinaceous extracellular matrix	growth factor activity				0						actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BICD2	23299	broad.mit.edu	37	9	95514616	95514617	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95514616_95514617insA	uc004aso.1	-						BICD2_uc004asp.1_Intron	NM_015250	NP_056065	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 isoform 2						microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1						ggaagcactttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115824350	115824351	+	IGR	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115824350_115824351delTG								ZFP37 (5354 upstream) : C9orf110 (42655 downstream)																							cctgtgtgtatgtgtgtgtgtg	0.460													5	3	---	---	---	---	
RBM18	92400	broad.mit.edu	37	9	125011987	125011988	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125011987_125011988insA	uc004bma.2	-						RBM18_uc004blz.2_Intron|RBM18_uc010mvy.2_Intron|RBM18_uc011lyp.1_Intron	NM_033117	NP_149108	Q96H35	RBM18_HUMAN	RNA binding motif protein 18								nucleotide binding|RNA binding				0						gaccctgtctcaaaaaaaaaaa	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	131959108	131959109	+	IGR	INS	-	TCCTTCCG	TCCTTCCG	rs149599727	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131959108_131959109insTCCTTCCG								IER5L (18568 upstream) : C9orf106 (124186 downstream)																							cctcccttccttccttccttcc	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11724663	11724664	+	IGR	INS	-	CTCCTCCTT	CTCCTCCTT	rs147502325	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11724663_11724664insCTCCTCCTT								USP6NL (70984 upstream) : ECHDC3 (59692 downstream)																							tcctctccctcctcctcctctc	0.134													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	13441305	13441305	+	IGR	DEL	A	-	-	rs111944975		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13441305delA								SEPHS1 (51025 upstream) : BEND7 (39179 downstream)																							ccccatctctaaaaaaaaaaa	0.000													6	3	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18754612	18754613	+	Intron	DEL	TT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18754612_18754613delTT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc009xkb.1_Intron|CACNB2_uc010qcm.1_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qcn.1_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	CAACttcttctttttttttttt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	23017413	23017414	+	IGR	INS	-	G	G	rs149433321	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23017413_23017414insG								PIP4K2A (13910 upstream) : ARMC3 (199540 downstream)																							ttagtagagatgggatttcact	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31325348	31325348	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31325348delG								ZNF438 (4482 upstream) : LOC220930 (280110 downstream)																							TTATCCCTCTGGTAACTCGGA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31965886	31965886	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31965886delG								ZEB1 (147759 upstream) : ARHGAP12 (129339 downstream)																							ACTGGACTGAGGGGTGGAAGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38876350	38876350	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38876350delG								LOC399744 (135270 upstream) : None (None downstream)																							atcatcaaatggactcgaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42657140	42657140	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42657140delT								None (None upstream) : LOC441666 (170175 downstream)																							AGCATTTTAGTAcagtcacac	0.174													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46953986	46953987	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46953986_46953987insA								FAM35B (14843 upstream) : SYT15 (1457 downstream)																							ccgtttctactaaaaaatacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46983189	46983193	+	IGR	DEL	AAAAC	-	-	rs10560214		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46983189_46983193delAAAAC								SYT15 (12588 upstream) : GPRIN2 (10353 downstream)																							ctcagtctcaaaaacaaaacaaaac	0.000													5	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	57023332	57023332	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57023332delG	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						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)				caaccccaaagggccaataga	0.000										HNSCC(58;0.16)			4	2	---	---	---	---	
CISD1	55847	broad.mit.edu	37	10	60042857	60042857	+	Intron	DEL	A	-	-	rs34137602		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60042857delA	uc001jkc.3	+						CISD1_uc001jkd.3_Intron	NM_018464	NP_060934	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1							integral to membrane|mitochondrial outer membrane	2 iron, 2 sulfur cluster binding|metal ion binding				0						GATTTGAGTTAATGATACTTT	0.383													3	4	---	---	---	---	
HERC4	26091	broad.mit.edu	37	10	69836884	69836885	+	5'Flank	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69836884_69836885insA	uc001jng.3	-						HERC4_uc001jnh.3_5'Flank|HERC4_uc009xpr.2_5'Flank|HERC4_uc001jni.3_5'Flank|HERC4_uc001jnj.2_5'Flank|HERC4_uc001jnk.2_5'Flank	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						aactccatctcaaaaaaaaaaa	0.025													3	3	---	---	---	---	
H2AFY2	55506	broad.mit.edu	37	10	71836752	71836755	+	Intron	DEL	CCTT	-	-	rs72374022		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71836752_71836755delCCTT	uc001jqm.2	+						H2AFY2_uc001jqn.2_Intron	NM_018649	NP_061119	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2						chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding			skin(1)	1						GCATCATGAGCCTTCCTTCCTCTT	0.490													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	83489344	83489344	+	IGR	DEL	G	-	-	rs66462997		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83489344delG								None (None upstream) : NRG3 (145726 downstream)																							aaggaaggaaggggggggaaa	0.174													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102204383	102204384	+	IGR	INS	-	A	A	rs141327473		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102204383_102204384insA								C10orf75 (56269 upstream) : WNT8B (18428 downstream)																							aactctgtctcaaaaaaaaaaa	0.178													4	2	---	---	---	---	
PAX2	5076	broad.mit.edu	37	10	102584110	102584111	+	Intron	INS	-	AC	AC	rs35197216		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102584110_102584111insAC	uc001krk.3	+						PAX2_uc001krl.3_Intron|PAX2_uc001krm.3_Intron|PAX2_uc001kro.3_Intron|PAX2_uc001krn.3_Intron|PAX2_uc010qps.1_Intron|PAX2_uc001krp.1_Intron	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e						anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of metanephric glomerulus development|positive regulation of optic nerve formation|positive regulation of transcription from RNA polymerase II promoter|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter maturation|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|superoxide-generating NADPH oxidase activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		CAAAGGCAGATacacacacaca	0.337													4	2	---	---	---	---	
FBXW4	6468	broad.mit.edu	37	10	103378650	103378650	+	Intron	DEL	A	-	-	rs75454639		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103378650delA	uc001kto.2	-							NM_022039	NP_071322	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		CCCTTGGCAGAAAAAAAAAAC	0.587													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	105633726	105633727	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105633726_105633727insA								SH3PXD2A (18562 upstream) : OBFC1 (3593 downstream)																							caaacaaaaccaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	110664910	110664911	+	IGR	DEL	AG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110664910_110664911delAG								None (None upstream) : XPNPEP1 (959613 downstream)																							GAGTAAAAACAGAGAGAAGAGG	0.292													4	2	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121153757	121153758	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121153757_121153758delTG	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		tgtgggtgtctgtgtgtggatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123385367	123385368	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123385367_123385368insA								FGFR2 (27395 upstream) : ATE1 (117258 downstream)																							gagactgtctcaaaaaaaaaaa	0.084													4	2	---	---	---	---	
ADAM12	8038	broad.mit.edu	37	10	127737235	127737235	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127737235delA	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		AAGTTTGGTGAAAAAAAAAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	131989528	131989528	+	IGR	DEL	T	-	-	rs71494350		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131989528delT								GLRX3 (6744 upstream) : TCERG1L (901128 downstream)																							ccctgctgcctccccccgtga	0.015													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132281193	132281193	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132281193delT								GLRX3 (298409 upstream) : TCERG1L (609463 downstream)																							GGACTGCATGTTGTCAATGGA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132690806	132690806	+	IGR	DEL	A	-	-	rs11352446		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132690806delA								GLRX3 (708022 upstream) : TCERG1L (199850 downstream)																							CTCTTTCTGGAAAAAAAAAAT	0.488													3	3	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	132974693	132974696	+	Intron	DEL	ACAC	-	-	rs71917773		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132974693_132974696delACAC	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		AGACACATGTACACACAGAGATAC	0.137													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133488770	133488770	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133488770delC								TCERG1L (378786 upstream) : PPP2R2D (259190 downstream)																							CAGCCCTGAGCCTGGAGAACA	0.592													3	3	---	---	---	---	
JAKMIP3	282973	broad.mit.edu	37	10	133968467	133968472	+	Intron	DEL	ATCATG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133968467_133968472delATCATG	uc001lkx.3	+						JAKMIP3_uc009yba.1_Intron	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		gataatggttatcatgatggtgatca	0.073													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134635444	134635445	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134635444_134635445delTG	uc010qux.1	-							NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																		tgatgtgtgctgtgtgtgcgct	0.000													6	3	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1477161	1477161	+	Intron	DEL	C	-	-	rs111757092		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1477161delC	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron|BRSK2_uc009ycw.2_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		GAGGGCACAGCCCCAGCCCCG	0.692													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1515187	1515188	+	IGR	INS	-	A	A	rs71464142		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1515187_1515188insA								MOB2 (7211 upstream) : DUSP8 (60093 downstream)																							ctggaaaacttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	32575382	32575384	+	IGR	DEL	TCT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32575382_32575384delTCT								WIT1 (107121 upstream) : EIF3M (30007 downstream)																							ttcttcttcctcttcttcttctt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43283606delA	uc001mxe.1	-	2		c.1330delT								Homo sapiens cDNA FLJ44864 fis, clone BRALZ2013621, moderately similar to Heterogeneous nuclear ribonucleoprotein K.																		AAGCAAATGTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
TP53I11	9537	broad.mit.edu	37	11	44967168	44967168	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44967168delT	uc001myi.2	-						TP53I11_uc001myf.1_Intron|TP53I11_uc001myj.2_Intron|TP53I11_uc001myk.2_Intron|TP53I11_uc001myl.2_Intron|TP53I11_uc001mym.2_Intron	NM_006034	NP_006025	O14683	P5I11_HUMAN	p53-induced protein						negative regulation of cell proliferation|response to stress	integral to membrane				ovary(1)	1						CTCCCTTGGGTTAAGGCCCTG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45513805	45513805	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45513805delC								SYT13 (205921 upstream) : CHST1 (156622 downstream)																							tgccttctttcttactgttat	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45667668	45667679	+	IGR	DEL	TGAATGAATGAA	-	-	rs113009882		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45667668_45667679delTGAATGAATGAA								SYT13 (359784 upstream) : CHST1 (2748 downstream)																							TGCACATACTtgaatgaatgaatgaatgaatg	0.382													6	4	---	---	---	---	
PHF21A	51317	broad.mit.edu	37	11	45952456	45952457	+	3'UTR	INS	-	C	C	rs141879629	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45952456_45952457insC	uc001ncc.3	-	18					PHF21A_uc001ncb.3_3'UTR|PHF21A_uc009ykx.2_3'UTR|PHF21A_uc001nca.1_3'UTR	NM_001101802	NP_001095272	Q96BD5	PF21A_HUMAN	BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2						GTGGTCACAGGCCCCCCCCCCT	0.614													5	4	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46504570	46504571	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46504570_46504571insA	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		aaaaaaaaaagaaaaaaaaaaa	0.208													5	9	---	---	---	---	
PACSIN3	29763	broad.mit.edu	37	11	47205906	47205907	+	Intron	DEL	CT	-	-	rs112564612		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47205906_47205907delCT	uc001ndw.2	-						PACSIN3_uc001ndx.2_Intron|PACSIN3_uc001ndy.2_Intron|PACSIN3_uc001ndz.2_Intron|PACSIN3_uc001nea.2_Intron	NM_016223	NP_057307	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in						endocytosis|negative regulation of endocytosis|positive regulation of membrane protein ectodomain proteolysis	cytoplasm|plasma membrane	cytoskeletal protein binding				0						GTCACTTCCCCTGTTTCTCTGT	0.550													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48387918	48387918	+	IGR	DEL	T	-	-	rs66829866		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48387918delT								OR4C45 (13919 upstream) : OR4A47 (122427 downstream)																							CCAAGCAAGATGAATTCCGTT	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50763966	50763966	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50763966delT								LOC646813 (384163 upstream) : OR4A5 (647482 downstream)																							tgaaacactctttttgtagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56270341	56270341	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56270341delT								OR5M8 (11495 upstream) : OR5M11 (39476 downstream)																							cataattaagttcaagggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	62518019	62518024	+	IGR	DEL	ACCCCT	-	-	rs112016105		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62518019_62518024delACCCCT								TTC9C (11914 upstream) : ZBTB3 (413 downstream)																							GAGCAGTCTGACCCCTACCCCTACCC	0.320													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64652876	64652877	+	IGR	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64652876_64652877delAC								EHD1 (5727 upstream) : MIR192 (5732 downstream)																							acacacacatacacacacacac	0.213													4	2	---	---	---	---	
SLC25A45	283130	broad.mit.edu	37	11	65148608	65148608	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65148608delT	uc001odp.1	-						SLC25A45_uc009yqi.1_Intron|SLC25A45_uc001odq.1_Intron|SLC25A45_uc001odr.1_Intron|SLC25A45_uc001ods.1_Intron|SLC25A45_uc001odt.1_Intron	NM_001077241	NP_001070709	Q8N413	S2545_HUMAN	solute carrier family 25, member 45 isoform b						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						GAACCCAGACttttttttttt	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69442884	69442885	+	IGR	INS	-	CTT	CTT	rs147663327	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69442884_69442885insCTT								MYEOV (286435 upstream) : CCND1 (12988 downstream)																							gcagctgacaccttcagcacca	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69830734	69830734	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69830734delG								FGF3 (196542 upstream) : ANO1 (93674 downstream)																							CAGGCCTGGTGGGGAGGAGGA	0.622													4	2	---	---	---	---	
UVRAG	7405	broad.mit.edu	37	11	75691186	75691187	+	Intron	DEL	TC	-	-	rs116302370	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75691186_75691187delTC	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc009yuh.1_Intron	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6						taatttaatttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76558831	76558832	+	IGR	INS	-	T	T	rs139412255	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76558831_76558832insT								TSKU (49634 upstream) : ACER3 (13085 downstream)																							agacttctttcttttttttttg	0.000													4	2	---	---	---	---	
PAK1	5058	broad.mit.edu	37	11	77171205	77171205	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77171205delA	uc001oyh.3	-						PAK1_uc001oyg.3_Intron	NM_002576	NP_002567	Q13153	PAK1_HUMAN	p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)					TGTAGAATagaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79258178	79258179	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79258178_79258179insT								ODZ4 (106483 upstream) : None (None downstream)																							CTCACCTTTTATTCCCTCTATG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	83137775	83137775	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83137775delT								CCDC90B (140361 upstream) : DLG2 (28281 downstream)																							TATGTTCAggttgggcatggt	0.144													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83323880	83323881	+	Intron	INS	-	C	C	rs139950958	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83323880_83323881insC	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				tgaggctccatccagggctttt	0.084													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84498870	84498870	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84498870delA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				gacctggcacagtggctcatg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87321535	87321536	+	IGR	INS	-	AAAA	AAAA	rs112800661		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87321535_87321536insAAAA								TMEM135 (286967 upstream) : RAB38 (524895 downstream)																							tgtctactatcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91715448	91715448	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91715448delG								None (None upstream) : FAT3 (369814 downstream)																							TAGGTTACTAGGATCTTGTGC	0.483													4	2	---	---	---	---	
MTMR2	8898	broad.mit.edu	37	11	95636645	95636646	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95636645_95636646insA	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240	Q13614	MTMR2_HUMAN	myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				cgagttgacagaaaaaaaacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	100457925	100457926	+	IGR	INS	-	T	T	rs113389542		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100457925_100457926insT								CNTN5 (230453 upstream) : ARHGAP42 (100481 downstream)																							aatttactgacttttttttttt	0.000													4	2	---	---	---	---	
BIRC3	330	broad.mit.edu	37	11	102188320	102188321	+	Intron	DEL	GT	-	-	rs57970279		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102188320_102188321delGT	uc001pgx.2	+							NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3						anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		AGGAAGGCTGgtgtgtgtgtgt	0.525			T	MALT1	MALT								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102418585	102418586	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102418585_102418586insT								MMP7 (17107 upstream) : MMP20 (28981 downstream)																							tcagtgtttccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112693363	112693363	+	IGR	DEL	G	-	-	rs144926574		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112693363delG								PTS (552686 upstream) : NCAM1 (138632 downstream)																							AGAGCAGCATGGAAGAGATGA	0.522													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	113831007	113831009	+	IGR	DEL	AAA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113831007_113831009delAAA								HTR3B (13725 upstream) : HTR3A (14788 downstream)																							atctcaggagaaaaaaaaaaaag	0.005													4	2	---	---	---	---	
CEP164	22897	broad.mit.edu	37	11	117229665	117229665	+	Intron	DEL	T	-	-	rs72208926		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117229665delT	uc001prc.2	+						CEP164_uc001prb.2_Intron|CEP164_uc010rxk.1_Intron|CEP164_uc001prf.2_5'Flank	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa						cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		ggcagggttcttttttttttt	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	125012005	125012006	+	IGR	INS	-	AGGA	AGGA	rs148003832	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125012005_125012006insAGGA								TMEM218 (30530 upstream) : PKNOX2 (22553 downstream)																							CATAAAGCTTGAGGAAGGCGGG	0.436											OREG0021469	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132551850	132551850	+	Intron	DEL	A	-	-	rs35562833		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132551850delA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		attccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NINJ2	4815	broad.mit.edu	37	12	762859	762860	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:762859_762860insA	uc001qil.2	-						NINJ2_uc010sds.1_Intron	NM_016533	NP_057617	Q9NZG7	NINJ2_HUMAN	ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			ccaccaaaggcaaaaaaaaaag	0.000													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	6025187	6025187	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6025187delA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						tcacccctctaatcccagcac	0.000													1	5	---	---	---	---	
ZNF384	171017	broad.mit.edu	37	12	6800285	6800285	+	5'Flank	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6800285delT	uc010sfh.1	-						ZNF384_uc001qpz.2_5'Flank|ZNF384_uc001qqa.2_5'Flank|ZNF384_uc001qqb.2_5'Flank|ZNF384_uc001qqc.2_5'Flank|ZNF384_uc001qqd.2_5'Flank|ZNF384_uc001qqe.2_5'Flank	NM_001135734	NP_001129206	Q8TF68	ZN384_HUMAN	nuclear matrix transcription factor 4 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8						CTTTATCACATTTTTGGGCTC	0.353			T	EWSR1|TAF15 	ALL								4	2	---	---	---	---	
DPPA3	359787	broad.mit.edu	37	12	7861976	7861976	+	5'Flank	DEL	T	-	-	rs34890034		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7861976delT	uc001qtf.2	+							NM_199286	NP_954980	Q6W0C5	DPPA3_HUMAN	stella							cytoplasm|nucleus					0				Kidney(36;0.0887)		tttatttgtcttttttttttt	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8791730	8791733	+	IGR	DEL	ACTC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8791730_8791733delACTC								AICDA (26288 upstream) : MFAP5 (6807 downstream)																							aaggaTAATGACTCactcacattt	0.015													2	5	---	---	---	---	
CLEC9A	283420	broad.mit.edu	37	12	10200965	10200966	+	Intron	INS	-	A	A	rs35035367		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10200965_10200966insA	uc001qxa.2	+							NM_207345	NP_997228	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A						positive regulation of cytokine secretion|receptor-mediated endocytosis	cell surface|integral to membrane	receptor activity|sugar binding			ovary(1)	1						gtgagattccgaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14453595	14453597	+	IGR	DEL	AAC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14453595_14453597delAAC								GRIN2B (320573 upstream) : ATF7IP (65014 downstream)																							gtaaataacaaacaacaacaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15162389	15162389	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15162389delC								PDE6H (27592 upstream) : RERG (98329 downstream)																							taacgaagtacccaaaactgg	0.109													4	2	---	---	---	---	
RERGL	79785	broad.mit.edu	37	12	18234479	18234480	+	Intron	DEL	AG	-	-	rs3054571		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18234479_18234480delAG	uc001rdq.2	-						RERGL_uc001rdr.2_Intron	NM_024730	NP_079006	Q9H628	RERGL_HUMAN	RERG/RAS-like						signal transduction	membrane	GTP binding|GTPase activity				0						aaaaaaaaaCAGATTTATAACC	0.272													4	2	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18425977	18425978	+	Intron	INS	-	AG	AG	rs142553219	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18425977_18425978insAG	uc001rdt.2	+						PIK3C2G_uc010sia.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)				CACACagagatagagagagaga	0.139													2	4	---	---	---	---	
KIAA0528	9847	broad.mit.edu	37	12	22653186	22653186	+	Intron	DEL	A	-	-	rs78786341		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22653186delA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron|KIAA0528_uc009ziy.1_Intron	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						AAGGAGACAGAAAAAAAAAAA	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31757311	31757312	+	IGR	INS	-	TTTG	TTTG	rs142820253	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31757311_31757312insTTTG								DENND5B (13359 upstream) : C12orf72 (42782 downstream)																							gctaatgtttctttgtttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32012533	32012535	+	IGR	DEL	TTG	-	-	rs67402834		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32012533_32012535delTTG								H3F3C (67358 upstream) : C12orf35 (99818 downstream)																							ATCCATGAACTTGTTGTTGTAAG	0.365													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34471531	34471531	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34471531delG								ALG10 (290297 upstream) : None (None downstream)																							tttcgtccatggggggcccca	0.000													3	3	---	---	---	---	
LRRK2	120892	broad.mit.edu	37	12	40658502	40658502	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40658502delA	uc001rmg.3	+						LRRK2_uc001rmh.1_Intron	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTCTCCGGAGAAATAACCTCT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43332488	43332488	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43332488delT								PRICKLE1 (348916 upstream) : ADAMTS20 (415525 downstream)																							cgcccttccctgcaacaagcc	0.000													4	2	---	---	---	---	
NR4A1	3164	broad.mit.edu	37	12	52440964	52440964	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52440964delG	uc010sno.1	+						NR4A1_uc001rzr.2_Intron	NM_173157	NP_775180	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)		CCATCTCCCCGACAATTAGCT	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53082493	53082493	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53082493delC								KRT1 (8302 upstream) : KRT77 (919 downstream)																							tccctcatctccccacccaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55933633	55933633	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55933633delA								OR6C68 (46535 upstream) : OR6C4 (11378 downstream)																							tctggtttgcaaaaggccaag	0.000													4	2	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64263247	64263248	+	Intron	INS	-	TG	TG	rs140346013	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64263247_64263248insTG	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TATGGTATGTATGTGTGTGTGT	0.243													4	3	---	---	---	---	
RAB3IP	117177	broad.mit.edu	37	12	70154472	70154472	+	Intron	DEL	T	-	-	rs80084025		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70154472delT	uc001svp.2	+						RAB3IP_uc001svl.1_Intron|RAB3IP_uc001svm.2_Intron|RAB3IP_uc001svn.2_Intron|RAB3IP_uc001svo.2_Intron|RAB3IP_uc001svq.2_Intron|RAB3IP_uc001svr.2_Intron|RAB3IP_uc001svs.2_Intron	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2						cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			agattgataattttttttttt	0.000													4	2	---	---	---	---	
RAB3IP	117177	broad.mit.edu	37	12	70173325	70173325	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70173325delT	uc001svp.2	+						RAB3IP_uc001svl.1_Intron|RAB3IP_uc001svm.2_Intron|RAB3IP_uc001svn.2_Intron|RAB3IP_uc001svo.2_Intron|RAB3IP_uc001svq.2_Intron|RAB3IP_uc001svr.2_Intron|RAB3IP_uc001svs.2_Intron|RAB3IP_uc001svt.2_Intron	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2						cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			ctctttagtcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74915842	74915851	+	IGR	DEL	TGTGTGTGTG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74915842_74915851delTGTGTGTGTG								None (None upstream) : ATXN7L3B (15700 downstream)																							tgtgtgtgtatgtgtgtgtgcgtgtgtggg	0.000													3	4	---	---	---	---	
GLIPR1	11010	broad.mit.edu	37	12	75884362	75884363	+	Intron	DEL	AC	-	-	rs150016880		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75884362_75884363delAC	uc001sxs.2	+						GLIPR1_uc009zsb.1_Intron	NM_006851	NP_006842	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1 precursor						cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3						AAAAACAACAACAAAAAAAAAC	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76168593	76168594	+	IGR	INS	-	T	T	rs143761125	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76168593_76168594insT								KRR1 (263175 upstream) : PHLDA1 (250634 downstream)																							TGAGTGAtttcttttttttctt	0.173													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76733155	76733156	+	IGR	DEL	TC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76733155_76733156delTC								NAP1L1 (254417 upstream) : BBS10 (5110 downstream)																							ATATAAAAGATCTCTCTCTCTC	0.307													4	2	---	---	---	---	
SYT1	6857	broad.mit.edu	37	12	79389563	79389563	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79389563delC	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						GTGCCCAATTCCTGCAGTTGT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	84008340	84008340	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84008340delC								TMTC2 (480277 upstream) : None (None downstream)																							TGCTTTTGTTCCTACTGCAAG	0.353													4	2	---	---	---	---	
CCDC41	51134	broad.mit.edu	37	12	94734213	94734213	+	Intron	DEL	T	-	-	rs143511419		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94734213delT	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen												0						TGTCTCTAGAttttttttttt	0.259													4	2	---	---	---	---	
NDUFA12	55967	broad.mit.edu	37	12	95389446	95389447	+	Intron	DEL	AC	-	-	rs10554904		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95389446_95389447delAC	uc001tdl.2	-							NM_018838	NP_061326	Q9UI09	NDUAC_HUMAN	13kDa differentiation-associated protein						respiratory electron transport chain|respiratory gaseous exchange|response to oxidative stress|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)	agtagctgggaccataggcatg	0.054													4	2	---	---	---	---	
VEZT	55591	broad.mit.edu	37	12	95674301	95674302	+	Intron	DEL	AC	-	-	rs148227689		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95674301_95674302delAC	uc001tdz.2	+						VEZT_uc009ztb.1_Intron|VEZT_uc009ztc.1_Intron|VEZT_uc001tdy.2_Intron	NM_017599	NP_060069	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane							acrosomal vesicle|adherens junction|integral to membrane|nucleus				ovary(1)	1						tcatatgtgtacacacacacac	0.139													3	3	---	---	---	---	
NTN4	59277	broad.mit.edu	37	12	96126017	96126020	+	Intron	DEL	TCTG	-	-	rs35979011		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96126017_96126020delTCTG	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052	Q9HB63	NET4_HUMAN	netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2						tctttctttctctgtctttctttc	0.157													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96525014	96525017	+	IGR	DEL	GAAA	-	-	rs140643700		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96525014_96525017delGAAA								LTA4H (87716 upstream) : ELK3 (63190 downstream)																							tttaataggcgaaagaaagagaag	0.000													3	3	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99431954	99431954	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99431954delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		AATGCTTCTAtgtatcattgc	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	100401876	100401876	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100401876delT								ANKS1B (23444 upstream) : UHRF1BP1L (28989 downstream)																							cctaggtttcttccatttttc	0.000													4	2	---	---	---	---	
CHST11	50515	broad.mit.edu	37	12	104957553	104957555	+	Intron	DEL	TGG	-	-	rs10602298		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104957553_104957555delTGG	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883	Q9NPF2	CHSTB_HUMAN	carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0						TGTTTGCTCTTGGTGGTTTTCAG	0.537													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108859890	108859890	+	IGR	DEL	T	-	-	rs35729318		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108859890delT								CMKLR1 (126796 upstream) : FICD (49161 downstream)																							gttttttgggttttttttttt	0.184													3	3	---	---	---	---	
SVOP	55530	broad.mit.edu	37	12	109337649	109337651	+	Intron	DEL	TCT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109337649_109337651delTCT	uc010sxh.1	-							NM_018711	NP_061181	Q8N4V2	SVOP_HUMAN	SV2 related protein							cell junction|integral to membrane|synaptic vesicle membrane	ion transmembrane transporter activity				0						ttcctcttcctcttcttcttctt	0.000													6	4	---	---	---	---	
RPH3A	22895	broad.mit.edu	37	12	113012611	113012612	+	5'Flank	DEL	GA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113012611_113012612delGA	uc010syl.1	+							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)		gtggaggagggagagggggtgg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	113482066	113482067	+	IGR	DEL	AG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113482066_113482067delAG								OAS2 (32539 upstream) : DTX1 (13595 downstream)																							ctaaagagaaagagagagagag	0.000													4	2	---	---	---	---	
IQCD	115811	broad.mit.edu	37	12	113658514	113658514	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113658514delG	uc001tuv.1	-						IQCD_uc001tuu.2_Intron|TPCN1_uc001tux.2_5'Flank|TPCN1_uc001tuw.2_5'Flank	NM_138451	NP_612460	Q96DY2	IQCD_HUMAN	IQ motif containing D											ovary(1)	1						TGTTTGACTTGAAATAAGTTA	0.507													4	2	---	---	---	---	
TPCN1	53373	broad.mit.edu	37	12	113681175	113681175	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113681175delA	uc001tuw.2	+						TPCN1_uc001tux.2_Intron|TPCN1_uc010syt.1_5'Flank	NM_017901	NP_060371	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1 isoform 2							endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated ion channel activity			skin(2)|ovary(1)	3						accctgtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115327875	115327876	+	IGR	DEL	CA	-	-	rs144653030		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115327875_115327876delCA								TBX3 (205906 upstream) : None (None downstream)																							GAATCATGTGcacacacacaca	0.361													5	3	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119444146	119444148	+	Intron	DEL	CTT	-	-	rs146225071		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119444146_119444148delCTT	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						GCGACTACTCCTTCTTTTCCTGG	0.468													3	4	---	---	---	---	
CCDC64	92558	broad.mit.edu	37	12	120529147	120529147	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120529147delT	uc001txl.1	+						CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACCTGATTGCTTAAAGTTAAA	0.438													4	2	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	130943835	130943835	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130943835delA	uc001uil.2	-						RIMBP2_uc001uim.2_Intron	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		gctatatacgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132641292	132641293	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132641292_132641293insA								NOC4L (4306 upstream) : GALNT9 (39625 downstream)																							actacacacacaccactacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	25581150	25581151	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25581150_25581151insA								TPTE2P1 (38543 upstream) : PABPC3 (89125 downstream)																							aaacaaaacagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30552284	30552284	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30552284delT								UBL3 (127464 upstream) : KATNAL1 (224484 downstream)																							agaaagtaggttgtcaggggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	34989411	34989412	+	IGR	INS	-	GT	GT	rs145358835	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34989411_34989412insGT								RFC3 (448717 upstream) : NBEA (527044 downstream)																							CTCCATtgtgagtgtgtgtgtg	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51732227	51732227	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51732227delT								GUCY1B2 (77229 upstream) : FAM124A (64280 downstream)																							tattcattccttcaatgacta	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60910889	60910889	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60910889delA								DIAPH3 (172770 upstream) : TDRD3 (59702 downstream)																							TGGGGGTGGGAGGTGATTAAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63632524	63632527	+	IGR	DEL	TTTG	-	-	rs71734546		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63632524_63632527delTTTG								None (None upstream) : OR7E156P (679041 downstream)																							ctttccttgctttgtttgtgcatt	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95960333	95960334	+	IGR	DEL	AG	-	-	rs71113912		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95960333_95960334delAG								ABCC4 (6646 upstream) : CLDN10 (125519 downstream)																							aatgggggacaggggttgcatt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107280357	107280358	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107280357_107280358delGT								ARGLU1 (59843 upstream) : FAM155A (540522 downstream)																							ATTTGTGCTGGTGGAACTAGGA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112220660	112220660	+	IGR	DEL	C	-	-	rs67626455		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112220660delC								C13orf16 (224067 upstream) : SOX1 (501253 downstream)																							GACCTTGTCACCCCCCACGCT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112270209	112270209	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112270209delA								C13orf16 (273616 upstream) : SOX1 (451704 downstream)																							ATATAGCATTAAAAAAACCAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112528516	112528517	+	IGR	DEL	GG	-	-	rs35200520		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112528516_112528517delGG								C13orf16 (531923 upstream) : SOX1 (193396 downstream)																							tgtagatcatgggttggtttcc	0.153													4	2	---	---	---	---	
ATP11A	23250	broad.mit.edu	37	13	113519306	113519307	+	Intron	INS	-	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113519306_113519307insG	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc010ago.2_Intron	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a						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			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				AATTCAGTGCAGCCCGCGCAGC	0.589													2	4	---	---	---	---	
DCUN1D2	55208	broad.mit.edu	37	13	114115171	114115171	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114115171delC	uc001vtr.1	-						DCUN1D2_uc001vts.1_Intron|DCUN1D2_uc010agw.1_Intron	NM_001014283	NP_001014305	Q6PH85	DCNL2_HUMAN	DCN1, defective in cullin neddylation 1, domain												0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)			CCCGGAGTGGCCCCAGCTCAG	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19030656	19030658	+	IGR	DEL	ATC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19030656_19030658delATC								None (None upstream) : OR11H12 (346936 downstream)																							aaactactcaatcaaaagaaacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19032347	19032348	+	IGR	INS	-	C	C	rs145631421		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19032347_19032348insC								None (None upstream) : OR11H12 (345246 downstream)																							tctacaaaaaaagagtttcaaa	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20315828	20315829	+	IGR	INS	-	T	T	rs150158951	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20315828_20315829insT								OR4N2 (19298 upstream) : OR4K2 (28598 downstream)																							TTTCTCAGATCTTTTTTTGCAC	0.416													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20670214	20670214	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20670214delT								OR11G2 (3684 upstream) : OR11H6 (21655 downstream)																							AGGCATTGTCTTTTTGCAAGT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22207653	22207653	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22207653delA	uc010aip.1	+											SubName: Full=Putative uncharacterized protein ENSP00000374934;																		tgttgggtacaatgtacacta	0.065													4	2	---	---	---	---	
SLC7A8	23428	broad.mit.edu	37	14	23634201	23634201	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23634201delA	uc001wiz.2	-						SLC7A8_uc010akj.2_Intron	NM_012244	NP_036376	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	accctgcctcaaaaaaaaaaa	0.169													4	2	---	---	---	---	
THTPA	79178	broad.mit.edu	37	14	23989604	23989605	+	Intron	INS	-	G	G	rs139291003	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23989604_23989605insG	uc001wkb.3	+						uc001wkc.1_Intron			Q9BU02	THTPA_HUMAN	Homo sapiens thiamine triphosphatase mRNA, complete cds.						dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity				0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)	GTGGGCCTCCAGGGGGGCAGCA	0.550													2	4	---	---	---	---	
KHNYN	23351	broad.mit.edu	37	14	24907508	24907509	+	3'UTR	INS	-	A	A	rs141940505	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24907508_24907509insA	uc001wph.3	+	8					KHNYN_uc010tpc.1_3'UTR|KHNYN_uc010alw.2_3'UTR	NM_015299	NP_056114	O15037	KHNYN_HUMAN	hypothetical protein LOC23351											ovary(2)|liver(1)	3						GATTTTTCACCAATCGATGAAG	0.416													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27633460	27633460	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27633460delG								NOVA1 (566500 upstream) : None (None downstream)																							tacggtccatggacagtggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38657302	38657303	+	IGR	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38657302_38657303delAC								FOXA1 (592813 upstream) : SSTR1 (19901 downstream)																							AAAAAGTCATACACACACACAC	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57442685	57442688	+	IGR	DEL	CCTT	-	-	rs36154882		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57442685_57442688delCCTT								OTX2 (165501 upstream) : EXOC5 (226508 downstream)																							ATGTATTTAGccttccttccttcc	0.176													4	2	---	---	---	---	
ACTN1	87	broad.mit.edu	37	14	69441269	69441270	+	Intron	INS	-	CA	CA	rs147500352	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69441269_69441270insCA	uc001xkl.2	-						ACTN1_uc010ttb.1_Intron|ACTN1_uc001xkm.2_Intron|ACTN1_uc001xkn.2_Intron|ACTN1_uc001xko.1_Intron|ACTN1_uc010ttd.1_Intron	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b						focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCCTACAACATcacacacacac	0.500													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	73382504	73382513	+	IGR	DEL	TGTGTGTGTG	-	-	rs79361675		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73382504_73382513delTGTGTGTGTG								DPF3 (21695 upstream) : DCAF4 (10527 downstream)																							tttatatctctgtgtgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84423413	84423413	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84423413delG								None (None upstream) : None (None downstream)																							gaagctgaaaggtgggaagcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85760478	85760479	+	IGR	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85760478_85760479delAC								None (None upstream) : FLRT2 (236009 downstream)																							ATCACACCAAacacacacacac	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87509934	87509943	+	IGR	DEL	TGTGTGTGTG	-	-	rs72015193		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87509934_87509943delTGTGTGTGTG								None (None upstream) : GALC (794221 downstream)																							TGGATTCAATtgtgtgtgtgtgtgtgtgtg	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88478502	88478503	+	IGR	DEL	GG	-	-	rs3055739		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88478502_88478503delGG								GPR65 (88 upstream) : KCNK10 (167951 downstream)																							aaagtatgtaggggactgtttc	0.188													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88618364	88618365	+	IGR	DEL	AA	-	-	rs76021456		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88618364_88618365delAA								GPR65 (139950 upstream) : KCNK10 (28089 downstream)																							ctcatgaaggaaaaaaaaaaaa	0.059													4	2	---	---	---	---	
KCNK10	54207	broad.mit.edu	37	14	88707860	88707861	+	Intron	INS	-	AT	AT	rs140356810	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88707860_88707861insAT	uc001xwo.2	-						KCNK10_uc001xwm.2_Intron|KCNK10_uc001xwn.2_Intron	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10						signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5						CACACACACACATCGCTCTTTT	0.312													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89790788	89790795	+	Intron	DEL	GTGTGTGT	-	-	rs145404871		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89790788_89790795delGTGTGTGT	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						AAgtgtgtgcgtgtgtgtgtgtgtgtgt	0.298													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89837344	89837345	+	Intron	DEL	CT	-	-	rs35510295		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89837344_89837345delCT	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						TTCAGCACCACTGTCTTTCCCT	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90135140	90135141	+	IGR	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90135140_90135141delAC								FOXN3 (49646 upstream) : C14orf143 (128330 downstream)																							catcacacatacacacacacac	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96069319	96069320	+	IGR	INS	-	ACAC	ACAC	rs142675915	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96069319_96069320insACAC								GLRX5 (58264 upstream) : TCL6 (47515 downstream)																							aaacaaacaaaacacacacaca	0.000													4	4	---	---	---	---	
BDKRB2	624	broad.mit.edu	37	14	96679833	96679842	+	Intron	DEL	ACACACACAC	-	-	rs66460667		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96679833_96679842delACACACACAC	uc010avm.1	+						BDKRB2_uc010avl.1_Intron|BDKRB2_uc010twu.1_Intron|BDKRB2_uc001yfg.2_Intron	NM_000623	NP_000614	P30411	BKRB2_HUMAN	bradykinin receptor B2						arachidonic acid secretion|elevation of cytosolic calcium ion concentration|transmembrane receptor protein tyrosine kinase signaling pathway	endosome|integral to plasma membrane	bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding			ovary(3)|breast(1)|kidney(1)	5		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)		ACCGACCCAAacacacacacacacacacac	0.395													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99530191	99530191	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99530191delG								C14orf177 (346094 upstream) : BCL11B (105436 downstream)																							aagtccctgcggagtacGTCA	0.234													4	2	---	---	---	---	
YY1	7528	broad.mit.edu	37	14	100717985	100717985	+	Intron	DEL	T	-	-	rs73351477	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100717985delT	uc001ygy.1	+							NM_003403	NP_003394	P25490	TYY1_HUMAN	YY1 transcription factor						cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)				ATAAAGGGGCTTTTTTTGCAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	103381044	103381044	+	IGR	DEL	A	-	-	rs35916256		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103381044delA								TRAF3 (8416 upstream) : AMN (7949 downstream)																							TCTAGGAGCCAGGGGCACAGC	0.632													3	3	---	---	---	---	
BRF1	2972	broad.mit.edu	37	14	105682370	105682371	+	Intron	INS	-	CA	CA	rs147569782	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105682370_105682371insCA	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc001yqk.2_Intron|BRF1_uc001yql.2_Intron|BRF1_uc001yqo.2_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.1_Intron	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		acagacacaggcacacacactg	0.000													2	4	---	---	---	---	
BRF1	2972	broad.mit.edu	37	14	105689751	105689754	+	Intron	DEL	AACA	-	-	rs35511483		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105689751_105689754delAACA	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc001yqk.2_5'Flank|BRF1_uc001yql.2_Intron|BRF1_uc001yqo.2_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.1_5'Flank	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		aatacaaacgaacaaaccattgat	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106034410	106034411	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106034410_106034411delTG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						tttatgtgtctgtgtgtgtgtg	0.223													4	2	---	---	---	---	
KIAA0125	9834	broad.mit.edu	37	14	106387222	106387223	+	Intron	INS	-	G	G	rs34863885		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106387222_106387223insG	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron|KIAA0125_uc001yss.2_Intron|KIAA0125_uc001yst.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0						tctcttggtgcggggggtggag	0.272													3	4	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106824931	106824932	+	Intron	INS	-	CT	CT	rs145829689	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106824931_106824932insCT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TAGAGCTGCCCGTTTTCAGTGG	0.559													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107111917	107111918	+	Intron	INS	-	A	A	rs112077215		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107111917_107111918insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						gaaagacaagtgtctgaaggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20144683	20144683	+	IGR	DEL	C	-	-	rs143228371		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20144683delC								None (None upstream) : GOLGA6L6 (592411 downstream)																							aaacaactctcttcattatac	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20514120	20514122	+	IGR	DEL	ATG	-	-	rs149937568		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20514120_20514122delATG								None (None upstream) : GOLGA6L6 (222972 downstream)																							ataaaatgaaatgatgagatgaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21922306	21922306	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21922306delA								NF1P1 (787681 upstream) : LOC646214 (10208 downstream)																							AAATTCACCTAATTTTTATTA	0.244													4	2	---	---	---	---	
OR4N4	283694	broad.mit.edu	37	15	22325871	22325872	+	Intron	INS	-	C	C	rs143935447	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22325871_22325872insC	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)		gacccataggtcaatggaacag	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24876222	24876222	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24876222delC								PWRN1 (43298 upstream) : C15orf2 (44319 downstream)																							ggatcagttaccccaacaaac	0.015													4	2	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	26950333	26950333	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26950333delG	uc001zaz.2	-						GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	tcaaggtgctggcataatctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31409854	31409855	+	IGR	INS	-	A	A	rs112661796		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31409854_31409855insA								TRPM1 (15930 upstream) : KLF13 (209228 downstream)																							ctgtctcaaagaaaaaaaaaaa	0.000													2	6	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31867123	31867123	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31867123delG	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron|OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		cctccactttgggcctgctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35453897	35453898	+	IGR	DEL	CT	-	-	rs150856630		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35453897_35453898delCT								ZNF770 (173443 upstream) : LOC723972 (75629 downstream)																							agtgtgctcgctctctctctct	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37866203	37866203	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37866203delA								MEIS2 (472703 upstream) : TMCO5A (360624 downstream)																							tctccagaagaaaaaaaaaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41175906	41175906	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41175906delA								RHOV (9419 upstream) : VPS18 (10722 downstream)																							actccatttcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44344179	44344179	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44344179delT	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		aagttaactcttttttttttt	0.000													4	2	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44416570	44416570	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44416570delA	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		agaaggaaggaaaaaaagagg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45120167	45120167	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45120167delT								TRIM69 (60142 upstream) : C15orf43 (128736 downstream)																							cctcccAttcttttttttttt	0.134													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46016315	46016318	+	IGR	DEL	TGTT	-	-	rs138475646		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46016315_46016318delTGTT								SQRDL (32837 upstream) : None (None downstream)																							CAAATGTGTGTGTTTGTTTTTCTG	0.387													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	51498314	51498314	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51498314delC								TNFAIP8L3 (100841 upstream) : CYP19A1 (1941 downstream)																							GAGACACTGGCCATATGTGTT	0.244													4	2	---	---	---	---	
CCPG1	9236	broad.mit.edu	37	15	55780319	55780319	+	Intron	DEL	T	-	-	rs113637708		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55780319delT	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		tttctttttcttttttttttt	0.318													4	2	---	---	---	---	
SLTM	79811	broad.mit.edu	37	15	59192257	59192258	+	Intron	INS	-	A	A	rs35822874		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59192257_59192258insA	uc002afp.2	-						SLTM_uc002afo.2_Intron|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron|SLTM_uc002afr.1_Intron	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						GGAAGTTAGGGAAAAAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60026398	60026399	+	IGR	INS	-	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60026398_60026399insG								BNIP2 (44756 upstream) : FOXB1 (270022 downstream)																							gctgcagtgcaggggaaatatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60085219	60085219	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60085219delA								BNIP2 (103577 upstream) : FOXB1 (211202 downstream)																							GATGTGAGACAAATAAACAAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62118892	62118893	+	IGR	INS	-	A	A	rs143697074	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62118892_62118893insA								RORA (597390 upstream) : VPS13C (25699 downstream)																							ACACATTTTTTAAAAAAAAATC	0.282													4	2	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62242755	62242755	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62242755delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						AAAGCCATTCAAAAAAAAAAA	0.279													4	2	---	---	---	---	
OSTBETA	123264	broad.mit.edu	37	15	65344105	65344106	+	Intron	INS	-	AAAC	AAAC	rs140336932	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65344105_65344106insAAAC	uc002aog.2	+						OSTBETA_uc002aoh.2_Intron	NM_178859	NP_849190	Q86UW2	OSTB_HUMAN	organic solute transporter beta							integral to membrane|plasma membrane					0						CAAGCTGTTaaaaacaaacaaa	0.465													4	2	---	---	---	---	
SNUPN	10073	broad.mit.edu	37	15	75902905	75902905	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75902905delC	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692	O95149	SPN1_HUMAN	snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1						TGCAACCACACCATGCTTACT	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78178341	78178344	+	IGR	DEL	CACA	-	-	rs72168317		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78178341_78178344delCACA								LINGO1 (189866 upstream) : LOC645752 (28215 downstream)																							cgcgcgcgtgcacacacacacaca	0.181													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78726383	78726383	+	IGR	DEL	A	-	-	rs35031532		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78726383delA								CRABP1 (85811 upstream) : IREB2 (4135 downstream)																							actctctctcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86397860	86397861	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86397860_86397861delGT								KLHL25 (59671 upstream) : AGBL1 (287381 downstream)																							GTCCTCTGGGgtgtgtgtgtgt	0.406											OREG0023428	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	15	89246374	89246375	+	IGR	INS	-	TGG	TGG			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89246374_89246375insTGG								ISG20 (47495 upstream) : ACAN (100299 downstream)																							tacgttggtgctggtggtggtg	0.000													1	5	---	---	---	---	
LOC283761	283761	broad.mit.edu	37	15	90069036	90069037	+	5'Flank	INS	-	A	A	rs35380797		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90069036_90069037insA	uc002bob.2	-						LOC283761_uc002bod.2_5'Flank|LOC283761_uc010upt.1_5'Flank|LOC283761_uc010upu.1_5'Flank|LOC283761_uc002boc.2_5'Flank	NR_027075				Homo sapiens cDNA FLJ25381 fis, clone TST02166.												0						gactctgtctcaaaaaaaaaaa	0.054													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90722813	90722813	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90722813delT								IDH2 (77105 upstream) : SEMA4B (5339 downstream)																							GCCTCAGGGCTTTTTTTTTTT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95390025	95390025	+	IGR	DEL	A	-	-	rs138601945		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95390025delA								MCTP2 (362845 upstream) : LOC145820 (586297 downstream)																							caaaacatacaaaaattagcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97218181	97218181	+	IGR	DEL	T	-	-	rs5814750		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97218181delT								NR2F2 (334691 upstream) : SPATA8 (108498 downstream)																							CCCCTCTCTCTTTTTTTTTTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98539000	98539001	+	IGR	INS	-	G	G			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98539000_98539001insG								ARRDC4 (21933 upstream) : FAM169B (441390 downstream)																							AAGGAAAACGAGGGAAGAGAAC	0.431													4	2	---	---	---	---	
CACNA1H	8912	broad.mit.edu	37	16	1240032	1240032	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1240032delA	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,						aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	CAGGGAGATGAAGGAGGGAGG	0.602													4	2	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4939225	4939226	+	Intron	INS	-	TT	TT	rs140073794	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4939225_4939226insTT	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						GCAAAAGGCAGTTTTTTTGTTG	0.198													9	5	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6823366	6823367	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6823366_6823367delTG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_5'Flank	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		ggggtgcatttgtgtgtgtgtg	0.198													4	2	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10195430	10195431	+	Intron	INS	-	G	G	rs140223025	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10195430_10195431insG	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GGGGTCATTTAGGTGGTGATGT	0.485													2	5	---	---	---	---	
EMP2	2013	broad.mit.edu	37	16	10631618	10631619	+	Intron	DEL	CA	-	-	rs34790340		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10631618_10631619delCA	uc002czx.2	-							NM_001424	NP_001415	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation	integral to membrane					0						TGCATGCGCCcacacacacaca	0.342													4	2	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12798200	12798200	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12798200delG	uc002dca.3	-						CPPED1_uc002dcb.3_Intron|CPPED1_uc002dbz.3_Intron	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						acttaggctagggtctgttct	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	14390800	14390800	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14390800delC								MKL2 (30171 upstream) : MIR193B (7024 downstream)																							ctccttccctcctaccttccc	0.000													4	2	---	---	---	---	
ABCC1	4363	broad.mit.edu	37	16	16168804	16168804	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16168804delC	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	ttttctttttctttttttttt	0.159													4	2	---	---	---	---	
C16orf62	57020	broad.mit.edu	37	16	19679914	19679915	+	Intron	DEL	GT	-	-	rs72312067		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19679914_19679915delGT	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						TTTAAGCTGAgtgtgtgtgtgt	0.228													4	2	---	---	---	---	
KIAA0556	23247	broad.mit.edu	37	16	27618054	27618054	+	Intron	DEL	T	-	-	rs112061995		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27618054delT	uc002dow.2	+							NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						tttttctaacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28617930	28617931	+	Intron	INS	-	G	G	rs143299878	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28617930_28617931insG	uc010vct.1	-						SULT1A1_uc002dqi.2_Intron|SULT1A1_uc002dqj.2_Intron|SULT1A1_uc002dqk.2_Intron|SULT1A1_uc002dql.2_Intron|SULT1A1_uc002dqm.2_Intron|SULT1A1_uc002dqn.2_Intron|SULT1A1_uc002dqo.2_Intron|SULT1A1_uc002dqp.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		AGGTGGGGCCTTAGTGGGGAGG	0.653													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32123215	32123215	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32123215delG								ZNF267 (194589 upstream) : HERC2P4 (39395 downstream)																							tattctagaaGGATAAATTAT	0.035													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32453205	32453205	+	IGR	DEL	A	-	-	rs35560090		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32453205delA								HERC2P4 (289331 upstream) : TP53TG3B (231636 downstream)																							cataaccaccacctaaatccc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32525841	32525842	+	IGR	INS	-	A	A	rs143512379		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32525841_32525842insA								HERC2P4 (361967 upstream) : TP53TG3B (158999 downstream)																							tcacagaaaggaaaaaaactgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32535370	32535370	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32535370delG								HERC2P4 (371496 upstream) : TP53TG3B (149471 downstream)																							ttttgccattgacttccatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33855145	33855146	+	IGR	INS	-	T	T	rs139175767		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33855145_33855146insT								SLC6A10P (958682 upstream) : MIR1826 (110362 downstream)																							agctgatgagcttaaaaaaaag	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33976749	33976749	+	IGR	DEL	G	-	-	rs111283986		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33976749delG								MIR1826 (11157 upstream) : UBE2MP1 (427053 downstream)																							ggcctatggtgaaaaaaggaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33978278	33978278	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33978278delG								MIR1826 (12686 upstream) : UBE2MP1 (425524 downstream)																							aacgctttgaggcctattgtg	0.000													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34372418	34372418	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34372418delT								MIR1826 (406826 upstream) : UBE2MP1 (31384 downstream)																							ATGTTTTCTCTTTTCCTGCCA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46444744	46444744	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46444744delC								None (None upstream) : ANKRD26P1 (58505 downstream)																							gaatcatcatcaaatggagtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50473175	50473175	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50473175delA								BRD7 (70346 upstream) : NKD1 (109066 downstream)																							ataagaaaacaagccaattaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52615862	52615862	+	Intron	DEL	T	-	-	rs71376171		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52615862delT	uc002egx.2	-											Homo sapiens cDNA clone IMAGE:5172237.																		gcaaatttaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54299089	54299089	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54299089delC								FTO (150711 upstream) : IRX3 (18123 downstream)																							GGAGGCGGCGCCCTTCACAGG	0.493													4	2	---	---	---	---	
CES7	221223	broad.mit.edu	37	16	55939283	55939284	+	Intron	INS	-	T	T	rs74529762	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55939283_55939284insT	uc002eir.2	-						CES7_uc002eiq.2_Intron			Q6NT32	EST5A_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000383269; Flags: Fragment;							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		TTAAATCTGACttttttttttt	0.238													4	3	---	---	---	---	
CETP	1071	broad.mit.edu	37	16	57007961	57007961	+	Intron	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57007961delG	uc002eki.2	+						CETP_uc002ekj.2_Intron	NM_000078	NP_000069	P11597	CETP_HUMAN	cholesteryl ester transfer protein, plasma						cholesterol homeostasis|cholesterol metabolic process|high-density lipoprotein particle remodeling|lipoprotein metabolic process|low-density lipoprotein particle remodeling|phosphatidylcholine metabolic process|phospholipid homeostasis|receptor-mediated endocytosis|regulation of cholesterol efflux|triglyceride homeostasis|triglyceride metabolic process|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle|vesicle	cholesterol binding|cholesterol transporter activity|phosphatidylcholine binding|phospholipid transporter activity|triglyceride binding			central_nervous_system(1)|skin(1)	2						accaggcttaggtcaggtagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64845065	64845065	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64845065delC								None (None upstream) : CDH11 (135620 downstream)																							GGAGAAAGATCCCCAAAGGGA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	69448639	69448639	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69448639delA								TERF2 (28766 upstream) : CYB5B (9859 downstream)																							tagcccggccAAAAAAGGATA	0.045													4	2	---	---	---	---	
CALB2	794	broad.mit.edu	37	16	71416057	71416064	+	Intron	DEL	AAGAAAAT	-	-	rs145128266	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71416057_71416064delAAGAAAAT	uc002faa.3	+						CALB2_uc010vme.1_Intron|CALB2_uc002fac.3_Intron	NM_001740	NP_001731	P22676	CALB2_HUMAN	calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)				gaaggaaggaaagaaaataaaggaagga	0.130													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73163613	73163614	+	IGR	INS	-	TG	TG	rs138662914	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73163613_73163614insTG								HTA (35943 upstream) : None (None downstream)																							gtgcatgtgtatgtgtgtgtgt	0.183													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78628094	78628095	+	Intron	INS	-	A	A	rs139449775	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78628094_78628095insA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		AGGGCCTTTTTAACCCCATATA	0.441													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	82873988	82873988	+	Intron	DEL	A	-	-	rs144671900		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82873988delA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TCTGAAAAGGAAAAAAAAAAA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	3313409	3313409	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3313409delT								OR1E1 (11705 upstream) : OR3A3 (10453 downstream)																							ctgaggggactttttttttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4726765	4726766	+	IGR	INS	-	CCT	CCT	rs138338670	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4726765_4726766insCCT								PLD2 (38 upstream) : MINK1 (9917 downstream)																							GCTCGTTCCAGCCTCCCGTTCC	0.500													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5692761	5692761	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5692761delT	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																		GCCCCCTCCCTTTTTTTTTTT	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5918278	5918278	+	IGR	DEL	C	-	-	rs112623399		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5918278delC								NLRP1 (430446 upstream) : WSCD1 (54159 downstream)																							cccgtctccaccaaaaaattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6464173	6464174	+	IGR	INS	-	TCC	TCC	rs151105597	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6464173_6464174insTCC								PITPNM3 (4296 upstream) : KIAA0753 (17472 downstream)																							tcccctccttttcctcctcctc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10749965	10749982	+	IGR	DEL	TGGTGGAAGTGGAGGTGA	-	-	rs151101254		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10749965_10749982delTGGTGGAAGTGGAGGTGA								PIRT (8547 upstream) : SHISA6 (394758 downstream)																							gtgatggtggtggtggaagtggaggtgatggtggagat	0.000													4	2	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11584306	11584307	+	Intron	DEL	AG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11584306_11584307delAG	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAGCAGCTGCAGACCAGTTAAT	0.455													4	2	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20772512	20772513	+	Intron	INS	-	A	A	rs148647596	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20772512_20772513insA	uc002gyf.2	-						uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						atggaggggggaagaggataat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21244375	21244376	+	IGR	INS	-	G	G	rs146713246		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21244375_21244376insG								MAP2K3 (25826 upstream) : KCNJ12 (35323 downstream)																							actccatctccaaaaaaaaaaa	0.243													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21324811	21324815	+	IGR	DEL	AGGGT	-	-	rs141749648		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21324811_21324815delAGGGT								KCNJ12 (1632 upstream) : C17orf51 (106757 downstream)																							aggcccccacagggtagttcctcaa	0.190													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21520057	21520058	+	IGR	INS	-	ATGG	ATGG	rs142565682	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21520057_21520058insATGG								C17orf51 (42326 upstream) : FAM27L (305312 downstream)																							aagatgtatttatggtaagaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21542186	21542186	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21542186delT								C17orf51 (64455 upstream) : FAM27L (283184 downstream)																							ATTACTTGGCTTTTTTTGATG	0.244													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22253548	22253549	+	IGR	INS	-	C	C	rs138638530		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22253548_22253549insC								FLJ36000 (340478 upstream) : None (None downstream)																							agaatcttcttgtgatgtttgc	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25291852	25291853	+	IGR	INS	-	TTTCTTC	TTTCTTC	rs137936696		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25291852_25291853insTTTCTTC								None (None upstream) : WSB1 (329253 downstream)																							TGCTTGCCATTTTTGTTCCCCT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25301908	25301908	+	IGR	DEL	C	-	-	rs62058878	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25301908delC								None (None upstream) : WSB1 (319198 downstream)																							GGTATTCTTACAGCAGGAGTG	0.358													4	2	---	---	---	---	
MRPL45	84311	broad.mit.edu	37	17	36464397	36464399	+	Intron	DEL	TTT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36464397_36464399delTTT	uc002hpy.2	+							NM_032351	NP_115727	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45 precursor						intracellular protein transport|translation	mitochondrial inner membrane presequence translocase complex|ribosome	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|structural constituent of ribosome				0	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAAAACAttgttttttttttgtt	0.020													6	4	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44235730	44235732	+	Intron	DEL	TTT	-	-	rs71941311		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44235730_44235732delTTT	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				CATTAGAGACttttttttttttt	0.163													4	2	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46218141	46218141	+	Intron	DEL	T	-	-	rs71366836		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46218141delT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						cttcttcttcttttttttttt	0.000													4	3	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46408186	46408187	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46408186_46408187insA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						CCAGGGGGCGGAAAAAAAAAAA	0.431													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47351672	47351672	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47351672delT								PHOSPHO1 (43544 upstream) : ZNF652 (14897 downstream)																							tccatatgtcttttttttttt	0.000													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	49760161	49760163	+	Intron	DEL	AAG	-	-	rs66961550		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49760161_49760163delAAG	uc002itw.3	-						CA10_uc002itu.3_Intron|CA10_uc002itv.3_Intron|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)			ACGTGGGGCAAAGAAGGGAAACC	0.227													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53631004	53631006	+	IGR	DEL	TTC	-	-	rs141966077		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53631004_53631006delTTC								MMD (131663 upstream) : TMEM100 (165984 downstream)																							tttttctgttttcttttcttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58624741	58624741	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58624741delA								APPBP2 (21161 upstream) : PPM1D (52813 downstream)																							gcctggcTATAAAAAAAAAAC	0.015													4	2	---	---	---	---	
LRRC37A3	374819	broad.mit.edu	37	17	62917739	62917741	+	5'Flank	DEL	AAC	-	-	rs67572836		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62917739_62917741delAAC	uc002jey.2	-						LRRC37A3_uc010wqg.1_5'Flank	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3							integral to membrane					0						ATCATTTTTAAACAACTTTAGAA	0.241													2	4	---	---	---	---	
APOH	350	broad.mit.edu	37	17	64222740	64222740	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64222740delA	uc002jfn.3	-							NM_000042	NP_000033	P02749	APOH_HUMAN	apolipoprotein H precursor						blood coagulation, intrinsic pathway|negative regulation of angiogenesis|negative regulation of blood coagulation|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of myeloid cell apoptosis|negative regulation of smooth muscle cell apoptosis|plasminogen activation|positive regulation of lipoprotein lipase activity|triglyceride metabolic process|triglyceride transport	cell surface|chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	eukaryotic cell surface binding|glycoprotein binding|heparin binding|lipoprotein lipase activator activity|phospholipid binding				0			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			ctccgtctccaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68207053	68207054	+	IGR	INS	-	TC	TC	rs140837334	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68207053_68207054insTC								KCNJ2 (30872 upstream) : None (None downstream)																							ctctctcactgtctctctctct	0.084													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68917358	68917359	+	IGR	INS	-	TG	TG	rs34413452		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68917358_68917359insTG								KCNJ2 (741177 upstream) : None (None downstream)																							TCTATGTAAATtgtgtgtgtgt	0.223													4	3	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70916477	70916478	+	Intron	INS	-	C	C	rs146998034	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70916477_70916478insC	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						ccattttatttcccccttcctc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75834424	75834424	+	IGR	DEL	T	-	-	rs113192099		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75834424delT								SEPT9 (337748 upstream) : FLJ45079 (40685 downstream)																							GCCTCCAAGATTTCGGGCCGT	0.572													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77853236	77853236	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77853236delG								CBX4 (40023 upstream) : TBC1D16 (60585 downstream)																							ccagcattttgggaggctgag	0.020													4	2	---	---	---	---	
BAHCC1	57597	broad.mit.edu	37	17	79372733	79372734	+	5'Flank	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79372733_79372734insA	uc002kaf.2	+							NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)			GGAAGGTTATTAAAAAAAAAAA	0.465													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4199272	4199272	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4199272delT	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				CTTGCTTGCCTTCAGACATCT	0.428													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4442603	4442604	+	Intron	INS	-	A	A	rs138716316	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4442603_4442604insA	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				ACAGAAAGGACAAAGAATGAGA	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5000864	5000867	+	IGR	DEL	CACA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5000864_5000867delCACA								DLGAP1 (545598 upstream) : LOC642597 (142805 downstream)																							ggtatctcagcacacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8848783	8848783	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8848783delA								KIAA0802 (16008 upstream) : NDUFV2 (253892 downstream)																							TCTGTCTGATAATAGACTCAT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19782639	19782640	+	IGR	DEL	GT	-	-	rs72199360		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19782639_19782640delGT								GATA6 (412 upstream) : CTAGE1 (210924 downstream)																							TCCATAGCCAgtgtgtgtgtgt	0.351													4	2	---	---	---	---	
DSC2	1824	broad.mit.edu	37	18	28654582	28654582	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28654582delA	uc002kwl.3	-						DSC2_uc002kwk.3_Intron	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TATTTCATACAAAAAAAAAAA	0.348													4	2	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30891372	30891375	+	Intron	DEL	AGAG	-	-	rs149984823		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30891372_30891375delAGAG	uc002kxn.2	-						C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						TAAAAAAGACAGAGAGGCCACATG	0.446													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35877917	35877917	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35877917delA								CELF4 (731917 upstream) : LOC647946 (908971 downstream)																							GAAGAGGGTTAAATATTTAAA	0.363													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37381893	37381894	+	5'Flank	DEL	AT	-	-	rs144679049		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37381893_37381894delAT	uc002lal.1	-											Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						TATGTGTCACATGTGTCCTTTG	0.351													2	4	---	---	---	---	
LOXHD1	125336	broad.mit.edu	37	18	44079632	44079633	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44079632_44079633delTG	uc010xcw.1	-						LOXHD1_uc002lcd.3_Intron|LOXHD1_uc002lce.3_Intron|LOXHD1_uc002lcf.3_Intron|LOXHD1_uc010xcv.1_Intron|LOXHD1_uc010xcu.1_Intron	NM_144612	NP_653213	Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1 isoform 1						sensory perception of sound	stereocilium	protein binding				0						ggtgtgtgtttgtgtgtgtgtg	0.361													4	2	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45844795	45844795	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45844795delT	uc010dnw.2	-						ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						CCCTTCTGCCTTCCCGGCTGG	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45989982	45989982	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45989982delA								ZBTB7C (54319 upstream) : KIAA0427 (75445 downstream)																							acctactagcaaaaaagacca	0.000													4	2	---	---	---	---	
BCL2	596	broad.mit.edu	37	18	60885923	60885924	+	Intron	INS	-	C	C			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60885923_60885924insC	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)	cctccactcatcccattctcca	0.035			T	IGH@	NHL|CLL								4	2	---	---	---	---	
BCL2	596	broad.mit.edu	37	18	60885993	60885994	+	Intron	INS	-	CAT	CAT	rs111996677		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60885993_60885994insCAT	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)	ccactcatccccctctactcat	0.079			T	IGH@	NHL|CLL								8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	66024607	66024607	+	IGR	DEL	T	-	-	rs77940791		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66024607delT								DSEL (840640 upstream) : TMX3 (316320 downstream)																							aggggatgcattttttttttc	0.000													4	2	---	---	---	---	
MBP	4155	broad.mit.edu	37	18	74779996	74779997	+	Intron	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74779996_74779997delTG	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1						central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)		tgtgtgtgtttgtgtgtgtgtg	0.455											OREG0025075	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77458769	77458770	+	Intron	INS	-	C	C	rs149955339	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77458769_77458770insC	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CCTTACCAGTTCTAAAGGTTCC	0.530													4	3	---	---	---	---	
CTDP1	9150	broad.mit.edu	37	18	77502182	77502183	+	Intron	DEL	GA	-	-	rs35935192		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77502182_77502183delGA	uc002lnh.1	+						CTDP1_uc002lni.1_Intron|CTDP1_uc010drd.1_Intron	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CATGAAGCATgagagagagaga	0.574													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	1867927	1867934	+	IGR	DEL	GTGTGTGT	-	-	rs72395295		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1867927_1867934delGTGTGTGT								KLF16 (4363 upstream) : FAM108A1 (9042 downstream)																							ATGTAAGGACgtgtgtgtgtgtgtgtgt	0.221													4	2	---	---	---	---	
GNA15	2769	broad.mit.edu	37	19	3160237	3160246	+	Intron	DEL	CTCTTGGCCT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3160237_3160246delCTCTTGGCCT	uc002lxf.2	+							NM_002068	NP_002059	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		gCTCTTGGCACTCTTGGCctctctctctgt	0.143													6	3	---	---	---	---	
ZFR2	23217	broad.mit.edu	37	19	3816241	3816242	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3816241_3816242insT	uc002lyw.2	-							NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		Cttcttgtatcttttttttttt	0.069													5	3	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7482716	7482716	+	Intron	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7482716delA	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				TGGGAGAGTGAAGGCTGGTGG	0.512													4	2	---	---	---	---	
LASS4	79603	broad.mit.edu	37	19	8302744	8302745	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8302744_8302745insA	uc002mjg.2	+						LASS4_uc002mjh.2_Intron|LASS4_uc002mji.2_Intron|LASS4_uc010dvz.2_Intron	NM_024552	NP_078828	Q9HA82	CERS4_HUMAN	LAG1 homolog, ceramide synthase 4							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1						caaaacaaaacaaaaaaaagtg	0.010													3	3	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13105126	13105127	+	5'Flank	INS	-	GT	GT	rs139318180	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13105126_13105127insGT	uc002mwd.2	+							NM_002501	NP_002492	Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			TGGGCAACCCAgtgtgtgtgtg	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14616770	14616771	+	IGR	INS	-	TG	TG			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14616770_14616771insTG								GIPC1 (9826 upstream) : DNAJB1 (8811 downstream)																							CACACCAGGCCtgtgtgtgtgt	0.540													6	3	---	---	---	---	
C19orf44	84167	broad.mit.edu	37	19	16628260	16628261	+	Intron	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16628260_16628261delAC	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167												0						GGGGTGATGGACACACACACAC	0.579													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27829509	27829509	+	IGR	DEL	G	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27829509delG								None (None upstream) : LOC148189 (451893 downstream)																							aggactcaaagcgctccaaat	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27843421	27843421	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27843421delT								None (None upstream) : LOC148189 (437981 downstream)																							taatagtttctttttcaccac	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28492857	28492859	+	IGR	DEL	TGT	-	-	rs140260955		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28492857_28492859delTGT								LOC148189 (208009 upstream) : LOC148145 (963181 downstream)																							TGCAGACAAATGTTGTTAGTGAC	0.335													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45107270	45107271	+	IGR	INS	-	G	G	rs143317332	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45107270_45107271insG								CEACAM22P (47120 upstream) : PVR (39827 downstream)																							ctgcagagagagggggtcccaa	0.000													5	4	---	---	---	---	
MARK4	57787	broad.mit.edu	37	19	45754179	45754180	+	5'Flank	INS	-	TC	TC			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45754179_45754180insTC	uc002pbb.1	+						MARK4_uc002paz.1_5'Flank|MARK4_uc002pba.1_5'Flank			Q96L34	MARK4_HUMAN	RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		gtctccctgcgtctctctctct	0.000													2	4	---	---	---	---	
MYPOP	339344	broad.mit.edu	37	19	46400495	46400496	+	Intron	INS	-	T	T	rs35760449		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46400495_46400496insT	uc002pdt.2	-							NM_001012643	NP_001012661	Q86VE0	MYPOP_HUMAN	Myb protein P42POP							nucleus	DNA binding				0						taatttttgtatttttagtaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47803957	47803964	+	IGR	DEL	TCCTTCCT	-	-	rs34256769		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47803957_47803964delTCCTTCCT								PRR24 (24978 upstream) : C5AR1 (9140 downstream)																							TCTCTATTTCtccttccttccttccttc	0.067													3	3	---	---	---	---	
CARD8	22900	broad.mit.edu	37	19	48724209	48724209	+	Intron	DEL	G	-	-	rs113441226		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48724209delG	uc002pie.3	-						CARD8_uc002pii.3_Intron|CARD8_uc002pid.1_5'Flank|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Intron|CARD8_uc010xzk.1_Intron|CARD8_uc002pif.3_Intron|CARD8_uc002pig.3_Intron|CARD8_uc002pih.3_Intron|CARD8_uc010xzl.1_Intron|CARD8_uc010xzm.1_Intron	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		agaaaggaaaggaaaggaagg	0.000													4	4	---	---	---	---	
TULP2	7288	broad.mit.edu	37	19	49396814	49396815	+	Intron	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49396814_49396815insT	uc002pkz.2	-							NM_003323	NP_003314	O00295	TULP2_HUMAN	tubby like protein 2						visual perception	cytoplasm|extracellular region				ovary(1)|kidney(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		ttctttctttcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53559322	53559323	+	IGR	INS	-	ATTC	ATTC	rs146814029	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53559322_53559323insATTC								ZNF702P (62538 upstream) : ZNF160 (10545 downstream)																							taaaactttttattcattcatt	0.000													4	2	---	---	---	---	
CACNG8	59283	broad.mit.edu	37	19	54483312	54483313	+	Intron	DEL	GT	-	-	rs71949256		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54483312_54483313delGT	uc002qcs.1	+						MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGGCGCGCACgtgtgtgtgtgt	0.530													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56282343	56282344	+	IGR	INS	-	T	T	rs145866117	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56282343_56282344insT								RFPL4A (7804 upstream) : NLRP11 (14426 downstream)																							attattttggcttttttttctt	0.000													4	2	---	---	---	---	
ZNF418	147686	broad.mit.edu	37	19	58443216	58443216	+	Intron	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58443216delT	uc002qqs.1	-						ZNF418_uc010yhn.1_Intron|ZNF418_uc010yho.1_Intron	NM_133460	NP_597717	Q8TF45	ZN418_HUMAN	zinc finger protein 418						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		agtgctgggattacagcatga	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1821317	1821317	+	IGR	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1821317delC								SIRPG (182892 upstream) : SIRPA (53496 downstream)																							cagaagccaacaagagagaaa	0.055													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1943171	1943172	+	Intron	INS	-	GG	GG	rs144048419	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1943171_1943172insGG	uc002wfu.1	+											Homo sapiens cDNA FLJ33362 fis, clone BRACE2005337.																		AGGGGAAGCCTGGGGGGGTTGG	0.554													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16077036	16077036	+	IGR	DEL	G	-	-	rs141896193		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16077036delG								MACROD2 (43197 upstream) : KIF16B (175713 downstream)																							ATTAAGGTTAGGGGACAGATA	0.498													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16755451	16755452	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16755451_16755452insA								OTOR (22643 upstream) : PCSK2 (451300 downstream)																							agaaagaaaggaaggaaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25103266	25103267	+	IGR	DEL	CA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25103266_25103267delCA								VSX1 (40499 upstream) : LOC284798 (18167 downstream)																							CACACACACTCACACACACACa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29447606	29447606	+	IGR	DEL	A	-	-	rs111907465		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29447606delA								None (None upstream) : FRG1B (164273 downstream)																							actgtggatgaaaaccaatat	0.114													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29591052	29591053	+	IGR	INS	-	A	A	rs73621638		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29591052_29591053insA								None (None upstream) : FRG1B (20826 downstream)																							tacttgcaaagcactgtgtgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29600270	29600270	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600270delA								None (None upstream) : FRG1B (11609 downstream)																							caaaaaatacaaacgactaat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32727952	32727952	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32727952delT								EIF2S2 (27867 upstream) : ASIP (120219 downstream)																							ggagaattgcttgaacccagg	0.000													4	2	---	---	---	---	
C20orf152	140894	broad.mit.edu	37	20	34598697	34598697	+	Intron	DEL	A	-	-	rs112198652		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34598697delA	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron			Q96M20	CT152_HUMAN	SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)					gaaaaaaaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41895437	41895437	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41895437delT								PTPRT (76880 upstream) : SFRS6 (191067 downstream)																							AACACTTTAATTTTTTTCCTC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42378912	42378913	+	IGR	DEL	TG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42378912_42378913delTG								GTSF1L (23270 upstream) : TOX2 (164579 downstream)																							TTGGGGGTGATGTGTGTGTGTG	0.584											OREG0025703	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	20	43366231	43366231	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43366231delC	uc002xml.1	-						uc002xmm.1_Intron					Homo sapiens cDNA FLJ33523 fis, clone BRAMY2006411.																		GGAGAATATTCCACTATGCTA	0.433													4	2	---	---	---	---	
FAM65C	140876	broad.mit.edu	37	20	49237656	49237657	+	Intron	DEL	AC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49237656_49237657delAC	uc002xvm.2	-						FAM65C_uc010zyt.1_Intron|FAM65C_uc010zyu.1_Intron|FAM65C_uc002xvn.1_Intron	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876											ovary(2)	2						GAACAGCTTGACAAAAAAAAAA	0.465													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51227471	51227474	+	IGR	DEL	CTTC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51227471_51227474delCTTC								ZFP64 (418947 upstream) : TSHZ2 (361403 downstream)																							ccttccttgtcttccttccttcct	0.000													9	6	---	---	---	---	
ZNF831	128611	broad.mit.edu	37	20	57786835	57786836	+	Intron	DEL	TG	-	-	rs33961636		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57786835_57786836delTG	uc002yan.2	+							NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831							intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					GAGCTGACCTtgtgtgtgtgtg	0.391													4	2	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62056551	62056551	+	Intron	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62056551delC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	tccaggatgacctcatctcaa	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9652894	9652895	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9652894_9652895insT								None (None upstream) : None (None downstream)																							TGGGTTTCTGGTTTAGCAGGTC	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9667742	9667742	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9667742delT								None (None upstream) : None (None downstream)																							CATCTGCCCCTCCCCCCGACA	0.517													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9828576	9828577	+	IGR	INS	-	CC	CC	rs77169237		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9828576_9828577insCC								None (None upstream) : None (None downstream)																							ATTATCTGGAGTCACACCTTGA	0.342													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10788037	10788038	+	IGR	INS	-	GAATG	GAATG	rs61127042		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10788037_10788038insGAATG								None (None upstream) : TPTE (118705 downstream)																							ggaattaaatagaatggaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10791306	10791310	+	IGR	DEL	ATAGA	-	-	rs113449614		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10791306_10791310delATAGA								None (None upstream) : TPTE (115433 downstream)																							gttgaatgctatagaatggaatgga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10829388	10829392	+	IGR	DEL	GAATG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10829388_10829392delGAATG								None (None upstream) : TPTE (77351 downstream)																							taatggtctcgaatggaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10831001	10831005	+	IGR	DEL	TACTT	-	-	rs57093114		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10831001_10831005delTACTT								None (None upstream) : TPTE (75738 downstream)																							gaatggaatgtacttgaatggaatg	0.000													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037534	11037537	+	Intron	DEL	AAAT	-	-	rs140499714		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037534_11037537delAAAT	uc002yit.1	-						TPTE_uc002yis.1_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)		ACAAAACAAAAAATACTTACTGGA	0.270													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088488	11088488	+	Intron	DEL	G	-	-	rs113519528	by1000genomes	TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088488delG	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ttgtttttttgttgttgttgt	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11114402	11114402	+	IGR	DEL	A	-	-	rs138581689		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11114402delA								BAGE (15465 upstream) : None (None downstream)																							ACTTTCTGTCAAAAAAAGTGA	0.254													4	2	---	---	---	---	
ITSN1	6453	broad.mit.edu	37	21	35253711	35253713	+	Intron	DEL	AAA	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35253711_35253713delAAA	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc010gmn.1_Intron|ITSN1_uc002ytk.1_Intron	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						actctgtctcaaaaaaaaaaaaa	0.212													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35343812	35343817	+	IGR	DEL	ACACAC	-	-	rs138324381		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35343812_35343817delACACAC								ATP5O (55654 upstream) : MRPS6 (102006 downstream)																							AATCCTGCTAacacacacacacacac	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16691266	16691267	+	IGR	DEL	GG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16691266_16691267delGG								OR11H1 (241462 upstream) : CCT8L2 (380381 downstream)																							ggctaagacaggggctgttata	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17392546	17392547	+	IGR	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17392546_17392547insA								HSFYL1 (82321 upstream) : GAB4 (50282 downstream)																							ATTGAATCTGTAAAAAAAAAAA	0.168													3	3	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26317783	26317784	+	Intron	DEL	GT	-	-	rs72080044		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26317783_26317784delGT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						AATAGCAATAgtgtgtgtgtgt	0.223													4	2	---	---	---	---	
MN1	4330	broad.mit.edu	37	22	28182831	28182832	+	Intron	DEL	CA	-	-	rs68170646		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28182831_28182832delCA	uc003adj.2	-						MN1_uc010gvg.2_Intron	NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						TGCCCGTGCGcacacacacaca	0.431			T	ETV6	AML|meningioma								4	2	---	---	---	---	
DRG1	4733	broad.mit.edu	37	22	31818095	31818096	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31818095_31818096insA	uc003aku.2	+							NM_004147	NP_004138	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1						multicellular organismal development|transcription, DNA-dependent	cytoplasm|intermediate filament cytoskeleton|nucleus	GTP binding|transcription factor binding			central_nervous_system(1)	1						gactccgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34449171	34449171	+	IGR	DEL	T	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34449171delT								LARGE (130587 upstream) : None (None downstream)																							agtgtgccaattacatgatgt	0.199													4	2	---	---	---	---	
SERHL	94009	broad.mit.edu	37	22	42947578	42947579	+	Intron	DEL	CC	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42947578_42947579delCC	uc011apm.1	+						SERHL2_uc011apn.1_5'Flank|SERHL2_uc003bcr.2_5'Flank|SERHL2_uc010gyz.2_5'Flank|SERHL2_uc010gyy.2_5'Flank|SERHL2_uc011apo.1_5'Flank					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0						gggtttttctccccatgtgcag	0.000													4	2	---	---	---	---	
MPPED1	758	broad.mit.edu	37	22	43895661	43895663	+	Intron	DEL	GGT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43895661_43895663delGGT	uc011apv.1	+						MPPED1_uc011apw.1_Intron|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Intron|MPPED1_uc011apz.1_Intron	NM_001044370	NP_001037835	O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1								hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)				tgatggtggaggtggtggtggtg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1237043	1237044	+	IGR	INS	-	T	T			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1237043_1237044insT								SHOX (616898 upstream) : CRLF2 (77843 downstream)																							tctcccttttcttttttttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68161125	68161126	+	IGR	DEL	GT	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68161125_68161126delGT								EFNB1 (95096 upstream) : PJA1 (219456 downstream)																							tcactatggggtgtgtgtgtgt	0.168													4	2	---	---	---	---	
ATRX	546	broad.mit.edu	37	X	76996288	76996289	+	Intron	INS	-	A	A			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76996288_76996289insA	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron|ATRX_uc004ecr.2_Intron|ATRX_uc010nlx.1_Intron|ATRX_uc010nly.1_Intron	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	aaatggggaggaaaaaaattaa	0.000			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115461568	115461568	+	IGR	DEL	A	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115461568delA								AGTR2 (155345 upstream) : SLC6A14 (106206 downstream)																							tccatctcggaaaaaaaaaaa	0.000													5	4	---	---	---	---	
DCAF12L1	139170	broad.mit.edu	37	X	125685932	125685932	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125685932delC	uc004eul.2	-	1	911	c.660delG	c.(658-660)TGGfs	p.W220fs		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	220	WD 2.									skin(3)|ovary(1)	4						GGTCCATCCGCCACAGCGCCA	0.652													12	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13433457	13433458	+	IGR	DEL	AG	-	-			TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13433457_13433458delAG								None (None upstream) : None (None downstream)																							agaaaaaGAAAGAAAACCAGAA	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13843008	13843012	+	IGR	DEL	AGTCA	-	-	rs76111096		TCGA-66-2771-01	TCGA-66-2771-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13843008_13843012delAGTCA								None (None upstream) : TTTY15 (931286 downstream)																							aatggaatggagtcaaatggaatag	0.000													4	3	---	---	---	---	
