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
TARDBP	23435	broad.mit.edu	37	1	11077007	11077007	+	Silent	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11077007A>C	uc001art.2	+	3	479	c.345A>C	c.(343-345)ACA>ACC	p.T115T	TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein	115	RRM 1.			Missing: Completely abolishes RNA binding.	3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		CATGGAAAACAACCGAACAGG	0.388													14	67	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11307700	11307700	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11307700G>A	uc001asd.2	-	8	1328	c.1207C>T	c.(1207-1209)CGA>TGA	p.R403*		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	403					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						GCAGAAGGTCGGAATGCAGCC	0.478													17	48	---	---	---	---	PASS
PRAMEF12	390999	broad.mit.edu	37	1	12837350	12837350	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12837350G>T	uc001aui.2	+	3	1087	c.1060G>T	c.(1060-1062)GAC>TAC	p.D354Y		NM_001080830	NP_001074299	O95522	PRA12_HUMAN	PRAME family member 12	354	LRR 2.									ovary(3)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGACCCTGGACTTAGAGGA	0.592													25	92	---	---	---	---	PASS
ZBTB8A	653121	broad.mit.edu	37	1	33059073	33059073	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33059073A>G	uc001bvn.2	+	3	1026	c.541A>G	c.(541-543)AAT>GAT	p.N181D	ZBTB8A_uc001bvk.2_RNA|ZBTB8A_uc001bvm.2_Missense_Mutation_p.N181D	NM_001040441	NP_001035531	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	181					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAAATCTTGGAATAAGTATAA	0.418													15	47	---	---	---	---	PASS
LHX8	431707	broad.mit.edu	37	1	75609574	75609574	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75609574G>C	uc001dgo.2	+	7	1319	c.655G>C	c.(655-657)GTT>CTT	p.V219L	LHX8_uc001dgq.2_Missense_Mutation_p.V158L	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	219						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						AGAGCAAGATGTTAACCATCC	0.413													13	53	---	---	---	---	PASS
ZZZ3	26009	broad.mit.edu	37	1	78031388	78031388	+	Silent	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78031388G>A	uc001dhq.2	-	15	3125	c.2649C>T	c.(2647-2649)TAC>TAT	p.Y883Y	ZZZ3_uc001dhr.2_Silent_p.Y389Y|ZZZ3_uc001dhp.2_Silent_p.Y882Y	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	883					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						GAGACACACAGTAGTCTCTGT	0.378													11	38	---	---	---	---	PASS
PTGFR	5737	broad.mit.edu	37	1	79002271	79002271	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79002271G>T	uc001din.2	+	3	1245	c.979G>T	c.(979-981)GTC>TTC	p.V327F	PTGFR_uc001dim.2_3'UTR	NM_000959	NP_000950	P43088	PF2R_HUMAN	prostaglandin F receptor isoform a precursor	327	Cytoplasmic (Potential).				parturition	extracellular region|integral to plasma membrane	prostaglandin F receptor activity			ovary(3)|breast(2)|skin(1)	6				Colorectal(170;0.248)	Bimatoprost(DB00905)|Latanoprost(DB00654)|Travoprost(DB00287)	TGGAGTGCATGTCATCAGCTT	0.393													12	57	---	---	---	---	PASS
AMY2B	280	broad.mit.edu	37	1	104116399	104116399	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104116399G>T	uc001duq.2	+	6	1199	c.583G>T	c.(583-585)GCC>TCC	p.A195S	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Missense_Mutation_p.A195S|AMY2B_uc001dus.1_5'Flank	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	195					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TTCCAAGATTGCCGAATATAT	0.413													39	233	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144882752	144882752	+	Silent	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144882752G>A	uc001elw.3	-	24	3558	c.3267C>T	c.(3265-3267)ACC>ACT	p.T1089T	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Silent_p.T96T	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1089					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GACCCTCTTTGGTTACCACAG	0.493			T	PDGFRB	MPD								28	235	---	---	---	---	PASS
ANKRD35	148741	broad.mit.edu	37	1	145549315	145549315	+	5'UTR	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145549315C>A	uc001eob.1	+	1					NBPF10_uc001emp.3_Intron|ANKRD35_uc010oyx.1_5'UTR	NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35											ovary(4)|skin(1)	5	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCGACCCCGGCCATGAAGCGT	0.637													4	24	---	---	---	---	PASS
LCE1B	353132	broad.mit.edu	37	1	152785226	152785226	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152785226G>T	uc001faq.2	+	1	780	c.304G>T	c.(304-306)GGC>TGC	p.G102C		NM_178349	NP_848126	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	102	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCCTCCGGGGGCTCCAGCTG	0.622													11	27	---	---	---	---	PASS
S100A2	6273	broad.mit.edu	37	1	153536362	153536362	+	5'UTR	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153536362G>A	uc001fcb.2	-	2						NM_005978	NP_005969	P29034	S10A2_HUMAN	S100 calcium binding protein A2						endothelial cell migration		calcium ion binding			ovary(1)	1	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATGGATCTGTGGCTGCAGAGG	0.582													8	20	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156814587	156814587	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156814587T>C	uc010pht.1	-	13	2740	c.2486A>G	c.(2485-2487)AAG>AGG	p.K829R	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	829	Fibronectin type-III 3.|Extracellular (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GACACTGTTCTTGCTGGAGGC	0.592													11	38	---	---	---	---	PASS
FCRL5	83416	broad.mit.edu	37	1	157514242	157514242	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157514242C>G	uc001fqu.2	-	5	812	c.654G>C	c.(652-654)GAG>GAC	p.E218D	FCRL5_uc009wsm.2_Missense_Mutation_p.E218D|FCRL5_uc010phv.1_Missense_Mutation_p.E218D|FCRL5_uc010phw.1_Missense_Mutation_p.E133D|FCRL5_uc001fqv.1_Missense_Mutation_p.E218D|FCRL5_uc010phx.1_5'UTR	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	218	Extracellular (Potential).|Ig-like C2-type 2.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CATCTGACCTCTCTAGAGAGA	0.567													28	109	---	---	---	---	PASS
FCRL5	83416	broad.mit.edu	37	1	157514827	157514827	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157514827G>T	uc001fqu.2	-	4	511	c.353C>A	c.(352-354)TCT>TAT	p.S118Y	FCRL5_uc009wsm.2_Missense_Mutation_p.S118Y|FCRL5_uc010phv.1_Missense_Mutation_p.S118Y|FCRL5_uc010phw.1_Missense_Mutation_p.S33Y|FCRL5_uc001fqv.1_Missense_Mutation_p.S118Y|FCRL5_uc010phx.1_Translation_Start_Site	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	118	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CAGAACCACAGAGTCTCCTTC	0.408													14	45	---	---	---	---	PASS
CD1C	911	broad.mit.edu	37	1	158262495	158262495	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158262495G>T	uc001fru.2	+	4	1012	c.720G>T	c.(718-720)ATG>ATT	p.M240I	CD1C_uc001frv.2_Missense_Mutation_p.M43I	NM_001765	NP_001756	P29017	CD1C_HUMAN	CD1C antigen precursor	240	Extracellular (Potential).|Ig-like.				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|skin(1)|pancreas(1)	4	all_hematologic(112;0.0378)					TGACATGGATGCGGAATGAAC	0.542													10	78	---	---	---	---	PASS
CD1B	910	broad.mit.edu	37	1	158299801	158299801	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158299801C>T	uc001frx.2	-	3	556	c.448G>A	c.(448-450)GTG>ATG	p.V150M	CD1B_uc001frw.2_Missense_Mutation_p.V43M	NM_001764	NP_001755	P29016	CD1B_HUMAN	CD1B antigen precursor	150	Extracellular (Potential).				antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)					GGGGAAGGCACACATGAAGCA	0.468													44	169	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158651411	158651411	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158651411A>G	uc001fst.1	-	4	636	c.437T>C	c.(436-438)CTG>CCG	p.L146P		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	146	Spectrin 2.				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)					CTCCAGGGTCAGCTCTAACAG	0.547													22	89	---	---	---	---	PASS
MNDA	4332	broad.mit.edu	37	1	158815386	158815386	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158815386A>C	uc001fsz.1	+	5	780	c.580A>C	c.(580-582)ACC>CCC	p.T194P		NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	194					B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)					GAATCAGGAAACCCAGGCCCA	0.363													7	22	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160098516	160098516	+	Silent	SNP	G	T	T	rs55741021		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160098516G>T	uc001fvc.2	+	9	1224	c.1092G>T	c.(1090-1092)ACG>ACT	p.T364T	ATP1A2_uc001fvb.2_Silent_p.T364T|ATP1A2_uc010piz.1_Silent_p.T209T|ATP1A2_uc001fvd.2_Silent_p.T100T|ATP1A2_uc009wtg.1_Silent_p.T52T	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	364	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CGGTGGAGACGCTGGGCTCCA	0.582													18	71	---	---	---	---	PASS
KLHL20	27252	broad.mit.edu	37	1	173754391	173754391	+	3'UTR	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173754391G>A	uc001gjc.2	+	12					KLHL20_uc010pmr.1_3'UTR|KLHL20_uc009wwf.2_3'UTR	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						GGTGAACACAGAGAAGACAGT	0.403													4	30	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175325455	175325455	+	Missense_Mutation	SNP	G	C	C	rs146606650		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175325455G>C	uc001gkp.1	-	14	3199	c.3118C>G	c.(3118-3120)CTC>GTC	p.L1040V	TNR_uc009wwu.1_Missense_Mutation_p.L1040V	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1040	Fibronectin type-III 9.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					ATGTACTCACGAGTAGAAAAG	0.493													20	86	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175372396	175372396	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175372396C>A	uc001gkp.1	-	2	937	c.856G>T	c.(856-858)GGC>TGC	p.G286C	TNR_uc009wwu.1_Missense_Mutation_p.G286C|TNR_uc010pmz.1_Missense_Mutation_p.G286C	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	286	Cys-rich.|EGF-like 4.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					CCAACGTAGCCCTCCTCGCAT	0.612													12	44	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	180044231	180044231	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180044231G>C	uc001gnt.2	+	28	6025	c.5642G>C	c.(5641-5643)CGT>CCT	p.R1881P	CEP350_uc009wxl.2_Missense_Mutation_p.R1880P|CEP350_uc001gnv.2_Missense_Mutation_p.R16P	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	1881	Potential.					centrosome|nucleus|spindle				ovary(4)	4						TGGAAGCGACGTTTAGATGCA	0.428													15	42	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197316598	197316598	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197316598A>C	uc001gtz.2	+	4	1112	c.977A>C	c.(976-978)CAC>CCC	p.H326P	CRB1_uc010poz.1_Missense_Mutation_p.H257P|CRB1_uc001gty.1_Missense_Mutation_p.H326P|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Missense_Mutation_p.H326P|CRB1_uc010ppc.1_RNA	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	326	Extracellular (Potential).|EGF-like 8.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						TACACTTGTCACTGCTGGCCT	0.373													13	40	---	---	---	---	PASS
NFASC	23114	broad.mit.edu	37	1	204951142	204951142	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204951142G>T	uc001hbj.2	+	21	2792	c.2464G>T	c.(2464-2466)GAA>TAA	p.E822*	NFASC_uc010pra.1_Nonsense_Mutation_p.E818*|NFASC_uc001hbi.2_Nonsense_Mutation_p.E818*|NFASC_uc010prb.1_Nonsense_Mutation_p.E833*|NFASC_uc010prc.1_Nonsense_Mutation_p.E389*|NFASC_uc001hbk.1_Nonsense_Mutation_p.E628*|NFASC_uc001hbl.1_Nonsense_Mutation_p.E72*	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	822	Extracellular (Potential).				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TTACTCCGGAGAAGATTGTGA	0.612													5	12	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233134126	233134126	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233134126C>G	uc001hvl.2	-	32	5897	c.5662G>C	c.(5662-5664)GGA>CGA	p.G1888R	PCNXL2_uc001hvk.1_Missense_Mutation_p.G540R|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1888						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				GCCCCTCCTCCGTCCACGTCT	0.617													8	22	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237604759	237604759	+	Silent	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237604759G>A	uc001hyl.1	+	13	1266	c.1146G>A	c.(1144-1146)GTG>GTA	p.V382V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	382	Cytoplasmic (By similarity).|MIR 5.				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)			TGAAATCCGTGAGAATGGGAT	0.348													16	83	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237778056	237778056	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237778056A>T	uc001hyl.1	+	37	5748	c.5628A>T	c.(5626-5628)CAA>CAT	p.Q1876H		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1876	Cytoplasmic (By similarity).|4 X approximate repeats.				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)			CAAAGCTGCAAGGAGCTGGTG	0.532													8	41	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237817703	237817703	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237817703C>T	uc001hyl.1	+	52	8074	c.7954C>T	c.(7954-7956)CTG>TTG	p.L2652L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2652	Modulator (Potential).|Cytoplasmic (By similarity).|4 X approximate repeats.				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)			TTTTGATGCCCTGTCTCAAAA	0.383													6	28	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248201806	248201806	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248201806G>C	uc001idw.2	+	1	333	c.237G>C	c.(235-237)AAG>AAC	p.K79N	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	79	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TTGTTCCAAAGAtggtttatg	0.299													32	157	---	---	---	---	PASS
SH3BP5L	80851	broad.mit.edu	37	1	249106437	249106437	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249106437G>A	uc001iew.1	-	7	1396	c.844C>T	c.(844-846)CAC>TAC	p.H282Y	SH3BP5L_uc010pzp.1_Missense_Mutation_p.H175Y|SH3BP5L_uc010pzq.1_Missense_Mutation_p.H250Y|SH3BP5L_uc001iev.1_Missense_Mutation_p.H163Y	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	282											0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CCCAGGGGGTGGGGAGGCAGA	0.716													4	15	---	---	---	---	PASS
TPO	7173	broad.mit.edu	37	2	1544431	1544431	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1544431G>A	uc002qww.2	+	16	2775	c.2684G>A	c.(2683-2685)AGA>AAA	p.R895K	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.R838K|TPO_uc002qwr.2_Missense_Mutation_p.R895K|TPO_uc002qwx.2_Missense_Mutation_p.R838K|TPO_uc010yio.1_Missense_Mutation_p.R722K|TPO_uc010yip.1_Missense_Mutation_p.R851K|TPO_uc002qwy.1_Missense_Mutation_p.R191K|TPO_uc002qwz.2_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	895	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CCCGAGCTGAGATGCGGAAAG	0.637													13	49	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11696853	11696853	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11696853C>T	uc002rbk.1	+	2	413	c.113C>T	c.(112-114)TCC>TTC	p.S38F	GREB1_uc002rbl.2_Missense_Mutation_p.S38F|GREB1_uc002rbm.2_Intron|GREB1_uc002rbn.1_Missense_Mutation_p.S38F	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	38						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCCATCTTTTCCCAGCTGTAC	0.522													5	38	---	---	---	---	PASS
SFRS7	6432	broad.mit.edu	37	2	38975742	38975742	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38975742C>T	uc002rqz.2	-	4	678	c.440G>A	c.(439-441)CGC>CAC	p.R147H	SFRS7_uc002rra.2_RNA|SFRS7_uc010ynp.1_Missense_Mutation_p.R147H|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7	147	Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)				GCTCCTGCTGCGTGAGCGAGA	0.398													12	59	---	---	---	---	PASS
C2orf86	51057	broad.mit.edu	37	2	63486509	63486509	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63486509C>A	uc002sch.2	-	14	2294	c.1848G>T	c.(1846-1848)TTG>TTT	p.L616F	C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Missense_Mutation_p.L457F|C2orf86_uc010ypu.1_RNA|C2orf86_uc002scg.2_Missense_Mutation_p.L424F	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	616					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						CAGCTAGTGCCAATTCACCTT	0.358													11	48	---	---	---	---	PASS
C2orf78	388960	broad.mit.edu	37	2	74043036	74043036	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74043036C>T	uc002sjr.1	+	3	1807	c.1686C>T	c.(1684-1686)ATC>ATT	p.I562I		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	562	Lys-rich.									ovary(2)	2						CCAGCAGGATCAGCAAAACTA	0.473													9	40	---	---	---	---	PASS
CD8A	925	broad.mit.edu	37	2	87017523	87017523	+	Missense_Mutation	SNP	C	A	A	rs121918660		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87017523C>A	uc002srt.2	-	2	1220	c.331G>T	c.(331-333)GGC>TGC	p.G111C	RMND5A_uc002srs.3_Intron|CD8A_uc002srv.2_Missense_Mutation_p.G111C|CD8A_uc010ytn.1_Missense_Mutation_p.G152C|CD8A_uc002sru.2_Missense_Mutation_p.G111C	NM_001768	NP_001759	P01732	CD8A_HUMAN	CD8 antigen alpha polypeptide isoform 1	111	Ig-like V-type.|Extracellular (Potential).		G -> S (in CD8 deficiency; prevents CD8 expression).	G->R: Prevents CD8 expression.	antigen processing and presentation|regulation of immune response|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane|T cell receptor complex	coreceptor activity|MHC class I protein binding			ovary(1)	1						AAATAGTAGCCCTCGTTCTCT	0.652													12	50	---	---	---	---	PASS
LIMS1	3987	broad.mit.edu	37	2	109276214	109276214	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109276214C>T	uc002teg.2	+	2	269	c.150C>T	c.(148-150)TTC>TTT	p.F50F	LIMS1_uc002tef.2_Silent_p.F62F|LIMS1_uc002teh.2_Silent_p.F50F|LIMS1_uc002tei.2_Silent_p.F50F|LIMS1_uc002tej.2_Silent_p.F87F|LIMS1_uc002tek.3_Silent_p.F112F	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	50	LIM zinc-binding 1.				cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						AAGGACTCTTCTATGAGGTGA	0.552													12	69	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116548748	116548748	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116548748C>T	uc002tla.1	+	18	2080	c.1623C>T	c.(1621-1623)GAC>GAT	p.D541D	DPP10_uc002tlb.1_Silent_p.D491D|DPP10_uc002tlc.1_Silent_p.D537D|DPP10_uc002tle.2_Silent_p.D545D|DPP10_uc002tlf.1_Silent_p.D534D	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	541	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TTCATATTGACGACTATGGTA	0.328													5	47	---	---	---	---	PASS
WDR33	55339	broad.mit.edu	37	2	128522490	128522490	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128522490C>A	uc002tpg.1	-	6	721	c.538G>T	c.(538-540)GAC>TAC	p.D180Y	WDR33_uc002tph.1_Missense_Mutation_p.D180Y|WDR33_uc002tpi.1_Missense_Mutation_p.D180Y	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	180	WD 2.				postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CCTCCGTGGTCTGCTGTCAAC	0.468													8	45	---	---	---	---	PASS
ARHGAP15	55843	broad.mit.edu	37	2	144194488	144194488	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144194488G>T	uc002tvm.3	+	8	731	c.580G>T	c.(580-582)GAT>TAT	p.D194Y	ARHGAP15_uc010zbl.1_Missense_Mutation_p.D194Y|ARHGAP15_uc002tvn.2_5'UTR	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15	194					regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		CCAGCCAAAGGATTCAAGTTG	0.333													9	33	---	---	---	---	PASS
CACNB4	785	broad.mit.edu	37	2	152732997	152732997	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152732997A>G	uc002tya.2	-	5	532	c.464T>C	c.(463-465)CTC>CCC	p.L155P	CACNB4_uc002txy.2_Missense_Mutation_p.L121P|CACNB4_uc002txz.2_Missense_Mutation_p.L137P|CACNB4_uc010fnz.2_Missense_Mutation_p.L155P|CACNB4_uc002tyb.2_Missense_Mutation_p.L121P	NM_000726	NP_000717	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4	155					axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)	CTCCAATCTGAGTGGACTTGG	0.398													10	31	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167330361	167330361	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167330361C>T	uc002udu.1	-	4	518	c.391G>A	c.(391-393)GAT>AAT	p.D131N	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	131	Helical; Name=S1 of repeat I; (By similarity).				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						AATACGCAATCAATCAGGACA	0.219													8	30	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179616205	179616205	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179616205G>A	uc002unb.2	-	46	11146	c.10922C>T	c.(10921-10923)CCC>CTC	p.P3641L	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)			TTTGTTAAAGGGAGAGCCAGT	0.373													19	80	---	---	---	---	PASS
MYO1B	4430	broad.mit.edu	37	2	192246304	192246304	+	Intron	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192246304A>G	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002ust.1_Intron	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			TAATGTTGAAATGCTATTTTT	0.259													6	28	---	---	---	---	PASS
PARD3B	117583	broad.mit.edu	37	2	206480475	206480475	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206480475G>C	uc002var.1	+	23	3763	c.3556G>C	c.(3556-3558)GAC>CAC	p.D1186H	PARD3B_uc002vao.1_Missense_Mutation_p.D1085H|PARD3B_uc002vap.1_Missense_Mutation_p.D1124H|PARD3B_uc002vaq.1_Missense_Mutation_p.D1117H|uc010fuc.1_5'Flank	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	1186					cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GGGCAGCCCAGACCAGTACCC	0.617													11	49	---	---	---	---	PASS
IKZF2	22807	broad.mit.edu	37	2	213886856	213886856	+	Splice_Site	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213886856T>A	uc002vem.2	-	6	744	c.575_splice	c.e6-1	p.V192_splice	IKZF2_uc010fuu.2_Splice_Site_p.M47_splice|IKZF2_uc002vej.2_Splice_Site_p.V139_splice|IKZF2_uc002vek.2_Splice_Site|IKZF2_uc010fuv.2_Splice_Site_p.V166_splice|IKZF2_uc002vel.2_Splice_Site_p.V113_splice|IKZF2_uc010fuw.2_Splice_Site|IKZF2_uc010fux.2_Splice_Site|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Splice_Site_p.V166_splice	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GTTTACCCACTGTGAAGAGAA	0.443													11	44	---	---	---	---	PASS
ATIC	471	broad.mit.edu	37	2	216190789	216190789	+	Silent	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216190789G>C	uc002vex.3	+	6	633	c.459G>C	c.(457-459)GTG>GTC	p.V153V	ATIC_uc010zjo.1_Silent_p.V94V|ATIC_uc002vey.3_Silent_p.V152V	NM_004044	NP_004035	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide	153					IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)	ACTATGTGGTGGTGTCCACGG	0.493			T	ALK	ALCL								6	43	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216262583	216262583	+	Intron	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216262583A>C	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TAGAGGAAGGAATGCAAAGTA	0.473													6	33	---	---	---	---	PASS
FAM124B	79843	broad.mit.edu	37	2	225266389	225266389	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225266389C>G	uc002vnx.2	-	1	323	c.97G>C	c.(97-99)GAT>CAT	p.D33H	FAM124B_uc002vnw.2_Missense_Mutation_p.D33H	NM_001122779	NP_001116251	Q9H5Z6	F124B_HUMAN	hypothetical protein LOC79843 isoform a	33							protein binding			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		CAAATGCAATCCAGGAGCTGG	0.572													12	41	---	---	---	---	PASS
UGT1A4	54657	broad.mit.edu	37	2	234628211	234628211	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234628211G>T	uc002vux.2	+	1	774	c.745G>T	c.(745-747)GTC>TTC	p.V249F	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Missense_Mutation_p.V249F	NM_007120	NP_009051	P22310	UD14_HUMAN	UDP glycosyltransferase 1 family, polypeptide A4	249					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Imipramine(DB00458)|Lamotrigine(DB00555)|Paricalcitol(DB00910)|Trifluoperazine(DB00831)	GGTGGATCTTGTCAGCTATGC	0.527													32	121	---	---	---	---	PASS
OR6B2	389090	broad.mit.edu	37	2	240968955	240968955	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240968955T>A	uc002vyr.2	-	2	938	c.892A>T	c.(892-894)AAG>TAG	p.K298*	OR6B2_uc010zoc.1_Nonsense_Mutation_p.K298*	NM_001005853	NP_001005853	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B,	298	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		AAGGCGTCCTTAAATTCCTTG	0.418													16	97	---	---	---	---	PASS
MTERFD2	130916	broad.mit.edu	37	2	242039030	242039030	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242039030C>G	uc002wan.1	-	1	881	c.388G>C	c.(388-390)GAC>CAC	p.D130H	MTERFD2_uc010zoj.1_Intron|MTERFD2_uc010zok.1_Missense_Mutation_p.D101H	NM_182501	NP_872307	Q7Z6M4	MTER2_HUMAN	MTERF domain containing 2	101										ovary(1)	1		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		AAACCCATGTCCAGGAGGGAA	0.488													24	99	---	---	---	---	PASS
PASK	23178	broad.mit.edu	37	2	242054777	242054777	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242054777C>A	uc002wao.1	-	13	3216	c.3124G>T	c.(3124-3126)GAG>TAG	p.E1042*	PASK_uc010zol.1_Nonsense_Mutation_p.E856*|PASK_uc010zom.1_Nonsense_Mutation_p.E1007*|PASK_uc010fzl.1_Nonsense_Mutation_p.E1042*|PASK_uc010zon.1_Nonsense_Mutation_p.E823*|PASK_uc002wap.2_Nonsense_Mutation_p.E585*|PASK_uc002waq.2_Nonsense_Mutation_p.E1042*	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1042	Protein kinase.				regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TTGGGATCCTCAATCCAACAA	0.463													11	66	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38835434	38835434	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38835434T>C	uc003ciq.2	-	1	68	c.68A>G	c.(67-69)GAG>GGG	p.E23G		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	23					sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	CTTCTCTATCTCCACCAGTGA	0.488													24	83	---	---	---	---	PASS
CSRNP1	64651	broad.mit.edu	37	3	39184890	39184890	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39184890C>T	uc003cjg.2	-	5	1640	c.1426G>A	c.(1426-1428)GGC>AGC	p.G476S	CSRNP1_uc003cjh.2_Missense_Mutation_p.G476S	NM_033027	NP_149016	Q96S65	CSRN1_HUMAN	AXIN1 up-regulated 1	476					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(4)|skin(1)	5						GGAAGGCTGCCTTCCCTTGAC	0.552													5	20	---	---	---	---	PASS
CCDC13	152206	broad.mit.edu	37	3	42784378	42784378	+	Intron	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42784378C>A	uc003cly.3	-							NM_144719	NP_653320	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13											ovary(1)	1						CCTCCTCAGGCACGCGTTACC	0.562													27	80	---	---	---	---	PASS
ATRIP	84126	broad.mit.edu	37	3	48506925	48506925	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48506925T>C	uc003ctf.1	+	13	2380	c.2348T>C	c.(2347-2349)GTG>GCG	p.V783A	ATRIP_uc011bbj.1_Missense_Mutation_p.V656A|ATRIP_uc003ctg.1_Missense_Mutation_p.V756A|TREX1_uc010hjy.2_5'UTR|TREX1_uc003ctj.2_5'UTR|TREX1_uc003ctk.2_5'Flank|TREX1_uc010hjz.2_5'Flank|TREX1_uc010hka.2_5'Flank	NM_130384	NP_569055	Q8WXE1	ATRIP_HUMAN	ATR interacting protein isoform 1	783					DNA damage checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding|protein serine/threonine kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GAAACCGATGTGGAAGACCCC	0.592								Other_conserved_DNA_damage_response_genes			OREG0015557	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	32	---	---	---	---	PASS
DAG1	1605	broad.mit.edu	37	3	49548205	49548205	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49548205G>T	uc003cxc.3	+	2	656	c.238G>T	c.(238-240)GTG>TTG	p.V80L		NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein	80	Required for laminin recognition.				cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTCATTTCGAGTGACCATTCC	0.488													7	17	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	120977942	120977942	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120977942A>G	uc003eec.3	+	18	2025	c.1885A>G	c.(1885-1887)ATT>GTT	p.I629V	STXBP5L_uc011bji.1_Missense_Mutation_p.I629V	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	629	WD 9.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		AGAACTTGTTATTCAATTGGT	0.363													18	54	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130442333	130442333	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130442333G>C	uc003enj.2	-	7	2487	c.1906C>G	c.(1906-1908)CTT>GTT	p.L636V		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	636					fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						AGGGCATAAAGAGCTTTCACA	0.423													13	61	---	---	---	---	PASS
SLCO2A1	6578	broad.mit.edu	37	3	133692622	133692622	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133692622C>A	uc003eqa.3	-	3	556	c.282G>T	c.(280-282)CGG>CGT	p.R94R	SLCO2A1_uc003eqb.3_Silent_p.R94R|SLCO2A1_uc011blv.1_Silent_p.R94R|SLCO2A1_uc010htw.1_5'UTR	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,	94	Cytoplasmic (Potential).				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1						GACGGTGCACCCGGCTGCCAA	0.572													6	24	---	---	---	---	PASS
SLCO2A1	6578	broad.mit.edu	37	3	133692623	133692623	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133692623C>A	uc003eqa.3	-	3	555	c.281G>T	c.(280-282)CGG>CTG	p.R94L	SLCO2A1_uc003eqb.3_Missense_Mutation_p.R94L|SLCO2A1_uc011blv.1_Missense_Mutation_p.R94L|SLCO2A1_uc010htw.1_5'UTR	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,	94	Cytoplasmic (Potential).				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1						ACGGTGCACCCGGCTGCCAAA	0.577													6	25	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164712183	164712183	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164712183G>T	uc003fei.2	-	41	4765	c.4703C>A	c.(4702-4704)CCC>CAC	p.P1568H		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1568	Sucrase.|Lumenal.				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)	CCAGGAAGCGGGATCTTGTCT	0.299										HNSCC(35;0.089)			15	71	---	---	---	---	PASS
TNIK	23043	broad.mit.edu	37	3	170857278	170857278	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170857278T>C	uc003fhh.2	-	14	1745	c.1400A>G	c.(1399-1401)CAT>CGT	p.H467R	TNIK_uc003fhi.2_Missense_Mutation_p.H467R|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Missense_Mutation_p.H467R|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Missense_Mutation_p.H467R|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1	467	Mediates interaction with NEDD4.				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGCTTGTTCATGCAGTAGCTG	0.408													28	120	---	---	---	---	PASS
ABCC5	10057	broad.mit.edu	37	3	183685506	183685506	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183685506G>C	uc003fmg.2	-	12	1975	c.1810C>G	c.(1810-1812)CTC>GTC	p.L604V	ABCC5_uc011bqt.1_Missense_Mutation_p.L132V|ABCC5_uc010hxl.2_Missense_Mutation_p.L604V	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	604	ABC transporter 1.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GCTGAAATGAGAGAGGTTTTT	0.433													29	290	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505742	195505742	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505742G>C	uc011bto.1	-	3	12785	c.12325C>G	c.(12325-12327)CAC>GAC	p.H4109D	MUC4_uc003fva.2_5'UTR|MUC4_uc003fvb.2_5'UTR|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_5'UTR|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_5'UTR|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_5'UTR|MUC4_uc011bti.1_5'UTR|MUC4_uc011btj.1_5'UTR|MUC4_uc011btk.1_5'UTR|MUC4_uc011btl.1_5'UTR|MUC4_uc011btm.1_5'UTR|MUC4_uc011btn.1_5'UTR|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Missense_Mutation_p.H849D	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	994	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGCGTGACCTGTGGAT	0.587													5	31	---	---	---	---	PASS
CPZ	8532	broad.mit.edu	37	4	8602977	8602977	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8602977C>A	uc003glm.2	+	3	375	c.249C>A	c.(247-249)AGC>AGA	p.S83R	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_5'UTR|CPZ_uc003glo.2_Missense_Mutation_p.S72R|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	83	FZ.				proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						TCCTGCTGAGCGTTCTACACC	0.662													4	48	---	---	---	---	PASS
SLC2A9	56606	broad.mit.edu	37	4	9998458	9998458	+	Silent	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9998458G>A	uc003gmc.2	-	3	418	c.357C>T	c.(355-357)ATC>ATT	p.I119I	SLC2A9_uc003gmd.2_Silent_p.I90I	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	solute carrier family 2, member 9 protein	119	Helical; Name=2; (Potential).				glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3						CAAGTCCACCGATGGCGAATA	0.493													10	47	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20533637	20533637	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20533637G>T	uc003gpr.1	+	17	1848	c.1644G>T	c.(1642-1644)TTG>TTT	p.L548F	SLIT2_uc003gps.1_Missense_Mutation_p.L540F	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	548	LRR 12.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						TTACCGTGTTGGAAGCCACAG	0.303													5	26	---	---	---	---	PASS
KCNIP4	80333	broad.mit.edu	37	4	21950183	21950183	+	Intron	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21950183T>A	uc003gqi.1	-							NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				CGCAAGCTTATTGCATCCTAC	0.632													4	11	---	---	---	---	PASS
GPR125	166647	broad.mit.edu	37	4	22444340	22444340	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22444340C>T	uc003gqm.1	-	7	1118	c.853G>A	c.(853-855)GAA>AAA	p.E285K	GPR125_uc010ieo.1_Missense_Mutation_p.E159K|GPR125_uc003gqn.1_Missense_Mutation_p.E59K|GPR125_uc003gqo.2_Missense_Mutation_p.E285K	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	285	Extracellular (Potential).|Ig-like.				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				TCATCGGTTTCAACTATTCTC	0.373													8	41	---	---	---	---	PASS
APBB2	323	broad.mit.edu	37	4	41016138	41016138	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41016138C>A	uc003gvl.2	-	6	927	c.297G>T	c.(295-297)CTG>CTT	p.L99L	APBB2_uc003gvm.2_Silent_p.L99L|APBB2_uc003gvn.2_Silent_p.L99L|APBB2_uc011byt.1_Silent_p.L82L	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	99					cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						CATTTTTCACCAGCTTGATGT	0.542													9	44	---	---	---	---	PASS
BEND4	389206	broad.mit.edu	37	4	42145770	42145770	+	Silent	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42145770A>G	uc003gwn.2	-	3	1309	c.729T>C	c.(727-729)TCT>TCC	p.S243S	BEND4_uc003gwm.2_Silent_p.S243S|BEND4_uc011byy.1_Silent_p.S243S	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a	243											0						TCAAAAAGGCAGAAGTTTGTT	0.463													10	64	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46067427	46067427	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46067427G>T	uc003gxb.2	-	4	648	c.496C>A	c.(496-498)CGT>AGT	p.R166S		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	166	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		CGAAGCAGACGATTAGGAGTT	0.338													12	60	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46067487	46067487	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46067487G>T	uc003gxb.2	-	4	588	c.436C>A	c.(436-438)CCT>ACT	p.P146T		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	146	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		AAAGTGTCAGGAATCCAAATT	0.358													4	52	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69682026	69682026	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69682026T>C	uc003hee.2	+	1	314	c.289T>C	c.(289-291)TCA>CCA	p.S97P	UGT2B10_uc011cam.1_Missense_Mutation_p.S97P	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	97					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						TAAGAGATTGTCAGAAATTCA	0.313													14	58	---	---	---	---	PASS
GRSF1	2926	broad.mit.edu	37	4	71702001	71702001	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71702001G>C	uc010iia.1	-	2	471	c.388C>G	c.(388-390)CCA>GCA	p.P130A	GRSF1_uc011caz.1_Missense_Mutation_p.P12A|GRSF1_uc003hfs.2_5'UTR	NM_002092	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1 isoform 1	130	RRM 1.				mRNA polyadenylation		mRNA binding|nucleotide binding				0		all_hematologic(202;0.21)	Lung(101;0.235)			GGGGGTGGTGGAAGGTCTTCC	0.413													6	54	---	---	---	---	PASS
PRKG2	5593	broad.mit.edu	37	4	82065400	82065400	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82065400T>G	uc003hmh.2	-	9	1253	c.1239A>C	c.(1237-1239)GAA>GAC	p.E413D	PRKG2_uc011ccf.1_5'UTR|PRKG2_uc011ccg.1_5'UTR|PRKG2_uc011cch.1_Missense_Mutation_p.E413D	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	413	cGMP 2.				platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						CATGTCTTTTTTCATCATCAC	0.423													9	46	---	---	---	---	PASS
NKX6-1	4825	broad.mit.edu	37	4	85414579	85414579	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85414579C>A	uc003hpa.1	-	3	973	c.967G>T	c.(967-969)GAC>TAC	p.D323Y		NM_006168	NP_006159	P78426	NKX61_HUMAN	NK6 transcription factor related, locus 1	323	Involved in DNA-binding (By similarity).				detection of glucose|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|type B pancreatic cell maturation	nucleus					0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		TAGTCGTCGTCCTCTTCCTCG	0.607													14	91	---	---	---	---	PASS
GRID2	2895	broad.mit.edu	37	4	94693265	94693265	+	Silent	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94693265T>A	uc011cdt.1	+	16	2898	c.2640T>A	c.(2638-2640)CGT>CGA	p.R880R	GRID2_uc011cdu.1_Silent_p.R785R	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	880	Cytoplasmic (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	TCCATAGACGTGTAAATAGCT	0.423													19	81	---	---	---	---	PASS
USP38	84640	broad.mit.edu	37	4	144109067	144109067	+	Silent	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144109067T>C	uc003ijb.2	+	2	1305	c.771T>C	c.(769-771)ACT>ACC	p.T257T	USP38_uc003ija.3_Silent_p.T257T|USP38_uc003ijc.2_RNA	NM_032557	NP_115946	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	257					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)					GGAGCCTTACTACGGATCCAA	0.403													6	34	---	---	---	---	PASS
ZNF827	152485	broad.mit.edu	37	4	146770699	146770699	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770699C>A	uc003ikn.2	-	6	2044	c.1996G>T	c.(1996-1998)GAA>TAA	p.E666*	ZNF827_uc003ikm.2_Nonsense_Mutation_p.E666*|ZNF827_uc010iox.2_Nonsense_Mutation_p.E316*	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	666					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					ATCTGTGTTTCCTTGTAGCTT	0.443													25	93	---	---	---	---	PASS
KIAA0922	23240	broad.mit.edu	37	4	154548808	154548808	+	Silent	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154548808T>A	uc003inm.3	+	31	4225	c.4173T>A	c.(4171-4173)CCT>CCA	p.P1391P	KIAA0922_uc010ipp.2_Silent_p.P1392P|KIAA0922_uc010ipq.2_Silent_p.P1160P	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	1391	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				CCAGCCTTCCTGCCGGGCCCA	0.532													5	27	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187178488	187178488	+	Missense_Mutation	SNP	G	A	A	rs150832692		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187178488G>A	uc003iyy.2	+	14	1765	c.1694G>A	c.(1693-1695)GGC>GAC	p.G565D	KLKB1_uc011clc.1_Missense_Mutation_p.G363D|KLKB1_uc011cld.1_Intron	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	565	Peptidase S1.				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)		GTCTGTGCTGGCTATAAAGAA	0.318													11	79	---	---	---	---	PASS
ZNF622	90441	broad.mit.edu	37	5	16451871	16451871	+	Silent	SNP	T	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16451871T>G	uc003jfq.2	-	6	1449	c.1329A>C	c.(1327-1329)CGA>CGC	p.R443R		NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622	443						cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1						ACTGCATGTCTCGCTCTCGCA	0.433													38	78	---	---	---	---	PASS
SLC45A2	51151	broad.mit.edu	37	5	33982512	33982512	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33982512T>C	uc003jid.2	-	2	483	c.391A>G	c.(391-393)ATT>GTT	p.I131V	SLC45A2_uc003jie.2_Missense_Mutation_p.I131V|SLC45A2_uc003jif.3_Missense_Mutation_p.I131V|SLC45A2_uc011coe.1_Missense_Mutation_p.I131V	NM_016180	NP_057264	Q9UMX9	S45A2_HUMAN	membrane-associated transporter protein isoform	131	Helical; Name=3; (Potential).				melanin biosynthetic process|response to stimulus|transmembrane transport|visual perception	integral to membrane|melanosome membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						GGGTTAGCAATCAAAGCTAAA	0.398													7	28	---	---	---	---	PASS
PCYOX1L	78991	broad.mit.edu	37	5	148745559	148745559	+	Silent	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148745559C>G	uc003lqk.2	+	4	587	c.525C>G	c.(523-525)CTC>CTG	p.L175L	PCYOX1L_uc003lql.2_Silent_p.L158L|PCYOX1L_uc010jgz.2_Intron|PCYOX1L_uc003lqm.2_Silent_p.L57L|PCYOX1L_uc003lqn.2_Silent_p.L85L	NM_024028	NP_076933	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like precursor	175					prenylcysteine catabolic process	extracellular region	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGCTGCTCTACTCACTGG	0.547													14	38	---	---	---	---	PASS
ANXA6	309	broad.mit.edu	37	5	150505989	150505989	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150505989C>A	uc003ltl.1	-	14	1182	c.1030G>T	c.(1030-1032)GAA>TAA	p.E344*	ANXA6_uc011dcp.1_Nonsense_Mutation_p.E312*|ANXA6_uc003ltm.1_Nonsense_Mutation_p.E344*|ANXA6_uc003ltn.1_Nonsense_Mutation_p.E137*|ANXA6_uc003lto.1_Intron	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1	344						melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCACTAAGTTCCCACATCTGA	0.572											OREG0016946	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	11	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169474568	169474568	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169474568G>C	uc003maf.2	+	40	4101	c.4021G>C	c.(4021-4023)GAC>CAC	p.D1341H	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Missense_Mutation_p.D833H	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1341	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCCCAAACCAGACTACTTTGC	0.507													9	29	---	---	---	---	PASS
FBXW11	23291	broad.mit.edu	37	5	171305017	171305017	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171305017C>A	uc003mbm.1	-	7	1277	c.906G>T	c.(904-906)GTG>GTT	p.V302V	FBXW11_uc011dey.1_Silent_p.V270V|FBXW11_uc003mbl.1_Silent_p.V289V|FBXW11_uc003mbn.1_Silent_p.V268V	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform	302	WD 2.				cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCACTCACCTCACCGTAGAAT	0.458													13	32	---	---	---	---	PASS
PHACTR1	221692	broad.mit.edu	37	6	13053641	13053641	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13053641G>A	uc010jpc.2	+	5	627	c.295G>A	c.(295-297)GTC>ATC	p.V99I	PHACTR1_uc011dir.1_Missense_Mutation_p.V99I|PHACTR1_uc003nag.1_Missense_Mutation_p.V99I|PHACTR1_uc003nah.1_Missense_Mutation_p.V99I	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	99						cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			TGACTCCCTCGTCCCAGGCAC	0.478													8	19	---	---	---	---	PASS
BTN2A2	10385	broad.mit.edu	37	6	26385438	26385438	+	Missense_Mutation	SNP	G	A	A	rs144702884	byFrequency	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26385438G>A	uc003nhq.2	+	3	376	c.290G>A	c.(289-291)CGG>CAG	p.R97Q	BTN2A2_uc011dkf.1_Intron|BTN2A2_uc011dkg.1_Missense_Mutation_p.R97Q|BTN2A2_uc003nhr.2_Intron|BTN2A2_uc011dkh.1_Intron|BTN2A2_uc003nhs.2_Missense_Mutation_p.R97Q|BTN2A2_uc003nht.2_Missense_Mutation_p.R97Q	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a	97	Extracellular (Potential).|Ig-like V-type.				negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						GAGGAGTACCGGGGAAGAATC	0.552													22	64	---	---	---	---	PASS
HIST1H2AH	85235	broad.mit.edu	37	6	27115008	27115008	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27115008T>G	uc003niz.2	+	1	101	c.101T>G	c.(100-102)CTG>CGG	p.L34R	HIST1H2BK_uc003nix.1_5'Flank|hsa-mir-3143|MI0014167_5'Flank	NM_080596	NP_542163	Q96KK5	H2A1H_HUMAN	histone cluster 1, H2ah	34					nucleosome assembly	nucleosome|nucleus	DNA binding				0						GTGCACCGCCTGCTCCGCAAG	0.652													10	47	---	---	---	---	PASS
PGBD1	84547	broad.mit.edu	37	6	28268508	28268508	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28268508G>T	uc003nky.2	+	7	1247	c.877G>T	c.(877-879)GCA>TCA	p.A293S	PGBD1_uc003nkz.2_Missense_Mutation_p.A293S	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	293					viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4						CAGAGAGTGTGCACCCCAGAT	0.423													6	62	---	---	---	---	PASS
OR2W1	26692	broad.mit.edu	37	6	29012694	29012694	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29012694C>A	uc003nlw.2	-	1	259	c.259G>T	c.(259-261)GGA>TGA	p.G87*		NM_030903	NP_112165	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W,	87	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3						TTATCAGGTCCCCACAAGTTG	0.438													8	48	---	---	---	---	PASS
C6orf27	80737	broad.mit.edu	37	6	31734925	31734925	+	Intron	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31734925A>G	uc011dog.1	-						C6orf27_uc003nxd.2_Intron	NM_025258	NP_079534	Q9Y334	G7C_HUMAN	G7c protein precursor							extracellular region				ovary(3)	3						GGCTCAGGGAATAAATGTACC	0.393													2	6	---	---	---	---	PASS
C6orf10	10665	broad.mit.edu	37	6	32261379	32261379	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32261379C>T	uc011dpy.1	-	12	1244	c.1071G>A	c.(1069-1071)GGG>GGA	p.G357G	C6orf10_uc011dpx.1_Silent_p.G139G	NM_006781	NP_006772	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	357						integral to membrane				skin(1)	1						GTACAACCAACCCACTCTTCG	0.478													36	87	---	---	---	---	PASS
FTSJD2	23070	broad.mit.edu	37	6	37420895	37420895	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37420895C>G	uc003ons.2	+	7	935	c.682C>G	c.(682-684)CGA>GGA	p.R228G	FTSJD2_uc010jwu.2_Intron	NM_015050	NP_055865	Q8N1G2	MTR1_HUMAN	FtsJ methyltransferase domain containing 2	228					mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						TGAGATGATCCGAGGAGTCTT	0.507													15	74	---	---	---	---	PASS
C6orf154	221424	broad.mit.edu	37	6	43475056	43475056	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43475056G>T	uc003ovk.1	-						C6orf154_uc003ovj.1_Intron	NM_001012974	NP_001012992	Q5JTD7	CF154_HUMAN	hypothetical protein LOC221424												0	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			TCTGTGGAAGGGCAGAGAAGT	0.562											OREG0017453	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	36	---	---	---	---	PASS
CENPQ	55166	broad.mit.edu	37	6	49459937	49459937	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49459937G>T	uc003ozh.1	+	9	845	c.756G>T	c.(754-756)AAG>AAT	p.K252N		NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	252					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					CACAGATGAAGAGCATGTCAA	0.323													7	30	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70909429	70909429	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70909429C>G	uc003pfc.1	+	49	3329	c.3212C>G	c.(3211-3213)CCT>CGT	p.P1071R		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	1071	Triple-helical region 6 (COL6).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						CCAGGAGACCCTGGACCCCAA	0.468													17	24	---	---	---	---	PASS
KIAA1009	22832	broad.mit.edu	37	6	84910599	84910599	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84910599G>C	uc010kbp.2	-	9	840	c.743C>G	c.(742-744)TCT>TGT	p.S248C	KIAA1009_uc003pkj.3_Missense_Mutation_p.S172C|KIAA1009_uc003pkk.2_Missense_Mutation_p.S248C	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	248					cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		CTCTGCAACAGAGTCTAATGA	0.333													17	82	---	---	---	---	PASS
HACE1	57531	broad.mit.edu	37	6	105259227	105259227	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105259227C>A	uc003pqu.1	-	7	853	c.576G>T	c.(574-576)AGG>AGT	p.R192S	HACE1_uc010kcy.1_5'UTR|HACE1_uc010kcz.1_Missense_Mutation_p.R192S	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	192	ANK 4.				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)		ATACATTTGGCCTGTTAATAT	0.313													17	61	---	---	---	---	PASS
AKD1	221264	broad.mit.edu	37	6	109867265	109867265	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109867265C>T	uc003ptn.2	-	26	3107	c.3030G>A	c.(3028-3030)CAG>CAA	p.Q1010Q	AKD1_uc011eat.1_Silent_p.Q89Q	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	1010					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						TTTCTGCCAACTGTCTTCCAC	0.448													12	89	---	---	---	---	PASS
C6orf204	387119	broad.mit.edu	37	6	118791756	118791756	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118791756C>T	uc003pxz.1	-	11	2554	c.1966G>A	c.(1966-1968)GAA>AAA	p.E656K		NM_001042475	NP_001035940	Q5SZL2	CF204_HUMAN	chromosome 6 open reading frame 204 isoform a	656	Potential.					centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)		TCCAGCTCTTCCATCATCTTT	0.318													13	34	---	---	---	---	PASS
C6orf204	387119	broad.mit.edu	37	6	118887127	118887127	+	Silent	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118887127T>C	uc003pxz.1	-	3	1173	c.585A>G	c.(583-585)CAA>CAG	p.Q195Q	C6orf204_uc003pya.1_Silent_p.Q198Q|C6orf204_uc003pyb.2_Silent_p.Q195Q|C6orf204_uc011ebj.1_Silent_p.Q93Q|C6orf204_uc003pyc.2_Silent_p.Q198Q|C6orf204_uc011ebl.1_Silent_p.Q93Q	NM_001042475	NP_001035940	Q5SZL2	CF204_HUMAN	chromosome 6 open reading frame 204 isoform a	195						centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)		TTGTCCTCAGTTGTGATGTTA	0.453													15	53	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165842174	165842174	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165842174G>A	uc003qun.2	-	11	1038	c.797C>T	c.(796-798)GCA>GTA	p.A266V	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Missense_Mutation_p.A196V|PDE10A_uc003quo.2_Missense_Mutation_p.A276V	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	266	GAF 2.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	AGAATCTATTGCAACTATGTT	0.308													7	19	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168311987	168311987	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168311987A>G	uc003qwd.2	+	15	1994	c.1852A>G	c.(1852-1854)ATT>GTT	p.I618V	MLLT4_uc003qwb.1_Missense_Mutation_p.I603V|MLLT4_uc003qwc.1_Missense_Mutation_p.I619V|MLLT4_uc003qwf.2_Missense_Mutation_p.I304V|MLLT4_uc003qwg.1_5'Flank	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	619					adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TTTGTCTGCCATTATAAATTA	0.328			T	MLL	AL								44	75	---	---	---	---	PASS
MAD1L1	8379	broad.mit.edu	37	7	2269698	2269698	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2269698C>A	uc003slh.1	-	3	337	c.71G>T	c.(70-72)CGT>CTT	p.R24L	MAD1L1_uc003slf.1_Missense_Mutation_p.R24L|MAD1L1_uc003slg.1_Missense_Mutation_p.R24L|MAD1L1_uc010ksh.1_Missense_Mutation_p.R24L|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Missense_Mutation_p.R24L|MAD1L1_uc010ksj.2_Missense_Mutation_p.R24L	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	24					cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		TCCCTCCACACGCTGAGAGAT	0.537													9	12	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21744181	21744181	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21744181G>C	uc003svc.2	+	39	6455	c.6424G>C	c.(6424-6426)GAA>CAA	p.E2142Q		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2142					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GCTGCACTTTGAACAGATGGT	0.537									Kartagener_syndrome				18	37	---	---	---	---	PASS
ZPBP	11055	broad.mit.edu	37	7	50057903	50057903	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50057903A>T	uc003tou.2	-	6	786	c.716T>A	c.(715-717)CTA>CAA	p.L239Q	ZPBP_uc011kci.1_Missense_Mutation_p.L165Q|ZPBP_uc010kyw.2_Missense_Mutation_p.L238Q	NM_007009	NP_008940	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein isoform 1	239					binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)					TTCAGTGTCTAGAGATGAAAC	0.299													4	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	100549773	100549773	+	5'Flank	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100549773C>G	uc003uxk.1	+						uc003uxl.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		CTCCACCCACCGTGTTGGTCT	0.527													19	125	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100686315	100686315	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100686315G>A	uc003uxp.1	+	3	11671	c.11618G>A	c.(11617-11619)AGC>AAC	p.S3873N	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3873	Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AGTGAAAGAAGCACTCCATTA	0.473													25	69	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101847741	101847741	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101847741A>T	uc003uyx.3	+	19	3016	c.2978A>T	c.(2977-2979)CAG>CTG	p.Q993L	CUX1_uc003uys.3_Missense_Mutation_p.Q1004L|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	993	CUT 2.				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						AAGCTGACGCAGAAAGGCCGA	0.632													22	56	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122047684	122047684	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122047684C>A	uc010lkp.2	-	19	2819	c.2656G>T	c.(2656-2658)GAT>TAT	p.D886Y	CADPS2_uc011knx.1_Missense_Mutation_p.D261Y|CADPS2_uc003vkg.3_Missense_Mutation_p.D580Y|CADPS2_uc010lkq.2_Missense_Mutation_p.D880Y	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	886	Interaction with DRD2.|MHD1.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						GTGTCCATATCCACTGTAAAT	0.403													9	20	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700549	136700549	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700549G>T	uc003vtf.1	+	4	1560	c.937G>T	c.(937-939)GGC>TGC	p.G313C	CHRM2_uc003vtg.1_Missense_Mutation_p.G313C|CHRM2_uc003vtj.1_Missense_Mutation_p.G313C|CHRM2_uc003vtk.1_Missense_Mutation_p.G313C|CHRM2_uc003vtl.1_Missense_Mutation_p.G313C|CHRM2_uc003vtm.1_Missense_Mutation_p.G313C|CHRM2_uc003vti.1_Missense_Mutation_p.G313C|CHRM2_uc003vto.1_Missense_Mutation_p.G313C|CHRM2_uc003vtn.1_Missense_Mutation_p.G313C|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	313	Cytoplasmic (By similarity).				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)	CACTTCCCTGGGCCATTCCAA	0.463													34	58	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142378620	142378620	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142378620G>T	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc011ksg.1_Intron|uc003waa.1_Missense_Mutation_p.R4S					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		TGACTATCAGGCTCCTCTGCT	0.463													6	7	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	144707409	144707409	+	IGR	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144707409C>T								TPK1 (174263 upstream) : None (None downstream)																							GTCGTGAAAACAGAAGTTGTG	0.418													50	102	---	---	---	---	PASS
INSIG1	3638	broad.mit.edu	37	7	155099999	155099999	+	3'UTR	SNP	T	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155099999T>G	uc003wly.2	+	6					INSIG1_uc011kvu.1_Missense_Mutation_p.I156M|INSIG1_uc003wlz.2_3'UTR	NM_005542	NP_005533	O15503	INSI1_HUMAN	insulin induced gene 1 isoform 1						cell proliferation|ER-nuclear sterol response pathway	endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AACCACCGATTCTGAGAGCAA	0.348													15	42	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3224705	3224705	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3224705C>T	uc011kwk.1	-	20	3357	c.2967G>A	c.(2965-2967)GAG>GAA	p.E989E	CSMD1_uc011kwj.1_Silent_p.E381E|CSMD1_uc003wqe.2_Silent_p.E145E	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	989	Extracellular (Potential).|CUB 6.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AACTTCCATCCTCTGTGATCA	0.468													4	40	---	---	---	---	PASS
FUT10	84750	broad.mit.edu	37	8	33230332	33230332	+	Intron	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33230332G>A	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron	NM_032664	NP_116053	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CCTGCAGGAAGAGAAAAGAGA	0.443													19	32	---	---	---	---	PASS
ANK1	286	broad.mit.edu	37	8	41554238	41554238	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41554238C>T	uc003xok.2	-	25	2775	c.2691G>A	c.(2689-2691)GAG>GAA	p.E897E	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.E213E|ANK1_uc003xoi.2_Silent_p.E897E|ANK1_uc003xoj.2_Silent_p.E897E|ANK1_uc003xol.2_Silent_p.E897E|ANK1_uc003xom.2_Silent_p.E938E	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	897					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGTCTGAGGTCTCGGTGGCCG	0.647													10	16	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61654299	61654299	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61654299C>T	uc003xue.2	+	2	785	c.308C>T	c.(307-309)TCG>TTG	p.S103L		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	103					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TCTCCGCACTCGCAGTATCAC	0.547													15	26	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86050585	86050585	+	Silent	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86050585G>C	uc003ycw.2	+	17	2869	c.2715G>C	c.(2713-2715)CGG>CGC	p.R905R	LRRCC1_uc003ycx.2_Silent_p.R812R|LRRCC1_uc003ycy.2_Silent_p.R885R	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	905					cell division|mitosis	centriole|nucleus					0						CACTGAATCGGAAGTGGCATG	0.289													18	53	---	---	---	---	PASS
AZIN1	51582	broad.mit.edu	37	8	103848592	103848592	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103848592T>C	uc003ykx.2	-	7	1218	c.476A>G	c.(475-477)GAT>GGT	p.D159G	AZIN1_uc003yky.2_Missense_Mutation_p.D159G	NM_015878	NP_056962	O14977	AZIN1_HUMAN	ornithine decarboxylase antizyme inhibitor	159					polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	catalytic activity|protein binding				0	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			TCCAATATTATCTTCTGTTGC	0.413													22	77	---	---	---	---	PASS
RLN2	6019	broad.mit.edu	37	9	5300281	5300281	+	Silent	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5300281G>C	uc003zja.1	-	2	375	c.375C>G	c.(373-375)CTC>CTG	p.L125L	RLN2_uc003ziz.1_3'UTR	NM_134441	NP_604390	P04090	REL2_HUMAN	relaxin 2 isoform 1 preproprotein	125					female pregnancy	extracellular region	hormone activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)		ATTCTTCAAAGAGAAGACTGG	0.398													13	45	---	---	---	---	PASS
OR13F1	138805	broad.mit.edu	37	9	107267037	107267037	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107267037C>A	uc011lvm.1	+	1	494	c.494C>A	c.(493-495)CCA>CAA	p.P165Q		NM_001004485	NP_001004485	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)|skin(1)	3						TCTGTGCTGCCACTGTCTCTC	0.473													17	32	---	---	---	---	PASS
TOR1B	27348	broad.mit.edu	37	9	132565604	132565604	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132565604C>T	uc004byk.1	+	1	173	c.113C>T	c.(112-114)TCG>TTG	p.S38L		NM_014506	NP_055321	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B) precursor	38					chaperone mediated protein folding requiring cofactor|response to unfolded protein	endoplasmic reticulum lumen	ATP binding|nucleoside-triphosphatase activity|unfolded protein binding				0		Ovarian(14;0.0586)				GGGGCCGCGTCGGCCATCACC	0.736													4	4	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30336572	30336572	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30336572C>T	uc001iux.2	-	1	229	c.170G>A	c.(169-171)CGT>CAT	p.R57H	KIAA1462_uc001iuy.2_Missense_Mutation_p.R57H|KIAA1462_uc001iuz.2_5'UTR|KIAA1462_uc009xle.1_Missense_Mutation_p.R57H	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	57										ovary(4)	4						GGACGTCTTACGATGTGCGAG	0.662													12	38	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31809073	31809073	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31809073C>T	uc001ivs.3	+	7	873	c.810C>T	c.(808-810)TGC>TGT	p.C270C	ZEB1_uc001ivr.3_Silent_p.C52C|ZEB1_uc010qee.1_Silent_p.C52C|ZEB1_uc010qef.1_Silent_p.C52C|ZEB1_uc009xlj.1_Silent_p.C196C|ZEB1_uc010qeg.1_Silent_p.C129C|ZEB1_uc009xlk.1_Silent_p.C52C|ZEB1_uc001ivt.3_Silent_p.C52C|ZEB1_uc001ivu.3_Silent_p.C271C|ZEB1_uc001ivv.3_Silent_p.C250C|ZEB1_uc010qeh.1_Silent_p.C203C|ZEB1_uc009xlo.1_Silent_p.C253C|ZEB1_uc009xlp.2_Silent_p.C254C	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	270	C2H2-type 4; atypical.				cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				CATATGAATGCCCAAACTGCA	0.358													8	19	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37431132	37431132	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37431132C>T	uc001iza.1	+	7	1238	c.1139C>T	c.(1138-1140)TCT>TTT	p.S380F		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	436						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						AGAGTAACATCTAATAAAACT	0.388													27	64	---	---	---	---	PASS
FRMPD2	143162	broad.mit.edu	37	10	49431303	49431303	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49431303G>C	uc001jgi.2	-	11	1286	c.1179C>G	c.(1177-1179)TTC>TTG	p.F393L	FRMPD2_uc001jgh.2_Missense_Mutation_p.F362L|FRMPD2_uc001jgj.2_Missense_Mutation_p.F371L	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3	393	FERM.				tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		CCAGGAAAAAGAACTCTTTGC	0.478													8	36	---	---	---	---	PASS
UNC5B	219699	broad.mit.edu	37	10	73047494	73047494	+	Silent	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73047494G>A	uc001jro.2	+	6	1318	c.873G>A	c.(871-873)CAG>CAA	p.Q291Q	UNC5B_uc001jrp.2_Silent_p.Q291Q	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	291	TSP type-1 1.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3						AGGCATTCCAGAAGACCGCCT	0.657													14	28	---	---	---	---	PASS
TUBGCP2	10844	broad.mit.edu	37	10	135095751	135095751	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135095751C>A	uc001lmg.1	-	16	2742	c.2385G>T	c.(2383-2385)CGG>CGT	p.R795R	TUBGCP2_uc001lmf.1_Silent_p.R388R|TUBGCP2_uc010qvc.1_Silent_p.R823R|TUBGCP2_uc009ybk.1_Silent_p.R818R|TUBGCP2_uc010qvd.1_Silent_p.R665R|TUBGCP2_uc001lmh.1_RNA	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	795					G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		CCTTCCGGGCCCGCTCCTCGG	0.667													9	9	---	---	---	---	PASS
OR51S1	119692	broad.mit.edu	37	11	4869932	4869932	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4869932G>C	uc010qyo.1	-	1	507	c.507C>G	c.(505-507)TTC>TTG	p.F169L		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	169	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGGCCAGCAGGAATGGCAGGG	0.552													21	76	---	---	---	---	PASS
SYT9	143425	broad.mit.edu	37	11	7437270	7437270	+	Intron	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7437270C>A	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		GCTTTCTCAACAGGACAACGT	0.478													15	81	---	---	---	---	PASS
TEAD1	7003	broad.mit.edu	37	11	12785988	12785988	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12785988G>T	uc001mkj.3	+							NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TATGGTAAGTGGCCTGGAACA	0.478													25	52	---	---	---	---	PASS
CSRP3	8048	broad.mit.edu	37	11	19207795	19207795	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19207795A>T	uc001mpk.2	-	4	499	c.382T>A	c.(382-384)TAT>AAT	p.Y128N		NM_003476	NP_003467	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3	128	LIM zinc-binding 2.				cell differentiation|skeletal muscle tissue development	cytoskeleton|nucleus	protein binding|zinc ion binding				0						TCAGCAGCATAGACTGACTTG	0.527													9	56	---	---	---	---	PASS
LRP4	4038	broad.mit.edu	37	11	46893077	46893077	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46893077T>C	uc001ndn.3	-	31	4837	c.4691A>G	c.(4690-4692)CAG>CGG	p.Q1564R	uc001ndl.2_Intron	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	1564	Extracellular (Potential).|LDL-receptor class B 19.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		AGCCAGTACCTGTGTGAGGGC	0.542													3	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	56143187	56143187	+	IGR	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56143187C>A								OR8J1 (14516 upstream) : OR5R1 (41549 downstream)																							CCTCTTTGTGCTATTCTTATC	0.458													34	96	---	---	---	---	PASS
MS4A3	932	broad.mit.edu	37	11	59828788	59828788	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59828788G>A	uc001nom.2	+	2	283	c.155G>A	c.(154-156)GGG>GAG	p.G52E	MS4A3_uc001non.2_Missense_Mutation_p.G52E|MS4A3_uc001noo.2_Intron	NM_006138	NP_006129	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member	52	Helical; (Potential).					endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)|skin(1)	3		all_epithelial(135;0.245)				CAAGTTCTTGGGGTAAGTCAG	0.318													17	68	---	---	---	---	PASS
MS4A4A	51338	broad.mit.edu	37	11	60059779	60059779	+	Silent	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60059779A>T	uc001noz.2	+	2	133	c.123A>T	c.(121-123)GGA>GGT	p.G41G	MS4A4A_uc001npa.2_Silent_p.G22G|MS4A4A_uc001npb.2_Silent_p.G22G|MS4A4A_uc001npc.2_Silent_p.G22G	NM_148975	NP_683876	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member	41	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						CCCAGCTGGGAAACATGGCTG	0.488													10	37	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60183397	60183397	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60183397A>G	uc001npj.2	+	5	1521	c.956A>G	c.(955-957)GAC>GGC	p.D319G	MS4A14_uc001npi.2_Missense_Mutation_p.D207G|MS4A14_uc001npn.2_Missense_Mutation_p.D57G|MS4A14_uc001npk.2_Missense_Mutation_p.D302G|MS4A14_uc001npl.2_Missense_Mutation_p.D57G|MS4A14_uc001npm.2_Missense_Mutation_p.D57G	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	319						integral to membrane	receptor activity			breast(1)	1						TCACCTGAAGACTTGCCATCC	0.453													13	64	---	---	---	---	PASS
CAPN1	823	broad.mit.edu	37	11	64977857	64977857	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64977857G>A	uc009yqd.1	+	20	2104	c.1993G>A	c.(1993-1995)GAG>AAG	p.E665K	CAPN1_uc001odf.1_Missense_Mutation_p.E665K|CAPN1_uc001odg.1_Missense_Mutation_p.E665K|CAPN1_uc010roa.1_Missense_Mutation_p.E406K	NM_005186	NP_005177	P07384	CAN1_HUMAN	calpain 1, large subunit	665	Domain IV.				positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CCGCTACTCGGAGCCCGACCT	0.592													3	15	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78380075	78380075	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78380075G>T	uc001ozl.3	-	32	7778	c.7315C>A	c.(7315-7317)CTT>ATT	p.L2439I	ODZ4_uc001ozk.3_Missense_Mutation_p.L664I|ODZ4_uc009yvb.1_Missense_Mutation_p.L1023I	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	2439	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						CTGCTACTAAGGTGCTTCCAC	0.507													10	40	---	---	---	---	PASS
CASP1	834	broad.mit.edu	37	11	104899950	104899950	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104899950C>A	uc010rve.1	-	7	924	c.907G>T	c.(907-909)GGA>TGA	p.G303*	CASP1_uc001pig.2_Nonsense_Mutation_p.G210*|CASP1_uc001pik.2_Nonsense_Mutation_p.G266*|CASP1_uc010rvf.1_Nonsense_Mutation_p.G210*|CASP1_uc010rvg.1_Nonsense_Mutation_p.G282*|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Nonsense_Mutation_p.G303*|CASP1_uc009yxi.2_Nonsense_Mutation_p.G282*|CASP1_uc010rvj.1_Nonsense_Mutation_p.G303*|CASP1_uc009yxj.2_Nonsense_Mutation_p.G148*|CASP1_uc010rvk.1_Nonsense_Mutation_p.G264*	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor	303					cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	GATAGGTTTCCAGAAACTCCT	0.418													7	23	---	---	---	---	PASS
CD163L1	283316	broad.mit.edu	37	12	7527242	7527242	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7527242C>T	uc001qsy.2	-	13	3231	c.3205G>A	c.(3205-3207)GAT>AAT	p.D1069N	CD163L1_uc010sge.1_Missense_Mutation_p.D1079N	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	1069	SRCR 10.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity	p.D1069fs*27(1)		ovary(8)|skin(2)|central_nervous_system(1)	11						ACGTGGGCATCGCTCAGGTCC	0.617											OREG0021653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	47	---	---	---	---	PASS
KLRG1	10219	broad.mit.edu	37	12	9147764	9147764	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9147764G>A	uc001qvh.2	+	3	248	c.237G>A	c.(235-237)TGG>TGA	p.W79*	KLRG1_uc001qvg.2_Nonsense_Mutation_p.W79*	NM_005810	NP_005801	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G,	79	Extracellular (Potential).				cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1						CAGACCGCTGGATGAAATATG	0.483													5	39	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546519	11546519	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546519G>C	uc010shk.1	-	3	528	c.493C>G	c.(493-495)CAA>GAA	p.Q165E		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			TTGTCTCCTTGTGGGGGTGGT	0.607													27	261	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15654796	15654796	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15654796A>C	uc001rcv.1	+	5	1078	c.904A>C	c.(904-906)AGT>CGT	p.S302R	PTPRO_uc001rcw.1_Missense_Mutation_p.S302R|PTPRO_uc001rcu.1_Missense_Mutation_p.S302R	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	302	Fibronectin type-III 3.|Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				TTGGTGGGACAGTGCATCTGC	0.443													7	25	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21242966	21242966	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242966C>A	uc010sil.1	+	16	2238	c.2173C>A	c.(2173-2175)CAA>AAA	p.Q725K	LST-3TM12_uc010sim.1_Missense_Mutation_p.Q664K|LST-3TM12_uc010sin.1_Missense_Mutation_p.Q617K			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					AAATGAAAGACAAGTAATGGA	0.313													8	28	---	---	---	---	PASS
PFKM	5213	broad.mit.edu	37	12	48535133	48535133	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48535133G>C	uc001rrc.2	+	15	1551	c.1381G>C	c.(1381-1383)GGC>CGC	p.G461R	PFKM_uc001rra.1_Missense_Mutation_p.G146R|PFKM_uc001rrb.1_Missense_Mutation_p.G532R|PFKM_uc001rrd.2_Missense_Mutation_p.G146R|PFKM_uc001rre.1_Missense_Mutation_p.G461R|PFKM_uc001rrg.1_Missense_Mutation_p.G430R	NM_000289	NP_000280	P08237	K6PF_HUMAN	phosphofructokinase, muscle	461					fructose 6-phosphate metabolic process|glycolysis|muscle cell homeostasis	6-phosphofructokinase complex|apical plasma membrane	6-phosphofructokinase activity|ATP binding|identical protein binding|kinase binding|metal ion binding|protein C-terminus binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4						GGGCTGGACTGGCCAAGGTGG	0.537													20	60	---	---	---	---	PASS
NCKAP5L	57701	broad.mit.edu	37	12	50186238	50186238	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50186238C>G	uc009zlk.2	-	12	3985	c.3783G>C	c.(3781-3783)AGG>AGC	p.R1261S	NCKAP5L_uc001rvc.3_Missense_Mutation_p.R465S|NCKAP5L_uc001rvb.2_Missense_Mutation_p.R854S	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1257	Pro-rich.									central_nervous_system(1)	1						CCATGGGGGTCCTGGGCAGCC	0.612													4	15	---	---	---	---	PASS
KRT81	3887	broad.mit.edu	37	12	52682248	52682248	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52682248G>T	uc001sab.2	-						KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT81_uc001sac.2_Intron	NM_002281	NP_002272	Q14533	KRT81_HUMAN	keratin, hair, basic, 1							keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATCCTGGAAAGGTGGGGAGTG	0.602													5	160	---	---	---	---	PASS
SUOX	6821	broad.mit.edu	37	12	56397818	56397818	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56397818C>T	uc001six.2	+	6	971	c.645C>T	c.(643-645)TTC>TTT	p.F215F	SUOX_uc001siy.2_Silent_p.F215F|SUOX_uc001siz.2_Silent_p.F215F|SUOX_uc001sja.2_Silent_p.F215F	NM_000456	NP_000447	P51687	SUOX_HUMAN	sulfite oxidase precursor	215	Molybdenum-pterin domain (By similarity).|Molybdenum-pterin-binding (By similarity).					mitochondrial intermembrane space	electron carrier activity|molybdenum ion binding|sulfite oxidase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			CTATCTTCTTCACCCGGAACC	0.552													17	69	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56722284	56722284	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56722284G>A	uc001skx.2	-	3	797	c.424C>T	c.(424-426)CGT>TGT	p.R142C	PAN2_uc001skz.2_Missense_Mutation_p.R142C|PAN2_uc001sky.2_Missense_Mutation_p.R142C	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	142					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						AGGCCCCCACGGGCCATATAC	0.488													26	83	---	---	---	---	PASS
CRADD	8738	broad.mit.edu	37	12	94072576	94072576	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94072576T>A	uc001tda.2	+	2	130	c.26T>A	c.(25-27)CTC>CAC	p.L9H	CRADD_uc010sur.1_Missense_Mutation_p.L9H|CRADD_uc010sus.1_RNA	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with	9	CARD.				apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						AAACAAGTACTCCGCTCACTT	0.488													17	34	---	---	---	---	PASS
APAF1	317	broad.mit.edu	37	12	99061383	99061383	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99061383C>G	uc001tfz.2	+	10	2032	c.1455C>G	c.(1453-1455)AAC>AAG	p.N485K	APAF1_uc001tfy.2_Missense_Mutation_p.N474K|APAF1_uc001tga.2_Missense_Mutation_p.N474K|APAF1_uc001tgb.2_Missense_Mutation_p.N485K|APAF1_uc001tgc.2_Intron	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	485					activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	ATTGGTACAACTTTCTGGCCT	0.393													16	49	---	---	---	---	PASS
SLC5A8	160728	broad.mit.edu	37	12	101555843	101555843	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101555843C>G	uc001thz.3	-	13	1929	c.1539G>C	c.(1537-1539)ATG>ATC	p.M513I		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	solute carrier family 5 (iodide transporter),	513	Extracellular (Potential).				apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0						ACCAGTTATCCATCAGTGGAG	0.388													27	67	---	---	---	---	PASS
C12orf43	64897	broad.mit.edu	37	12	121442168	121442168	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121442168A>C	uc001tzh.1	-	6	600	c.577T>G	c.(577-579)TTG>GTG	p.L193V	C12orf43_uc009zxa.1_Missense_Mutation_p.L224V|C12orf43_uc010szo.1_Missense_Mutation_p.L152V|C12orf43_uc010szp.1_Missense_Mutation_p.L183V|C12orf43_uc001tzi.1_Missense_Mutation_p.L194V	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897	193	Lys-rich.										0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCTTTTTCAACTTCCTTTTC	0.587													19	50	---	---	---	---	PASS
MPHOSPH8	54737	broad.mit.edu	37	13	20224398	20224398	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20224398C>T	uc001umh.2	+	5	1583	c.1574C>T	c.(1573-1575)TCA>TTA	p.S525L	MPHOSPH8_uc001umg.2_Missense_Mutation_p.S525L|MPHOSPH8_uc001umi.2_Missense_Mutation_p.S222L	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	525					cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		GATGAGAATTCAGGTGAGTTT	0.398													42	56	---	---	---	---	PASS
PCDH17	27253	broad.mit.edu	37	13	58299048	58299048	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58299048T>A	uc001vhq.1	+	4	3992	c.3100T>A	c.(3100-3102)TCA>ACA	p.S1034T	PCDH17_uc010aec.1_Missense_Mutation_p.S1033T|PCDH17_uc001vhr.1_Missense_Mutation_p.S123T	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	1034	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		AGAGGTCCCCTCAGCATCAAG	0.522													28	49	---	---	---	---	PASS
RNF219	79596	broad.mit.edu	37	13	79219120	79219120	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79219120C>A	uc001vkw.1	-	2	144	c.85G>T	c.(85-87)GTC>TTC	p.V29F	RNF219_uc010afb.1_5'UTR|RNF219_uc010afc.2_Missense_Mutation_p.V29F	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	29	RING-type; degenerate.						zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		ATGCATATGACAGGCTGACGT	0.383													25	34	---	---	---	---	PASS
IPO5	3843	broad.mit.edu	37	13	98673325	98673325	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98673325G>C	uc001vne.2	+	28	3379	c.3199G>C	c.(3199-3201)GAG>CAG	p.E1067Q		NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5	1049					interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3						AGAAATGCACGAGGCAATTAA	0.418													44	124	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111099172	111099172	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111099172G>T	uc001vqx.2	+	18	1328	c.1039G>T	c.(1039-1041)GGA>TGA	p.G347*		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	347	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)			AGGGCCCCCTGGACTACCTGC	0.473													22	41	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111099173	111099173	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111099173G>C	uc001vqx.2	+	18	1329	c.1040G>C	c.(1039-1041)GGA>GCA	p.G347A		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	347	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)			GGGCCCCCTGGACTACCTGCC	0.478													22	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22322268	22322268	+	Intron	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22322268G>A	uc010tmf.1	+						uc001wbw.2_Intron|uc010tmg.1_Intron|uc001wby.2_Intron|uc001wcc.2_Silent_p.R73R					SubName: Full=Putative uncharacterized protein ENSP00000374943;																		AGCCTTGGAGGGTAGCAAGTA	0.418													11	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22521260	22521260	+	Intron	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22521260T>C	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_RNA					SubName: Full=Alpha-chain C region; Flags: Fragment;																		CGTAGTACTTTATACATTGCA	0.468													8	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22952008	22952008	+	Intron	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22952008G>A	uc001wbw.2	+						uc010aja.1_RNA|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_RNA|uc010aje.1_Intron|uc001wcp.2_Missense_Mutation_p.S117N|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Missense_Mutation_p.S114N|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Missense_Mutation_p.S114N|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_5'Flank|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_RNA					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AGTGGAGGTAGCAACTATAAA	0.448													26	40	---	---	---	---	PASS
TSSK4	283629	broad.mit.edu	37	14	24676618	24676618	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24676618A>T	uc001wng.2	+	3	875	c.707A>T	c.(706-708)CAT>CTT	p.H236L	TM9SF1_uc010tob.1_Intron|TSSK4_uc001wne.2_Missense_Mutation_p.H160L|TSSK4_uc001wnf.2_Missense_Mutation_p.H166L|TSSK4_uc001wnh.2_Missense_Mutation_p.H246L	NM_174944	NP_777604	Q6SA08	TSSK4_HUMAN	testis-specific serine kinase 4	236	Protein kinase.				cell differentiation|multicellular organismal development|positive regulation of CREB transcription factor activity|spermatogenesis		ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity				0				GBM - Glioblastoma multiforme(265;0.018)		GTGGTCGCCCATCTGCCCTTT	0.517													34	65	---	---	---	---	PASS
MDGA2	161357	broad.mit.edu	37	14	47504430	47504430	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47504430G>A	uc001wwj.3	-	8	1592	c.1396C>T	c.(1396-1398)CAA>TAA	p.Q466*	MDGA2_uc001wwi.3_Nonsense_Mutation_p.Q237*|MDGA2_uc010ani.2_Nonsense_Mutation_p.Q26*	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	466	Ig-like 5.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						CCAGTTACTTGACATTGCAGT	0.408													16	67	---	---	---	---	PASS
KTN1	3895	broad.mit.edu	37	14	56083372	56083372	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56083372G>T	uc001xcb.2	+	4	963	c.661G>T	c.(661-663)GTC>TTC	p.V221F	KTN1_uc001xce.2_Missense_Mutation_p.V221F|KTN1_uc001xcc.2_Missense_Mutation_p.V221F|KTN1_uc001xcd.2_Missense_Mutation_p.V221F|KTN1_uc010trb.1_Missense_Mutation_p.V221F|KTN1_uc001xcf.1_Missense_Mutation_p.V221F	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a	221	Lumenal (Potential).				microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7						GACAGAAAATGGTGAGATGTT	0.388			T	RET	papillary thryoid								6	66	---	---	---	---	PASS
C14orf37	145407	broad.mit.edu	37	14	58563647	58563647	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58563647C>G	uc001xdc.2	-	5	1995	c.1884G>C	c.(1882-1884)GAG>GAC	p.E628D	C14orf37_uc010tro.1_Missense_Mutation_p.E666D|C14orf37_uc001xdd.2_Missense_Mutation_p.E628D	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	628	Extracellular (Potential).|Glu-rich.					integral to membrane	binding				0						cctcatcttcctcttcttcat	0.279													13	29	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64443309	64443309	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64443309A>T	uc001xgm.2	+	12	1387	c.1157A>T	c.(1156-1158)TAT>TTT	p.Y386F	SYNE2_uc001xgl.2_Missense_Mutation_p.Y386F	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	386	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAGCTAAATTATGCCTTGCCC	0.378													78	144	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72138134	72138134	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72138134G>T	uc001xms.2	+	8	2902	c.2554G>T	c.(2554-2556)GAG>TAG	p.E852*	SIPA1L1_uc001xmt.2_Nonsense_Mutation_p.E852*|SIPA1L1_uc001xmu.2_Nonsense_Mutation_p.E852*|SIPA1L1_uc001xmv.2_Nonsense_Mutation_p.E852*|SIPA1L1_uc010ttm.1_Nonsense_Mutation_p.E327*	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	852					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)		TCCAGGAGCCGAGCTCAGCAG	0.502													18	41	---	---	---	---	PASS
RGS6	9628	broad.mit.edu	37	14	72976929	72976929	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72976929G>A	uc001xna.3	+	14	1556	c.1033G>A	c.(1033-1035)GTG>ATG	p.V345M	RGS6_uc010ttn.1_Missense_Mutation_p.V345M|RGS6_uc001xmx.3_Missense_Mutation_p.V345M|RGS6_uc010tto.1_RNA|RGS6_uc001xmy.3_Missense_Mutation_p.V345M|RGS6_uc010ttp.1_Missense_Mutation_p.V276M|RGS6_uc001xmz.1_Missense_Mutation_p.V206M	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6	345	RGS.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		GAAGGACCAGGTGGGGCGGGA	0.468													64	114	---	---	---	---	PASS
KCNK10	54207	broad.mit.edu	37	14	88652109	88652109	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88652109T>C	uc001xwo.2	-	7	1844	c.1387A>G	c.(1387-1389)AAG>GAG	p.K463E	KCNK10_uc001xwm.2_Missense_Mutation_p.K468E|KCNK10_uc001xwn.2_Missense_Mutation_p.K468E	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	463	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5						GGCAAGGTCTTTTTGAGGTCC	0.507													17	94	---	---	---	---	PASS
FBLN5	10516	broad.mit.edu	37	14	92357691	92357691	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92357691G>T	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)				TCTGGAAACAGAAATGCAAGC	0.478													4	70	---	---	---	---	PASS
BTBD7	55727	broad.mit.edu	37	14	93727992	93727992	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93727992A>G	uc001ybo.2	-	5	1729	c.1403T>C	c.(1402-1404)ATT>ACT	p.I468T	BTBD7_uc010aur.2_5'UTR|BTBD7_uc010two.1_Intron|BTBD7_uc001ybp.2_Missense_Mutation_p.I117T|BTBD7_uc001ybq.3_Missense_Mutation_p.I383T	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1	468										pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TCCCCATTTAATCAGATATTT	0.303													7	78	---	---	---	---	PASS
BTBD7	55727	broad.mit.edu	37	14	93761256	93761256	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93761256T>C	uc001ybo.2	-	3	436	c.110A>G	c.(109-111)TAT>TGT	p.Y37C	BTBD7_uc010aur.2_5'UTR|BTBD7_uc010two.1_5'UTR|BTBD7_uc001ybp.2_Intron|BTBD7_uc001ybq.3_5'UTR|BTBD7_uc001ybr.2_Missense_Mutation_p.Y37C	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1	37										pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TTCGCAACCATAGCCTTGCTG	0.343													23	57	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103406186	103406186	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103406186C>G	uc001ymi.1	-	33	4922	c.4690G>C	c.(4690-4692)GAG>CAG	p.E1564Q		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	1564					actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TGCAGTCTCTCTTCCTCTGGG	0.612													66	123	---	---	---	---	PASS
MKRN3	7681	broad.mit.edu	37	15	23811224	23811224	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23811224A>T	uc001ywh.3	+	1	771	c.295A>T	c.(295-297)ATC>TTC	p.I99F	MKRN3_uc001ywi.2_Missense_Mutation_p.I99F|MKRN3_uc010ayi.1_Missense_Mutation_p.I99F	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	99	C3H1-type 1.					ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		GACAAAGCAGATCATCTGCAG	0.602													9	48	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	26026288	26026288	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26026288G>T	uc010ayu.2	-	2	638	c.532C>A	c.(532-534)CCT>ACT	p.P178T		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	178	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ATGTCCGCAGGGAAGATTTCG	0.527													10	55	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	26026289	26026289	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26026289G>T	uc010ayu.2	-	2	637	c.531C>A	c.(529-531)TTC>TTA	p.F177L		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	177	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGTCCGCAGGGAAGATTTCGT	0.527													9	56	---	---	---	---	PASS
ARHGAP11A	9824	broad.mit.edu	37	15	32928116	32928116	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32928116G>T	uc001zgy.1	+	11	2205	c.1483G>T	c.(1483-1485)GGT>TGT	p.G495C	ARHGAP11A_uc010ubw.1_Missense_Mutation_p.G306C|ARHGAP11A_uc001zgw.2_Missense_Mutation_p.G495C|ARHGAP11A_uc001zgx.2_Missense_Mutation_p.G467C|ARHGAP11A_uc010ubx.1_Missense_Mutation_p.G306C	NM_014783	NP_055598	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A isoform 1	495					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		ACCAAAGAAAGGTACATTTAC	0.294													11	23	---	---	---	---	PASS
RAD51	5888	broad.mit.edu	37	15	40993374	40993374	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40993374G>T	uc001zmi.3	+	3	499	c.200G>T	c.(199-201)AGT>ATT	p.S67I	RAD51_uc010bbw.2_Missense_Mutation_p.S67I|RAD51_uc010bbx.2_Missense_Mutation_p.S67I|RAD51_uc001zmk.3_RNA|RAD51_uc001zml.3_Missense_Mutation_p.S67I|RAD51_uc001zmm.1_RNA|RAD51_uc001zmn.1_5'UTR	NM_002875	NP_002866	Q06609	RAD51_HUMAN	RAD51 homolog protein isoform 1	67	HhH.				DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		AAGGGAATTAGTGAAGCCAAA	0.403								Homologous_recombination					17	81	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42693865	42693865	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42693865C>T	uc001zpn.1	+	11	1687	c.1381C>T	c.(1381-1383)CGT>TGT	p.R461C	CAPN3_uc001zpk.1_Missense_Mutation_p.R234C|CAPN3_uc001zpl.1_Missense_Mutation_p.R374C|CAPN3_uc010udf.1_Missense_Mutation_p.R374C|CAPN3_uc010udg.1_Missense_Mutation_p.R326C|CAPN3_uc001zpo.1_Missense_Mutation_p.R461C|CAPN3_uc001zpp.1_Missense_Mutation_p.R413C|CAPN3_uc001zpq.1_5'Flank	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	461	Domain III.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		CCCTCAGTACCGTCTGAAGCT	0.582													13	38	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42702775	42702775	+	Intron	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42702775T>A	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron|CAPN3_uc001zpq.1_Intron|CAPN3_uc010bcv.1_Intron|CAPN3_uc001zpr.1_Intron|CAPN3_uc001zps.1_Intron|CAPN3_uc001zpt.1_Intron	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		CCTCAAATTTTCTATTGCCAG	0.468													10	39	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45427450	45427450	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45427450C>T	uc001zus.1	+	6	802	c.456C>T	c.(454-456)GAC>GAT	p.D152D	DUOX1_uc001zut.1_Silent_p.D152D|DUOX1_uc010bee.1_5'UTR	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	152	Peroxidase-like; mediates peroxidase activity.|Extracellular (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GCCGCTGGGACCCCGAGACCG	0.716													5	16	---	---	---	---	PASS
CEP152	22995	broad.mit.edu	37	15	49031141	49031141	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49031141C>T	uc001zwy.2	-	26	4304	c.4270G>A	c.(4270-4272)GAC>AAC	p.D1424N	CEP152_uc001zwz.2_Missense_Mutation_p.D1480N	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	1424					centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CTGAGTAGGTCTTTCTTCTTG	0.453													9	73	---	---	---	---	PASS
TEX9	374618	broad.mit.edu	37	15	56680704	56680704	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56680704C>A	uc002adp.2	+	5	303	c.298C>A	c.(298-300)CAT>AAT	p.H100N	TEX9_uc002ado.1_Missense_Mutation_p.H100N|TEX9_uc010ugl.1_Missense_Mutation_p.H25N|TEX9_uc002adq.1_Missense_Mutation_p.H25N	NM_198524	NP_940926	Q8N6V9	TEX9_HUMAN	testis expressed 9	100											0				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		AGTTCATCTTCATTCAGAAAC	0.328													5	41	---	---	---	---	PASS
AAGAB	79719	broad.mit.edu	37	15	67529170	67529170	+	Intron	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67529170T>C	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0						TAAAAATAAATGACAACATTA	0.333													4	12	---	---	---	---	PASS
HMG20A	10363	broad.mit.edu	37	15	77769937	77769937	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77769937C>T	uc002bcr.2	+	8	857	c.656C>T	c.(655-657)CCT>CTT	p.P219L	HMG20A_uc002bcs.2_Missense_Mutation_p.P219L	NM_018200	NP_060670	Q9NP66	HM20A_HUMAN	high-mobility group 20A	219					chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						TTTGACATCCCTATATTTACA	0.328													5	26	---	---	---	---	PASS
NARFL	64428	broad.mit.edu	37	16	780560	780560	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:780560C>T	uc002cjr.2	-	11	1300	c.1288G>A	c.(1288-1290)GAG>AAG	p.E430K	NARFL_uc002cjp.2_Missense_Mutation_p.E328K|NARFL_uc002cjq.2_Missense_Mutation_p.E328K|NARFL_uc002cjs.2_Missense_Mutation_p.E212K	NM_022493	NP_071938	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	430					iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)				TCGGGCGCCTCAGCCCGGACC	0.667													6	46	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9857679	9857679	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9857679C>T	uc002czo.3	-	13	4270	c.3722G>A	c.(3721-3723)CGG>CAG	p.R1241Q	GRIN2A_uc010uym.1_Missense_Mutation_p.R1241Q|GRIN2A_uc010uyn.1_Missense_Mutation_p.R1084Q|GRIN2A_uc002czr.3_Missense_Mutation_p.R1241Q	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1241	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)	GTTCCCCATCCGCAGGCAGGC	0.582													10	91	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24920378	24920378	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24920378C>A	uc002dmu.2	+	14	1843	c.1611C>A	c.(1609-1611)TCC>TCA	p.S537S	SLC5A11_uc002dms.2_Silent_p.S473S|SLC5A11_uc010vcd.1_Silent_p.S502S|SLC5A11_uc002dmt.2_Silent_p.S381S|SLC5A11_uc010vce.1_Silent_p.S467S|SLC5A11_uc010bxt.2_Silent_p.S473S|SLC5A11_uc002dmv.2_Silent_p.S160S	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	537	Helical; (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		TCACTGTCTCCACCGTGAGCT	0.468													12	39	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27784413	27784413	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27784413G>T	uc002dow.2	+							NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						TTAATAAAGTGTCCCAGTCAT	0.408													3	13	---	---	---	---	PASS
NFATC2IP	84901	broad.mit.edu	37	16	28967563	28967563	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28967563G>T	uc002dru.2	+	5	766	c.751G>T	c.(751-753)GTC>TTC	p.V251F	uc010vct.1_Intron|NFATC2IP_uc002drt.2_Intron|NFATC2IP_uc002drv.2_5'UTR|NFATC2IP_uc010vdh.1_5'Flank	NM_032815	NP_116204	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells,	251						cytoplasm|nucleus				ovary(1)	1						GGATGAAGTGGTCTTGGTGGA	0.607													14	31	---	---	---	---	PASS
C16orf57	79650	broad.mit.edu	37	16	58043878	58043878	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58043878C>T	uc002emz.2	+	3	394	c.311C>T	c.(310-312)CCC>CTC	p.P104L	C16orf57_uc010via.1_Missense_Mutation_p.P104L|C16orf57_uc002emy.2_RNA|C16orf57_uc010vib.1_Missense_Mutation_p.P104L|C16orf57_uc010vic.1_Missense_Mutation_p.P53L	NM_024598	NP_078874	Q9BQ65	CP057_HUMAN	hypothetical protein LOC79650	104											0						GTGTTGCTGCCCCATGCCCAG	0.592													34	77	---	---	---	---	PASS
PDP2	57546	broad.mit.edu	37	16	66918398	66918398	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66918398G>T	uc002eqk.1	+	2	373	c.211G>T	c.(211-213)GAT>TAT	p.D71Y		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	71					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		AACAGAGGAAGATGATTTTCA	0.488													5	73	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72992122	72992122	+	Silent	SNP	C	T	T	rs150601682	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72992122C>T	uc002fck.2	-	2	2596	c.1923G>A	c.(1921-1923)GAG>GAA	p.E641E	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	641	C2H2-type 2.				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)				ATTTGGGGCACTCCACGCCAC	0.642													7	16	---	---	---	---	PASS
TUBB3	10381	broad.mit.edu	37	16	90001435	90001435	+	Silent	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90001435G>T	uc002fph.1	+	4	641	c.576G>T	c.(574-576)CTG>CTT	p.L192L	TUBB3_uc002fpf.2_Silent_p.L539L|TUBB3_uc010ciz.1_Silent_p.L120L|TUBB3_uc002fpg.1_Silent_p.L46L|TUBB3_uc002fpi.1_Silent_p.L120L|TUBB3_uc002fpj.1_Silent_p.L120L|TUBB3_uc010cjb.1_Silent_p.L46L|TUBB3_uc002fpk.1_Silent_p.L46L	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4	192					'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		TCCACCAGCTGGTGGAGAACA	0.612													52	105	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7579311	7579311	+	Splice_Site	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7579311C>A	uc002gim.2	-	4	569	c.375_splice	c.e4+1	p.T125_splice	TP53_uc002gig.1_Splice_Site_p.T125_splice|TP53_uc002gih.2_Splice_Site_p.T125_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Splice_Site_p.T125_splice|TP53_uc010cni.1_Splice_Site_p.T125_splice|TP53_uc002gij.2_Splice_Site_p.T125_splice|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Splice_Site_p.T86_splice	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.?(11)|p.0?(7)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GGGCAACTGACCGTGCAAGTC	0.532		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			11	45	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29663350	29663350	+	Splice_Site	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29663350G>T	uc002hgg.2	+	41	6340	c.6007_splice	c.e41-1	p.I2003_splice	NF1_uc002hgh.2_Splice_Site_p.I1982_splice|NF1_uc010cso.2_Splice_Site_p.I191_splice|NF1_uc010wbt.1_5'Flank|NF1_uc010wbu.1_5'Flank	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCTTCAACTAGATTACAGATC	0.328			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			9	26	---	---	---	---	PASS
HSF5	124535	broad.mit.edu	37	17	56540167	56540167	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56540167T>G	uc002iwi.1	-	4	1642	c.1518A>C	c.(1516-1518)GAA>GAC	p.E506D		NM_001080439	NP_001073908	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	506						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATGGTGGCCCTTCCTGCACAA	0.433													15	113	---	---	---	---	PASS
WIPI1	55062	broad.mit.edu	37	17	66417912	66417912	+	3'UTR	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66417912C>A	uc010dey.2	-	13					WIPI1_uc002jhd.3_RNA|WIPI1_uc010wqo.1_3'UTR|WIPI1_uc002jhe.3_RNA	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting						macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						GTGTGCTTCTCATCATGACTG	0.463													14	58	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28934971	28934971	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28934971A>T	uc002kwp.2	+	15	3024	c.2812A>T	c.(2812-2814)AGT>TGT	p.S938C	DSG1_uc010xbp.1_Missense_Mutation_p.S297C	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	938	Desmoglein repeat 5.|Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			AGGTAGTCTGAGTATGCACCC	0.483													107	175	---	---	---	---	PASS
DCC	1630	broad.mit.edu	37	18	50976931	50976931	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50976931C>A	uc002lfe.1	+	23	3878	c.3291C>A	c.(3289-3291)AAC>AAA	p.N1097K	DCC_uc010dpf.1_Missense_Mutation_p.N732K	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	1097	Extracellular (Potential).				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGAACAGCAACCTGCTTGTGA	0.527													14	29	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59203723	59203723	+	Intron	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59203723C>A	uc010dps.1	+						CDH20_uc002lif.2_Intron	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				CATGTTTCTGCAGATACTCCA	0.433													42	80	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59212249	59212249	+	Intron	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59212249C>T	uc010dps.1	+						CDH20_uc002lif.2_Intron	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				GATTTCATGTCCCTCCCTCAG	0.512													16	26	---	---	---	---	PASS
TRIP10	9322	broad.mit.edu	37	19	6751103	6751103	+	Missense_Mutation	SNP	G	C	C	rs139253875	byFrequency	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6751103G>C	uc002mfs.2	+	15	1753	c.1687G>C	c.(1687-1689)GAG>CAG	p.E563Q	TRIP10_uc010dux.1_Silent_p.P516P|TRIP10_uc002mfr.2_Missense_Mutation_p.E507Q|TRIP10_uc010duy.2_RNA|TRIP10_uc010duz.2_Missense_Mutation_p.E326Q	NM_004240	NP_004231	Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	563	Interaction with PDE6G (By similarity).|SH3.|Required for podosome formation.|Interaction with ARHGAP17, DAAM1, DIAPH1 and DIAPH2.|Interaction with DNM1 and WASL.|Required for interaction with FASLG and localization to lysosomes.|Interaction with WAS.				actin cytoskeleton organization|cell communication|endocytosis|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell projection|cytoskeleton|cytosol|Golgi apparatus|lysosome|perinuclear region of cytoplasm|phagocytic cup	GTPase activator activity|identical protein binding|lipid binding			ovary(1)	1						CTCTATGGCCGAGGGTGAAGA	0.527													13	29	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8971706	8971706	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8971706T>A	uc002mkp.2	-	78	43090	c.42886A>T	c.(42886-42888)ACC>TCC	p.T14296S	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.T1096S|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	14379	Extracellular (Potential).			Missing (in Ref. 3; AAK74120).	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						AACTGGTAGGTGGAGCCCAGC	0.527													13	15	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14736383	14736383	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14736383C>G	uc002mzi.3	-	15	1989	c.1841G>C	c.(1840-1842)AGA>ACA	p.R614T	EMR3_uc010dzp.2_Missense_Mutation_p.R562T|EMR3_uc010xnv.1_Missense_Mutation_p.R488T	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	614	Cytoplasmic (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						TACGATCTCTCTAAACCACTT	0.418													11	65	---	---	---	---	PASS
CEACAM5	1048	broad.mit.edu	37	19	42213940	42213940	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42213940G>A	uc002ork.2	+	2	527	c.406G>A	c.(406-408)GGC>AGC	p.G136S	CEACAM5_uc010ehz.1_Missense_Mutation_p.G136S|CEACAM5_uc002orj.1_Missense_Mutation_p.G136S|CEACAM5_uc002orl.2_Missense_Mutation_p.G136S	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	136	Ig-like 1.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane				skin(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		AGAAGCAACTGGCCAGTTCCG	0.517													36	170	---	---	---	---	PASS
CD37	951	broad.mit.edu	37	19	49838976	49838976	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49838976C>A	uc002pnd.2	+	2	196	c.75C>A	c.(73-75)CTC>CTA	p.L25L	uc002pnb.1_Intron|CD37_uc002pnc.2_RNA|CD37_uc010yam.1_Silent_p.L25L|CD37_uc010yan.1_5'UTR|CD37_uc002pnf.3_5'UTR|CD37_uc002pne.2_5'UTR	NM_001774	NP_001765	P11049	CD37_HUMAN	CD37 antigen isoform A	25	Helical; (Potential).					integral to membrane					0		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		CCCAGGTCCTCGGCAGCCTGA	0.657													67	236	---	---	---	---	PASS
TSKS	60385	broad.mit.edu	37	19	50247496	50247496	+	Silent	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50247496G>C	uc002ppm.2	-	8	1364	c.1353C>G	c.(1351-1353)CGC>CGG	p.R451R		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	451							protein binding			large_intestine(1)|skin(1)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ACCTGGCACAGCGGGCACAGT	0.582													10	41	---	---	---	---	PASS
PTOV1	53635	broad.mit.edu	37	19	50357725	50357725	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50357725C>T	uc002pqf.1	+	2	404	c.234C>T	c.(232-234)CTC>CTT	p.L78L	uc002ppy.3_5'Flank|PTOV1_uc010ybf.1_Silent_p.L46L|PTOV1_uc002ppz.3_RNA|PTOV1_uc002pqb.3_Silent_p.L46L|PTOV1_uc002pqa.2_RNA|PTOV1_uc002pqc.1_RNA|PTOV1_uc002pqd.2_RNA|PTOV1_uc002pqe.1_RNA	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	78					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		GGCTCACCCTCGGGGGTCTGG	0.667													8	80	---	---	---	---	PASS
ZNF415	55786	broad.mit.edu	37	19	53612438	53612438	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53612438A>T	uc002qax.2	-	7	1353	c.1004T>A	c.(1003-1005)CTT>CAT	p.L335H	ZNF415_uc002qat.2_Missense_Mutation_p.L299H|ZNF415_uc002qaw.2_Missense_Mutation_p.L287H|ZNF415_uc010yds.1_Missense_Mutation_p.L287H|ZNF415_uc010ydt.1_Missense_Mutation_p.L287H|ZNF415_uc002qau.2_Missense_Mutation_p.L274H|ZNF415_uc002qav.2_Missense_Mutation_p.L299H|ZNF415_uc002qba.2_Missense_Mutation_p.L57H|ZNF415_uc002qay.2_Missense_Mutation_p.L274H|ZNF415_uc002qaz.2_Missense_Mutation_p.L335H	NR_028343		Q09FC8	ZN415_HUMAN	RecName: Full=Zinc finger protein 415;	335	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.0191)		ATGTAGTGCAAGGCATGAGTT	0.413													7	54	---	---	---	---	PASS
EPS8L1	54869	broad.mit.edu	37	19	55597214	55597214	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55597214G>A	uc002qis.3	+	15	1495	c.1391G>A	c.(1390-1392)CGA>CAA	p.R464Q	EPS8L1_uc010ess.1_Missense_Mutation_p.R478Q|EPS8L1_uc010yfr.1_Missense_Mutation_p.R400Q|EPS8L1_uc010esu.1_RNA|EPS8L1_uc002qiu.2_Missense_Mutation_p.R337Q|EPS8L1_uc002qiv.2_Missense_Mutation_p.R142Q|EPS8L1_uc002qiw.2_Missense_Mutation_p.R243Q	NM_133180	NP_573441	Q8TE68	ES8L1_HUMAN	epidermal growth factor receptor pathway	464						cytoplasm					0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CTCAGTCACCGAGACTTGGAG	0.577													15	73	---	---	---	---	PASS
U2AF2	11338	broad.mit.edu	37	19	56185293	56185293	+	Intron	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56185293C>A	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron|EPN1_uc002qlw.2_5'Flank|EPN1_uc002qlv.2_5'Flank|EPN1_uc010etd.2_5'Flank|EPN1_uc002qlx.2_5'Flank	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CTCTCCTTTCCCCACAGATCT	0.577													5	50	---	---	---	---	PASS
ZNF667	63934	broad.mit.edu	37	19	56953294	56953294	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56953294G>A	uc002qnd.2	-	5	1232	c.1070C>T	c.(1069-1071)CCG>CTG	p.P357L	ZNF667_uc010etl.2_Missense_Mutation_p.P139L|ZNF667_uc002qne.2_Missense_Mutation_p.P357L|ZNF667_uc010etm.2_Missense_Mutation_p.P300L	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	357					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		ACATTTGTACGGTTTCTCTGA	0.353													11	55	---	---	---	---	PASS
AURKC	6795	broad.mit.edu	37	19	57746259	57746259	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57746259A>G	uc002qoe.2	+	6	781	c.592A>G	c.(592-594)ACA>GCA	p.T198A	AURKC_uc002qoc.2_Missense_Mutation_p.T179A|AURKC_uc002qod.2_Missense_Mutation_p.T164A|AURKC_uc010etv.2_Missense_Mutation_p.T195A	NM_001015878	NP_001015878	Q9UQB9	AURKC_HUMAN	aurora kinase C isoform 1	198	Protein kinase.			T->A: Impairs kinase activity.	cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		TAGGAGGAAGACAATGTGTGG	0.483													6	46	---	---	---	---	PASS
PDYN	5173	broad.mit.edu	37	20	1961247	1961247	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961247G>A	uc010gaj.2	-	3	729	c.487C>T	c.(487-489)CTC>TTC	p.L163F	uc002wfu.1_Intron|PDYN_uc002wfv.2_Missense_Mutation_p.L163F|PDYN_uc010zpt.1_Missense_Mutation_p.L8F	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	163					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2						TCCTCAGCGAGATAGAGTGTG	0.602													23	75	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2575614	2575614	+	Splice_Site	SNP	G	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2575614G>A	uc002wgf.1	+	9	1091	c.1076_splice	c.e9+1	p.S359_splice	TMC2_uc002wgg.1_Splice_Site_p.S343_splice|TMC2_uc010zpw.1_Splice_Site_p.S191_splice|TMC2_uc010zpx.1_Splice_Site_p.S190_splice	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3						TCATTCGATCGTAAGTATGAC	0.557													12	54	---	---	---	---	PASS
C20orf79	140856	broad.mit.edu	37	20	18794684	18794684	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18794684C>A	uc002wrk.2	+	1	315	c.225C>A	c.(223-225)ACC>ACA	p.T75T	uc002wrj.1_Intron	NM_178483	NP_848578	Q9UJQ7	CT079_HUMAN	hypothetical protein LOC140856	75	SCP2.						sterol binding			skin(3)	3						TGGACATCACCAAAAATGGGA	0.493													19	65	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20486081	20486081	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20486081C>A	uc002wrz.2	-	34	5169	c.5026G>T	c.(5026-5028)GAC>TAC	p.D1676Y	RALGAPA2_uc010gcx.2_Missense_Mutation_p.D1380Y|RALGAPA2_uc010zsg.1_Missense_Mutation_p.D1124Y|RALGAPA2_uc002wsa.1_Missense_Mutation_p.D448Y	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1676	Rap-GAP.				activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GCAACAAAGTCTTCATATGCT	0.403													5	10	---	---	---	---	PASS
PLK1S1	55857	broad.mit.edu	37	20	21143751	21143751	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21143751A>T	uc002wsb.2	+	6	1436	c.1303A>T	c.(1303-1305)AGC>TGC	p.S435C	PLK1S1_uc010zsh.1_Missense_Mutation_p.S332C|PLK1S1_uc010zsi.1_Missense_Mutation_p.S302C|PLK1S1_uc010zsj.1_RNA|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_RNA	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1	435					spindle organization	centrosome	protein kinase binding				0						GCAAACCCTAAGCTCTCCTGA	0.373													35	139	---	---	---	---	PASS
C20orf185	359710	broad.mit.edu	37	20	31659950	31659950	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31659950C>A	uc002wym.1	+	13	1301	c.1301C>A	c.(1300-1302)GCA>GAA	p.A434E		NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3 precursor	434					innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4						GTGGTCGGGGCAGTGTATGCA	0.522													9	38	---	---	---	---	PASS
PCK1	5105	broad.mit.edu	37	20	56139260	56139260	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56139260T>C	uc002xyn.3	+	7	1160	c.997T>C	c.(997-999)TTC>CTC	p.F333L	PCK1_uc010zzm.1_Missense_Mutation_p.F16L	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	333					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AAATGGCTTTTTCGGTGTCGC	0.478													5	31	---	---	---	---	PASS
MIR646	693231	broad.mit.edu	37	20	58883553	58883553	+	RNA	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58883553G>T	hsa-mir-646|MI0003661	+			c.22G>T			uc002ybl.2_Intron|uc010gjw.1_Intron																	0						tgccagtggagtcagcacacc	0.000													8	26	---	---	---	---	PASS
YTHDF1	54915	broad.mit.edu	37	20	61834312	61834312	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61834312C>A	uc002yeh.2	-	4	1274	c.980G>T	c.(979-981)CGC>CTC	p.R327L	YTHDF1_uc011aaq.1_Missense_Mutation_p.R277L	NM_017798	NP_060268	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	327	Gln/Pro-rich.									ovary(2)	2						GGCAACCCAGCGGGTCTGGGG	0.657													10	14	---	---	---	---	PASS
TIAM1	7074	broad.mit.edu	37	21	32513671	32513671	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32513671C>T	uc002yow.1	-	22	4099	c.3627G>A	c.(3625-3627)GCG>GCA	p.A1209A	TIAM1_uc011adk.1_Silent_p.A1209A|TIAM1_uc011adl.1_Silent_p.A1149A	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1209	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						CCTCGCTCTCCGCATCGGTCA	0.597													7	63	---	---	---	---	PASS
CRYAA	1409	broad.mit.edu	37	21	44589369	44589369	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44589369C>T	uc002zdd.1	+	1	229	c.160C>T	c.(160-162)CGC>TGC	p.R54C		NM_000394	NP_000385	P02489	CRYAA_HUMAN	crystallin, alpha A	54					anti-apoptosis|negative regulation of intracellular transport|protein homooligomerization|response to heat|visual perception	cytoplasm|nucleus	structural constituent of eye lens|unfolded protein binding			breast(1)|central_nervous_system(1)	2						GTCCCTCTTCCGCACCGTGCT	0.637													32	41	---	---	---	---	PASS
CECR1	51816	broad.mit.edu	37	22	17670825	17670825	+	Intron	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17670825G>C	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc002zmj.1_Intron	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				TTCACAGCATGGGTTACCAGG	0.587													8	39	---	---	---	---	PASS
PPIL2	23759	broad.mit.edu	37	22	22039088	22039088	+	Silent	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22039088A>T	uc010gtj.1	+	10	716	c.600A>T	c.(598-600)ACA>ACT	p.T200T	PPIL2_uc002zvh.3_Silent_p.T200T|PPIL2_uc002zvi.3_Silent_p.T200T|PPIL2_uc002zvg.3_Silent_p.T200T|PPIL2_uc011aij.1_Silent_p.T179T|PPIL2_uc002zvk.3_5'Flank	NM_148175	NP_680480	Q13356	PPIL2_HUMAN	peptidylprolyl isomerase-like 2 isoform a	200	Potential.				blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)					TGAAAAATACAAATGCCGAGA	0.542													9	51	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26422777	26422777	+	Silent	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26422777C>T	uc003abz.1	+	43	7087	c.6837C>T	c.(6835-6837)CCC>CCT	p.P2279P	MYO18B_uc003aca.1_Silent_p.P2160P|MYO18B_uc010guy.1_Silent_p.P2161P|MYO18B_uc010guz.1_Silent_p.P2159P|MYO18B_uc011aka.1_Silent_p.P1433P|MYO18B_uc011akb.1_Silent_p.P1792P|MYO18B_uc010gva.1_Silent_p.P262P|MYO18B_uc010gvb.1_RNA	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2279						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						CCACTCTCCCCATTTACCAGA	0.642													6	11	---	---	---	---	PASS
SFI1	9814	broad.mit.edu	37	22	31924666	31924666	+	Intron	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31924666C>T	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|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						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						CTTTCGTCCTCAAATTTAAGG	0.378													12	48	---	---	---	---	PASS
SFI1	9814	broad.mit.edu	37	22	31924738	31924738	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31924738C>G	uc003ale.2	+	3	548	c.155C>G	c.(154-156)TCT>TGT	p.S52C	SFI1_uc003ald.1_Missense_Mutation_p.S52C|SFI1_uc003alf.2_Missense_Mutation_p.S52C|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Missense_Mutation_p.S52C|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	52					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						AACAAGAAGTCTTCTGCATCC	0.443													14	77	---	---	---	---	PASS
ST13	6767	broad.mit.edu	37	22	41223120	41223120	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41223120C>G	uc003aze.2	-	11	1104	c.961G>C	c.(961-963)GAG>CAG	p.E321Q	ST13_uc011aow.1_Missense_Mutation_p.E311Q	NM_003932	NP_003923	P50502	F10A1_HUMAN	heat shock 70kD protein binding protein	321	STI1.						protein binding, bridging				0						GCAAGAACCTCTGGATCACTA	0.453													7	62	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42042926	42042926	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42042926T>C	uc003bao.1	+	7	870	c.800T>C	c.(799-801)ATA>ACA	p.I267T	XRCC6_uc003bap.1_Missense_Mutation_p.I226T|XRCC6_uc011apc.1_Missense_Mutation_p.I217T|XRCC6_uc003baq.1_Missense_Mutation_p.I267T|XRCC6_uc003bar.1_Missense_Mutation_p.I267T|XRCC6_uc003bas.1_Missense_Mutation_p.I217T	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	267	Ku.				DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						AACAAAGATATAGTGATCTCT	0.398								Direct_reversal_of_damage|NHEJ					31	149	---	---	---	---	PASS
DHRSX	207063	broad.mit.edu	37	X	2161142	2161142	+	Silent	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2161142C>A	uc004cqf.3	-	6	775	c.726G>T	c.(724-726)GTG>GTT	p.V242V		NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked	242							binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCGTGTTGACCACCCCGGGGT	0.622													11	36	---	---	---	---	PASS
EGFL6	25975	broad.mit.edu	37	X	13645160	13645160	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13645160T>A	uc004cvi.2	+	11	1556	c.1316T>A	c.(1315-1317)TTG>TAG	p.L439*	EGFL6_uc004cvj.2_Nonsense_Mutation_p.L440*	NM_015507	NP_056322	Q8IUX8	EGFL6_HUMAN	epidermal growth factor-like protein 6	439	MAM.				cell adhesion|cell cycle|cell differentiation|multicellular organismal development	basement membrane|extracellular space|membrane	calcium ion binding|integrin binding			breast(2)	2						GTTCCGGCCTTGGCAGGTCAC	0.433													31	24	---	---	---	---	PASS
FUNDC1	139341	broad.mit.edu	37	X	44383470	44383470	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44383470C>T	uc004dgc.2	-	5	585	c.442G>A	c.(442-444)GGC>AGC	p.G148S		NM_173794	NP_776155	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1	148											0						AGCAAAAAGCCTCCCACAAAT	0.333													7	16	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65423336	65423336	+	Silent	SNP	T	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65423336T>C	uc011moz.1	+	13	2277	c.2217T>C	c.(2215-2217)TAT>TAC	p.Y739Y	HEPH_uc004dwn.2_Silent_p.Y739Y|HEPH_uc004dwo.2_Silent_p.Y469Y|HEPH_uc010nkr.2_Silent_p.Y547Y|HEPH_uc011mpa.1_Silent_p.Y739Y|HEPH_uc010nks.2_Silent_p.Y28Y	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	736	Extracellular (Potential).|Plastocyanin-like 5.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						GAATCTACTATATCATGGCAG	0.527													6	12	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73045917	73045917	+	RNA	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73045917A>T	uc004ebn.2	+	1		c.33878A>T			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						CATAACCATCACTAGAAATCC	0.502													28	46	---	---	---	---	PASS
CYLC1	1538	broad.mit.edu	37	X	83129612	83129612	+	Silent	SNP	A	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83129612A>T	uc004eei.1	+	4	1917	c.1896A>T	c.(1894-1896)CCA>CCT	p.P632P	CYLC1_uc004eeh.1_Silent_p.P631P	NM_021118	NP_066941	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head	632	Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis	acrosomal matrix|cytoskeletal calyx	structural molecule activity			ovary(4)|skin(1)	5						TGCCTCCTCCACCTCCAAAAC	0.393													12	6	---	---	---	---	PASS
SATL1	340562	broad.mit.edu	37	X	84363064	84363064	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84363064G>C	uc011mqx.1	-	1	911	c.911C>G	c.(910-912)TCA>TGA	p.S304*	SATL1_uc004een.2_Nonsense_Mutation_p.S304*	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	117	Gln-rich.						N-acetyltransferase activity			breast(2)	2						GTTTGTACCTGATTGCCTCAT	0.478													10	17	---	---	---	---	PASS
CXorf66	347487	broad.mit.edu	37	X	139047560	139047560	+	Intron	SNP	G	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139047560G>T	uc004fbb.2	-							NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor							integral to membrane					0						TTAAGGTTAGGCACCTACCTG	0.328													11	35	---	---	---	---	PASS
MAGEA11	4110	broad.mit.edu	37	X	148797503	148797503	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148797503C>A	uc004fdq.2	+	5	459	c.357C>A	c.(355-357)CAC>CAA	p.H119Q	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Missense_Mutation_p.H90Q	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	119						cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GAAGTCAGCACTGCAAGCCTG	0.587													15	36	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2367874	2367881	+	IGR	DEL	TCCTCCCT	-	-	rs141324068	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2367874_2367881delTCCTCCCT								PEX10 (23864 upstream) : PLCH2 (39873 downstream)																							CCTTTctccctcctcccttcctcccttc	0.091													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2762165	2762165	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2762165delT								MMEL1 (197684 upstream) : ACTRT2 (175881 downstream)																							gcaaagacccttttttccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	8376358	8376359	+	IGR	INS	-	C	C	rs142570272	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8376358_8376359insC								ERRFI1 (289965 upstream) : SLC45A1 (8031 downstream)																							CTGTTCCTGTACCCCCCCACCT	0.569													6	3	---	---	---	---	
MFN2	9927	broad.mit.edu	37	1	12058607	12058611	+	Intron	DEL	AAAAC	-	-	rs113209787		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12058607_12058611delAAAAC	uc001atn.3	+						MFN2_uc009vni.2_Intron	NM_014874	NP_055689	O95140	MFN2_HUMAN	mitofusin 2						blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion	cytosol|integral to membrane|intrinsic to mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		tcTATATCCAaaaacaaaacaaaac	0.195													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14594966	14594967	+	IGR	INS	-	A	A	rs71570195		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14594966_14594967insA								PRDM2 (443394 upstream) : KAZ (330246 downstream)																							GACACTGTGTTAAAAAAAAAAA	0.371													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15374918	15374919	+	Intron	INS	-	TG	TG	rs139436450	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15374918_15374919insTG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						atgtgtgtgtatgtgtgtgtgt	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16438410	16438411	+	IGR	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16438410_16438411delCA								FAM131C (38283 upstream) : EPHA2 (12421 downstream)																							CCACCACGTGcacacacacaca	0.307													3	3	---	---	---	---	
FBXO42	54455	broad.mit.edu	37	1	16636856	16636856	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16636856delA	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron|FBXO42_uc001ayh.2_Intron	NM_018994	NP_061867	Q6P3S6	FBX42_HUMAN	F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		gttccatctgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17098015	17098018	+	Intron	DEL	ACAG	-	-	rs72381779		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17098015_17098018delACAG	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		acacacacacacagacacacacac	0.098													5	4	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17231626	17231626	+	Intron	DEL	C	-	-	rs67781706		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17231626delC	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGGTGGTGCTCGGGGCAAGTG	0.587													4	2	---	---	---	---	
PADI6	353238	broad.mit.edu	37	1	17719645	17719645	+	Intron	DEL	A	-	-	rs12128561	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17719645delA	uc001bak.1	+							NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		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;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	gtctcaaaagaaaaaaaaaaa	0.229													4	2	---	---	---	---	
ALDH4A1	8659	broad.mit.edu	37	1	19219052	19219053	+	Intron	INS	-	G	G	rs147706590	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19219052_19219053insG	uc001bbb.2	-						ALDH4A1_uc010ocu.1_5'Flank|ALDH4A1_uc001bbc.2_Intron	NM_170726	NP_733844	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4A1 isoform a precursor						proline biosynthetic process|proline catabolic process	mitochondrial matrix	1-pyrroline-5-carboxylate dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	NADH(DB00157)	tagaaggaggcgggggggggct	0.149													5	5	---	---	---	---	
PQLC2	54896	broad.mit.edu	37	1	19641389	19641389	+	Intron	DEL	T	-	-	rs3215559		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19641389delT	uc001bby.2	+						AKR7A2_uc001bbw.2_5'Flank|AKR7A2_uc001bbx.2_5'Flank|AKR7A2_uc009vpi.1_5'Flank|PQLC2_uc001bbz.2_Intron|PQLC2_uc001bca.2_Intron|PQLC2_uc001bcb.2_Intron|PQLC2_uc001bcc.2_Intron	NM_017765	NP_060235	Q6ZP29	PQLC2_HUMAN	PQ loop repeat containing 2 isoform 1							integral to membrane					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GACTATATGGTTTtttttttg	0.259													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20594605	20594606	+	IGR	INS	-	C	C	rs146897685	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20594605_20594606insC								UBXN10 (74664 upstream) : VWA5B1 (22806 downstream)																							CTGTGAACCCTCCCCCTGCAGC	0.347													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22125418	22125418	+	IGR	DEL	T	-	-	rs67336070		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22125418delT								USP48 (15730 upstream) : LDLRAD2 (13340 downstream)																							tttcttcttcttttttttttt	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22881578	22881583	+	IGR	DEL	CACGCG	-	-	rs5012140	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22881578_22881583delCACGCG								ZBTB40 (23928 upstream) : EPHA8 (8421 downstream)																							cacacacacacacgcgcgcgcgcgcg	0.248													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	23410469	23410470	+	IGR	INS	-	TT	TT	rs141111131	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23410469_23410470insTT								KDM1A (285 upstream) : LUZP1 (46 downstream)																							TATTAGGAAACTTTGGATGCAC	0.485													3	5	---	---	---	---	
GRHL3	57822	broad.mit.edu	37	1	24671547	24671548	+	Intron	INS	-	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24671547_24671548insC	uc001biy.2	+						GRHL3_uc001bix.2_Intron|GRHL3_uc001biz.2_Intron	NM_021180	NP_067003	Q8TE85	GRHL3_HUMAN	sister-of-mammalian grainyhead protein isoform						regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		CCACACCTGTGCCCCTCCACAC	0.668													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31551036	31551036	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31551036delT								PUM1 (12273 upstream) : NKAIN1 (101557 downstream)																							CTAGCTTGTCttttttttttt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31909152	31909153	+	IGR	INS	-	T	T	rs144508675	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31909152_31909153insT								SERINC2 (1628 upstream) : LOC284551 (74883 downstream)																							CAAGTGGGCAAttttttttttc	0.213													4	2	---	---	---	---	
COL16A1	1307	broad.mit.edu	37	1	32165094	32165095	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32165094_32165095delCA	uc001btk.1	-						COL16A1_uc001btj.1_5'Flank|COL16A1_uc001btl.3_Intron	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		cgcatgtgcgcacacacacaca	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	32474307	32474308	+	IGR	INS	-	GTTT	GTTT	rs111904301		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32474307_32474308insGTTT								PTP4A2 (70319 upstream) : KHDRBS1 (5183 downstream)																							ctctgTTTTTGgtttgtttgtt	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33771916	33771916	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33771916delT								ZNF362 (5596 upstream) : PHC2 (17308 downstream)																							atgtttcctcttttgtatctc	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34913748	34913748	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34913748delC								C1orf94 (229019 upstream) : MIR552 (221452 downstream)																							GGgtctgcttcccttcatgct	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38254740	38254741	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38254740_38254741insA								EPHA10 (23916 upstream) : MANEAL (5033 downstream)																							catctctaccgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	50810117	50810118	+	IGR	INS	-	TCTTTACGCA	TCTTTACGCA	rs141486984	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50810117_50810118insTCTTTACGCA								ELAVL4 (142577 upstream) : DMRTA2 (73111 downstream)																							TTACGCATCTTTCTCCCAGAAA	0.416													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51681853	51681853	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51681853delT								C1orf185 (68101 upstream) : RNF11 (20092 downstream)																							tctctttctcttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56051517	56051517	+	Intron	DEL	C	-	-	rs11326567		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56051517delC	uc001cyi.1	+											SubName: Full=cDNA FLJ45337 fis, clone BRHIP3007960;																		ctttttttttctctctctttt	0.085													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56070242	56070243	+	Intron	INS	-	T	T	rs151235799		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56070242_56070243insT	uc001cyi.1	+											SubName: Full=cDNA FLJ45337 fis, clone BRHIP3007960;																		CTTCTCCTGCCTTTTTTTTTTT	0.421													5	3	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58783236	58783236	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58783236delC	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						aacattggtgcccccctggct	0.000													4	2	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62246330	62246331	+	Intron	INS	-	T	T	rs34053510		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62246330_62246331insT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TTGGAGTGGCATTTTTTTTTTT	0.292													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68759279	68759280	+	IGR	INS	-	AC	AC	rs149858749		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68759279_68759280insAC								WLS (61026 upstream) : RPE65 (135227 downstream)																							ACTGCATTAAAacacacacaca	0.386													6	3	---	---	---	---	
AK5	26289	broad.mit.edu	37	1	78022664	78022664	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78022664delT	uc001dhn.2	+						AK5_uc001dho.2_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						ACCCTCTACCTTTTTTTTTTC	0.358													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	81586441	81586442	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81586441_81586442delTG								None (None upstream) : LPHN2 (185403 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.208													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83966804	83966804	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83966804delC								None (None upstream) : TTLL7 (368255 downstream)																							TACTTACATTCCCCTATCGCA	0.448													4	2	---	---	---	---	
MCOLN2	255231	broad.mit.edu	37	1	85434859	85434859	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85434859delC	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		ttacaataaaccagtaaatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91522603	91522604	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91522603_91522604delTG								ZNF644 (34932 upstream) : HFM1 (203720 downstream)																							ACGttttttttgtttgtttttc	0.139													4	2	---	---	---	---	
C1orf146	388649	broad.mit.edu	37	1	92682284	92682285	+	5'Flank	INS	-	T	T	rs72510798	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92682284_92682285insT	uc001doq.2	+						C1orf146_uc010ote.1_5'Flank	NM_001012425	NP_001012425	Q5VVC0	CA146_HUMAN	hypothetical protein LOC388649											ovary(1)	1		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		agcagaatctggcatatagatg	0.005													1	5	---	---	---	---	
RTCD1	8634	broad.mit.edu	37	1	100733959	100733960	+	Intron	INS	-	T	T	rs146892533		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100733959_100733960insT	uc001dtc.2	+						RTCD1_uc010ouh.1_Intron|RTCD1_uc001dtd.2_Intron	NM_003729	NP_003720	O00442	RTC1_HUMAN	RNA terminal phosphate cyclase domain 1 isoform						RNA processing	mitochondrion|nucleoplasm	ATP binding|protein binding|RNA binding|RNA-3'-phosphate cyclase activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0513)|all cancers(265;0.0902)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)		CTACttttatgttttttttttt	0.040													3	4	---	---	---	---	
RTCD1	8634	broad.mit.edu	37	1	100752033	100752034	+	Intron	DEL	CG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100752033_100752034delCG	uc001dtc.2	+						RTCD1_uc001dtd.2_Intron	NM_003729	NP_003720	O00442	RTC1_HUMAN	RNA terminal phosphate cyclase domain 1 isoform						RNA processing	mitochondrion|nucleoplasm	ATP binding|protein binding|RNA binding|RNA-3'-phosphate cyclase activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0513)|all cancers(265;0.0902)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)		aaaaaaaaaacgaaaaaCAAAA	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101093299	101093300	+	IGR	DEL	GT	-	-	rs112016709		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101093299_101093300delGT								GPR88 (85717 upstream) : VCAM1 (91997 downstream)																							CATATtgtgcgtgtgtgtgtgt	0.252													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	105009092	105009092	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105009092delA								AMY1A (801920 upstream) : None (None downstream)																							gaccttgtttaagtttgcgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	106519440	106519440	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106519440delA								None (None upstream) : None (None downstream)																							agctgtggctaaaaggtgcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108091505	108091506	+	IGR	INS	-	TGTT	TGTT	rs141004784		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108091505_108091506insTGTT								NTNG1 (67034 upstream) : VAV3 (22276 downstream)																							ccttgacacactgtctccttct	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	109621685	109621686	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109621685_109621686insA								TAF13 (3061 upstream) : TMEM167B (11717 downstream)																							ctccatctcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112352273	112352274	+	Intron	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112352273_112352274delGT	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		CACATTTCCCgtgtgtgtgtgt	0.198													5	3	---	---	---	---	
TRIM33	51592	broad.mit.edu	37	1	115041254	115041254	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115041254delA	uc001eew.2	-						TRIM33_uc001eex.2_Intron	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		actccatctcaaaaaaaaaag	0.000			T	RET	papillary thyroid								4	2	---	---	---	---	
DENND2C	163259	broad.mit.edu	37	1	115182205	115182205	+	Intron	DEL	A	-	-	rs111485406		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115182205delA	uc001efd.1	-						DENND2C_uc001eez.2_Intron|DENND2C_uc001efc.1_Intron	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-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)		ctccatcttgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118501390	118501391	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118501390_118501391insT	uc001ehk.2	-						WDR3_uc001ehi.2_Intron|WDR3_uc010oxe.1_Intron	NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACTTCTTTGGCTTTTTTTTTTT	0.307													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142574780	142574780	+	IGR	DEL	A	-	-	rs150032502		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142574780delA								None (None upstream) : None (None downstream)																							actctgtctcaaaaaaaaaaa	0.139													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143161859	143161860	+	Intron	INS	-	TTTG	TTTG	rs144570074	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143161859_143161860insTTTG	uc001eiw.1	+						uc001ejf.1_Intron|hsa-mir-3118-2|MI0014132_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		GTTGttgtttatttgtttgttt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143474835	143474835	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143474835delT								None (None upstream) : LOC100286793 (172804 downstream)																							TCATATCGTCTTATTTTTTTA	0.234													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143532978	143532979	+	IGR	INS	-	TG	TG	rs138972237		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143532978_143532979insTG								None (None upstream) : LOC100286793 (114660 downstream)																							ACTTTTTTTTTGTCTTCATACT	0.248													7	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145005442	145005443	+	Intron	INS	-	T	T	rs77544116		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145005442_145005443insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		aaaaaaaaaaaaaaacaaaaca	0.188			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145215122	145215123	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145215122_145215123insT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	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)		TTGTTTGTTTGTTTTTTGAGAG	0.297													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145227546	145227547	+	Intron	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145227546_145227547delGT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	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)		gtgtgtgtgcgtgtgtgtgtgt	0.218													4	2	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	147720385	147720385	+	Intron	DEL	T	-	-	rs111322116		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147720385delT	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						gcattcaccattttttttttt	0.000													5	4	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148349431	148349432	+	5'Flank	INS	-	G	G	rs67020224		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148349431_148349432insG	uc001eqf.2	-						LOC200030_uc001eqe.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'Flank|uc010paw.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GGGCTGACACTGGGGGGCCAGA	0.559													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148854642	148854642	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148854642delA								NBPF16 (96331 upstream) : LOC645166 (73644 downstream)																							CGCGGCGGCGAGGGGGGCAAA	0.697													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149207401	149207406	+	IGR	DEL	TTATTC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149207401_149207406delTTATTC								LOC645166 (254347 upstream) : LOC388692 (72070 downstream)																							aGTCAAGAAATTAttcttattcttta	0.024													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149224051	149224051	+	IGR	DEL	A	-	-	rs67690860		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149224051delA								LOC645166 (270997 upstream) : LOC388692 (55425 downstream)																							TTTAAACTACAAAAAATcagg	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149227975	149227976	+	5'Flank	INS	-	C	C	rs144607986	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149227975_149227976insC	uc010pbe.1	+											Homo sapiens cDNA clone IMAGE:4734071, partial cds.																		ctgaacagactccctcttggct	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149272669	149272690	+	IGR	DEL	GGCTTAGCCAAGGAGAGTTCTT	-	-	rs150844468		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149272669_149272690delGGCTTAGCCAAGGAGAGTTCTT								LOC645166 (319615 upstream) : LOC388692 (6786 downstream)																							ccaaaattggggcttagccaaggagagttcttggctttgccc	0.009													4	2	---	---	---	---	
VPS45	11311	broad.mit.edu	37	1	150054597	150054597	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150054597delA	uc001etp.2	+						VPS45_uc010pbp.1_Intron|VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron|VPS45_uc009wlm.1_Intron	NM_007259	NP_009190	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			actctgtctcaaaaaaaaaaa	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152506888	152506889	+	IGR	INS	-	A	A	rs150512742	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152506888_152506889insA								CRCT1 (18408 upstream) : LCE3E (31242 downstream)																							AAAGGTGGCGCCGTTCTGTACA	0.545													4	2	---	---	---	---	
TDRD10	126668	broad.mit.edu	37	1	154507319	154507319	+	Intron	DEL	G	-	-	rs113936460		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154507319delG	uc009wow.2	+						TDRD10_uc001ffd.2_Intron|TDRD10_uc001ffe.2_Intron	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a								nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			gcagtgttcaggtcagcgtgg	0.035													3	5	---	---	---	---	
DCST2	127579	broad.mit.edu	37	1	154993916	154993916	+	Intron	DEL	T	-	-	rs112439021		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154993916delT	uc001fgm.2	-						DCST2_uc009wpb.2_Intron	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			cccATCCCCCTACTTGATTTC	0.085													5	4	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155360742	155360743	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155360742_155360743insT	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			acctgCCTGTGttttttttttt	0.020													4	3	---	---	---	---	
IQGAP3	128239	broad.mit.edu	37	1	156541258	156541259	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156541258_156541259delCA	uc001fpf.2	-						IQGAP3_uc009wsb.1_Intron	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CACATGCGTGCACACACACACA	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157306180	157306181	+	IGR	INS	-	AGTT	AGTT	rs140101871	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157306180_157306181insAGTT								ETV3 (197797 upstream) : FCRL5 (176987 downstream)																							agttctcactcagttcacacga	0.000													5	4	---	---	---	---	
KCNJ9	3765	broad.mit.edu	37	1	160051116	160051116	+	5'Flank	DEL	T	-	-	rs77918900		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160051116delT	uc001fuy.1	+						KCNJ9_uc001fux.1_5'Flank|KCNJ9_uc009wte.1_5'Flank	NM_004983	NP_004974	Q92806	IRK9_HUMAN	potassium inwardly-rectifying channel subfamily						synaptic transmission	integral to membrane|plasma membrane	G-protein activated inward rectifier potassium channel activity|protein binding			ovary(1)|skin(1)	2	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			tttcttcttcttttttttttt	0.423													4	2	---	---	---	---	
ATF6	22926	broad.mit.edu	37	1	161914747	161914747	+	Intron	DEL	G	-	-	rs72633698		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161914747delG	uc001gbr.2	+							NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			TAAATGCAGTGTTTGGCATTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162793601	162793602	+	IGR	DEL	TC	-	-	rs68015535		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162793601_162793602delTC								HSD17B7 (10994 upstream) : C1orf110 (646 downstream)																							ACATGGGCATtctctctctctc	0.173													4	2	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164680512	164680512	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164680512delT	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						ttctcttttctttttttgaaa	0.229			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								4	2	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165191181	165191182	+	Intron	INS	-	ACAT	ACAT	rs148884855	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165191181_165191182insACAT	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					cacacacacacgcacacgcaca	0.134													3	3	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165247351	165247354	+	Intron	DEL	AAGG	-	-	rs71759641		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165247351_165247354delAAGG	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					taacttggccaaggaaggtcacaa	0.054													4	2	---	---	---	---	
SELP	6403	broad.mit.edu	37	1	169590667	169590676	+	Intron	DEL	TGTGTGTGTG	-	-	rs113988780		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169590667_169590676delTGTGTGTGTG	uc001ggi.3	-						SELP_uc001ggh.2_5'Flank|SELP_uc009wvr.2_Intron	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor						platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	AGTGTGAGGTtgtgtgtgtgtgtgtgtgtg	0.443													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174201898	174201899	+	Intron	INS	-	A	A	rs71735162		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174201898_174201899insA	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						gacgccatctcaaaaaaaaaaa	0.163													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175563376	175563376	+	Intron	DEL	T	-	-	rs113397882		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175563376delT	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)					CCTCTGAGCATTTTTTTTTTC	0.428													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175678445	175678448	+	Intron	DEL	ACAC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175678445_175678448delACAC	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)					acacacacatacacacacacacac	0.304													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175742192	175742197	+	IGR	DEL	GGAGAA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175742192_175742197delGGAGAA								TNR (29440 upstream) : RFWD2 (171770 downstream)																							ggaggaggagggagaaggagaaggag	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176314147	176314148	+	IGR	INS	-	G	G	rs142313615	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176314147_176314148insG								RFWD2 (137777 upstream) : PAPPA2 (118159 downstream)																							ctggacatctaggctttactgt	0.000													4	2	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176778843	176778843	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176778843delA	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						GAAGAGGTAGAGAGTAGCTGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177307006	177307007	+	IGR	INS	-	T	T	rs145966399	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177307006_177307007insT								FAM5B (55449 upstream) : SEC16B (590482 downstream)																							agatgtgtttgttatatacgtg	0.000													4	4	---	---	---	---	
ACBD6	84320	broad.mit.edu	37	1	180370923	180370924	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180370923_180370924insA	uc001gog.2	-							NM_032360	NP_115736	Q9BR61	ACBD6_HUMAN	acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1						attctgtccagaaaaaaaaaaa	0.158													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181094404	181094404	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181094404delA								IER5 (34427 upstream) : CACNA1E (358312 downstream)																							tgaagaaaataaaataaagta	0.095													4	2	---	---	---	---	
RGSL1	353299	broad.mit.edu	37	1	182526979	182526979	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182526979delA	uc009wxw.2	+						RGSL1_uc009wxx.1_Intron	NM_001137669	NP_001131141	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1							integral to membrane	signal transducer activity			central_nervous_system(1)	1						TCCCAGATCTAACATGTTCTA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	186965453	186965454	+	IGR	INS	-	CA	CA	rs35771151		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186965453_186965454insCA								PLA2G4A (7348 upstream) : None (None downstream)																							CAGATGACCAGcacacacacac	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	189980610	189980610	+	IGR	DEL	T	-	-	rs34097675		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189980610delT								None (None upstream) : FAM5C (86187 downstream)																							gtaccaatccttttgacacta	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191977591	191977594	+	IGR	DEL	GAAG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191977591_191977594delGAAG								None (None upstream) : RGS18 (149998 downstream)																							aacagtacaagaaggaaggaagga	0.000													3	3	---	---	---	---	
CDC73	79577	broad.mit.edu	37	1	193137661	193137661	+	Intron	DEL	T	-	-	rs78606230		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193137661delT	uc001gtb.2	+							NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						taactctgccttttttttttt	0.000									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				3	3	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202174542	202174543	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202174542_202174543delAC	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						acacctccaaacacacacacac	0.045													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	204150189	204150190	+	IGR	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204150189_204150190delGT								REN (14724 upstream) : KISS1 (9280 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.431													4	2	---	---	---	---	
PIK3C2B	5287	broad.mit.edu	37	1	204449022	204449022	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204449022delC	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TCCCATCCAGCCAGGGCACCA	0.562													4	2	---	---	---	---	
TMCC2	9911	broad.mit.edu	37	1	205235739	205235739	+	Intron	DEL	A	-	-	rs1779412	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205235739delA	uc001hbz.1	+						TMCC2_uc010prf.1_Intron|TMCC2_uc001hca.2_Intron|TMCC2_uc001hcb.1_Intron|TMCC2_uc001hcc.1_Intron|TMCC2_uc001hcd.2_5'Flank	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2							integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			aaaaacaaataaaaaaaaAAA	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	206670493	206670494	+	IGR	INS	-	T	T	rs41299902	byFrequency	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206670493_206670494insT								IKBKE (271 upstream) : RASSF5 (10385 downstream)																							AGGTATTCTTCTTTTTTTTTTT	0.455													3	3	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208251766	208251766	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208251766delA	uc001hgz.2	-							NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TGAAGCAGGGAAAAGGATGGT	0.473													4	2	---	---	---	---	
BATF3	55509	broad.mit.edu	37	1	212869935	212869936	+	Intron	INS	-	T	T	rs142147899	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212869935_212869936insT	uc001hjl.1	-							NM_018664	NP_061134	Q9NR55	BATF3_HUMAN	basic leucine zipper transcription factor,						transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)		GACAACAGGTGTAACTACTCTT	0.337													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	217419503	217419504	+	IGR	DEL	GT	-	-	rs149761658		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217419503_217419504delGT								ESRRG (108406 upstream) : GPATCH2 (184330 downstream)																							TGTGTGTTGCGTGTGTGTTGTA	0.243													2	4	---	---	---	---	
IARS2	55699	broad.mit.edu	37	1	220307287	220307287	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220307287delA	uc001hmc.2	+						IARS2_uc001hmd.2_5'Flank	NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	tggaaagaggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223361295	223361295	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223361295delC								TLR5 (44671 upstream) : SUSD4 (32868 downstream)																							ctggaaacaacccccgtgtcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226699485	226699486	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226699485_226699486delTG								PARP1 (103684 upstream) : C1orf95 (37015 downstream)																							accaatagaatgtgtgtgtgtg	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229884527	229884528	+	IGR	INS	-	CAAA	CAAA	rs150323046	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229884527_229884528insCAAA								URB2 (88581 upstream) : GALNT2 (309008 downstream)																							aaactctgtctcaaacaaacaa	0.000													5	4	---	---	---	---	
CAPN9	10753	broad.mit.edu	37	1	230886160	230886160	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230886160delC	uc001htz.1	+						CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Intron	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1						digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CATTCTCGTACCCCTATCTGT	0.423													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231807043	231807043	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231807043delT	uc001huz.2	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc010pwm.1_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				cttttcattatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232729914	232729914	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232729914delA								SIPA1L2 (78671 upstream) : KIAA1383 (210724 downstream)																							GTCGGACTAGAACAGGCTTGT	0.498													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233127233	233127233	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233127233delC	uc001hvl.2	-						PCNXL2_uc001hvk.1_Intron|PCNXL2_uc001hvm.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				catgttccctccccagactcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234722895	234722896	+	IGR	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234722895_234722896delTC								TARBP1 (108046 upstream) : IRF2BP2 (17121 downstream)																							GTTAATCAAATCTCTCTCTCTC	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234869071	234869072	+	IGR	INS	-	ACAG	ACAG	rs144648710	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234869071_234869072insACAG								IRF2BP2 (123800 upstream) : TOMM20 (403588 downstream)																							ctggaaagaccacaggccctga	0.223													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235007425	235007425	+	IGR	DEL	C	-	-	rs113762650		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235007425delC								IRF2BP2 (262154 upstream) : TOMM20 (265235 downstream)																							CCAGCCAAGACAAAAGGTAAC	0.418													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235053412	235053413	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235053412_235053413delGA								IRF2BP2 (308141 upstream) : TOMM20 (219247 downstream)																							tcacatggtggagagagagagg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238877695	238877696	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238877695_238877696delGA								LOC339535 (228378 upstream) : CHRM3 (672169 downstream)																							CAAGAGCTCTGAGAGAGAGAGA	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242080137	242080137	+	IGR	DEL	T	-	-	rs34707443		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242080137delT								EXO1 (27090 upstream) : MAP1LC3C (78655 downstream)																							tttttttgtcttttttttttt	0.164													4	3	---	---	---	---	
PLD5	200150	broad.mit.edu	37	1	242572759	242572759	+	Intron	DEL	A	-	-	rs75430640		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242572759delA	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)			TGGTGCAAGCAGAAGCTGAAA	0.418													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244450407	244450418	+	IGR	DEL	GCTGGGATTACA	-	-	rs112323189		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244450407_244450418delGCTGGGATTACA								ZNF238 (229631 upstream) : C1orf100 (65519 downstream)																							ctcccaaagtgctgggattacaggcgtgagcc	0.024													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	245060944	245060944	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245060944delG								HNRNPU (33117 upstream) : EFCAB2 (72227 downstream)																							gtggagaggtggagggaacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	245104394	245104395	+	IGR	DEL	AC	-	-	rs112475238		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245104394_245104395delAC								HNRNPU (76567 upstream) : EFCAB2 (28776 downstream)																							ctgtctcaaaacacacacacac	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	246700146	246700146	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246700146delG								SMYD3 (29532 upstream) : TFB2M (3722 downstream)																							ccttacagcagggacaatagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247953070	247953070	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247953070delT								OR1C1 (31362 upstream) : OR14A16 (25032 downstream)																							tctgtctgcattttactgttc	0.000													4	2	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	2184755	2184756	+	Intron	INS	-	CT	CT	rs149254565	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2184755_2184756insCT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		tgtgtgtgtacctgtgtgtgct	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2587392	2587393	+	IGR	DEL	GG	-	-	rs113069189		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2587392_2587393delGG								MYT1L (252347 upstream) : TSSC1 (605348 downstream)																							GGACTCAGCTGGGGGCACAGCA	0.386													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4517860	4517861	+	IGR	INS	-	GAGGAA	GAGGAA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4517860_4517861insGAGGAA								ALLC (767602 upstream) : None (None downstream)																							acaaggaggaggaggagaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5495520	5495520	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5495520delA								None (None upstream) : SOX11 (337279 downstream)																							GCTAACCTGGAAAAGACATGT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7456340	7456340	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7456340delA								RNF144A (272033 upstream) : LOC339788 (606218 downstream)																							gacattctggaaaagaaagga	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12281564	12281565	+	Intron	INS	-	TGTA	TGTA	rs10174466	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12281564_12281565insTGTA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		gtgtgtgtgtgtgtttgtgAAG	0.411													4	2	---	---	---	---	
RAD51AP2	729475	broad.mit.edu	37	2	17696275	17696275	+	Intron	DEL	A	-	-	rs34060092		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17696275delA	uc002rcl.1	-						RAD51AP2_uc010exn.1_Intron	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCTTGCTGGAAAAAAAAAAA	0.308													5	3	---	---	---	---	
EFR3B	22979	broad.mit.edu	37	2	25280281	25280282	+	Intron	INS	-	A	A	rs111600205		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25280281_25280282insA	uc010eyh.2	+						EFR3B_uc002rfw.2_Intron	NM_014971	NP_055786	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B								binding				0						gcatggctaACAAAAAAAAAAA	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	27399157	27399157	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27399157delT								TCF23 (23424 upstream) : SLC5A6 (23302 downstream)																							gcacagtggctcacacctgta	0.000													3	4	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28361616	28361616	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28361616delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					aggcatcctatttttgacctc	0.129													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28406606	28406607	+	Intron	INS	-	CTCTCACACA	CTCTCACACA	rs142432868	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28406606_28406607insCTCTCACACA	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					TGGATGAAGATcacacacacac	0.342													3	4	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29860575	29860576	+	Intron	INS	-	AAA	AAA	rs70958274		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29860575_29860576insAAA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	actccgtctccaaaaaaaaaaa	0.000			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	31527244	31527245	+	IGR	DEL	CT	-	-	rs77163982		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31527244_31527245delCT								EHD3 (35985 upstream) : XDH (29943 downstream)																							TCTCGACACCCTAAGGAATGGC	0.530													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	31541509	31541510	+	IGR	INS	-	T	T	rs74524668		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31541509_31541510insT								EHD3 (50250 upstream) : XDH (15678 downstream)																							GTCATTTTTCCTTTTTTTTTTT	0.431													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	32270778	32270778	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32270778delA								MEMO1 (5916 upstream) : SPAST (17902 downstream)																							ccctgtcttgaaaaaaaaaaa	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37976146	37976146	+	IGR	DEL	T	-	-	rs67724115		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37976146delT								CDC42EP3 (76820 upstream) : FAM82A1 (176316 downstream)																							TTGATTTATATTCAGTTAGAA	0.373													5	4	---	---	---	---	
C2orf58	285154	broad.mit.edu	37	2	38371694	38371695	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38371694_38371695delCA	uc010faj.1	+							NR_027252				Homo sapiens chromosome 2 open reading frame 58, mRNA (cDNA clone IMAGE:5197672).												0						tctctacatgcacacacacaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51768966	51768966	+	IGR	DEL	A	-	-	rs11693342		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51768966delA								NRXN1 (509292 upstream) : None (None downstream)																							gcaaaacaggaaaaaaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56079904	56079904	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56079904delG								PNPT1 (158893 upstream) : EFEMP1 (13199 downstream)																							atatttatttgggaatagggt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58731267	58731267	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58731267delG								FANCL (262752 upstream) : None (None downstream)																							gcttgtacaaggacagagaag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66355494	66355495	+	IGR	INS	-	TCCC	TCCC	rs150726147	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66355494_66355495insTCCC								SPRED2 (695838 upstream) : MEIS1 (307037 downstream)																							cctgcctttcttccctccctcc	0.243													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73524770	73524770	+	IGR	DEL	T	-	-	rs77845457		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73524770delT								EGR4 (3941 upstream) : ALMS1 (88116 downstream)																							ccactccCTCTTTTTTTTTTC	0.264													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82961639	82961639	+	IGR	DEL	T	-	-	rs76657459		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82961639delT								None (None upstream) : None (None downstream)																							TCTGCTCTGCTTTTTTTTTTT	0.333													5	3	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87588348	87588349	+	Intron	INS	-	GA	GA	rs147207680		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87588348_87588349insGA	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						aatgatgaaatgatgagatgag	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90048090	90048091	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90048090_90048091delCA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		cacacacactcacacacacaca	0.238													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90468342	90468350	+	IGR	DEL	AAGATGGTG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90468342_90468350delAAGATGGTG								None (None upstream) : None (None downstream)																							cagcctggccaagatggtgaaaccccatc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91629286	91629287	+	IGR	DEL	TA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91629286_91629287delTA								None (None upstream) : LOC654342 (175905 downstream)																							ACAGCATcattatatgacagaa	0.124													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92041823	92041823	+	IGR	DEL	C	-	-	rs143409613		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92041823delC								GGT8P (71670 upstream) : FKSG73 (87336 downstream)																							aaacagaaaacaaaaacaatg	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92097334	92097334	+	IGR	DEL	C	-	-	rs12479288		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92097334delC								GGT8P (127181 upstream) : FKSG73 (31825 downstream)																							aagaaaaaaacaacccatcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95751661	95751661	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95751661delT								MAL (31926 upstream) : MRPS5 (1292 downstream)																							tttatgacaattttttttttt	0.000													5	3	---	---	---	---	
NCAPH	23397	broad.mit.edu	37	2	97022407	97022407	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97022407delC	uc002svz.1	+						NCAPH_uc010fhu.1_Intron|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				ATGGcaggctccagtccacac	0.194													4	2	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101666296	101666296	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101666296delT	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron|TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						GCTACATGTCttttttttttt	0.164													5	3	---	---	---	---	
MAP4K4	9448	broad.mit.edu	37	2	102499800	102499800	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102499800delT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_Intron|MAP4K4_uc002tbl.2_Intron	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						ACCAAAACTCttttttttttt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108599550	108599550	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108599550delT								RGPD4 (90551 upstream) : SLC5A7 (3445 downstream)																							TGAAATGACCTTTTTTTTATT	0.229													4	2	---	---	---	---	
SULT1C2	6819	broad.mit.edu	37	2	108919566	108919567	+	Intron	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108919566_108919567delAG	uc002tdy.2	+						SULT1C2_uc010ywp.1_Intron|SULT1C2_uc002tdx.2_Intron|SULT1C2_uc010ywq.1_Intron	NM_001056	NP_001047	O00338	ST1C2_HUMAN	sulfotransferase family, cytosolic, 1C, member 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine metabolic process|sulfation|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	sulfotransferase activity			ovary(1)	1						AAGTTGGAGAAGAGAAGATGGG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121221282	121221282	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121221282delC								INHBB (111899 upstream) : LOC84931 (629 downstream)																							CCTGGTCCTGCCATTGGCAGG	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123117081	123117082	+	IGR	INS	-	CT	CT	rs138576392	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123117081_123117082insCT								TSN (591655 upstream) : None (None downstream)																							tcctcttcctccccttcctcct	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123228934	123228935	+	IGR	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123228934_123228935delAG								TSN (703508 upstream) : None (None downstream)																							TACTTAAGGCagagagagagag	0.297													2	4	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	124993065	124993065	+	Intron	DEL	T	-	-	rs145473146		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124993065delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		cctgaccaagttggtgtataa	0.174													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132799958	132799960	+	IGR	DEL	AAG	-	-	rs150266949		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132799958_132799960delAAG								C2orf27B (240724 upstream) : NCRNA00164 (105204 downstream)																							gaaggagagaaagaagaagagaa	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133024477	133024478	+	IGR	DEL	GA	-	-	rs139217167	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133024477_133024478delGA								NCRNA00164 (8935 upstream) : GPR39 (149669 downstream)																							gacagacagggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133087871	133087872	+	IGR	INS	-	T	T	rs148498305	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133087871_133087872insT								NCRNA00164 (72329 upstream) : GPR39 (86275 downstream)																							aacccacgtgatttttttttct	0.000													4	3	---	---	---	---	
GPR39	2863	broad.mit.edu	37	2	133380971	133380971	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133380971delG	uc002ttl.2	+							NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0						GGCGCCTGAAGGGAAGGAGAG	0.403													4	2	---	---	---	---	
TMEM163	81615	broad.mit.edu	37	2	135214034	135214035	+	3'UTR	INS	-	A	A	rs149902154	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135214034_135214035insA	uc002ttx.2	-	8					TMEM163_uc002tty.2_RNA	NM_030923	NP_112185	Q8TC26	TM163_HUMAN	transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)		CTCCAGAGACTAAAAAACGCCA	0.554													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	144582902	144582930	+	IGR	DEL	CTTTCCTCTTCTTCCTTAATACAGATTTC	-	-	rs149474687		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144582902_144582930delCTTTCCTCTTCTTCCTTAATACAGATTTC								ARHGAP15 (56982 upstream) : GTDC1 (120653 downstream)																							GTGCTATGGGCTTTCCTCTTCTTCCTTAATACAGATTTCCTTTCCTCCT	0.358													3	3	---	---	---	---	
ZEB2	9839	broad.mit.edu	37	2	145272632	145272632	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145272632delC	uc002tvu.2	-						ZEB2_uc002tvv.2_Intron|ZEB2_uc010zbm.1_Intron|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Intron|ZEB2_uc002tvw.2_Intron|ZEB2_uc002tvx.1_Intron|ZEB2_uc002tvy.2_Intron|ZEB2_uc002tvz.2_Intron|ZEB2_uc002twa.2_Intron	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b							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)		ACTGCTAGGGCCAGGCTGGTC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146395555	146395556	+	IGR	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146395555_146395556delGT								None (None upstream) : PABPC1P2 (949069 downstream)																							gcacgcatgcgtgtgtgtgtgt	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	154618723	154618727	+	IGR	DEL	CTCTC	-	-	rs10604149		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154618723_154618727delCTCTC								RPRM (283401 upstream) : GALNT13 (109699 downstream)																							CACTATACTTCTCTCCTCTTTTTTT	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157216787	157216787	+	IGR	DEL	T	-	-	rs78158671		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157216787delT								NR4A2 (27500 upstream) : GPD2 (75178 downstream)																							TGTCAAGATCTTTTTTTTTTA	0.448													4	2	---	---	---	---	
CYTIP	9595	broad.mit.edu	37	2	158291325	158291334	+	Intron	DEL	TCTCTCTCTC	-	-	rs113065609		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158291325_158291334delTCTCTCTCTC	uc002tzj.1	-						CYTIP_uc010zcl.1_Intron	NM_004288	NP_004279	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein						regulation of cell adhesion	cell cortex|early endosome	protein binding			ovary(1)|kidney(1)|skin(1)	3						ATGTTCTAAAtctctctctctctctctctc	0.205													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162151691	162151692	+	IGR	INS	-	TTTG	TTTG	rs138667446	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162151691_162151692insTTTG								TANK (59009 upstream) : PSMD14 (13094 downstream)																							AATTATGTTTttttgttttttg	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164958397	164958397	+	IGR	DEL	A	-	-	rs35182122		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164958397delA								FIGN (365884 upstream) : GRB14 (390936 downstream)																							ctaaaaatacaaaaaaaaaaa	0.000													3	3	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166923992	166923993	+	Intron	INS	-	C	C	rs34449756		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166923992_166923993insC	uc010zcz.1	-							NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha							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)	TTTTTTTTTTTTCCACTGCTGT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170283040	170283040	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170283040delA								LRP2 (63918 upstream) : BBS5 (52966 downstream)																							CAAACCCAGCAAATGCAGAAT	0.562													4	2	---	---	---	---	
GAD1	2571	broad.mit.edu	37	2	171684687	171684688	+	Intron	DEL	CT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171684687_171684688delCT	uc002ugi.2	+						GAD1_uc002ugh.2_Intron	NM_000817	NP_000808	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 isoform GAD67						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	cctcgccctcctctctctgctg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	172116414	172116414	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172116414delA								TLK1 (28590 upstream) : METTL8 (57501 downstream)																							aaaaaagaagaaaaaaaaaag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177920708	177920709	+	IGR	INS	-	AACAAC	AACAAC	rs140275829	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177920708_177920709insAACAAC								MIR1246 (454928 upstream) : HNRNPA3 (156713 downstream)																							ctcaaaaagaaaacaacaacaa	0.193													2	4	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182879128	182879129	+	Intron	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182879128_182879129delTC	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.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)			acaaacagaatctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184773306	184773306	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184773306delT								NUP35 (746899 upstream) : ZNF804A (689787 downstream)																							cttactgtgcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	185908625	185908625	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185908625delC								ZNF804A (104413 upstream) : None (None downstream)																							ttctctgtcacccaggctgga	0.045													4	2	---	---	---	---	
MYO1B	4430	broad.mit.edu	37	2	192121673	192121673	+	Intron	DEL	T	-	-	rs68083534		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192121673delT	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			TTTCTGTGAATTTTTTTTTTA	0.413													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193330099	193330099	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193330099delG								TMEFF2 (270455 upstream) : PCGEM1 (284472 downstream)																							TTCCAGCCCAGGTACACTAAA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193801196	193801197	+	IGR	INS	-	T	T	rs148451752	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193801196_193801197insT								PCGEM1 (159575 upstream) : None (None downstream)																							tccctttagcattcttgtagta	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	194306838	194306839	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194306838_194306839insA								PCGEM1 (665217 upstream) : None (None downstream)																							CCATCTTTGCCAAAAAAAAAAA	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195119962	195119963	+	IGR	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195119962_195119963delCA								None (None upstream) : None (None downstream)																							accctgtgttcacttgctcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207195614	207195615	+	IGR	DEL	CG	-	-	rs34307820		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207195614_207195615delCG								ZDBF2 (16466 upstream) : ADAM23 (112753 downstream)																							cacacacacacgcacgcacgca	0.000													4	2	---	---	---	---	
ADAM23	8745	broad.mit.edu	37	2	207381294	207381295	+	Intron	DEL	AG	-	-	rs78226281	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207381294_207381295delAG	uc002vbq.2	+						ADAM23_uc010ziv.1_Intron	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein						cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		ttcatatggtagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	208950465	208950466	+	IGR	INS	-	TAT	TAT	rs146013187	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208950465_208950466insTAT								PLEKHM3 (60181 upstream) : CRYGD (35866 downstream)																							tttcagaagagtattctccact	0.035													2	4	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210829510	210829510	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210829510delA	uc010zjc.1	+						UNC80_uc002vdk.2_Intron|UNC80_uc002vdl.1_Intron|UNC80_uc010zjd.1_Intron|UNC80_uc010zje.1_Intron	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						actctgtctcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212401108	212401109	+	Intron	INS	-	G	G	rs72546109	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212401108_212401109insG	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		AACCCTAAACTTGAAAGATGGG	0.396										TSP Lung(8;0.080)			4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214926428	214926428	+	Intron	DEL	A	-	-	rs112243936		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214926428delA	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)		atgtttgaccaaaaactggat	0.000													5	3	---	---	---	---	
PECR	55825	broad.mit.edu	37	2	216916026	216916027	+	Intron	DEL	AG	-	-	rs58236871		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216916026_216916027delAG	uc002vft.2	-						PECR_uc010zjq.1_Intron|PECR_uc002vfr.2_Intron|PECR_uc002vfs.2_Intron	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	aaaaaaaaaaagaaaaTTAGGC	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221011563	221011563	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221011563delA								SLC4A3 (504862 upstream) : None (None downstream)																							gcagtgtgagaaggactaata	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221678832	221678833	+	IGR	DEL	TG	-	-	rs34172603		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221678832_221678833delTG								None (None upstream) : EPHA4 (603916 downstream)																							TTGATAAATAtgtgtgtgtgtg	0.243													4	2	---	---	---	---	
CUL3	8452	broad.mit.edu	37	2	225441405	225441406	+	Intron	DEL	GG	-	-	rs71879284		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225441405_225441406delGG	uc002vny.2	-						CUL3_uc010zls.1_Intron	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3						cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		tgaaaaaaaagggggggggggg	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	230961741	230961742	+	IGR	INS	-	C	C	rs138824926	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230961741_230961742insC								FBXO36 (13725 upstream) : SP110 (71903 downstream)																							gctcattgcaactcctcctcta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231418071	231418071	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231418071delA								SP100 (7754 upstream) : CAB39 (159486 downstream)																							caccaacaacaggcaagcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232255034	232255034	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232255034delC								ARMC9 (16428 upstream) : B3GNT7 (5301 downstream)																							ggtacccccgcccccccgcaa	0.000													4	2	---	---	---	---	
USP40	55230	broad.mit.edu	37	2	234397434	234397434	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234397434delC	uc010zmr.1	-						USP40_uc002vul.2_Intron|USP40_uc010zms.1_Intron|USP40_uc002vun.2_Intron	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		tgcctgaggtcccagctacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235247746	235247749	+	IGR	DEL	TCTC	-	-	rs72192359		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235247746_235247749delTCTC								SPP2 (261970 upstream) : ARL4C (153939 downstream)																							cctatctgggtctctctctctctc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236061428	236061429	+	IGR	INS	-	TTCC	TTCC	rs142875227	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236061428_236061429insTTCC								SH3BP4 (97072 upstream) : AGAP1 (341307 downstream)																							cctttctttctttccttccttc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236151149	236151149	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236151149delG								SH3BP4 (186793 upstream) : AGAP1 (251587 downstream)																							AAGTGAAGGAGGACAGCGTCC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239484613	239484613	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239484613delC								ASB1 (123723 upstream) : TWIST2 (272060 downstream)																							tcccctgcgtcccttcaGCCG	0.269													5	3	---	---	---	---	
NDUFA10	4705	broad.mit.edu	37	2	240919013	240919014	+	Intron	DEL	AG	-	-	rs146511504		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240919013_240919014delAG	uc002vyn.2	-							NM_004544	NP_004535	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)	TCTCGGGAAAAGAGACAGTGCc	0.267													2	4	---	---	---	---	
BOK	666	broad.mit.edu	37	2	242505717	242505718	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242505717_242505718insT	uc002wbq.2	+							NM_032515	NP_115904	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer						activation of caspase activity|cell proliferation|signal transduction by p53 class mediator resulting in induction of apoptosis	mitochondrial membrane|nucleus				ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		tttcttttttcttttttttttt	0.045													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	529640	529640	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:529640delT								CHL1 (78545 upstream) : CNTN6 (604980 downstream)																							agattctgccttatttttctt	0.000													4	2	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4731000	4731003	+	Intron	DEL	CACT	-	-	rs144124917		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4731000_4731003delCACT	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		tgcatGCACACACTCACTCACTCA	0.142													4	2	---	---	---	---	
IQSEC1	9922	broad.mit.edu	37	3	13094263	13094263	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13094263delT	uc011auw.1	-							NM_001134382	NP_001127854	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1						gccatgtctgttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14850742	14850742	+	IGR	DEL	A	-	-	rs148790230	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14850742delA								C3orf20 (36202 upstream) : FGD5 (9727 downstream)																							ctccacctctaccaccaccac	0.174													4	2	---	---	---	---	
RAB5A	5868	broad.mit.edu	37	3	20015347	20015347	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20015347delT	uc003cbn.2	+						RAB5A_uc010hey.2_Intron|RAB5A_uc011awg.1_Intron	NM_004162	NP_004153	P20339	RAB5A_HUMAN	RAB5A, member RAS oncogene family						blood coagulation|protein transport|receptor internalization|regulation of filopodium assembly|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GDP binding|GTP binding|GTPase activity				0						ATATATCTCATTAGACTTTGT	0.308													4	2	---	---	---	---	
VENTXP7	391518	broad.mit.edu	37	3	21447901	21447902	+	RNA	INS	-	CC	CC	rs143568999	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21447901_21447902insCC	uc003ccd.2	+	1		c.684_685insCC				NR_002311				Homo sapiens VENT homeobox (Xenopus laevis) pseudogene 7 (VENTXP7), non-coding RNA.												0						CTGGCATACCACCCCCCACGCC	0.663													3	3	---	---	---	---	
NKIRAS1	28512	broad.mit.edu	37	3	23968004	23968005	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23968004_23968005insT	uc003cck.2	-							NM_020345	NP_065078	Q9NYS0	KBRS1_HUMAN	kappa B-ras 1						I-kappaB kinase/NF-kappaB cascade|small GTPase mediated signal transduction	cytoplasm	GTP binding|GTPase activity				0						tcttcctcttcttttttttTGT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	39211939	39211939	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39211939delG								CSRNP1 (15886 upstream) : XIRP1 (12768 downstream)																							ccaaagtgctgggattaccgg	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	44040276	44040276	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44040276delA								ABHD5 (276060 upstream) : MIR138-1 (115428 downstream)																							GGAGGAAAGGAAAAAAAAAAA	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46959394	46959395	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46959394_46959395insT								PTH1R (14108 upstream) : CCDC12 (3825 downstream)																							cctcattttcattttttttttt	0.005													6	3	---	---	---	---	
GNAI2	2771	broad.mit.edu	37	3	50296331	50296331	+	3'UTR	DEL	A	-	-	rs71802167		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50296331delA	uc003cyq.1	+	9					GNAI2_uc003cyo.1_3'UTR|GNAI2_uc003cyp.1_3'UTR|GNAI2_uc010hlg.1_3'UTR|GNAI2_uc011bdn.1_3'UTR|GNAI2_uc003cyr.1_3'UTR|uc003cys.1_5'Flank	NM_002070	NP_002061	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein),						adenosine receptor signaling pathway|cell cycle|cell division|gamma-aminobutyric acid signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|platelet activation|response to nutrient|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		AAAGTAAAGGAAAAAAAAAAA	0.423													2	4	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57882416	57882416	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57882416delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GTGTTTGGGGAAAAAAAAAAC	0.353													9	4	---	---	---	---	
ADAMTS9	56999	broad.mit.edu	37	3	64520453	64520453	+	Intron	DEL	G	-	-	rs11328216		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64520453delG	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc011bfp.1_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		tcacaactgtgggggggcagg	0.030													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99262743	99262743	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99262743delC								DCBLD2 (642210 upstream) : COL8A1 (94711 downstream)																							TGCTTGAGTTCCTCATCTGCT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	107149639	107149640	+	5'Flank	DEL	GT	-	-	rs10526142		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107149639_107149640delGT	uc003dwj.2	+											Homo sapiens cDNA clone IMAGE:5312582.																		gtgtgtgtgcgtgtgtgtgtgt	0.351													4	5	---	---	---	---	
C3orf52	79669	broad.mit.edu	37	3	111838220	111838223	+	Intron	DEL	AACA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111838220_111838223delAACA	uc011bht.1	+						C3orf52_uc003dyr.1_Intron	NM_024616	NP_078892	Q5BVD1	TTMP_HUMAN	TPA-induced transmembrane protein							endoplasmic reticulum membrane|integral to membrane					0						gaaactccataacaaacaaacaaa	0.167													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	113682595	113682595	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113682595delA								ZDHHC23 (384 upstream) : KIAA1407 (391 downstream)																							gtctcaaaacaaaaaaaacac	0.114													4	2	---	---	---	---	
DRD3	1814	broad.mit.edu	37	3	113890131	113890132	+	Intron	INS	-	T	T	rs145915849	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113890131_113890132insT	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	ACATTCACTAATTTTTTTTTTC	0.441													3	4	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115647528	115647529	+	Intron	INS	-	GT	GT	rs149591505	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115647528_115647529insGT	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		CAGAGTGCAGGGGGTGAGGAGG	0.421													3	5	---	---	---	---	
POPDC2	64091	broad.mit.edu	37	3	119372844	119372845	+	Intron	INS	-	G	G	rs138591919	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119372844_119372845insG	uc003ecx.1	-						POPDC2_uc010hqw.1_Intron|POPDC2_uc003ecy.1_Intron	NM_022135	NP_071418	Q9HBU9	POPD2_HUMAN	popeye protein 2							integral to membrane				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.242)		GAAGCTGGTGAGGCTGTGGGGT	0.381													3	3	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	127954784	127954785	+	Intron	INS	-	GTTT	GTTT	rs138995700	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127954784_127954785insGTTT	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						GATGGGCAAAGgtttgtttgtt	0.302													5	3	---	---	---	---	
TMEM108	66000	broad.mit.edu	37	3	132956965	132956966	+	Intron	INS	-	CACA	CACA	rs150613146	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132956965_132956966insCACA	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4						cctccctcactcacacACATAC	0.183													6	3	---	---	---	---	
CEP63	80254	broad.mit.edu	37	3	134266403	134266404	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134266403_134266404insA	uc003eqo.1	+						CEP63_uc003eql.1_Intron|CEP63_uc003eqm.2_Intron|CEP63_uc003eqn.1_Intron|CEP63_uc003eqp.1_5'Flank	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a						cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1						ATAGTCATAGTAAAAAAAATAA	0.178													4	3	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134585531	134585531	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134585531delG	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						GGTTTTTGCAGGACATGCAGC	0.353													4	2	---	---	---	---	
TFDP2	7029	broad.mit.edu	37	3	141698756	141698757	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141698756_141698757insT	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						ctgtttttgggttttttttttt	0.000													4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142251897	142251897	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142251897delC	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						taccagtactcccagaggccc	0.015								Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147480079	147480079	+	IGR	DEL	A	-	-	rs11360904		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147480079delA								ZIC1 (345575 upstream) : AGTR1 (935579 downstream)																							actctgtctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154523222	154523222	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154523222delT								GPR149 (375718 upstream) : MME (218691 downstream)																							ttttctgaacttttatgctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155753126	155753131	+	IGR	DEL	CTCCTT	-	-	rs61125392		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155753126_155753131delCTCCTT								GMPS (97608 upstream) : KCNAB1 (85206 downstream)																							tctcctcctcctccttctccccctcc	0.073													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	156918196	156918196	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156918196delT								CCNL1 (39714 upstream) : VEPH1 (60502 downstream)																							tcttccactcttttttttttt	0.000													2	4	---	---	---	---	
RSRC1	51319	broad.mit.edu	37	3	157944956	157944956	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157944956delT	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			ggggatgttattgcccctatt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163949826	163949826	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163949826delT								MIR1263 (60482 upstream) : MIR720 (109303 downstream)																							TTAAAATGAAttttttttttt	0.119													6	3	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170859451	170859452	+	Intron	DEL	TG	-	-	rs67047406		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170859451_170859452delTG	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ccaaacatcctgtgcaaggcac	0.149													3	4	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170871944	170871947	+	Intron	DEL	AGTT	-	-	rs10565644		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170871944_170871947delAGTT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CACAATAAAAAGTTAGAGGCTTAG	0.363													3	4	---	---	---	---	
NCEH1	57552	broad.mit.edu	37	3	172412183	172412184	+	Intron	DEL	TC	-	-	rs34220450	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172412183_172412184delTC	uc011bpx.1	-						NCEH1_uc003fig.2_Intron|NCEH1_uc011bpw.1_Intron|NCEH1_uc011bpy.1_Intron	NM_001146276	NP_001139748	Q6PIU2	NCEH1_HUMAN	arylacetamide deacetylase-like 1 isoform a						lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0						tgtgtgtgtgtctgtgtgtgtg	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177413783	177413783	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177413783delT								TBL1XR1 (498735 upstream) : KCNMB2 (840441 downstream)																							cctctacccctttttggattc	0.000													4	2	---	---	---	---	
MFN1	55669	broad.mit.edu	37	3	179104879	179104879	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179104879delT	uc003fjs.2	+						MFN1_uc010hxb.2_Intron|MFN1_uc003fjt.2_Intron|MFN1_uc010hxc.2_Intron	NM_033540	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1						mitochondrial fusion	integral to membrane|mitochondrial outer membrane	GTP binding|GTPase activity			ovary(2)|large_intestine(1)	3	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			aattttttaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182479954	182479954	+	IGR	DEL	A	-	-	rs62727060		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182479954delA								None (None upstream) : ATP11B (31337 downstream)																							gactccatcCAAAAAAAAAAA	0.194													4	2	---	---	---	---	
C3orf70	285382	broad.mit.edu	37	3	184803980	184803980	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184803980delT	uc003fpd.2	-							NM_001025266	NP_001020437	A6NLC5	CC070_HUMAN	hypothetical protein LOC285382												0						ACTCCATCTCTTTTTTTTTCC	0.443													4	2	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185383106	185383108	+	Intron	DEL	AGA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185383106_185383108delAGA	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			gagcagaaggagaaggaggagga	0.000													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187970154	187970154	+	Intron	DEL	C	-	-	rs59363696		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187970154delC	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		gtttttttttcctctctctct	0.000			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188353879	188353879	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188353879delC	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		gtctacagctcccagcctgag	0.085			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190098016	190098029	+	IGR	DEL	TTCTTCCTTCCCTC	-	-	rs71750965	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190098016_190098029delTTCTTCCTTCCCTC								CLDN1 (57801 upstream) : CLDN16 (7812 downstream)																							ttccttccttttcttccttccctcccttccttcc	0.079													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190424837	190424838	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190424837_190424838insT								IL1RAP (48994 upstream) : LOC647309 (145688 downstream)																							atgcctggctattttttttttc	0.000													3	4	---	---	---	---	
LRRC15	131578	broad.mit.edu	37	3	194092595	194092596	+	5'Flank	DEL	AT	-	-	rs112884343	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194092595_194092596delAT	uc003ftu.2	-						LRRC15_uc003ftt.2_5'Flank	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b							integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		acacaaacacatacacacacac	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195237037	195237037	+	IGR	DEL	A	-	-	rs79705699		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195237037delA								ACAP2 (73220 upstream) : PPP1R2 (4186 downstream)																							ctgtctcaggaaaaaaaaaaa	0.040													4	2	---	---	---	---	
MUC20	200958	broad.mit.edu	37	3	195462031	195462032	+	3'UTR	INS	-	T	T	rs139052122	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195462031_195462032insT	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		cctcggcaccgtctttattccc	0.000													5	3	---	---	---	---	
MUC20	200958	broad.mit.edu	37	3	195462634	195462635	+	3'UTR	INS	-	TTTA	TTTA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195462634_195462635insTTTA	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		gtcatacatattttgttttctt	0.000													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195473757	195473758	+	3'UTR	DEL	GT	-	-	rs71634711		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195473757_195473758delGT	uc011bto.1	-	26					MUC4_uc010hzq.2_3'UTR|MUC4_uc003fuz.2_3'UTR|MUC4_uc003fva.2_3'UTR|MUC4_uc003fvb.2_3'UTR|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_3'UTR|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_3'UTR|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_3'UTR|MUC4_uc011bti.1_3'UTR|MUC4_uc011btj.1_3'UTR|MUC4_uc011btk.1_3'UTR|MUC4_uc011btl.1_3'UTR|MUC4_uc011btm.1_3'UTR|MUC4_uc011btn.1_3'UTR|MUC4_uc003fvo.2_3'UTR|MUC4_uc003fvp.2_3'UTR	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTATGAACTCgtgtgtgtgtgt	0.401													3	3	---	---	---	---	
SDHAP1	255812	broad.mit.edu	37	3	195714613	195714614	+	Intron	INS	-	A	A	rs139057401		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195714613_195714614insA	uc011btq.1	-						SDHAP1_uc003fvx.3_Intron|SDHAP1_uc011btp.1_Intron					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						aaaaacaaaagaaaaaaaaaaG	0.163													3	3	---	---	---	---	
WDR53	348793	broad.mit.edu	37	3	196294623	196294624	+	Intron	DEL	TG	-	-	rs35058038		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196294623_196294624delTG	uc003fwt.2	-						FBXO45_uc010iai.2_5'Flank	NM_182627	NP_872433	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53											breast(1)|skin(1)	2	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		CTGAAATTCTtgtgtgtgtgtg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197043150	197043151	+	IGR	DEL	AG	-	-	rs34675924		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197043150_197043151delAG								DLG1 (17007 upstream) : BDH1 (193504 downstream)																							cacattaaacagtgtctctgca	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37801	37801	+	IGR	DEL	T	-	-	rs146978263		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37801delT								None (None upstream) : ZNF595 (15426 downstream)																							taaaattctcttttttttttg	0.000													5	5	---	---	---	---	
GAK	2580	broad.mit.edu	37	4	863528	863529	+	Intron	INS	-	CA	CA	rs138892904	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:863528_863529insCA	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc010ibk.1_Intron|GAK_uc010ibi.2_5'Flank|GAK_uc010ibj.2_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase						cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		acacatgaatgcacacagtaca	0.040													4	3	---	---	---	---	
C4orf42	92070	broad.mit.edu	37	4	1276179	1276179	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1276179delA	uc003gcy.1	+											Homo sapiens cDNA FLJ31571 fis, clone NT2RI2001726.											ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0101)	Colorectal(103;0.188)		aagcaacaataaaaaaaaaaa	0.000													4	2	---	---	---	---	
C4orf50	389197	broad.mit.edu	37	4	5981742	5981743	+	Intron	INS	-	T	T	rs60012784	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5981742_5981743insT	uc003git.1	-							NM_207405	NP_997288	Q6ZRC1	CD050_HUMAN	hypothetical protein LOC389197											pancreas(2)|breast(1)	3						GTTTTTTGTTGTTTTTTTTTTC	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6745204	6745205	+	IGR	INS	-	TCTCCT	TCTCCT	rs139389744	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6745204_6745205insTCTCCT								CNO (25817 upstream) : KIAA0232 (39254 downstream)																							cttccccttcctctccttctcc	0.124													6	4	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7843634	7843634	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7843634delG	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						agggagaggagggcaggggag	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9742024	9742025	+	IGR	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9742024_9742025delTT								MIR548I2 (184087 upstream) : DRD5 (41233 downstream)																							tctctctctctttctttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13774896	13774897	+	Intron	INS	-	A	A	rs150635363	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13774896_13774897insA	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																		aggcgtgagcccagcgcctggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15244730	15244730	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15244730delT								CPEB2 (172956 upstream) : C1QTNF7 (96830 downstream)																							ATAAGTTCACttttttttttt	0.184													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19029280	19029280	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19029280delG								None (None upstream) : None (None downstream)																							AGGATCCTAAGGAAAGGCAGA	0.408													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21261508	21261509	+	Intron	INS	-	TG	TG	rs141943032	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21261508_21261509insTG	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				GCGCCCAAGACtgtgtgtgtgt	0.366													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31697427	31697428	+	IGR	DEL	TG	-	-	rs35293741		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31697427_31697428delTG								PCDH7 (549006 upstream) : None (None downstream)																							atatagttaatgtgtgtgtgtg	0.000													5	3	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39237897	39237898	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39237897_39237898delAC	uc003gtv.2	+						WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						aatgtggtatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	39808541	39808541	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39808541delA								UBE2K (24133 upstream) : PDS5A (15943 downstream)																							gctctgtttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
LIMCH1	22998	broad.mit.edu	37	4	41426160	41426160	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41426160delC	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						ACGTAGGGctccctctttccc	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49114594	49114598	+	IGR	DEL	ATGAA	-	-	rs146572145	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49114594_49114598delATGAA								CWH43 (50501 upstream) : None (None downstream)																							attccattccatgaaattccattcc	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49118535	49118543	+	IGR	DEL	TTGCGTTGT	-	-	rs148482734	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49118535_49118543delTTGCGTTGT								CWH43 (54442 upstream) : None (None downstream)																							taccattgcattgcgttgtttccattcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49142416	49142417	+	IGR	INS	-	TTCCC	TTCCC	rs140060257	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49142416_49142417insTTCCC								CWH43 (78323 upstream) : None (None downstream)																							tttccattcctctcgtgttgat	0.000													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54556281	54556282	+	Intron	INS	-	T	T	rs140329710	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54556281_54556282insT	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	atttgcttctcgtacactttta	0.000			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55378614	55378615	+	IGR	INS	-	AGAG	AGAG	rs146171334		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55378614_55378615insAGAG								PDGFRA (214203 upstream) : KIT (145480 downstream)																							gagagagagagagagagagaga	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	56908676	56908677	+	IGR	INS	-	CCTT	CCTT	rs149122671	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56908676_56908677insCCTT								CEP135 (9150 upstream) : KIAA1211 (127684 downstream)																							atccctccctcccttccttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61099958	61099959	+	IGR	DEL	TA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61099958_61099959delTA								None (None upstream) : LPHN3 (967015 downstream)																							ctgtagcagctattctgcccca	0.000													4	2	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62392333	62392333	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62392333delA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						ctgtctttataaaagaaaaaa	0.000													4	2	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73212023	73212023	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73212023delC	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTACAGGTTACCCACCTTGCT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	74951135	74951135	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74951135delC								PPBPL2 (30019 upstream) : CXCL2 (11629 downstream)																							aattctgactcaaaaaaaaag	0.000													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79376432	79376433	+	Intron	INS	-	GTCAAAA	GTCAAAA	rs142972914	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79376432_79376433insGTCAAAA	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						TGTTTTTACATGCCTCCCTTTG	0.396													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81528569	81528570	+	Intron	INS	-	AG	AG	rs144030262	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81528569_81528570insAG	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						GGTGgagaaacagagaaagtgg	0.178													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82326680	82326681	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82326680_82326681insA								PRKG2 (190462 upstream) : RASGEF1B (21538 downstream)																							gatcccttcttaaaaaaaaaaa	0.015													3	3	---	---	---	---	
TMEM150C	441027	broad.mit.edu	37	4	83483586	83483587	+	5'Flank	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83483586_83483587insT	uc003hmy.1	-						TMEM150C_uc011ccj.1_5'Flank	NM_001080506	NP_001073975	B9EJG8	T150C_HUMAN	transmembrane protein 150C							integral to membrane				ovary(1)	1						GCGGTTTTTGGTTTTTTTTTTT	0.495													4	2	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86707802	86707803	+	Intron	INS	-	AC	AC	rs149213511	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86707802_86707803insAC	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		ATCTCTTATGAACACACACACA	0.361													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97754945	97754945	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97754945delA								PDHA2 (992321 upstream) : C4orf37 (725089 downstream)																							TCTCCTTTTCAAATGCTGTGT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	99644348	99644349	+	IGR	DEL	CA	-	-	rs148260531		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99644348_99644349delCA								TSPAN5 (64621 upstream) : EIF4E (155258 downstream)																							TTTATTAAAGcacacacacaca	0.267													4	2	---	---	---	---	
TACR3	6870	broad.mit.edu	37	4	104557153	104557154	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104557153_104557154delCA	uc003hxe.1	-							NM_001059	NP_001050	P29371	NK3R_HUMAN	tachykinin receptor 3							integral to plasma membrane	tachykinin receptor activity			ovary(3)|lung(2)|breast(1)|skin(1)	7		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		cttcctctcTCATAGGCACACA	0.243													3	3	---	---	---	---	
TBCK	93627	broad.mit.edu	37	4	107215642	107215643	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107215642_107215643insT	uc010ilv.2	-						TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907	Q8TEA7	TBCK_HUMAN	TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5						ggaaaATAATCttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	107815192	107815192	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107815192delT								AIMP1 (544813 upstream) : DKK2 (27768 downstream)																							cactgccaagtttccttcccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109133464	109133464	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109133464delT								LEF1 (43886 upstream) : LOC285456 (325882 downstream)																							ATAGCAGTACTTTTTTTTTAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118391844	118391844	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118391844delC								TRAM1L1 (385108 upstream) : NDST3 (562929 downstream)																							aggatctcttccctggggata	0.000													4	2	---	---	---	---	
NDST3	9348	broad.mit.edu	37	4	119006277	119006278	+	Intron	INS	-	AAC	AAC	rs139423039	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119006277_119006278insAAC	uc003ibx.2	+						NDST3_uc011cgf.1_Intron	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						gactccgtAAAaacaacaacaa	0.114													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122147395	122147396	+	IGR	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122147395_122147396delAG								TNIP3 (9613 upstream) : QRFPR (102401 downstream)																							cacataggaaagagagagagag	0.074													4	2	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123236998	123236999	+	Intron	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123236998_123236999delTT	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TAATACTGTCTTTTAATCGAGT	0.297													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132671633	132671633	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132671633delC								None (None upstream) : None (None downstream)																							ctctctctctccccccccccc	0.194													4	2	---	---	---	---	
SLC10A7	84068	broad.mit.edu	37	4	147224527	147224528	+	Intron	INS	-	T	T	rs111238580		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147224527_147224528insT	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					ctttttctttcttttttttttt	0.054													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151848796	151848796	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151848796delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron|LRBA_uc010ipk.1_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					aacaatgactaaaatgtttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158390161	158390161	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158390161delG								GRIA2 (102937 upstream) : LOC340017 (103481 downstream)																							caagagtgcaggccgtctcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	162301387	162301394	+	Intron	DEL	ACACACAC	-	-	rs6148751		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162301387_162301394delACACACAC	uc010iqu.1	+											full-length cDNA clone CS0DK008YC04 of HeLa cells Cot 25-normalized of Homo sapiens (human).																		TCAAATTAAAacacacacacacacacac	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163937229	163937229	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163937229delA								FSTL5 (852043 upstream) : NAF1 (110631 downstream)																							catgctacagaagaatatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	168504295	168504296	+	IGR	INS	-	A	A	rs71588110		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168504295_168504296insA								SPOCK3 (348554 upstream) : ANXA10 (509411 downstream)																							gaagcagggggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NEK1	4750	broad.mit.edu	37	4	170490089	170490089	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170490089delA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron|NEK1_uc003isg.1_Intron	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		actccatttcaaaaaaaaaaa	0.114													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171465466	171465467	+	IGR	DEL	AG	-	-	rs34787160		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171465466_171465467delAG								AADAT (454094 upstream) : None (None downstream)																							GAGCCCTATCAGGGGATTAAAG	0.431													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183968067	183968068	+	IGR	INS	-	G	G	rs142884383	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183968067_183968068insG								FAM92A3 (6796 upstream) : C4orf38 (50106 downstream)																							ctggctaacatggtgaaaccct	0.000													4	2	---	---	---	---	
SNX25	83891	broad.mit.edu	37	4	186166140	186166140	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186166140delG	uc003ixh.2	+							NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		CTGGGGCTGTGGGATTGATTG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190604439	190604440	+	IGR	INS	-	CA	CA	rs147961780		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190604439_190604440insCA								None (None upstream) : FRG1 (257534 downstream)																							TTACCTTCACTCACAGagtttc	0.223													5	3	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	847521	847522	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:847521_847522insA	uc011cma.1	-						ZDHHC11_uc003jbj.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)			GACGCGGCCCCAAGAGGACCCT	0.678													4	2	---	---	---	---	
BRD9	65980	broad.mit.edu	37	5	871105	871106	+	Intron	INS	-	T	T	rs148077764	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:871105_871106insT	uc003jbq.2	-						BRD9_uc003jbl.2_Intron|BRD9_uc003jbm.2_Intron|BRD9_uc003jbn.2_Intron|BRD9_uc011cmb.1_Intron|BRD9_uc003jbo.2_Intron|BRD9_uc003jbp.2_Intron	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1								nucleic acid binding				0			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			TACAGCCACCCTAACACATACT	0.550													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3636315	3636316	+	IGR	INS	-	C	C	rs146018101	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3636315_3636316insC								IRX1 (34799 upstream) : None (None downstream)																							TATCTGAGATGCCCCTCTCAGT	0.416													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4171629	4171629	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4171629delA								IRX1 (570113 upstream) : LOC340094 (862843 downstream)																							GTGAGTTGCTAAAGTGGCTAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5892006	5892013	+	IGR	DEL	GTGTGTGT	-	-	rs149383035		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5892006_5892013delGTGTGTGT								KIAA0947 (401669 upstream) : FLJ33360 (418541 downstream)																							TTTCCCATGGgtgtgtgtgtgtgtgtgt	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5931234	5931235	+	IGR	INS	-	A	A	rs150057412	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5931234_5931235insA								KIAA0947 (440897 upstream) : FLJ33360 (379319 downstream)																							aatatatgcatacatgtgtatc	0.074													3	3	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10431739	10431740	+	Intron	DEL	GT	-	-	rs10574367		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10431739_10431740delGT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						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						GAgtgagtgagtgtgtgtgtgt	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13627616	13627617	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13627616_13627617insA								None (None upstream) : DNAH5 (62820 downstream)																							acatttgtaccaaaaaaaaaaa	0.020													1	5	---	---	---	---	
ANKH	56172	broad.mit.edu	37	5	14811113	14811113	+	Intron	DEL	G	-	-	rs35285662		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14811113delG	uc003jfm.3	-							NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1						GAAGAAGGAAGGGGGGGAATA	0.413													3	6	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15797921	15797921	+	Intron	DEL	T	-	-	rs74440785		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15797921delT	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						GAGAAATTTGTGACGTCTGTG	0.294													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16433560	16433561	+	IGR	DEL	GT	-	-	rs113407363		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16433560_16433561delGT								MARCH11 (253663 upstream) : ZNF622 (18068 downstream)																							ggaaaaaaaagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16507789	16507790	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16507789_16507790delCA	uc003jfs.2	-						FAM134B_uc003jfr.2_Intron	NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						TTATAATTACCACACACACAAA	0.351													4	2	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16697905	16697906	+	Intron	INS	-	AGG	AGG	rs141968674	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16697905_16697906insAGG	uc003jft.3	-						MYO10_uc011cnc.1_Intron|MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						aagaaaaaggaagaagacaaat	0.208													2	5	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21344713	21344713	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21344713delT	uc011cnn.1	+											Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ccttccttcctttccttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24673556	24673556	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24673556delT								CDH10 (28645 upstream) : None (None downstream)																							tctttccttcttttttttttG	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	26006603	26006604	+	IGR	DEL	TT	-	-	rs146539668		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26006603_26006604delTT								None (None upstream) : CDH9 (874105 downstream)																							TATGTTGGAGTTCTATTTTACA	0.257													4	3	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33652952	33652952	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33652952delC	uc003jia.1	-						ADAMTS12_uc010iuq.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						tccaattttgccagcaccatt	0.020										HNSCC(64;0.19)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35518843	35518843	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35518843delT								PRLR (288049 upstream) : SPEF2 (99146 downstream)																							ATCACACAGATTTTACAAGTC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	37086022	37086022	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37086022delA								NIPBL (20102 upstream) : C5orf42 (20308 downstream)																							AATTAATAGGAAAAAAAAaaa	0.204													4	2	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38372247	38372247	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38372247delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					ATACTGCTCCttttttttttt	0.239													4	3	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38450926	38450926	+	Intron	DEL	T	-	-	rs113724457		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38450926delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron|EGFLAM_uc003jlg.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					GCCTTGTTCCTTTGTCTGAGA	0.572													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	45954194	45954194	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45954194delC								HCN1 (257974 upstream) : None (None downstream)																							tggaaacagtctttttgtaca	0.000													8	5	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59136060	59136061	+	Intron	INS	-	CA	CA	rs142164308	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59136060_59136061insCA	uc003jsa.2	-						PDE4D_uc003jsb.2_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	acgtgcactgccacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62043416	62043418	+	IGR	DEL	TTA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62043416_62043418delTTA								IPO11 (119001 upstream) : ISCA1P1 (27784 downstream)																							GCCACAATTGTTATTATTATTAT	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62222640	62222641	+	IGR	INS	-	GT	GT	rs143924955	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62222640_62222641insGT								ISCA1P1 (149470 upstream) : None (None downstream)																							catgcattctagtgtgtgtgtg	0.010													5	3	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	79957763	79957763	+	Intron	DEL	G	-	-	rs34814946		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79957763delG	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		gagttagaaagggggtgcata	0.109								MMR					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	80179446	80179446	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80179446delC								MSH3 (6813 upstream) : RASGRF2 (77112 downstream)																							ctcaaggaggccccagtgtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82020862	82020863	+	IGR	INS	-	TGT	TGT	rs148969170	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82020862_82020863insTGT								ATP6AP1L (406716 upstream) : TMEM167A (327804 downstream)																							TGGTTTATTGCTGTTGTTGTCG	0.292													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85861710	85861710	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85861710delC								NBPF22P (268348 upstream) : COX7C (52074 downstream)																							cagtcagcttccaggtatgac	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91154234	91154234	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91154234delG								LOC100129716 (437703 upstream) : None (None downstream)																							GTCATGAGGTGGAGGTCTTTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109481424	109481425	+	IGR	INS	-	T	T	rs144746217	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109481424_109481425insT								MAN2A1 (277995 upstream) : TMEM232 (143509 downstream)																							ctttcctttccttccttccttc	0.015													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	136903891	136903891	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136903891delA								SPOCK1 (68873 upstream) : KLHL3 (49299 downstream)																							CCGGGGTTGGATTCTAATGTG	0.483													4	2	---	---	---	---	
CDC23	8697	broad.mit.edu	37	5	137541386	137541386	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137541386delA	uc003lcl.2	-							NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ggtaaattGGAAAAAAAAAAA	0.129													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141456885	141456886	+	IGR	INS	-	GGAGAG	GGAGAG			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141456885_141456886insGGAGAG								GNPDA1 (64265 upstream) : NDFIP1 (31438 downstream)																							agggagaccgtggagagggaga	0.040													4	2	---	---	---	---	
DPYSL3	1809	broad.mit.edu	37	5	146891950	146891950	+	5'Flank	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146891950delG	uc003loo.2	-							NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ttacctgtctggtactagcat	0.030													4	2	---	---	---	---	
AFAP1L1	134265	broad.mit.edu	37	5	148693997	148693999	+	Intron	DEL	TTG	-	-	rs59875305		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148693997_148693999delTTG	uc003lqh.2	+						AFAP1L1_uc010jgy.2_Intron|AFAP1L1_uc003lqi.1_5'Flank	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1								protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTGGTATTTTGGGTGGAGAGT	0.453													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	148836218	148836221	+	IGR	DEL	AGAG	-	-	rs143911630		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148836218_148836221delAGAG								LOC728264 (23819 upstream) : CSNK1A1 (36728 downstream)																							ggagaaagaaagagagagagagaa	0.005													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	148854599	148854600	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148854599_148854600insT								LOC728264 (42200 upstream) : CSNK1A1 (18349 downstream)																							cactcagctaattttttgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153198034	153198035	+	IGR	INS	-	AC	AC	rs148133313	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153198034_153198035insAC								GRIA1 (4606 upstream) : FAM114A2 (173236 downstream)																							cactaagtaaaacaagtttcga	0.109													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161669683	161669684	+	IGR	DEL	AT	-	-	rs67191899		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161669683_161669684delAT								GABRG2 (87139 upstream) : None (None downstream)																							ATGTGTTAAGATATAAGGGATG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170932151	170932151	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170932151delA								FGF18 (47989 upstream) : FBXW11 (356405 downstream)																							AGAGTGGTGGAAAATGGGTTG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173137429	173137430	+	IGR	INS	-	TT	TT	rs144117622	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173137429_173137430insTT								BOD1 (93763 upstream) : CPEB4 (177901 downstream)																							gtttttttctgtttttttgttt	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174018051	174018054	+	IGR	DEL	AAGA	-	-	rs79440752		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174018051_174018054delAAGA								HMP19 (481870 upstream) : MSX2 (133521 downstream)																							gaaaggaaggaagaaagaaagaaa	0.069													4	3	---	---	---	---	
CDHR2	54825	broad.mit.edu	37	5	176019518	176019519	+	Intron	INS	-	GTG	GTG			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176019518_176019519insGTG	uc003mem.1	+						CDHR2_uc003men.1_Intron	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor						homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2						ttatgatgatagtggtggtggt	0.000													5	3	---	---	---	---	
NSD1	64324	broad.mit.edu	37	5	176592771	176592773	+	Intron	DEL	TGT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176592771_176592773delTGT	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Intron	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		ggcaaatcactgttgttgttgtt	0.000			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	176909544	176909545	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176909544_176909545insA								DBN1 (8850 upstream) : PDLIM7 (850 downstream)																							AGGCCCTGCTGCAACTCCTCCT	0.594													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177407639	177407639	+	IGR	DEL	T	-	-	rs148992496		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177407639delT								LOC728554 (96372 upstream) : PROP1 (11597 downstream)																							tgtgtgtgtgtgACACACAGA	0.507													4	2	---	---	---	---	
LOC729678	729678	broad.mit.edu	37	5	180261938	180261939	+	RNA	DEL	CT	-	-	rs72473031		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180261938_180261939delCT	uc011dhd.1	+	3		c.2104_2105delCT			LOC729678_uc010jlj.2_RNA|LOC729678_uc003mmk.3_RNA|LOC729678_uc003mml.3_RNA	NR_027183				Homo sapiens cDNA FLJ37851 fis, clone BRSSN2014294.												0						caaaagcttgctctctctctct	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	367660	367661	+	IGR	DEL	AC	-	-	rs146534455		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:367660_367661delAC								DUSP22 (16307 upstream) : IRF4 (24091 downstream)																							atacagacatacacacacatac	0.149													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2013630	2013630	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2013630delA	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		agctttcaacaaaaaaaatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2381686	2381686	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2381686delA								GMDS (135840 upstream) : C6orf195 (241286 downstream)																							ACTTTGAGCTAAAAAAGCTCC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9010406	9010406	+	IGR	DEL	T	-	-	rs142258048		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9010406delT								HULC (356329 upstream) : None (None downstream)																							AACTCAATGAttttttttttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12509967	12509967	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12509967delA								EDN1 (212541 upstream) : PHACTR1 (206921 downstream)																							CTAGGATGCTAAAAAAGATGA	0.199													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21955099	21955099	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21955099delG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron|FLJ22536_uc011djj.1_Intron|FLJ22536_uc003ndk.1_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						AACAAAGTCTGGGCAGATGGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26473166	26473166	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26473166delA	uc003nie.1	-											Homo sapiens cDNA FLJ40220 fis, clone TESTI2021667.																		gtgagtatgcaaaaaaggtta	0.000													4	2	---	---	---	---	
HIST1H2BK	85236	broad.mit.edu	37	6	27117086	27117086	+	5'Flank	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27117086delT	uc003nix.1	-							NM_080593	NP_542160	O60814	H2B1K_HUMAN	histone cluster 1, H2bk						defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0						cctttttaactcctctgtggg	0.000													4	2	---	---	---	---	
HCG18	414777	broad.mit.edu	37	6	30288479	30288480	+	Intron	INS	-	GT	GT	rs139932441	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30288479_30288480insGT	uc003npw.2	-						HCG18_uc003npx.2_Intron|HCG18_uc003npy.2_Intron					Homo sapiens cDNA FLJ13272 fis, clone OVARC1001004.												0						GACAGGTAGGGGTGTGTGTGTG	0.356													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30644100	30644100	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30644100delC								DHX16 (3270 upstream) : KIAA1949 (68 downstream)																							ATTTTCCTCTCCCCCAGCCAC	0.493													4	2	---	---	---	---	
C6orf106	64771	broad.mit.edu	37	6	34590316	34590316	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34590316delA	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3						ggctactactaaaaaaaaaaa	0.000													4	3	---	---	---	---	
ZNF76	7629	broad.mit.edu	37	6	35262831	35262831	+	Intron	DEL	A	-	-	rs113114842		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35262831delA	uc003oki.1	+						ZNF76_uc003okj.1_Intron|DEF6_uc003okk.2_5'Flank|DEF6_uc010jvs.2_5'Flank|DEF6_uc010jvt.2_5'Flank	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGGGAGAGTCAAAAAAAAAAG	0.502													4	2	---	---	---	---	
CLPS	1208	broad.mit.edu	37	6	35766317	35766318	+	5'Flank	INS	-	TC	TC	rs140155385	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35766317_35766318insTC	uc003ole.1	-						CLPS_uc003olf.1_5'Flank	NM_001832	NP_001823	P04118	COL_HUMAN	colipase preproprotein						lipid catabolic process|lipid digestion|retinoid metabolic process|steroid metabolic process	extracellular region					0						ttgagacaaggtctcactctgt	0.198													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	36911291	36911291	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36911291delA								C6orf89 (14553 upstream) : PI16 (10918 downstream)																							tctcaggaataaaaaaaaaaa	0.005													4	2	---	---	---	---	
FGD2	221472	broad.mit.edu	37	6	36977790	36977790	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36977790delA	uc010jwp.1	+						FGD2_uc011dtu.1_Intron|FGD2_uc003ong.2_Intron|FGD2_uc011dtv.1_Intron	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3						actctgtctcaaaaaaaaaaa	0.020													4	2	---	---	---	---	
ZFAND3	60685	broad.mit.edu	37	6	37897539	37897540	+	Intron	INS	-	T	T	rs71542149		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37897539_37897540insT	uc003onx.2	+							NM_021943	NP_068762	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1						ttatatttttgttttttttttt	0.282													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44668815	44668816	+	IGR	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44668815_44668816delGT								CDC5L (254036 upstream) : SUPT3H (108238 downstream)																							TCTTCATCCAgtgtgtgtgtgt	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57121513	57121514	+	IGR	DEL	CA	-	-	rs10527830		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57121513_57121514delCA								RAB23 (34412 upstream) : PRIM2 (60908 downstream)																							ctctcactttcacacacacaca	0.114													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57218933	57218933	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57218933delA	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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)		ATGCCTAGAGAAATGAACCTT	0.264													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57391533	57391534	+	Intron	INS	-	A	A	rs66613378		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57391533_57391534insA	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)		CTTCTATATTGAAAAAATGGTA	0.277													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57394864	57394865	+	Intron	INS	-	C	C	rs112404107		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57394864_57394865insC	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)		gagacaactttccccccgagtt	0.000													7	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57402022	57402023	+	Intron	INS	-	G	G	rs144916181		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402022_57402023insG	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)		actttgttaatttttttttctc	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57408104	57408118	+	Intron	DEL	TTTAAAAAGCTTATC	-	-	rs71839638	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57408104_57408118delTTTAAAAAGCTTATC	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)		TTTAGCACTGTTTAAAAAGCTTATCTTTTCTTCCA	0.353													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57414398	57414399	+	Intron	INS	-	A	A	rs151258963		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57414398_57414399insA	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)		ATTGTGCCTTGAGGCCTCTTAC	0.287													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57431675	57431676	+	Intron	DEL	AA	-	-	rs33996904		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57431675_57431676delAA	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)		GTTTCAGACTAAGTCATATGCC	0.183													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57512931	57512932	+	3'UTR	INS	-	T	T	rs143949713		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57512931_57512932insT	uc003pdx.2	+	18						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)		ttttgtagagggggggtctccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57580214	57580215	+	IGR	INS	-	C	C	rs143340678	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57580214_57580215insC								PRIM2 (66839 upstream) : GUSBL2 (665944 downstream)																							tttctaagccaccagccatggt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58775897	58775897	+	IGR	DEL	C	-	-	rs112764199		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58775897delC								GUSBL2 (488173 upstream) : None (None downstream)																							aacgggatttcttcatataaa	0.035													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65288514	65288515	+	Intron	INS	-	GTGT	GTGT	rs148608224	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65288514_65288515insGTGT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						gtgtgtgtgtggtgtgtgtgtg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67421880	67421880	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67421880delG								MCART3P (922505 upstream) : None (None downstream)																							agagtgaacaggcaacctgca	0.000													3	3	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69931566	69931566	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69931566delG	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				CTAGTTTTGTGGAATTTCGTA	0.333													4	2	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84417119	84417119	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84417119delT	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TAAATTCATCTTTTTTTTTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85678868	85678869	+	IGR	INS	-	AGCCAGTT	AGCCAGTT	rs139001389	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85678868_85678869insAGCCAGTT								TBX18 (204969 upstream) : NT5E (480433 downstream)																							actaccactgaagccagttagc	0.124													4	2	---	---	---	---	
SYNCRIP	10492	broad.mit.edu	37	6	86350406	86350406	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86350406delA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		TCTATACCTGAAAAAAAAAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87977775	87977776	+	IGR	INS	-	C	C	rs34184494		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87977775_87977776insC								ZNF292 (4371 upstream) : GJB7 (14921 downstream)																							tttTTTTTTTTCAAGTAATTTC	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92177183	92177183	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92177183delA								MAP3K7 (880276 upstream) : None (None downstream)																							TTGAATCTCCAAAAAATAGTC	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92796756	92796759	+	IGR	DEL	AATT	-	-	rs151118062		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92796756_92796759delAATT								None (None upstream) : None (None downstream)																							TCAAGACATAAATTATTTTAGTGT	0.309													1	5	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97621624	97621624	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97621624delA	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		AACTTCTTGGAAAAAAAAAGG	0.363													4	2	---	---	---	---	
ASCC3	10973	broad.mit.edu	37	6	101196202	101196202	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101196202delA	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GGGAGAAATTAAAAAAAAAAT	0.333													4	2	---	---	---	---	
DDO	8528	broad.mit.edu	37	6	110715312	110715312	+	Intron	DEL	T	-	-	rs142234892		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110715312delT	uc003puc.2	-						C6orf186_uc003pub.2_Intron|DDO_uc003pud.2_Intron	NM_003649	NP_003640	Q99489	OXDD_HUMAN	D-aspartate oxidase isoform a						aspartate catabolic process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		cttcagaatattttttttttt	0.000													4	3	---	---	---	---	
RSPH4A	345895	broad.mit.edu	37	6	116937274	116937275	+	5'Flank	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116937274_116937275delTC	uc003pxe.2	+						RSPH4A_uc010kee.2_5'Flank	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						cttccttccttctctctctctc	0.297									Kartagener_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	121795008	121795008	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121795008delA								GJA1 (24136 upstream) : HSF2 (925688 downstream)																							gactccatctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NCOA7	135112	broad.mit.edu	37	6	126225771	126225771	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126225771delT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		taccccAGCCTTAGACACTTC	0.224													4	2	---	---	---	---	
ENPP1	5167	broad.mit.edu	37	6	132164800	132164800	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132164800delT	uc011ecf.1	+							NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GCATGTCGTCTTTTTTTTTTT	0.433													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134267196	134267197	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134267196_134267197insA								TCF21 (48039 upstream) : TBPL1 (6156 downstream)																							gactttgtcttaaaaaaaaaaa	0.000													4	3	---	---	---	---	
PDE7B	27115	broad.mit.edu	37	6	136266620	136266621	+	Intron	INS	-	CTC	CTC	rs146213434	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136266620_136266621insCTC	uc003qgp.2	+						uc003qgq.1_Intron	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)	CAACTGTCCATCTCCACATAAT	0.401													2	4	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136943224	136943224	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136943224delA	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		actccgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
HECA	51696	broad.mit.edu	37	6	139482318	139482318	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139482318delC	uc003qin.2	+							NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase						respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		TCTGACTATTCCCGAGGTCCA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153146711	153146711	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153146711delA								VIP (65813 upstream) : FBXO5 (144949 downstream)																							agggaagcctaaggagaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153200743	153200743	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153200743delA								VIP (119845 upstream) : FBXO5 (90917 downstream)																							aagaagaagtaaagcatgacc	0.000													4	2	---	---	---	---	
SERAC1	84947	broad.mit.edu	37	6	158553035	158553036	+	Intron	INS	-	AG	AG	rs146754268	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158553035_158553036insAG	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250	Q96JX3	SRAC1_HUMAN	serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		actactcgtgtagagagagaGA	0.218													4	5	---	---	---	---	
PNLDC1	154197	broad.mit.edu	37	6	160220810	160220810	+	5'Flank	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160220810delG	uc003qsx.1	+						PNLDC1_uc003qsy.1_5'Flank	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TGAAGACAGTGGTAAGGTGGA	0.498													4	2	---	---	---	---	
AGPAT4	56895	broad.mit.edu	37	6	161613068	161613069	+	Intron	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161613068_161613069delTT	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_Intron|AGPAT4_uc011egc.1_Intron|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		TGTGCATTCCTTTTTTTTTTTT	0.406													3	3	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162560922	162560923	+	Intron	INS	-	A	A	rs79585060		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162560922_162560923insA	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		gactccatctcaaaaaaaaaaa	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164035966	164035966	+	IGR	DEL	A	-	-	rs11302380		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164035966delA								QKI (41074 upstream) : None (None downstream)																							cctcatgaataagaataatgc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164888317	164888317	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164888317delA								QKI (893425 upstream) : C6orf118 (804838 downstream)																							accctgtctcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
PDE10A	10846	broad.mit.edu	37	6	166032898	166032902	+	Intron	DEL	TAGTG	-	-	rs149600436	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166032898_166032902delTAGTG	uc003qun.2	-						PDE10A_uc003quo.2_Intron	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	tagtgtagtctagtgtagtgtagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167690251	167690252	+	IGR	INS	-	A	A	rs150612716	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167690251_167690252insA								TCP10L2 (93856 upstream) : UNC93A (14551 downstream)																							CAAGTCTAAGCAAAAAAAATGT	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169240095	169240100	+	IGR	DEL	GAGGAC	-	-	rs71008040	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169240095_169240100delGAGGAC								SMOC2 (171424 upstream) : THBS2 (375776 downstream)																							CGGTGCTGATGAGGACGCGGTGCTGA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170763830	170763831	+	IGR	INS	-	G	G	rs139128866	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170763830_170763831insG								FAM120B (49594 upstream) : PSMB1 (16276 downstream)																							TGTCCCAGACAGAAGTGGTAAC	0.564													2	7	---	---	---	---	
PSMB1	5689	broad.mit.edu	37	6	170821774	170821775	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170821774_170821775delAC	uc003qxq.2	-							NM_002793		P20618	PSB1_HUMAN	proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)	TGCAGGAGGGACACACACACAC	0.376													6	3	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	946233	946253	+	Intron	DEL	GAAGGGAGAAAGGGAGAAAGG	-	-	rs55791165	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:946233_946253delGAAGGGAGAAAGGGAGAAAGG	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						ggagaaaggagaagggagaaagggagaaagggaaaggagaa	0.181													4	2	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1546840	1546840	+	5'Flank	DEL	T	-	-	rs111819550		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1546840delT	uc003skn.2	-						INTS1_uc003skq.2_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCAttattcttttttttttt	0.269													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4333379	4333380	+	IGR	INS	-	CAGTGTGTGTG	CAGTGTGTGTG	rs139589462	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4333379_4333380insCAGTGTGTGTG								SDK1 (24750 upstream) : FOXK1 (350008 downstream)																							gatatgcacacaatctcacaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4503999	4503999	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4503999delT								SDK1 (195370 upstream) : FOXK1 (179389 downstream)																							GCCCCACCCCTTCCACCTCTA	0.468													4	2	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	5985001	5985001	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5985001delG	uc003sph.1	-						RSPH10B2_uc003spg.1_Intron|RSPH10B2_uc010ktd.1_Intron|RSPH10B2_uc011jwk.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						tgtaatcccagcactttggga	0.119													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6689541	6689541	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6689541delA								ZNF853 (25622 upstream) : ZNF12 (38523 downstream)																							GATCAGGATCAAGGGAGAGGT	0.617													4	2	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8708163	8708163	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8708163delG	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		ggatccacttgggtagacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12028627	12028630	+	IGR	DEL	GTGA	-	-	rs72128033		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12028627_12028630delGTGA								THSD7A (156803 upstream) : TMEM106B (222218 downstream)																							gtgtgtgtgtgtgagtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13718729	13718729	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13718729delA								ARL4A (988173 upstream) : ETV1 (212129 downstream)																							caaagactggaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22882662	22882663	+	IGR	INS	-	A	A	rs35607464		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22882662_22882663insA								TOMM7 (20241 upstream) : SNORD93 (13569 downstream)																							AACAATTACGTAAAAAAAAAAA	0.431													3	4	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23765162	23765162	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23765162delA	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						accttatctcaaaaaaaGTAG	0.095													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23836558	23836558	+	Intron	DEL	A	-	-	rs148242178		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23836558delA	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron|STK31_uc003swv.1_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						aatggaaagcaaaaaaaaaag	0.000													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23855511	23855511	+	Intron	DEL	T	-	-	rs11360202		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23855511delT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron|STK31_uc003swv.1_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						TGACTAGATATAAAGAGGATA	0.328													0	6	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26342938	26342938	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26342938delA	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0						CTGGAAAGTCAAAAACTGAAG	0.468													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33984810	33984810	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33984810delC	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						gccttggcctcccaaagtgct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35975621	35975621	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35975621delA								SEPT7 (30706 upstream) : EEPD1 (217215 downstream)																							ccatcccaagaaaaaaaaaaa	0.214													4	2	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38613047	38613047	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38613047delA	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						AATGACAACCAAAATATAACA	0.318													4	2	---	---	---	---	
RALA	5898	broad.mit.edu	37	7	39721905	39721907	+	Intron	DEL	TGC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39721905_39721907delTGC	uc003thd.2	+							NM_005402	NP_005393	P11233	RALA_HUMAN	ras related v-ral simian leukemia viral oncogene						actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis	cell surface|cleavage furrow|cytosol|midbody|plasma membrane	Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity			lung(1)|skin(1)	2						GTAATACCATtgctgctgctgct	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57553753	57553753	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57553753delG								ZNF716 (20488 upstream) : None (None downstream)																							gaggagtggagaggagtggag	0.035													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57556565	57556566	+	IGR	INS	-	GAATG	GAATG	rs144037641		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57556565_57556566insGAATG								ZNF716 (23300 upstream) : None (None downstream)																							ggaatgtaattgaatggaatgg	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57701331	57701331	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57701331delT								ZNF716 (168066 upstream) : None (None downstream)																							AAGCAGATGCTTAACCCTGTC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62018607	62018607	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62018607delC								None (None upstream) : LOC643955 (733065 downstream)																							gaagatatttccatttccacc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62435864	62435865	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62435864_62435865insA								None (None upstream) : LOC643955 (315807 downstream)																							tgtttttgtacaattttcgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68404659	68404660	+	IGR	DEL	AG	-	-	rs72350561		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68404659_68404660delAG								None (None upstream) : AUTS2 (659245 downstream)																							TGATAGGCTAAGTCTATTCTCA	0.441													4	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69118630	69118630	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69118630delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GTGGGTTTGGTTTTTTTTTTT	0.358													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70621477	70621477	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70621477delT	uc003tvy.2	+							NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CTGCCTTTCCTTTCCCTTCCT	0.224													4	2	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71451041	71451042	+	Intron	INS	-	T	T	rs139744865	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71451041_71451042insT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				aaatctttctcttttttttttg	0.000													4	2	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71733783	71733784	+	Intron	INS	-	ACACAA	ACACAA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71733783_71733784insACACAA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				ccctgCcacacacacacacaca	0.144													5	3	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71810342	71810345	+	Intron	DEL	GAAG	-	-	rs72389743		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71810342_71810345delGAAG	uc003twb.3	-						CALN1_uc003twc.3_Intron	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				gaaagaaagagaaggaaggaagga	0.108													4	2	---	---	---	---	
CLIP2	7461	broad.mit.edu	37	7	73767481	73767481	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73767481delA	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3						accctatctcaaaaaaaaaag	0.015													4	2	---	---	---	---	
CD36	948	broad.mit.edu	37	7	80212931	80212931	+	Intron	DEL	T	-	-	rs66787314		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80212931delT	uc003uhc.2	+							NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1						CTTGGATCACTTTTTTTTTTT	0.378													3	3	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87193301	87193301	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87193301delG	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	gatacatagaggggaacaaca	0.000													3	3	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87203208	87203209	+	Intron	DEL	AT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87203208_87203209delAT	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	AACCTACACGATATATATATAT	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	94000823	94000824	+	IGR	INS	-	T	T	rs143155048	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94000823_94000824insT								BET1 (367133 upstream) : COL1A2 (23049 downstream)																							aaatttatttattttttttttC	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97264485	97264485	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97264485delC								ACN9 (453412 upstream) : TAC1 (96786 downstream)																							TGGTCCAAGACCATCAGTGAG	0.453													3	3	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100229247	100229247	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100229247delA	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					actccatctcaaaaaaaaaaa	0.035													4	2	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100373941	100373948	+	Intron	DEL	AGGGAGGG	-	-	rs3991185		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100373941_100373948delAGGGAGGG	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kke.1_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			actTGAaggaagggagggagggagggag	0.125													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100547835	100547836	+	5'Flank	INS	-	T	T	rs146275646		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100547835_100547836insT	uc003uxk.1	+						uc003uxl.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		CCAGCTCTGCCGTCACTCTCTT	0.624													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101413874	101413875	+	IGR	INS	-	TTTG	TTTG	rs147083768	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101413874_101413875insTTTG								MYL10 (141298 upstream) : CUX1 (45417 downstream)																							tcctttcttcctttctctttct	0.000													1	6	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103603094	103603097	+	Intron	DEL	TGTG	-	-	rs111928955		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103603094_103603097delTGTG	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCAAAGTTGTtgtgtgtgtgtgtg	0.324													3	5	---	---	---	---	
CDHR3	222256	broad.mit.edu	37	7	105612120	105612120	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105612120delG	uc003vdl.3	+						CDHR3_uc003vdk.2_Intron|CDHR3_uc011kls.1_Intron|CDHR3_uc003vdm.3_Intron|CDHR3_uc011klt.1_Intron	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN	hypothetical protein LOC222256 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						GGCAATATTTGGGGAGCATGG	0.493													4	2	---	---	---	---	
PNPLA8	50640	broad.mit.edu	37	7	108150621	108150622	+	Intron	INS	-	A	A	rs35880371		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108150621_108150622insA	uc003vff.1	-						PNPLA8_uc003vfg.1_Intron|PNPLA8_uc003vfh.1_Intron|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Intron|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8						fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2						taaagtataataaaaaaaaaaa	0.203													2	4	---	---	---	---	
FOXP2	93986	broad.mit.edu	37	7	114278197	114278197	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114278197delG	uc003vhb.2	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgz.2_Intron|FOXP2_uc003vha.2_Intron|FOXP2_uc011kmu.1_Intron|FOXP2_uc011kmv.1_Intron|FOXP2_uc010ljz.1_Intron|FOXP2_uc003vgx.2_Intron|FOXP2_uc003vhd.2_Intron|FOXP2_uc003vhc.2_Intron	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						TAGAAAGACTGGGAGGGGTAT	0.398													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116730309	116730310	+	Intron	DEL	AC	-	-	rs10537016		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116730309_116730310delAC	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7OT2_uc003viu.2_Intron|uc003vit.2_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		acacacacagacacacacacac	0.282													2	4	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127520769	127520770	+	Intron	INS	-	GT	GT	rs141703150	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127520769_127520770insGT	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						AGAATGCAGGGgtgtgtgtgtg	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128078110	128078110	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128078110delA								IMPDH1 (28074 upstream) : C7orf68 (17774 downstream)																							GAGCAAGTGgaaaaaaaaaac	0.154													4	2	---	---	---	---	
UBE2H	7328	broad.mit.edu	37	7	129531651	129531651	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129531651delA	uc003vpf.1	-						UBE2H_uc003vpg.1_Intron	NM_003344	NP_003335	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H isoform 1						protein K11-linked ubiquitination|protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin-protein ligase activity			skin(1)	1	Melanoma(18;0.0435)					aaacaaaaacaaaaaaaaaaa	0.124													0	6	---	---	---	---	
LUZP6	767558	broad.mit.edu	37	7	135622119	135622120	+	Intron	DEL	AC	-	-	rs112277111		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135622119_135622120delAC	uc003vte.3	-						LUZP6_uc010lmv.2_Intron	NM_145808	NP_665807	Q538Z0	LUZP6_HUMAN	myotrophin												0						CTAACTGGATacacacacacac	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136107896	136107898	+	IGR	DEL	ACT	-	-	rs143916437		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136107896_136107898delACT								LUZP6 (445692 upstream) : CHRM2 (445501 downstream)																							AATATTTCCCACTATTAAGACTG	0.271													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136540273	136540273	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136540273delC								LUZP6 (878069 upstream) : CHRM2 (13126 downstream)																							gcatagtattccatgctgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	137984167	137984167	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137984167delT								AKR1D1 (181117 upstream) : TRIM24 (160912 downstream)																							cattgattgatttgtgtatgt	0.000													4	2	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138787474	138787475	+	Intron	INS	-	AC	AC	rs145985433	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138787474_138787475insAC	uc003vun.2	-						ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						actgtctctatacacacacaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142007188	142007189	+	Intron	INS	-	GT	GT	rs141970212	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142007188_142007189insGT	uc011kro.1	+						uc011krp.1_5'Flank|uc003vxf.3_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		ACACTACCAAAgtgtgtgtgtg	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142353577	142353578	+	Intron	INS	-	TTTGT	TTTGT	rs147204686	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142353577_142353578insTTTGT	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_5'Flank|uc011ksi.1_5'Flank|uc003vzw.1_5'Flank|uc011ksg.1_5'Flank					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		CAGATCCAAGCtttgttttgtt	0.416													4	5	---	---	---	---	
ZYX	7791	broad.mit.edu	37	7	143077326	143077326	+	5'Flank	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143077326delA	uc003wcw.2	+						ZYX_uc011ktd.1_Intron|ZYX_uc003wcx.2_5'Flank|ZYX_uc011kte.1_5'Flank|ZYX_uc011ktf.1_5'Flank	NM_001010972	NP_001010972	Q15942	ZYX_HUMAN	zyxin						cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding				0	Melanoma(164;0.205)					CAGTGCaattaaaaaaaaaaa	0.498											OREG0018403	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148888416	148888419	+	IGR	DEL	CTCA	-	-	rs147356472		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148888416_148888419delCTCA								ZNF398 (8300 upstream) : ZNF282 (4158 downstream)																							gagatggagtctcactctgtcgcc	0.172													9	6	---	---	---	---	
LRRC61	65999	broad.mit.edu	37	7	150010730	150010730	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150010730delT	uc003wgv.2	+							NM_023942	NP_076431	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61												0			OV - Ovarian serous cystadenocarcinoma(82;0.011)			tctgaaccagtttttttcacg	0.015													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152112096	152112097	+	Intron	INS	-	ATTTTTT	ATTTTTT	rs144846176		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152112096_152112097insATTTTTT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		acatgcagctaattttttattt	0.000			N		medulloblastoma								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153184053	153184053	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153184053delC								ACTR3B (631590 upstream) : DPP6 (400366 downstream)																							aagcccaagacccattagctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155657302	155657303	+	IGR	INS	-	TTTA	TTTA	rs145584493	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155657302_155657303insTTTA								SHH (52335 upstream) : C7orf4 (675882 downstream)																							TATGCTAGCTTTTTATTAGGAT	0.460													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155739522	155739525	+	IGR	DEL	TTCC	-	-	rs5888641		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155739522_155739525delTTCC								SHH (134555 upstream) : C7orf4 (593660 downstream)																							ccttccttctttccttccttcctt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155746184	155746185	+	IGR	DEL	AA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155746184_155746185delAA								SHH (141217 upstream) : C7orf4 (587000 downstream)																							aaaactgtctaaaaaaaaacag	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157100312	157100313	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157100312_157100313delTG								UBE3C (38247 upstream) : DNAJB6 (29397 downstream)																							aggcaacgtttgttcaccagac	0.168													4	2	---	---	---	---	
CLN8	2055	broad.mit.edu	37	8	1724654	1724655	+	Intron	INS	-	A	A	rs141640229	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1724654_1724655insA	uc003wpo.3	+							NM_018941	NP_061764	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8						cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		TGAAATCTGTGCGGGCAGATGT	0.505													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2652217	2652217	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2652217delC								MYOM2 (558838 upstream) : CSMD1 (140659 downstream)																							GTTCAACCTGCCCGCCTTTCA	0.473													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3552334	3552334	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3552334delG	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGGGAGCCAGGGGAACGCGG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4916717	4916718	+	IGR	INS	-	ACAC	ACAC	rs139331389	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4916717_4916718insACAC								CSMD1 (64389 upstream) : None (None downstream)																							tacacacgtatacacacacaca	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6772549	6772549	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6772549delC								DEFB1 (37020 upstream) : DEFA6 (9672 downstream)																							CCACATCCCTCAGAATGTAGC	0.488													3	4	---	---	---	---	
RP1L1	94137	broad.mit.edu	37	8	10510181	10510181	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10510181delA	uc003wtc.2	-							NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)		TGTATTGAAGAAAAAAAAAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15223636	15223637	+	IGR	INS	-	T	T	rs143009313	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15223636_15223637insT								SGCZ (127844 upstream) : TUSC3 (174093 downstream)																							caaatagaaaatcaaacaagag	0.069													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21481269	21481269	+	IGR	DEL	T	-	-	rs5889992		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21481269delT								None (None upstream) : GFRA2 (68261 downstream)																							CTAGCAAGGGTTAGACTGAAG	0.488													4	2	---	---	---	---	
GFRA2	2675	broad.mit.edu	37	8	21615718	21615719	+	Intron	DEL	CA	-	-	rs76473239		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21615718_21615719delCA	uc003wzu.1	-						GFRA2_uc003wzv.1_Intron|GFRA2_uc003wzw.1_Intron|DOK2_uc003wzx.1_Intron	NM_001495	NP_001486	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		GCCCACTCCCcacacacacaca	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	22566954	22566955	+	IGR	INS	-	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22566954_22566955insG								EGR3 (16139 upstream) : PEBP4 (3810 downstream)																							tcaccatcacttcattatcacc	0.000													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25372244	25372244	+	Intron	DEL	A	-	-	rs33943178		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25372244delA	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GGGGTCAAACAGTTGAAACGT	0.338													2	4	---	---	---	---	
DPYSL2	1808	broad.mit.edu	37	8	26453114	26453114	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26453114delC	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CTGCCCTCTTCCCCGCTGCCT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	28467732	28467733	+	IGR	INS	-	TGTG	TGTG	rs71943886		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28467732_28467733insTGTG								FZD3 (45773 upstream) : EXTL3 (91420 downstream)																							aaaTAtgtatatgtgtgtgtgt	0.119													4	2	---	---	---	---	
HMBOX1	79618	broad.mit.edu	37	8	28777489	28777490	+	Intron	DEL	TG	-	-	rs148345782		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28777489_28777490delTG	uc003xhd.3	+						HMBOX1_uc010lvd.2_Intron|HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_Intron|HMBOX1_uc003xhe.2_Intron	NM_001135726	NP_001129198	Q6NT76	HMBX1_HUMAN	homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		AGTGAAGTTTtgtgtgtgtgtg	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29880944	29880944	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29880944delA								LOC286135 (69823 upstream) : TMEM66 (39688 downstream)																							ctccagtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37464006	37464007	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37464006_37464007delGA								KCNU1 (670365 upstream) : ZNF703 (89294 downstream)																							ATgagagagggagagagagaga	0.213													3	3	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38110159	38110160	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38110159_38110160insA	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc003xld.2_Intron	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			gacctcatctcaaaaaaaaaaa	0.163													5	3	---	---	---	---	
FGFR1	2260	broad.mit.edu	37	8	38284624	38284624	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38284624delA	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbr.1_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	gactccgtctaaaaaaaaaaa	0.000		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40986647	40986648	+	IGR	INS	-	GAGAC	GAGAC	rs142690020	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40986647_40986648insGAGAC								ZMAT4 (231304 upstream) : SFRP1 (132831 downstream)																							GACATGGCACAGAGACGCTTCC	0.500													5	3	---	---	---	---	
SLC20A2	6575	broad.mit.edu	37	8	42378702	42378702	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42378702delA	uc010lxm.2	-						SLC20A2_uc003xpe.2_Intron	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			AGTATTAATCATCCTTTTAAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43808432	43808432	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43808432delT								POTEA (590104 upstream) : None (None downstream)																							tgaaccttcctttttgataga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	46882551	46882551	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46882551delA								None (None upstream) : BEYLA (869957 downstream)																							tagaaaatgcaagtggatatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53774657	53774658	+	IGR	INS	-	T	T	rs151145488	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53774657_53774658insT								RB1CC1 (147631 upstream) : NPBWR1 (77810 downstream)																							catgaccttggtttttttatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54008457	54008457	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54008457delA								NPBWR1 (155004 upstream) : OPRK1 (129819 downstream)																							aatgtccaccaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54874037	54874038	+	IGR	INS	-	CC	CC	rs138074487	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54874037_54874038insCC								RGS20 (2176 upstream) : TCEA1 (5079 downstream)																							ctgtgactcttccctccttttc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55121316	55121317	+	IGR	INS	-	TT	TT	rs34162406		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55121316_55121317insTT								MRPL15 (60242 upstream) : SOX17 (249178 downstream)																							tggctggctaattttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57384587	57384588	+	Intron	INS	-	GGC	GGC	rs143781481	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57384587_57384588insGGC	uc003xtb.1	+											Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																		GACAATGGGGGGGTGGTGGTGG	0.287													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58128069	58128070	+	IGR	INS	-	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58128069_58128070insC								IMPAD1 (221642 upstream) : C8orf71 (64032 downstream)																							TGAGAAGGTTGCATGGTGGACA	0.554													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65118823	65118823	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65118823delT								YTHDF3 (993478 upstream) : MIR124-2 (172883 downstream)																							gttaggtttattacctcattt	0.184													4	2	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69697038	69697039	+	Intron	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69697038_69697039delTG	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			tgtgtgtgtatgtgtgtgtgtg	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71875984	71875984	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71875984delG								XKR9 (227808 upstream) : EYA1 (233686 downstream)																							tatatttgttggctgcatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73170797	73170798	+	Intron	INS	-	A	A	rs146090764	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73170797_73170798insA	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																		aggatgaaatgaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75495747	75495747	+	IGR	DEL	T	-	-	rs34205996		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75495747delT								GDAP1 (216414 upstream) : MIR2052 (122181 downstream)																							TTTGACCAAGTTTTTTTTTTG	0.348													2	4	---	---	---	---	
HNF4G	3174	broad.mit.edu	37	8	76379277	76379277	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76379277delT	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			AGGAGTATACTTTTTCTTTTA	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79807197	79807198	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79807197_79807198delAC								IL7 (89439 upstream) : STMN2 (716182 downstream)																							AACCACAGGGACACACACACAG	0.416													3	3	---	---	---	---	
ATP6V0D2	245972	broad.mit.edu	37	8	87140592	87140595	+	Intron	DEL	AAAC	-	-	rs75696206		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87140592_87140595delAAAC	uc003ydp.1	+							NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0						ataaataaataaacaaacaaacaa	0.167													6	4	---	---	---	---	
CPNE3	8895	broad.mit.edu	37	8	87526084	87526084	+	5'Flank	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87526084delT	uc003ydv.2	+							NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2						TCTTGGTAACttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89722534	89722534	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89722534delC								MMP16 (382817 upstream) : None (None downstream)																							aaacacagcaccctctttata	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90258241	90258244	+	IGR	DEL	TCTT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90258241_90258244delTCTT								MMP16 (918524 upstream) : RIPK2 (511731 downstream)																							TCtctctccctctttctttctttc	0.044													3	3	---	---	---	---	
LRRC69	100130742	broad.mit.edu	37	8	92219079	92219079	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92219079delT	uc010mal.1	+						SLC26A7_uc003yex.2_5'Flank|SLC26A7_uc003yey.2_5'Flank|LRRC69_uc003yev.1_Intron|LRRC69_uc003yew.1_Intron	NM_001129890	NP_001123362	Q6ZNQ3	LRC69_HUMAN	leucine rich repeat containing 69												0						aaccaagtaattttgccaatt	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94480121	94480121	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94480121delT								C8orf83 (450220 upstream) : FAM92A1 (232652 downstream)																							caaaacactctttaggatatt	0.000													4	2	---	---	---	---	
TMEM67	91147	broad.mit.edu	37	8	94792770	94792770	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94792770delC	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TCAACTTTTGCATAGACTGTT	0.229													62	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96209937	96209938	+	IGR	INS	-	GAT	GAT	rs138586341	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96209937_96209938insGAT								PLEKHF2 (41026 upstream) : C8orf37 (48297 downstream)																							GAACCTTCTCAgatgatgatga	0.465													3	3	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	98066304	98066304	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98066304delA	uc003yhw.2	+							NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					tttcatgtggagaggtcaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98222483	98222485	+	IGR	DEL	TTG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98222483_98222485delTTG								PGCP (66762 upstream) : TSPYL5 (63230 downstream)																							ACAGGGAAACTTGTTGTTGGTTG	0.567													3	3	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100267272	100267272	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100267272delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.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)			ctcttttctctttttttccct	0.000													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100278483	100278484	+	Intron	INS	-	A	A	rs113518710		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100278483_100278484insA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.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)			cctgtctctacaaaaaaaaaac	0.144													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102289079	102289080	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102289079_102289080delAC								ZNF706 (71119 upstream) : NACAP1 (84942 downstream)																							AGTGAGACAGACACACACACAC	0.371													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102453311	102453312	+	IGR	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102453311_102453312delTC								NACAP1 (68376 upstream) : GRHL2 (51356 downstream)																							tccttagccatctctctctctc	0.064													4	2	---	---	---	---	
KLF10	7071	broad.mit.edu	37	8	103670754	103670755	+	5'Flank	DEL	AC	-	-	rs34889681		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103670754_103670755delAC	uc011lhk.1	-							NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a						cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			cacgtcgaatacacacacacac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103978487	103978487	+	IGR	DEL	T	-	-	rs68107697		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103978487delT								AZIN1 (102090 upstream) : ATP6V1C1 (54761 downstream)																							tAATTTATGAttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104090243	104090244	+	IGR	INS	-	T	T	rs138664736		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104090243_104090244insT								ATP6V1C1 (4959 upstream) : C8orf56 (54948 downstream)																							AGAACTCAGACTTTTTTCTTCT	0.475													4	2	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106784735	106784735	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106784735delA	uc003ymd.2	+						ZFPM2_uc011lhs.1_Intron	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AAGAGGAAGGAAAACAGAAGA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110162329	110162329	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110162329delA								TRHR (30519 upstream) : NUDCD1 (90820 downstream)																							agatctacttaaaaaaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116058425	116058425	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116058425delA								None (None upstream) : TRPS1 (362300 downstream)																							ctggatcctcatctcacctta	0.000													5	3	---	---	---	---	
MED30	90390	broad.mit.edu	37	8	118535449	118535450	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118535449_118535450insT	uc003yoj.2	+						MED30_uc011lib.1_Intron	NM_080651	NP_542382	Q96HR3	MED30_HUMAN	TRAP/Mediator complex component TRAP25						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding				0	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)			TTTTTTTTAAGTTTTTTTTTTT	0.327													9	4	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119404179	119404180	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119404179_119404180insA	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			AAGTTCTGGTTAAAAAAAAAAA	0.188													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126003122	126003122	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126003122delG								ZNF572 (11494 upstream) : SQLE (7598 downstream)																							tagttccagagggaggaatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127495057	127495057	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127495057delG								None (None upstream) : FAM84B (69630 downstream)																							gttctttagtggtaatatctg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127579689	127579689	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127579689delT								FAM84B (9223 upstream) : LOC727677 (722373 downstream)																							atttaagatgttaacgagaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127974969	127974969	+	IGR	DEL	T	-	-	rs35624905		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127974969delT								FAM84B (404503 upstream) : LOC727677 (327093 downstream)																							ATTTGTTAACTTTTTTTTTTT	0.219													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132466815	132466815	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132466815delG								ADCY8 (413980 upstream) : EFR3A (449544 downstream)																							gaagataaaagaaaaaataaa	0.000													4	2	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133493789	133493795	+	5'Flank	DEL	TCCCTCT	-	-	rs3840713		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133493789_133493795delTCCCTCT	uc003ytj.2	-						KCNQ3_uc010mdt.2_5'Flank	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			AGCTCGTGACtccctcttccctcttcc	0.502													6	3	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133929633	133929634	+	Intron	INS	-	TG	TG	rs141561412	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133929633_133929634insTG	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_5'Flank|TG_uc003ytx.1_5'Flank	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						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)		gtgcatgtatatgtgtgtgtgt	0.366													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134177786	134177786	+	IGR	DEL	C	-	-	rs66512720		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134177786delC								TG (30645 upstream) : WISP1 (25526 downstream)																							ACTGCTGAGGCCTCCCCTCCA	0.259													3	3	---	---	---	---	
ST3GAL1	6482	broad.mit.edu	37	8	134536114	134536114	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134536114delA	uc003yuk.2	-						ST3GAL1_uc003yum.2_Intron	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			atgtgggaagaagtgtcaaga	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134716973	134716974	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134716973_134716974delAC								ST3GAL1 (132790 upstream) : ZFAT (773059 downstream)																							ctaatcacctacatggtcattt	0.005													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139704411	139704414	+	Intron	DEL	GTGT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139704411_139704414delGTGT	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)			atgtgtggaggtgtgtgtgtatgt	0.000										HNSCC(7;0.00092)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140109796	140109797	+	IGR	INS	-	CC	CC	rs140227515	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140109796_140109797insCC								COL22A1 (183560 upstream) : KCNK9 (503285 downstream)																							AGAGGTGCAGGCCACTTAGAGA	0.455													5	3	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141047977	141047978	+	Intron	DEL	AC	-	-	rs10560088		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141047977_141047978delAC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						cacacctccaacacacacacac	0.178													4	2	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	141923054	141923054	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141923054delA	uc003yvu.2	-						PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			caaaaaaaagaaaaaagaaaa	0.000													4	2	---	---	---	---	
EXOSC4	54512	broad.mit.edu	37	8	145134151	145134152	+	Intron	INS	-	G	G	rs150826787	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145134151_145134152insG	uc003zau.2	+							NM_019037	NP_061910	Q9NPD3	EXOS4_HUMAN	exosome component 4						DNA deamination|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear mRNA surveillance|positive regulation of cell growth	cytosol|exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			aataaaccctttgttttgtgca	0.025													1	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	4333234	4333238	+	IGR	DEL	AGTGG	-	-	rs150496908	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4333234_4333238delAGTGG								GLIS3 (33199 upstream) : SLC1A1 (157206 downstream)																							gggaaggaaaagtggaggggaagga	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	12283163	12283163	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12283163delA								None (None upstream) : TYRP1 (410223 downstream)																							aggttcatggaaaaagaattt	0.000													4	2	---	---	---	---	
C9orf93	203238	broad.mit.edu	37	9	15588699	15588704	+	Intron	DEL	TTTTTT	-	-	rs137961065		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15588699_15588704delTTTTTT	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)		AGATGCAGACtttttttttttttttt	0.175													6	3	---	---	---	---	
BNC2	54796	broad.mit.edu	37	9	16786436	16786437	+	Intron	INS	-	A	A	rs112393165	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16786436_16786437insA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		GAAACGGAGGGAAAAAAAAAGT	0.366													4	2	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27359377	27359377	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27359377delG	uc003zqn.2	-							NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		gtgtgtgtgtggggggggggg	0.169													6	3	---	---	---	---	
IGFBPL1	347252	broad.mit.edu	37	9	38419861	38419863	+	Intron	DEL	CCT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38419861_38419863delCCT	uc004aba.2	-							NM_001007563	NP_001007564	Q8WX77	IBPL1_HUMAN	insulin-like growth factor binding protein-like						regulation of cell growth	extracellular region	insulin-like growth factor binding				0				GBM - Glioblastoma multiforme(29;0.0437)|Lung(182;0.116)		tcctcctccccctcctcctcctc	0.138													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43655316	43655317	+	IGR	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43655316_43655317delGT								FAM75A6 (24586 upstream) : None (None downstream)																							TTGTTTTGGGgtgtgtgtgtgt	0.406													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66464394	66464394	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66464394delG	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		CATTATTAAAGCAAAGTGAAA	0.294													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67039911	67039911	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67039911delG								LOC442421 (536884 upstream) : AQP7P1 (214356 downstream)																							gcatgacagaggggggcagtg	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68473056	68473056	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68473056delT								FAM27B (678867 upstream) : MIR1299 (529183 downstream)																							TAAAAAATGATTTttttttgt	0.194													6	4	---	---	---	---	
APBA1	320	broad.mit.edu	37	9	72045456	72045457	+	3'UTR	DEL	TG	-	-	rs35210525		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72045456_72045457delTG	uc004ahh.2	-	13						NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						CAAATGGGACtgtgtgtgtgtg	0.446													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	77852079	77852080	+	IGR	INS	-	A	A	rs142907892	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77852079_77852080insA								OSTF1 (89966 upstream) : PCSK5 (653480 downstream)																							cccataggttttgccacatggc	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81646753	81646754	+	IGR	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81646753_81646754delAG								PSAT1 (701746 upstream) : TLE4 (540124 downstream)																							ggagggaggaagagagagagag	0.059													4	2	---	---	---	---	
TLE4	7091	broad.mit.edu	37	9	82269146	82269146	+	Intron	DEL	T	-	-	rs35639126		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82269146delT	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						GTGTGGTTGattttttttttt	0.303													6	3	---	---	---	---	
SLC28A3	64078	broad.mit.edu	37	9	86962484	86962484	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86962484delA	uc004anu.1	-							NM_022127	NP_071410	Q9HAS3	S28A3_HUMAN	concentrative Na+-nucleoside cotransporter						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4						AAGTATATGCAAAAAAGGCTA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	89380332	89380333	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89380332_89380333delTG								ZCCHC6 (410954 upstream) : GAS1 (178946 downstream)																							aacgtatgtctgtgtgtgtgtg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	89607701	89607702	+	Intron	INS	-	C	C	rs139095311	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89607701_89607702insC	uc004aoy.2	+											Homo sapiens, clone IMAGE:5309572, mRNA.																		tgattttttggccctttttttt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95875794	95875803	+	IGR	DEL	CACACACACA	-	-	rs57069113		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95875794_95875803delCACACACACA								C9orf89 (230 upstream) : NINJ1 (7969 downstream)																							CCTCATGTGCcacacacacacacacacaca	0.500													3	3	---	---	---	---	
FAM120A	23196	broad.mit.edu	37	9	96316959	96316959	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96316959delA	uc004atw.2	+						FAM120A_uc004aty.2_Intron|FAM120A_uc004atz.2_Intron|FAM120A_uc010mrg.2_Intron	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0						tgtttcaaagaaaaaaaaaag	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	103711849	103711849	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103711849delC								MURC (361678 upstream) : LPPR1 (79182 downstream)																							AGCCCATCAACCCTCCAATGG	0.488													4	2	---	---	---	---	
RAD23B	5887	broad.mit.edu	37	9	110081279	110081279	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110081279delT	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1						TACATAATGCTTTTTTTTTTC	0.289								Direct_reversal_of_damage|NER					4	2	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111789621	111789621	+	Intron	DEL	T	-	-	rs35939859		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111789621delT	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		aaactagaggtttttttcccc	0.000													3	3	---	---	---	---	
MUSK	4593	broad.mit.edu	37	9	113519124	113519125	+	Intron	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113519124_113519125delTG	uc004bey.2	+							NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6						tcaagttgtatgtgtgtgtgtg	0.094													4	2	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116812722	116812723	+	3'UTR	INS	-	CA	CA	rs147537659	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116812722_116812723insCA	uc004bid.2	+	15					ZNF618_uc004bic.2_3'UTR|ZNF618_uc011lxi.1_3'UTR|ZNF618_uc011lxj.1_3'UTR|ZNF618_uc010mvb.2_3'UTR	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTGcacacacgcacacacacac	0.465													5	3	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	119011806	119011807	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119011806_119011807insT	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						tttaggacatctttttggctgt	0.000													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119264818	119264820	+	Intron	DEL	AGA	-	-	rs139490072		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119264818_119264820delAGA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|uc004bju.1_5'Flank	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						agaagtggatagaaggtcagaga	0.059													2	4	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119482839	119482840	+	Intron	INS	-	TC	TC	rs150369166	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119482839_119482840insTC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						ctcccctcttttctctctctct	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126940492	126940493	+	IGR	DEL	AA	-	-	rs68089291		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126940492_126940493delAA								LHX2 (145050 upstream) : NEK6 (79393 downstream)																							ctctgtctccaaaaaaaaaaaa	0.015													4	2	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127295935	127295935	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127295935delT	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						TAGGGGCACCttttttttttt	0.269													4	2	---	---	---	---	
PTGES2	80142	broad.mit.edu	37	9	130893424	130893443	+	5'Flank	DEL	AGCCAGTGGTTGCAGTAGGC	-	-	rs72466106		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130893424_130893443delAGCCAGTGGTTGCAGTAGGC	uc004bti.2	-						PTGES2_uc004btj.2_5'Flank|PTGES2_uc004btk.2_5'Flank|PTGES2_uc004btl.2_5'Flank|PTGES2_uc004btm.2_5'Flank	NM_025072	NP_079348	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2						cell redox homeostasis|prostaglandin biosynthetic process	Golgi membrane|integral to membrane|mitochondrion|perinuclear region of cytoplasm	electron carrier activity|prostaglandin-E synthase activity|protein binding|protein disulfide oxidoreductase activity				0						GTCTTTTGAAAGCCAGTGGTTGCAGTAGGCACATCCTCTC	0.477													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132231389	132231392	+	IGR	DEL	ATGT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132231389_132231392delATGT								C9orf106 (146507 upstream) : C9orf50 (143114 downstream)																							actgtgtcgaatgtgtgtgcacag	0.172													4	2	---	---	---	---	
ASS1	445	broad.mit.edu	37	9	133360187	133360188	+	Intron	DEL	CA	-	-	rs3030699		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133360187_133360188delCA	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	GCTTTAAacgcacacacacaca	0.386													5	3	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136657133	136657134	+	Intron	INS	-	CA	CA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136657133_136657134insCA	uc004ces.2	-						VAV2_uc004cer.2_Intron|VAV2_uc004cet.1_5'Flank	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GTGTGTGAATGAGCTGTGCTGG	0.351													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138901690	138901690	+	5'Flank	DEL	G	-	-	rs3841030		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138901690delG	uc011mds.1	-						uc004cgv.3_RNA					Homo sapiens cDNA FLJ30516 fis, clone BRAWH2000697.																		GCACACCGGAGGGGGTGCTGA	0.627													1	5	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	575419	575420	+	Intron	DEL	TT	-	-	rs142402925		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:575419_575420delTT	uc001ifp.2	-							NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GACACAAAAGTTAGTTCTCAAA	0.386													2	4	---	---	---	---	
AKR1C4	1109	broad.mit.edu	37	10	5236982	5236983	+	5'Flank	INS	-	A	A	rs143068057	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5236982_5236983insA	uc001ihw.2	+							NM_001818	NP_001809	P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4						androgen metabolic process|bile acid biosynthetic process	cytosol	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid transmembrane transporter activity|chlordecone reductase activity|electron carrier activity			ovary(1)	1					NADH(DB00157)	GGCATATTCTTagtctcgacat	0.144													4	3	---	---	---	---	
PRKCQ	5588	broad.mit.edu	37	10	6503063	6503066	+	Intron	DEL	ATCC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6503063_6503066delATCC	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						tccatcatttatccatccatccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10264744	10264744	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10264744delA								None (None upstream) : SFTA1P (561658 downstream)																							ctaatatgctaagggttctca	0.000													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11181802	11181803	+	Intron	INS	-	TT	TT			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11181802_11181803insTT	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						ACATCATTCAGTTTTTTTTTTT	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11488160	11488160	+	IGR	DEL	C	-	-	rs71511381		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11488160delC								CELF2 (109490 upstream) : USP6NL (14349 downstream)																							ccaacagcttccccatgtttc	0.000													3	4	---	---	---	---	
FAM171A1	221061	broad.mit.edu	37	10	15339062	15339063	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15339062_15339063insT	uc001iob.2	-							NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4						AGCtttttttcttttttttttt	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19465751	19465752	+	IGR	INS	-	CGTA	CGTA	rs140446090	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19465751_19465752insCGTA								ARL5B (498811 upstream) : PLXDC2 (639620 downstream)																							ctgtgtgtctgtgtgtgtgtgc	0.119													4	2	---	---	---	---	
ABI1	10006	broad.mit.edu	37	10	27075150	27075150	+	Intron	DEL	T	-	-	rs112500030		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27075150delT	uc001isx.2	-						ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Intron|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Intron|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Intron|ABI1_uc010qdj.1_Intron|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1						CTCTCTACACttttttttttt	0.189													4	2	---	---	---	---	
ITGB1	3688	broad.mit.edu	37	10	33224708	33224708	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33224708delC	uc001iws.3	-						ITGB1_uc001iwp.3_5'Flank|ITGB1_uc001iwq.3_5'Flank|ITGB1_uc001iwr.3_5'Flank|ITGB1_uc001iwt.3_Intron|ITGB1_uc001iwu.1_5'Flank	NM_133376	NP_596867	P05556	ITB1_HUMAN	integrin beta 1 isoform 1A precursor						axon guidance|blood coagulation|cell-cell adhesion mediated by integrin|cell-matrix adhesion|cellular defense response|homophilic cell adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|leukocyte migration|positive regulation of apoptosis|regulation of immune response	cell surface|cleavage furrow|focal adhesion|melanosome|neuromuscular junction|ruffle|sarcolemma	identical protein binding|protein heterodimerization activity|receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(717;1.34e-05)|Breast(68;0.0634)				CATACCAGAGCCCCAGAATCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33724980	33724980	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33724980delA								NRP1 (100974 upstream) : PARD3 (675118 downstream)																							GCCCCAGGATAAGCGTATGtt	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38939448	38939450	+	IGR	DEL	AAT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38939448_38939450delAAT								LOC399744 (198368 upstream) : None (None downstream)																							TCTTACCAACAATATTTGATTCA	0.222													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39082540	39082540	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39082540delT								LOC399744 (341460 upstream) : None (None downstream)																							cattccattcttttcctttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39101085	39101086	+	IGR	INS	-	AACTG	AACTG	rs75378691		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39101085_39101086insAACTG								LOC399744 (360005 upstream) : None (None downstream)																							cattccattccattccattcca	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42653182	42653182	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42653182delT								None (None upstream) : LOC441666 (174133 downstream)																							AAAAGAGAAATTCTTTCATTG	0.328													4	2	---	---	---	---	
LOC441666	441666	broad.mit.edu	37	10	42847207	42847207	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42847207delT	uc010qey.1	-							NR_024380				Homo sapiens noncoding mRNA sequence.												0						tcattctcacttatatgggga	0.000													4	2	---	---	---	---	
ZNF33B	7582	broad.mit.edu	37	10	43073899	43073899	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43073899delC	uc001jad.2	-									Q06732	ZN33B_HUMAN	Homo sapiens C2H2-type zinc finger protein mRNA, partial cds.							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						ATGCAACTGTCCCCTCTTCTC	0.547													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43556283	43556283	+	IGR	DEL	C	-	-	rs5784585		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43556283delC								BMS1 (225900 upstream) : RET (16234 downstream)																							TCtttcccttctttttttttt	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46989395	46989411	+	IGR	DEL	AACAGGGGGACTACAGA	-	-	rs72031633		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46989395_46989411delAACAGGGGGACTACAGA								SYT15 (18794 upstream) : GPRIN2 (4135 downstream)																							cagccttgggaacagggggactacagaaacatgccac	0.000													3	3	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47012503	47012503	+	RNA	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47012503delG	uc001jed.3	-	4		c.1054delC						P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						acacctctctgggcttagtcc	0.015													5	4	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47035469	47035470	+	Intron	INS	-	A	A	rs141068721		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47035469_47035470insA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						AAAtttcacacaaaaaaattat	0.277													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47071171	47071172	+	Intron	INS	-	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47071171_47071172insC	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						agaaagacccacccattgcagg	0.000													7	5	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47090315	47090316	+	Intron	INS	-	A	A	rs112966378		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47090315_47090316insA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						ccagaatttgcatgataacatc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54197957	54197959	+	IGR	DEL	TTT	-	-	rs146144307		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54197957_54197959delTTT								DKK1 (120541 upstream) : MBL2 (327182 downstream)																							aatttttgcattttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58708975	58708976	+	IGR	INS	-	T	T	rs143607093	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58708975_58708976insT								ZWINT (587941 upstream) : None (None downstream)																							gtcaccagcagttttttttgtc	0.000													0	6	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61444172	61444172	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61444172delA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TCCTAAAGTGAAAAAAAAAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65696713	65696714	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65696713_65696714insT								REEP3 (314742 upstream) : ANXA2P3 (888571 downstream)																							CTTTGGCAttcttttttttttt	0.173													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72343418	72343418	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72343418delC								KIAA1274 (15213 upstream) : PRF1 (13687 downstream)																							GGCAGGATTTCCCAGCCGTCA	0.363													4	2	---	---	---	---	
CAMK2G	818	broad.mit.edu	37	10	75586709	75586709	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75586709delC	uc001jvv.1	-						CAMK2G_uc001jvm.1_Intron|CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc010qkv.1_Intron|CAMK2G_uc009xrp.1_Intron|CAMK2G_uc001jvw.1_Intron|CAMK2G_uc001jvx.1_Intron	NM_172171	NP_751911	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)					GAAGAGGGGGCCCAGGAGTAG	0.562													4	3	---	---	---	---	
SAMD8	142891	broad.mit.edu	37	10	76897987	76897987	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76897987delG	uc001jwx.1	+						SAMD8_uc001jwy.1_Intron	NM_144660	NP_653261	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8						sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					agggagactagaaaggatact	0.159													4	2	---	---	---	---	
VDAC2	7417	broad.mit.edu	37	10	76989625	76989625	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76989625delT	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)	ttttctttgcttttttttttt	0.179													4	2	---	---	---	---	
ANXA11	311	broad.mit.edu	37	10	81967990	81967990	+	5'Flank	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81967990delA	uc001kbr.1	-						ANXA11_uc001kbs.1_5'Flank|ANXA11_uc001kbt.1_5'Flank|ANXA11_uc010qly.1_5'Flank|ANXA11_uc009xsq.1_5'Flank|ANXA11_uc001kbu.1_5'Flank|uc001kbv.2_Intron	NM_145869	NP_665876	P50995	ANX11_HUMAN	annexin A11						cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			catacaaggtaagggaaggtg	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85916204	85916205	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85916204_85916205insA								GHITM (2893 upstream) : C10orf99 (17349 downstream)																							AGTTTTCTGTGAAAAAAAAATT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	89138480	89138481	+	IGR	DEL	GC	-	-	rs945106	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89138480_89138481delGC								FAM22D (8028 upstream) : MINPP1 (125742 downstream)																							gtgtgtgtgtgcgcgtgtgtgt	0.401													4	2	---	---	---	---	
PTEN	5728	broad.mit.edu	37	10	89711960	89711960	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89711960delT	uc001kfb.2	+	7	1609	c.578delT	c.(577-579)CTGfs	p.L193fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	193	C2 tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.?(3)|p.G165fs*9(3)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.G165_K342del(1)|p.G165_*404del(1)|p.V191fs*7(1)|p.L193P(1)|p.L193del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CCAGTGGCACTGTTGTTTCAC	0.398		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			90	41	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91797542	91797543	+	IGR	INS	-	TC	TC	rs150051853	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91797542_91797543insTC								KIF20B (262842 upstream) : HTR7 (703035 downstream)																							ACActttctggtctgtgttcct	0.208													2	4	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98782812	98782812	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98782812delT	uc001kmw.2	-							NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		tacgtgcctcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102501167	102501171	+	IGR	DEL	AAAAA	-	-	rs10522882		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102501167_102501171delAAAAA								HIF1AN (187487 upstream) : PAX2 (4297 downstream)																							AAGCTCTTCCaaaaaaaaaaaaaaa	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103061102	103061102	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103061102delT								LBX1 (72385 upstream) : BTRC (52723 downstream)																							tctttctttctttttttcttt	0.000													4	4	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106527359	106527365	+	Intron	DEL	TCCCCCT	-	-	rs113518885		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106527359_106527365delTCCCCCT	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							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)		tttttattcctcccccttcccccttcc	0.077													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113141840	113141840	+	IGR	DEL	A	-	-	rs34671640		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113141840delA								ADRA2A (301180 upstream) : GPAM (767782 downstream)																							aaacaggaagagaggttctca	0.000													1	5	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114468372	114468372	+	Intron	DEL	A	-	-	rs7907407	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114468372delA	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		TCTGCATACTAATTAGCATTA	0.318													4	2	---	---	---	---	
CASP7	840	broad.mit.edu	37	10	115449108	115449108	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115449108delT	uc001lan.2	+						CASP7_uc001lam.2_Intron|CASP7_uc001lao.2_Intron|CASP7_uc001lap.2_Intron|CASP7_uc001laq.2_Intron|CASP7_uc010qsa.1_Intron	NM_033339	NP_203125	P55210	CASP7_HUMAN	caspase 7 isoform alpha						activation of caspase activity by cytochrome c|cellular component disassembly involved in apoptosis|induction of apoptosis by intracellular signals|proteolysis	cytosol|endoplasmic reticulum membrane|mitochondrial membrane|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		tggtttgtgatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121958975	121958979	+	IGR	DEL	TCCTG	-	-	rs142928381		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121958975_121958979delTCCTG								SEC23IP (257730 upstream) : PPAPDC1A (257487 downstream)																							ttcctttccttcctgtcctgtcctg	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122048096	122048097	+	IGR	DEL	CC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122048096_122048097delCC								SEC23IP (346851 upstream) : PPAPDC1A (168369 downstream)																							GCCTGCACTTCCCATTTCTTAC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122715675	122715676	+	IGR	INS	-	TG	TG	rs140381439	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122715675_122715676insTG								WDR11 (46640 upstream) : FGFR2 (522169 downstream)																							TAAACATCACTtgtgtgtgtgt	0.287													3	3	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126815305	126815305	+	Intron	DEL	C	-	-	rs5788695		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126815305delC	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CTGATCACCACCCCCCGCTAT	0.488													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126858361	126858362	+	IGR	DEL	TG	-	-	rs74759752		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126858361_126858362delTG								CTBP2 (8737 upstream) : LOC100169752 (404578 downstream)																							CCCAGggctttgtgagttgcaa	0.114													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126951801	126951802	+	IGR	DEL	TG	-	-	rs112403832		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126951801_126951802delTG								CTBP2 (102177 upstream) : LOC100169752 (311138 downstream)																							CTTTTCATTTtgtgtgtgtgtg	0.361													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129626583	129626586	+	IGR	DEL	TTCT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129626583_129626586delTTCT								FOXI2 (87133 upstream) : CLRN3 (49528 downstream)																							ttgtcttctcttctttctttctgt	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130262011	130262011	+	IGR	DEL	G	-	-	rs79754469		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130262011delG								MKI67 (337543 upstream) : None (None downstream)																							GCAGGAGGGAGGCTGGGGGCG	0.582													2	9	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	132974877	132974878	+	Intron	INS	-	CA	CA	rs143998824		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132974877_132974878insCA	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)		agagacacgtgcacacaccatg	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133625299	133625299	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133625299delC								TCERG1L (515315 upstream) : PPP2R2D (122661 downstream)																							GTACTGGGGTCAGTGATGAGC	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134237262	134237263	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134237262_134237263delTG								PWWP2B (5911 upstream) : C10orf91 (21451 downstream)																							tgtgtgtggctgtgtgtgtgtg	0.218													4	2	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	135026633	135026635	+	Intron	DEL	TCC	-	-	rs138714952		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135026633_135026635delTCC	uc001llz.1	+							NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CAAAGCTGAGTCCTCCTCTCCAG	0.685													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1978380	1978397	+	IGR	DEL	GGCGGAGAGGTGCCGTCG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1978380_1978397delGGCGGAGAGGTGCCGTCG								MRPL23 (543 upstream) : LOC100133545 (26043 downstream)																							GGAGAGCCATGGCGGAGAGGTGCCGTCGGGCGGAGAGG	0.688													4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10282474	10282474	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10282474delA	uc001mib.2	-							NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		gggagaaaagaaaaaaaAATA	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15614654	15614655	+	IGR	DEL	CT	-	-	rs147863986		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15614654_15614655delCT								INSC (345902 upstream) : SOX6 (373341 downstream)																							ggaaaacagactctgctcactc	0.084													3	3	---	---	---	---	
SAA4	6291	broad.mit.edu	37	11	18253712	18253713	+	Intron	INS	-	AGCCCCTGCACCC	AGCCCCTGCACCC	rs143986842	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18253712_18253713insAGCCCCTGCACCC	uc001mny.2	-							NM_006512	NP_006503	P35542	SAA4_HUMAN	serum amyloid A4, constitutive precursor						acute-phase response	high-density lipoprotein particle					0						ttacaggtgtgagcccctgcac	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	19306025	19306027	+	IGR	DEL	TTT	-	-	rs35583361		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19306025_19306027delTTT								E2F8 (42858 upstream) : NAV2 (66244 downstream)																							CTGGTTTGCCTTTTTTTTTTTTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26005932	26005932	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26005932delT								LUZP2 (901750 upstream) : ANO3 (204897 downstream)																							atattagctGTTTTTTTTTTT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28670354	28670354	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28670354delT								METT5D1 (315300 upstream) : None (None downstream)																							TTCCTTTTTCTTTTTTTTTTT	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28688651	28688652	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28688651_28688652delTG								METT5D1 (333597 upstream) : None (None downstream)																							AGGGAAAATTtgtgtgtgtgtg	0.297													6	3	---	---	---	---	
FBXO3	26273	broad.mit.edu	37	11	33791270	33791271	+	Intron	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33791270_33791271delGA	uc001muz.2	-						FBXO3_uc001muy.2_Intron|FBXO3_uc009ykb.2_Intron|FBXO3_uc001mva.1_Intron|FBXO3_uc001mvb.1_Intron|FBXO3_uc010rek.1_Intron	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1						proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		GAgaagtggggagagagagaga	0.203													4	2	---	---	---	---	
CD44	960	broad.mit.edu	37	11	35207119	35207120	+	Intron	INS	-	CCTC	CCTC	rs147232120	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35207119_35207120insCCTC	uc001mvu.2	+						CD44_uc001mvv.2_Intron|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	CTGCCTGTCTTCCTCCCTCCCT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35673153	35673156	+	IGR	DEL	AGAG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35673153_35673156delAGAG								FJX1 (30734 upstream) : TRIM44 (11197 downstream)																							CCCTAAGGACagagagagagagag	0.304													5	3	---	---	---	---	
TTC17	55761	broad.mit.edu	37	11	43379862	43379863	+	5'Flank	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43379862_43379863insA	uc001mxi.2	+						TTC17_uc001mxh.2_5'Flank	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17								binding			ovary(5)	5						aagacttagttaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45778965	45778965	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45778965delA								CHST1 (91793 upstream) : DKFZp779M0652 (14018 downstream)																							tggcccctgtaaaacttgagg	0.000													4	2	---	---	---	---	
C11orf49	79096	broad.mit.edu	37	11	47145490	47145491	+	Intron	INS	-	GA	GA	rs140803714	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47145490_47145491insGA	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018	Q9H6J7	CK049_HUMAN	hypothetical protein LOC79096 isoform 3												0						gtgacaagagtgactctgtctc	0.144													3	3	---	---	---	---	
MTCH2	23788	broad.mit.edu	37	11	47653910	47653910	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47653910delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0						GGCTTTTGCAttttttttttt	0.174													4	3	---	---	---	---	
OR4C45	403257	broad.mit.edu	37	11	48376212	48376212	+	5'Flank	DEL	T	-	-	rs33971529		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48376212delT	uc010rhw.1	-							NM_001005513	NP_001005513			olfactory receptor, family 4, subfamily C,												0						ATTCAAGTTCTTCTTTCAACT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57699418	57699418	+	IGR	DEL	T	-	-	rs34834685		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57699418delT								CTNND1 (112767 upstream) : OR9Q1 (91935 downstream)																							TAAGCTCTGATTTTTTTTTTT	0.423													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	58117699	58117699	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58117699delA								OR10W1 (81967 upstream) : OR5B17 (7901 downstream)																							CTGAGTGTGTAAATAGTTAAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69872357	69872358	+	IGR	INS	-	ATGATG	ATGATG	rs150618791	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69872357_69872358insATGATG								FGF3 (238165 upstream) : ANO1 (52050 downstream)																							tggtgatgacaatgatgatgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70286249	70286249	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70286249delT								CTTN (3560 upstream) : SHANK2 (27713 downstream)																							gcctggctaattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70291041	70291041	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70291041delT								CTTN (8352 upstream) : SHANK2 (22921 downstream)																							TACGGTAGGATTTTTTTTCCT	0.129													4	2	---	---	---	---	
ALG8	79053	broad.mit.edu	37	11	77850820	77850820	+	5'Flank	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77850820delG	uc001oza.1	-						ALG8_uc001oyz.1_5'Flank|ALG8_uc009yux.1_5'Flank|ALG8_uc009yuy.1_5'Flank	NM_024079	NP_076984	Q9BVK2	ALG8_HUMAN	dolichyl pyrophosphate Glc1Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GTCTCACCCCGGGCCGGAAGG	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	80797294	80797295	+	IGR	INS	-	AG	AG			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80797294_80797295insAG								None (None upstream) : None (None downstream)																							tgtcagcatgcagagttctggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	83018033	83018033	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83018033delC	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																		TCTAGCTTTTCCAGCCCATGA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	83117134	83117134	+	Intron	DEL	A	-	-	rs112327263		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83117134delA	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																		actccatcttaaaaaaaaaaa	0.174													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90523689	90523690	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90523689_90523690delGA								CHORDC1 (567157 upstream) : MIR1261 (78599 downstream)																							gagattgagggagagagagaga	0.000													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95904185	95904185	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95904185delT	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				tggccTCTACTTTTTTTTTTT	0.219			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	98890220	98890220	+	5'Flank	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98890220delA	uc001pga.2	+						CNTN5_uc009ywv.1_5'Flank|CNTN5_uc001pfz.2_5'Flank|CNTN5_uc001pgb.2_5'Flank	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TGGGGCAGAGAAAAAGCCACA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101913110	101913110	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101913110delA								KIAA1377 (41319 upstream) : C11orf70 (5064 downstream)																							agactgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109386076	109386076	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109386076delT								C11orf87 (86238 upstream) : ZC3H12C (577850 downstream)																							tgttgtttccttctttgtgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109687549	109687550	+	IGR	INS	-	C	C	rs147256951	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109687549_109687550insC								C11orf87 (387711 upstream) : ZC3H12C (276376 downstream)																							TAGAATGAATTCCCCCCCACTC	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110943310	110943311	+	IGR	INS	-	ACAC	ACAC	rs148596896	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110943310_110943311insACAC								ARHGAP20 (359398 upstream) : C11orf53 (183396 downstream)																							CTCTCCCTCAGacacacacaca	0.361													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116145687	116145688	+	IGR	DEL	GT	-	-	rs7121267		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116145687_116145688delGT								CADM1 (770446 upstream) : BUD13 (473200 downstream)																							CAGAGCAGGGgtgtgtgtgtgt	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119897688	119897688	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119897688delT								PVRL1 (298253 upstream) : TRIM29 (84307 downstream)																							tgtagcttcatttctgagtca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	126968230	126968233	+	Intron	DEL	CACA	-	-	rs112390928		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126968230_126968233delCACA	uc001qeg.1	+											Homo sapiens cDNA FLJ37868 fis, clone BRSSN2017297.																		TGTGcacatgcacacacacacaca	0.319													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128021680	128021680	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128021680delT								None (None upstream) : ETS1 (306976 downstream)																							TTCAATGGCCTTTCCTTATGT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129528233	129528233	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129528233delT								BARX2 (206060 upstream) : TMEM45B (157508 downstream)																							tagttggcggttttcccctcc	0.000													4	2	---	---	---	---	
PRDM10	56980	broad.mit.edu	37	11	129783608	129783608	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129783608delA	uc001qfm.2	-						PRDM10_uc001qfj.2_Intron|PRDM10_uc001qfk.2_Intron|PRDM10_uc001qfl.2_Intron|PRDM10_uc010sbx.1_Intron|PRDM10_uc001qfn.2_Intron	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		gcctgaagttaaaaacccTCC	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	169502	169503	+	IGR	INS	-	AAACG	AAACG	rs140976240	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169502_169503insAAACG								FAM138D (20090 upstream) : IQSEC3 (6700 downstream)																							aaagctaaggaaaaagctggct	0.000													4	3	---	---	---	---	
IQSEC3	440073	broad.mit.edu	37	12	259631	259631	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:259631delG	uc001qhw.1	+						IQSEC3_uc001qhu.1_Intron|uc001qhv.1_5'Flank	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		GTTGTTGAGAGGGGGATAGGG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	1647818	1647819	+	IGR	INS	-	TCTGCCTGTGTG	TCTGCCTGTGTG	rs146965235	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1647818_1647819insTCTGCCTGTGTG								ERC1 (42719 upstream) : FBXL14 (27341 downstream)																							TTTCGGTTTTTTCTGCCTGTGT	0.401													4	2	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	1954136	1954136	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1954136delT	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		ATGAGTTTCCTTTTTTTGAGC	0.468													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2681538	2681540	+	Intron	DEL	TCT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2681538_2681540delTCT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	ctccttctcctcttcctcctctt	0.034													4	2	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6152717	6152717	+	Intron	DEL	G	-	-	rs66491856		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6152717delG	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GCATCCTTCAGGATGTATGCG	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	6531793	6531794	+	IGR	INS	-	TTTC	TTTC	rs146457410	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6531793_6531794insTTTC								LTBR (31061 upstream) : LOC678655 (16373 downstream)																							TGCATTCTttttttctttcttt	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10345092	10345092	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10345092delT								C12orf59 (690 upstream) : GABARAPL1 (20397 downstream)																							TCACTAGTTATTTGTACCCCT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10703072	10703073	+	IGR	INS	-	A	A	rs145469786	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10703072_10703073insA								KLRC1 (96088 upstream) : KLRA1 (38005 downstream)																							gaagcaaatagaaaaaaaatgt	0.158													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13109246	13109249	+	IGR	DEL	CCTT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13109246_13109249delCCTT								GPRC5D (5928 upstream) : HEBP1 (18552 downstream)																							tccctctgtcccttcctttcctcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	18896590	18896591	+	IGR	INS	-	TTTGT	TTTGT	rs145907811	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18896590_18896591insTTTGT								CAPZA3 (4469 upstream) : PLEKHA5 (386057 downstream)																							CGtttgttttgtttgttttgtt	0.094													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25931815	25931816	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25931815_25931816delAC								IFLTD1 (130327 upstream) : RASSF8 (180153 downstream)																							CCTTATCCCAACACACACACAC	0.381													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26920204	26920204	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26920204delC	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					TATCTGGCTGCCAATGCCCAC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29016477	29016478	+	IGR	INS	-	CTTCCTTC	CTTCCTTC	rs138024408	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29016477_29016478insCTTCCTTC								CCDC91 (313379 upstream) : FAR2 (285754 downstream)																							tcccttcccctcttccttcctt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29298545	29298546	+	IGR	INS	-	G	G	rs140384302	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29298545_29298546insG								CCDC91 (595447 upstream) : FAR2 (3686 downstream)																							gcagggggcatggggggggtgg	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37895665	37895665	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37895665delG								None (None upstream) : ALG10B (814892 downstream)																							GAATGAATGCGAAGTCGGAGT	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38108817	38108817	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38108817delC								None (None upstream) : ALG10B (601740 downstream)																							atttggagggctttgtggcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39936264	39936264	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39936264delA								KIF21A (99346 upstream) : ABCD2 (8758 downstream)																							actccatctcaaaaaaaaaaa	0.005													3	3	---	---	---	---	
CNTN1	1272	broad.mit.edu	37	12	41298236	41298239	+	Intron	DEL	TTTC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41298236_41298239delTTTC	uc001rmm.1	+						CNTN1_uc009zjy.1_Intron|CNTN1_uc001rmn.1_Intron|CNTN1_uc001rmo.2_Intron	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				ttttttcttttttctttctttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47801961	47801961	+	IGR	DEL	A	-	-	rs58205141		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47801961delA								FAM113B (171520 upstream) : RPAP3 (253755 downstream)																							TCATTTTACCAGCATTTTGAA	0.343													5	4	---	---	---	---	
ANKRD33	341405	broad.mit.edu	37	12	52285209	52285210	+	3'UTR	INS	-	TA	TA	rs147140141	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52285209_52285210insTA	uc001rzf.3	+	6					ANKRD33_uc001rzh.3_3'UTR|ANKRD33_uc001rzd.2_3'UTR|ANKRD33_uc001rze.2_3'UTR|ANKRD33_uc001rzg.3_3'UTR|ANKRD33_uc001rzi.3_3'UTR	NM_001130015	NP_001123487	Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33 isoform 1												0				BRCA - Breast invasive adenocarcinoma(357;0.0969)		TGCTCTCAACCTatatatatac	0.302													2	5	---	---	---	---	
NR4A1	3164	broad.mit.edu	37	12	52423472	52423473	+	Intron	INS	-	AAAAACAAAAAC	AAAAACAAAAAC	rs147813148	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52423472_52423473insAAAAACAAAAAC	uc010sno.1	+							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)		accctgtctcaaaaaacaaaaa	0.228													4	2	---	---	---	---	
HOXC4	3221	broad.mit.edu	37	12	54426580	54426580	+	Intron	DEL	T	-	-	rs113659413		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54426580delT	uc001seu.2	+						HOXC5_uc001set.2_Intron|HOXC5_uc001sew.2_5'Flank|MIR615_hsa-mir-615|MI0003628_5'Flank	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TCCAAGAACcttttttttttt	0.413											OREG0021884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
LOC400043	400043	broad.mit.edu	37	12	54523160	54523161	+	Intron	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54523160_54523161delAG	uc001sez.3	+							NR_026656				Homo sapiens hypothetical gene supported by BC009385, mRNA (cDNA clone IMAGE:4127835).												0						gaaggcgggtagagagagagag	0.208													4	2	---	---	---	---	
PDE1B	5153	broad.mit.edu	37	12	54949973	54949973	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54949973delA	uc001sgd.1	+						PDE1B_uc010soz.1_Intron|PDE1B_uc010spa.1_Intron	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1						activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						AGCAGCAGAGAAAGAGGGACA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	66486337	66486337	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66486337delG								HMGA2 (126269 upstream) : LLPH (30513 downstream)																							CATGTCATCAGGGAAAAAAAA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67605376	67605376	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67605376delC								GRIP1 (407482 upstream) : CAND1 (57685 downstream)																							ggtgaaacagccaaaatggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69798413	69798413	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69798413delA								YEATS4 (13838 upstream) : FRS2 (65716 downstream)																							cagcctccagaaccatgagcg	0.035													4	2	---	---	---	---	
ZFC3H1	196441	broad.mit.edu	37	12	72022938	72022938	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72022938delT	uc001swo.2	-							NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						ATGATACGTAttttttttttt	0.119													6	3	---	---	---	---	
TBC1D15	64786	broad.mit.edu	37	12	72237797	72237798	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72237797_72237798insT	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0						tcagtaaataacctcatctaca	0.045													4	2	---	---	---	---	
TPH2	121278	broad.mit.edu	37	12	72346943	72346943	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72346943delT	uc009zrw.1	+						TPH2_uc001swy.2_Intron	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)	TTTTCCCTGCTTTTTTTTTTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	72509149	72509149	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72509149delA								TPH2 (82928 upstream) : LOC283392 (147179 downstream)																							tgttgcaaataacaggatctt	0.000													4	2	---	---	---	---	
CAPS2	84698	broad.mit.edu	37	12	75754980	75754980	+	Intron	DEL	A	-	-	rs36088782		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75754980delA	uc001sxm.3	-						CAPS2_uc009zsa.2_Intron|GLIPR1L1_uc001sxn.2_Intron|GLIPR1L1_uc001sxo.2_Intron			Q9BXY5	CAYP2_HUMAN	RecName: Full=Calcyphosin-2; AltName: Full=Calcyphosine-2;								calcium ion binding			ovary(2)	2						ttggtatgccaaaaaaaataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77299451	77299451	+	IGR	DEL	T	-	-	rs35465030		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77299451delT								CSRP2 (26652 upstream) : E2F7 (115576 downstream)																							cttttctttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	85986979	85986979	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85986979delC								ALX1 (291420 upstream) : RASSF9 (211352 downstream)																							ttgtccctttccatgtgtcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87489777	87489778	+	IGR	DEL	CA	-	-	rs34639495		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87489777_87489778delCA								MGAT4C (257096 upstream) : C12orf50 (884038 downstream)																							TAAAATAGTTcacacacacaca	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90897038	90897038	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90897038delA								LOC338758 (791310 upstream) : C12orf12 (448955 downstream)																							ggagaagactaagcaaaaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93576745	93576746	+	IGR	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93576745_93576746delTT								EEA1 (253638 upstream) : NUDT4 (194955 downstream)																							tctttttttctttttttttttt	0.084													3	3	---	---	---	---	
LTA4H	4048	broad.mit.edu	37	12	96435764	96435765	+	Intron	INS	-	TT	TT	rs150049972		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96435764_96435765insTT	uc010suy.1	-						LTA4H_uc010suz.1_Intron	NM_000895	NP_000886	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1						gtttttttttcttttttttttt	0.030													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99169397	99169398	+	Intron	INS	-	T	T	rs35251566		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99169397_99169398insT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc009ztq.2_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.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)		tattttctgtattttttttttt	0.000													3	3	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101240724	101240725	+	Intron	DEL	CC	-	-	rs11363490		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101240724_101240725delCC	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						tccttccacacccccccccaac	0.084										HNSCC(74;0.22)			4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107622345	107622345	+	IGR	DEL	T	-	-	rs34007168		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107622345delT								CRY1 (134747 upstream) : BTBD11 (89852 downstream)																							cctttctttcttttttttttt	0.303													4	2	---	---	---	---	
ANKRD13A	88455	broad.mit.edu	37	12	110452594	110452595	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110452594_110452595insT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc009zvm.1_Intron|ANKRD13A_uc010sxw.1_Intron	NM_033121	NP_149112	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13												0						CAtttctcttcttttttttttt	0.203													4	2	---	---	---	---	
ANKRD13A	88455	broad.mit.edu	37	12	110467031	110467031	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110467031delT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc010sxw.1_Intron|ANKRD13A_uc001tpy.2_Intron|ANKRD13A_uc001tpz.2_Intron|ANKRD13A_uc001tqa.2_5'Flank	NM_033121	NP_149112	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13												0						CTATCATTTCTTCATGCTTGC	0.398													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111617398	111617400	+	Intron	DEL	GTT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111617398_111617400delGTT	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						CATCGCCGTGgttgttgttgttg	0.236													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114203723	114203724	+	Intron	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114203723_114203724delTC	uc001tvk.1	-						uc001tvl.3_Intron					Homo sapiens cDNA FLJ39613 fis, clone SKNSH2009357.																		gctctctgtatctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114239331	114239331	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114239331delG								LHX5 (329454 upstream) : RBM19 (15212 downstream)																							atggggctgtggggaggattc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115174857	115174858	+	Intron	DEL	GT	-	-	rs147888391		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115174857_115174858delGT	uc001tvv.1	+											full-length cDNA clone CS0DI031YB14 of Placenta Cot 25-normalized of Homo sapiens (human).																		gtgtgtgtgcgtgtgtgtgtgt	0.337													3	4	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116595957	116595957	+	Intron	DEL	A	-	-	rs73200219	byFrequency	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116595957delA	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATTCAAGGGGAAAAAAAAAAA	0.418													3	4	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117249513	117249514	+	Intron	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117249513_117249514delTG	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		tgtgtgtgtctgtgtgtgtgtg	0.282													4	2	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119913954	119913954	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119913954delA	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CTATGCAGGGAAAAAAAAATC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	120029926	120029926	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120029926delA	uc001txf.2	-						TMEM233_uc010szd.1_5'Flank					Homo sapiens full length insert cDNA clone ZD48A05.																		aactcaaagtaaaaaaaaaaa	0.040													4	3	---	---	---	---	
MPHOSPH9	10198	broad.mit.edu	37	12	123707528	123707529	+	5'Flank	DEL	TA	-	-	rs60789595		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123707528_123707529delTA	uc001uel.2	-						MPHOSPH9_uc010tal.1_5'Flank|MPHOSPH9_uc010tam.1_5'Flank|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9						M phase of mitotic cell cycle	centriole|Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		tgtgtgtgtgtatatgtacgta	0.144													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124923650	124923651	+	Intron	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923650_124923651delGA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gagacagagggagagacagaga	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126571112	126571113	+	IGR	DEL	TG	-	-	rs35966007		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126571112_126571113delTG								TMEM132B (427523 upstream) : LOC100128554 (355914 downstream)																							gtgtgtgcaatgtgtgtgtgtg	0.000													4	4	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129691789	129691790	+	Intron	INS	-	AGATG	AGATG	rs147753169	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129691789_129691790insAGATG	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		ggacagtcagaagatgaataCA	0.064													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130702518	130702518	+	IGR	DEL	T	-	-	rs71843595		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130702518delT								FZD10 (52234 upstream) : PIWIL1 (120096 downstream)																							ggcatatttcttttttttttt	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131249603	131249605	+	IGR	DEL	TGA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131249603_131249605delTGA								RIMBP2 (48777 upstream) : STX2 (24544 downstream)																							TGTCATGtgttgatgatgtcact	0.039													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27277773	27277774	+	IGR	INS	-	A	A	rs35826664		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27277773_27277774insA								WASF3 (14693 upstream) : GPR12 (51567 downstream)																							ggatgtctgttaaaaaaaaaaa	0.000													3	6	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28605372	28605372	+	Intron	DEL	G	-	-	rs7319062	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28605372delG	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	ctcaaaaaaagaagaaaaaat	0.000			Mis|O		AML|ALL								4	2	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	30075070	30075070	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30075070delG	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron|MTUS2_uc010tdq.1_Intron	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						aagaaatgctggtcacattcc	0.080													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31572978	31572978	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31572978delG								C13orf26 (23827 upstream) : HSPH1 (137787 downstream)																							TCAGCAGGCTGGAGATGGAGG	0.517													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32611191	32611196	+	Intron	DEL	ACACAA	-	-	rs10530774	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32611191_32611196delACACAA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		acacacacacacacaaacacacacac	0.238													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33752065	33752066	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33752065_33752066insA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		aggaaggaaggaaggaaggaag	0.000													4	2	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49830213	49830214	+	Intron	INS	-	A	A	rs147882512	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49830213_49830214insA	uc001vcu.2	+						CDADC1_uc001vcs.1_Intron|CDADC1_uc001vct.1_Intron|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		CTCCTTTTTTTTAAAAAAAAAA	0.262													2	4	---	---	---	---	
DLEU7	220107	broad.mit.edu	37	13	51420839	51420839	+	5'Flank	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51420839delG	uc001vex.2	-						uc001vey.2_Intron|DLEU7_uc001vez.2_5'Flank	NM_198989	NP_945340	Q6UYE1	LEU7_HUMAN	deleted in lymphocytic leukemia, 7												0		Acute lymphoblastic leukemia(7;1.03e-07)|Lung NSC(96;0.000818)|Breast(56;0.00122)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.25e-08)		aATTGGTGGAGGGAGGATGAA	0.234													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52855276	52855277	+	Intron	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52855276_52855277delTG	uc001vgm.1	-											Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						ctggtgtgcttgtgtgtgtgtg	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61271466	61271467	+	IGR	INS	-	C	C	rs146485613	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61271466_61271467insC								TDRD3 (123454 upstream) : PCDH20 (712354 downstream)																							ttccttcccttcctcccttccc	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66525694	66525694	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66525694delC								None (None upstream) : PCDH9 (351273 downstream)																							ccctgacagaccccagtgtgt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68210233	68210233	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68210233delT								PCDH9 (405765 upstream) : None (None downstream)																							ACTTTCCTTCTTCACCTAGCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70740749	70740750	+	IGR	INS	-	G	G	rs146714617		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70740749_70740750insG								ATXN8OS (26864 upstream) : None (None downstream)																							aaggacttcattcatgtctaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73965914	73965915	+	IGR	DEL	AG	-	-	rs139332355	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73965914_73965915delAG								KLF5 (314239 upstream) : KLF12 (294235 downstream)																							tgaagggagaagagagagagag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80457779	80457790	+	Intron	DEL	GAGAGGAAGGGG	-	-	rs117938482		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80457779_80457790delGAGAGGAAGGGG	uc001vlh.2	+											Homo sapiens cDNA clone IMAGE:4825993.																		cacaaagggtgagaggaagggggagaggaaga	0.160													4	4	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	102029111	102029111	+	Frame_Shift_Del	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102029111delA	uc001vox.1	-	6	773	c.584delT	c.(583-585)TTAfs	p.L195fs	NALCN_uc001voy.2_5'UTR|NALCN_uc001voz.2_Frame_Shift_Del_p.L195fs|NALCN_uc001vpa.2_Frame_Shift_Del_p.L195fs	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	195	Helical; Name=S5 of repeat I; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGAACTCCTAAAATTCCATA	0.318													108	50	---	---	---	---	
ITGBL1	9358	broad.mit.edu	37	13	102370916	102370918	+	3'UTR	DEL	ATC	-	-	rs72332834		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102370916_102370918delATC	uc001vpc.3	+	11								O95965	ITGBL_HUMAN	SubName: Full=cDNA FLJ38556 fis, clone HCHON2003131, highly similar to Homo sapiens integrin, beta-like 1 (with EGF-like repeat domains) (ITGBL1), mRNA;						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGTTTGGCAAATCATCATCACTG	0.419													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107754095	107754095	+	IGR	DEL	T	-	-	rs1927764	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107754095delT								ARGLU1 (533581 upstream) : FAM155A (66785 downstream)																							tacttcattcttttttatggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111714010	111714010	+	IGR	DEL	G	-	-	rs76966792		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111714010delG								ANKRD10 (146594 upstream) : ARHGEF7 (53614 downstream)																							CATGAAGCAAGAACGTGTCAT	0.463													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19549326	19549327	+	IGR	INS	-	TG	TG	rs79571359	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19549326_19549327insTG								OR11H12 (170754 upstream) : POTEG (4038 downstream)																							acacacacacacacacacacgc	0.455													4	3	---	---	---	---	
THTPA	79178	broad.mit.edu	37	14	24010431	24010431	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24010431delT	uc001wkb.3	+						uc001wkc.1_Intron|uc001wkf.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)	CACCCCTTTCTTGACCAAGAC	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	24360022	24360023	+	IGR	DEL	AG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24360022_24360023delAG								DHRS2 (245176 upstream) : C14orf165 (31436 downstream)																							gatgaaagaaagagagagagag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	28471116	28471118	+	IGR	DEL	GTG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28471116_28471118delGTG								None (None upstream) : FOXG1 (765169 downstream)																							ctaagggcctgtggtggtggtgg	0.000													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	33814076	33814076	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33814076delA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GGAGAGAAGGAAGTCACAGGC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38510428	38510429	+	Intron	INS	-	T	T	rs76418623		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38510428_38510429insT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		ctgatgtatgcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39017057	39017057	+	IGR	DEL	A	-	-	rs113072639		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39017057delA								CLEC14A (291483 upstream) : SEC23A (484066 downstream)																							TTGTTAAAGGAAAAAAAAAAA	0.159													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44255219	44255219	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44255219delT								None (None upstream) : FSCB (718136 downstream)																							CCCCCTCAGATTTTTACGATT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51804978	51804978	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51804978delA								TMX1 (80608 upstream) : FRMD6 (150877 downstream)																							TATGACAACCAAAAAAACTTA	0.303													4	2	---	---	---	---	
NID2	22795	broad.mit.edu	37	14	52494351	52494352	+	Intron	INS	-	AC	AC	rs141906245	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52494351_52494352insAC	uc001wzo.2	-						NID2_uc010tqs.1_Intron|NID2_uc010tqt.1_Intron|NID2_uc001wzp.2_Intron	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor							basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					GAGCAATTGCTacacacacaca	0.252													5	3	---	---	---	---	
FERMT2	10979	broad.mit.edu	37	14	53326539	53326539	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53326539delT	uc001xad.2	-						FERMT2_uc001xac.2_Intron|FERMT2_uc001xae.2_Intron|FERMT2_uc001xaf.2_Intron	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					AGTACTAttcttttttttttt	0.174													4	2	---	---	---	---	
SAMD4A	23034	broad.mit.edu	37	14	55239545	55239545	+	Intron	DEL	A	-	-	rs35278828		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55239545delA	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404	Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0						ACAAACAAACAAAAAAAAAAA	0.403													3	3	---	---	---	---	
RPL13AP3	645683	broad.mit.edu	37	14	56233989	56233990	+	RNA	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56233989_56233990insA	uc010aos.2	+	1		c.1027_1028insA				NR_004844				Homo sapiens ribosomal protein L13a pseudogene, mRNA (cDNA clone IMAGE:5271409).												0						TACTTTTAAAGAAAAAAAAaac	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56413920	56413920	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56413920delT								C14orf34 (150528 upstream) : PELI2 (171173 downstream)																							ATAGGAATACttttttttttt	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	58217450	58217451	+	IGR	INS	-	TTG	TTG	rs143731317	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58217450_58217451insTTG								SLC35F4 (153835 upstream) : C14orf37 (253358 downstream)																							attatttgggtttgttgttgtt	0.000													4	2	---	---	---	---	
PRKCH	5583	broad.mit.edu	37	14	61677473	61677484	+	Intron	DEL	TCTCTCTCTCTC	-	-	rs113902485		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61677473_61677484delTCTCTCTCTCTC	uc010tsa.1	+							NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		AAGAGTCctttctctctctctctctctctctc	0.165													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	63648030	63648031	+	IGR	INS	-	CCA	CCA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63648030_63648031insCCA								KCNH5 (79446 upstream) : RHOJ (23114 downstream)																							aatcttatcctccacctcagac	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66854135	66854135	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66854135delA								FUT8 (644174 upstream) : C14orf53 (98974 downstream)																							actctgtctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
DPF3	8110	broad.mit.edu	37	14	73166692	73166692	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73166692delC	uc001xnc.2	-						DPF3_uc001xnd.1_Intron|DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AGCTTAGGATCAGGGCAGACC	0.537													4	2	---	---	---	---	
COQ6	51004	broad.mit.edu	37	14	74418079	74418079	+	Intron	DEL	T	-	-	rs35032560		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74418079delT	uc001xph.2	+						FAM161B_uc001xpd.1_5'Flank|COQ6_uc001xpe.2_Intron|COQ6_uc001xpf.2_Intron|COQ6_uc010tuk.1_Intron|COQ6_uc010tul.1_Intron|COQ6_uc010tum.1_Intron|COQ6_uc010tun.1_Intron|COQ6_uc001xpg.2_Intron	NM_182476	NP_872282	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 homolog isoform a						ubiquinone biosynthetic process	mitochondrion	flavin adenine dinucleotide binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.00337)		gtcttttcacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	74943822	74943823	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74943822_74943823delAC								TMEM90A (51017 upstream) : NPC2 (2821 downstream)																							CCCATTCCCAacacacacacac	0.342													4	2	---	---	---	---	
FLVCR2	55640	broad.mit.edu	37	14	76090708	76090709	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76090708_76090709insA	uc001xrs.2	+						FLVCR2_uc010tvd.1_Intron	NM_017791	NP_060261	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular						transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)		aaaaaataaagaaaaaaaaaaa	0.168													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77056750	77056750	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77056750delT								ESRRB (88572 upstream) : VASH1 (171485 downstream)																							CAGCATTCCAttttttttttt	0.199													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77145392	77145393	+	IGR	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77145392_77145393delCA								ESRRB (177214 upstream) : VASH1 (82842 downstream)																							cacacacgtgcacacacacaca	0.228													3	3	---	---	---	---	
C14orf148	122945	broad.mit.edu	37	14	77865261	77865261	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77865261delA	uc001xtr.2	-							NM_001113475	NP_001106946	Q6NXP6	CN148_HUMAN	hypothetical protein LOC122945 isoform 1						proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)		ccagtgagccaagatcgcgct	0.000													4	2	---	---	---	---	
ADCK1	57143	broad.mit.edu	37	14	78334752	78334752	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78334752delC	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Intron|ADCK1_uc001xuk.1_Intron	NM_020421	NP_065154	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1 isoform a							extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		GTCAGAGCCACCCAGTGGGCC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80841014	80841014	+	Intron	DEL	C	-	-	rs34331083		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80841014delC	uc001xuw.1	+											Homo sapiens, clone IMAGE:5167652, mRNA.																		ccacaccacacccggcACTCT	0.154													4	2	---	---	---	---	
FLRT2	23768	broad.mit.edu	37	14	86003942	86003943	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86003942_86003943delAC	uc001xvr.2	+						FLRT2_uc010atd.2_Intron	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTATAGTAAAacacacacacac	0.262													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87401328	87401328	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87401328delT								None (None upstream) : GALC (902836 downstream)																							ATATTTGATATTTTAGTATAC	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88092051	88092052	+	IGR	INS	-	TGTG	TGTG	rs148313202	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88092051_88092052insTGTG								None (None upstream) : GALC (212112 downstream)																							CTATATACATAtgtgtgtgtgt	0.178													4	2	---	---	---	---	
C14orf143	90141	broad.mit.edu	37	14	90330777	90330778	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90330777_90330778insT	uc001xxt.2	-						C14orf143_uc001xxs.2_Intron|C14orf143_uc001xxv.1_Intron	NM_145231	NP_660274	Q9BUY7	EFC11_HUMAN	hypothetical protein LOC90141								calcium ion binding				0		all_cancers(154;0.136)		Epithelial(152;0.194)		tgtttccttcctttttttttca	0.168													4	2	---	---	---	---	
CCDC88C	440193	broad.mit.edu	37	14	91830906	91830906	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91830906delG	uc010aty.2	-						CCDC88C_uc010twk.1_Intron	NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				CCACCCACCTGACAACACCCT	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94334835	94334835	+	IGR	DEL	A	-	-	rs67737519		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94334835delA								PRIMA1 (80069 upstream) : C14orf86 (36241 downstream)																							cctcttgaccaaaagtgatgc	0.144													2	4	---	---	---	---	
DICER1	23405	broad.mit.edu	37	14	95567512	95567512	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95567512delC	uc001ydw.2	-						DICER1_uc010avh.1_Intron|DICER1_uc001ydv.2_Intron|DICER1_uc001ydx.2_Intron|DICER1_uc001ydy.1_Intron	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1						negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AGAGCAAGGGCCCCAAGGCTG	0.547			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97602215	97602217	+	IGR	DEL	CAC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97602215_97602217delCAC								VRK1 (254265 upstream) : C14orf64 (789730 downstream)																							ccaacatcatcaccaccaccacc	0.000													4	2	---	---	---	---	
WARS	7453	broad.mit.edu	37	14	100810397	100810403	+	Intron	DEL	CTTCCCT	-	-	rs11276770		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100810397_100810403delCTTCCCT	uc001yhf.1	-						WARS_uc001yhe.1_Intron|WARS_uc001yhg.1_Intron|WARS_uc001yhh.1_Intron|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Intron	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a						angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	GTTATGATGGCTtccctcttccctctt	0.164													4	4	---	---	---	---	
MIR539	664612	broad.mit.edu	37	14	101513129	101513130	+	5'Flank	INS	-	TGG	TGG	rs138069781	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101513129_101513130insTGG	hsa-mir-539|MI0003514	+						MIR889_hsa-mir-889|MI0005540_5'Flank|MIR544_hsa-mir-544|MI0003515_5'Flank|MIR655_hsa-mir-655|MI0003677_5'Flank																	0						GAAACTATCATtggtggtggtg	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101656176	101656177	+	IGR	INS	-	GGAA	GGAA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101656176_101656177insGGAA								MIR656 (123038 upstream) : DIO3OS (362383 downstream)																							ATTggaagcagggaaggaagga	0.262													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101929208	101929208	+	IGR	DEL	C	-	-	rs35597202		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101929208delC								MIR656 (396070 upstream) : DIO3OS (89352 downstream)																							AAATCCTCCTCCCCCCTTCCA	0.562													2	6	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106846005	106846005	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106846005delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ACAAATAAAGAAAAAAAAACA	0.428													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107278989	107278989	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107278989delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ACACAGGTGTGGTCCTGCAGT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20003421	20003421	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20003421delA								None (None upstream) : GOLGA6L6 (733673 downstream)																							gacgatatttacttttccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20397406	20397406	+	IGR	DEL	G	-	-	rs55961858		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20397406delG								None (None upstream) : GOLGA6L6 (339688 downstream)																							CTGTAGTTTTGCACAATTTTG	0.348													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20481403	20481403	+	IGR	DEL	T	-	-	rs111588962		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20481403delT								None (None upstream) : GOLGA6L6 (255691 downstream)																							TCTTCAtttgtttttttttgt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20524821	20524822	+	IGR	INS	-	A	A	rs75144308		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20524821_20524822insA								None (None upstream) : GOLGA6L6 (212272 downstream)																							TTTTCTAAAATAAAAAAAAATC	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20857994	20857995	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20857994_20857995insA								GOLGA8C (76968 upstream) : BCL8 (12061 downstream)																							tgtccaatattaagatcatgat	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21086017	21086022	+	IGR	DEL	TTTCTA	-	-	rs74736528		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21086017_21086022delTTTCTA								POTEB (14040 upstream) : NF1P1 (35999 downstream)																							gtcatcattgtttctatttgtatttg	0.019													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21964093	21964093	+	IGR	DEL	T	-	-	rs149601786		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21964093delT								LOC646214 (23354 upstream) : CXADRP2 (50327 downstream)																							attctccccctggcagtctgt	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22512132	22512133	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22512132_22512133delGA								OR4N3P (97747 upstream) : MIR1268 (1096 downstream)																							CAGAGCCCAGGAGATTGGTGGC	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22533088	22533088	+	IGR	DEL	A	-	-	rs146102575		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22533088delA								MIR1268 (19808 upstream) : GOLGA8DP (169197 downstream)																							actctctctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27849752	27849753	+	IGR	DEL	GT	-	-	rs145099900		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27849752_27849753delGT								GABRG3 (71618 upstream) : OCA2 (150272 downstream)																							gagacagcaggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33256125	33256126	+	Intron	DEL	CA	-	-	rs35753530		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33256125_33256126delCA	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TCCTATGAATcacacacacaca	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36209687	36209687	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36209687delG								ATPBD4 (371283 upstream) : C15orf41 (662125 downstream)																							CTTTTTCAATGGCTTTTTATC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40614429	40614430	+	5'Flank	DEL	GT	-	-	rs34185101		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40614429_40614430delGT	uc001zlf.1	+											Homo sapiens cDNA FLJ41776 fis, clone IMR322013053.																		GGGCTTCCTCgtgtgtgtgtgt	0.460													4	2	---	---	---	---	
NUSAP1	51203	broad.mit.edu	37	15	41657923	41657923	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41657923delT	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443	Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		tttctttttcttttttttttt	0.030													4	2	---	---	---	---	
CATSPER2	117155	broad.mit.edu	37	15	43934300	43934301	+	Intron	INS	-	T	T	rs11440900		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43934300_43934301insT	uc001zsh.2	-						CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron|CATSPER2_uc001zsk.2_Intron	NM_172095	NP_742093	Q96P56	CTSR2_HUMAN	sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		aattaggatgcttttttttttt	0.084													4	2	---	---	---	---	
GABPB1	2553	broad.mit.edu	37	15	50635745	50635745	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50635745delT	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron|GABPB1_uc001zyc.2_Intron|GABPB1_uc001zyd.2_Intron|GABPB1_uc001zye.2_Intron|GABPB1_uc001zyf.2_Intron	NM_005254	NP_005245	Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1						ccctcaccTCtttttttttta	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53493134	53493134	+	IGR	DEL	A	-	-	rs71889566		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53493134delA								ONECUT1 (410925 upstream) : WDR72 (312804 downstream)																							tgtcaaaaggaaaaaaaaaaa	0.164													5	3	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57567557	57567558	+	Intron	INS	-	AC	AC	rs142758945	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57567557_57567558insAC	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron|TCF12_uc010ugp.1_Intron|TCF12_uc010ugq.1_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		tgtgtgtgtgtgtgtacgtatg	0.257			T	TEC	extraskeletal myxoid chondrosarcoma								4	2	---	---	---	---	
GCOM1	145781	broad.mit.edu	37	15	57922170	57922170	+	Intron	DEL	T	-	-	rs72160469		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57922170delT	uc002aei.2	+						GCOM1_uc002aej.2_Intron|GCOM1_uc002aek.2_Intron|GCOM1_uc002ael.2_Intron|GCOM1_uc002aem.2_Intron|GCOM1_uc002aeq.2_Intron|GCOM1_uc002aen.2_Intron|GCOM1_uc010bfy.2_Intron|GCOM1_uc002aeo.2_Intron|GCOM1_uc002aep.2_Intron|GCOM1_uc010bfx.2_Intron	NM_001018100	NP_001018110	P0CAP1	GCOM1_HUMAN	GRINL1A upstream protein isoform 7						intracellular signal transduction	extrinsic to internal side of plasma membrane|I band				ovary(1)	1						ctTCATTGGAttttttttttt	0.030													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	60836679	60836681	+	Intron	DEL	TTG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60836679_60836681delTTG	uc002agv.2	-						RORA_uc002agt.3_Intron|RORA_uc002agw.2_Intron|RORA_uc002agx.2_Intron	NM_134260	NP_599022	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform b						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						CTGCTTTTTTTTGTTGTTGTTGT	0.365													3	3	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	60982503	60982503	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60982503delC	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						agacatgtgaccaggaggggt	0.000													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61415975	61415978	+	Intron	DEL	GCCG	-	-	rs150991018		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61415975_61415978delGCCG	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						AGATTTCCCAGCCGGCCTCTGACC	0.363													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61699011	61699015	+	IGR	DEL	ATCTC	-	-	rs148312020		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61699011_61699015delATCTC								RORA (177509 upstream) : VPS13C (445577 downstream)																							TCTAAAGCTTATCTCATCTCTTATG	0.161													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63471478	63471478	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63471478delA								RPS27L (21737 upstream) : RAB8B (10250 downstream)																							CGCACCATCTAAACAACTGAT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	65017079	65017080	+	IGR	INS	-	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65017079_65017080insG								OAZ2 (21617 upstream) : RBPMS2 (15018 downstream)																							ctgtaatcccacactttgggag	0.000													4	2	---	---	---	---	
THSD4	79875	broad.mit.edu	37	15	71595417	71595417	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71595417delA	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						TTTCCTACCCAGGAGGATAAG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	73341274	73341274	+	IGR	DEL	T	-	-	rs150625116		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73341274delT								ADPGK (264607 upstream) : NEO1 (3601 downstream)																							atctgaactgttttttttttt	0.000													4	2	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	76666830	76666831	+	Intron	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76666830_76666831delTT	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						AGTAGGGGGCtttttttttttt	0.168													4	2	---	---	---	---	
IL16	3603	broad.mit.edu	37	15	81565263	81565264	+	Intron	INS	-	TGT	TGT	rs67106640		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81565263_81565264insTGT	uc002bgh.3	+						IL16_uc002bgc.2_Intron|IL16_uc010blq.1_Intron|IL16_uc002bge.3_Intron|IL16_uc010unp.1_Intron|IL16_uc002bgg.2_Intron	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2						immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						gttgttgttggtgttgttgttg	0.450													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82351382	82351396	+	IGR	DEL	CCTTCTCCTCCCCCT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82351382_82351396delCCTTCTCCTCCCCCT								MEX3B (13021 upstream) : EFTUD1 (71165 downstream)																							CCCCCTtcccccttctcctccccctccttctcctc	0.065													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82361974	82361975	+	IGR	INS	-	G	G	rs148071343	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82361974_82361975insG								MEX3B (23613 upstream) : EFTUD1 (60586 downstream)																							CAAAAGCAGTTGGTTCTGCAGC	0.426													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98583772	98583772	+	IGR	DEL	T	-	-	rs34967522		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98583772delT								ARRDC4 (66705 upstream) : FAM169B (396619 downstream)																							ACTTTCAGGGTTTTTTTTTTC	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98824030	98824031	+	IGR	DEL	AG	-	-	rs116617604	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98824030_98824031delAG								ARRDC4 (306963 upstream) : FAM169B (156360 downstream)																							ACTTCCATTcagagagagagag	0.391													4	2	---	---	---	---	
SYNM	23336	broad.mit.edu	37	15	99654982	99654983	+	Intron	INS	-	C	C	rs139805932	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99654982_99654983insC	uc002bup.2	+						SYNM_uc002buo.2_Intron|SYNM_uc002buq.2_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A						intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4						CCTTGGCATCACCCTCCTTTCC	0.629													2	4	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100598526	100598527	+	Intron	INS	-	T	T	rs144409944	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100598526_100598527insT	uc002bvv.1	-							NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TATCCCGGCTCTAACACCCCTA	0.584													4	4	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101998764	101998764	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101998764delC	uc002bwy.2	-						PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCGTCTGTCTCCAGGGACTGT	0.577													4	2	---	---	---	---	
ITFG3	83986	broad.mit.edu	37	16	306739	306740	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:306739_306740insT	uc002cgf.2	+						ITFG3_uc010bqr.2_Intron|ITFG3_uc002cgg.2_Intron|ITFG3_uc010uud.1_Intron|ITFG3_uc002cgh.2_Intron	NM_032039	NP_114428	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3							integral to membrane				central_nervous_system(1)	1		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				tgcctggctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	1977026	1977026	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1977026delC								HS3ST6 (8795 upstream) : SEPX1 (11209 downstream)																							GTCACTGAAGCCCCACCAACC	0.612													4	3	---	---	---	---	
ZNF598	90850	broad.mit.edu	37	16	2049882	2049883	+	In_Frame_Ins	INS	-	TCC	TCC	rs141374045	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2049882_2049883insTCC	uc002cof.1	-	11	1682_1683	c.1667_1668insGGA	c.(1666-1668)GAC>GAGGAC	p.555_556insE	ZNF598_uc002coe.1_5'UTR	NM_178167	NP_835461	Q86UK7	ZN598_HUMAN	zinc finger protein 598	555_556						intracellular	zinc ion binding			lung(1)|breast(1)	2						CCGGGCCGCCGTCCTCCTCCTC	0.703													6	8	---	---	---	---	
ALG1	56052	broad.mit.edu	37	16	5085790	5085790	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5085790delG	uc002cyj.2	+						NAGPA_uc002cyf.2_5'Flank|NAGPA_uc002cyg.2_5'Flank|NAGPA_uc002cyh.2_5'Flank|NAGPA_uc002cyi.2_5'Flank|NAGPA_uc010uxx.1_5'Flank	NM_019109	NP_061982	Q9BT22	ALG1_HUMAN	beta-1,4-mannosyltransferase						dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(90;0.0164)				CCACAGGTATGGGGGGACACA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8429569	8429569	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8429569delT								A2BP1 (666229 upstream) : TMEM114 (189934 downstream)																							AAGCAAGCAGTTTCCTTCTCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9127640	9127655	+	IGR	DEL	TCGGTCCCTCCCTCCC	-	-	rs7198349	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9127640_9127655delTCGGTCCCTCCCTCCC								USP7 (70299 upstream) : C16orf72 (57882 downstream)																							cttccttccttcggtccctccctccctccttccttc	0.102													5	5	---	---	---	---	
FAM18A	780776	broad.mit.edu	37	16	10898153	10898153	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10898153delA	uc010buo.1	-						FAM18A_uc010uyr.1_Intron|FAM18A_uc010uys.1_Intron|FAM18A_uc010uyt.1_Intron|FAM18A_uc010bun.2_Intron|FAM18A_uc010uyu.1_Intron|FAM18A_uc002dad.3_Intron|FAM18A_uc002daf.1_Intron	NM_001079512	NP_001072980	A6NH52	FA18A_HUMAN	hypothetical protein LOC780776							integral to membrane					0						TTTTCTCACCACTGTTTTCAG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11579834	11579834	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11579834delG	uc002dax.1	-											Homo sapiens cDNA FLJ44575 fis, clone UTERU3018154.																		tgtatgggtaggagggtggac	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13363886	13363886	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13363886delT								SHISA9 (29614 upstream) : ERCC4 (650128 downstream)																							TTACTCTACCTGCCACAGAAC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	14155013	14155014	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14155013_14155014insA								ERCC4 (108808 upstream) : MKL2 (10182 downstream)																							aaaaaaaaaacaaaaaaaaaca	0.000													4	2	---	---	---	---	
MKL2	57496	broad.mit.edu	37	16	14354211	14354212	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14354211_14354212insA	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dcj.2_Intron	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						ACTGTAATGATAAAAAAAAAAA	0.307													4	3	---	---	---	---	
C16orf45	89927	broad.mit.edu	37	16	15617713	15617713	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15617713delA	uc002ddo.2	+						C16orf45_uc002ddp.2_Intron	NM_033201	NP_149978	Q96MC5	CP045_HUMAN	hypothetical protein LOC89927 isoform 1											ovary(1)	1						GTCTCCAGAGAATTCCCAGAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20266820	20266820	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20266820delG								GPR139 (181720 upstream) : GP2 (54992 downstream)																							GTCTCACCCTGGTGGTTCCCA	0.517													4	2	---	---	---	---	
ACSM5	54988	broad.mit.edu	37	16	20441903	20441903	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20441903delA	uc002dhe.2	+							NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2						gggaggaaataaaggaaagag	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23819346	23819346	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23819346delC								CHP2 (49090 upstream) : PRKCB (27954 downstream)																							TACATAAAAGCCCAATACAAA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26306701	26306702	+	IGR	DEL	GT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26306701_26306702delGT								HS3ST4 (157693 upstream) : C16orf82 (771517 downstream)																							AAGCCAAAGAgtgtgtgtgtgt	0.262													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26385831	26385831	+	IGR	DEL	G	-	-	rs72532698		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26385831delG								HS3ST4 (236823 upstream) : C16orf82 (692388 downstream)																							tggatggaatgggtaagtaag	0.030													2	8	---	---	---	---	
IL21R	50615	broad.mit.edu	37	16	27435872	27435872	+	Intron	DEL	A	-	-	rs111439864		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27435872delA	uc002doq.1	+						IL21R_uc002dor.1_Intron|IL21R_uc002dos.1_5'Flank	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor						natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4						ACAGGACTTCAAATTCGATGA	0.224			T	BCL6	NHL								3	3	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27990887	27990888	+	Intron	INS	-	A	A	rs77066595		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27990887_27990888insA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						gagaatccatcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	28050924	28050925	+	Intron	INS	-	CA	CA	rs139661868	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28050924_28050925insCA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						acccacacttgcacacacacac	0.020													3	4	---	---	---	---	
PRSS36	146547	broad.mit.edu	37	16	31157693	31157695	+	Intron	DEL	CCT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31157693_31157695delCCT	uc002ebd.2	-						PRSS36_uc010vff.1_Intron|PRSS36_uc010vfg.1_Intron|PRSS36_uc010vfh.1_Intron	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor						proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1						TCTCAACTCCCCTCCTCCAGTCA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32384850	32384851	+	IGR	DEL	CT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32384850_32384851delCT								HERC2P4 (220976 upstream) : TP53TG3B (299990 downstream)																							gtgccgtttgctaagaccactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32653057	32653058	+	IGR	INS	-	C	C	rs141887857	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32653057_32653058insC								HERC2P4 (489183 upstream) : TP53TG3B (31783 downstream)																							gtgcagtggtgtatcttggctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32817064	32817065	+	IGR	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32817064_32817065delTT								TP53TG3B (128186 upstream) : SLC6A10P (71732 downstream)																							tttcatctcattttatcatttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32848034	32848034	+	IGR	DEL	A	-	-	rs75274373		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32848034delA								TP53TG3B (159156 upstream) : SLC6A10P (40763 downstream)																							tatttctttcattaaaaaatt	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33052524	33052524	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33052524delC								SLC6A10P (156061 upstream) : MIR1826 (912984 downstream)																							aacctgtgtactacattacta	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33337174	33337174	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33337174delG								SLC6A10P (440711 upstream) : MIR1826 (628334 downstream)																							ctggacaacagggtgaaactc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33387792	33387793	+	IGR	INS	-	TC	TC	rs142682927		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33387792_33387793insTC								SLC6A10P (491329 upstream) : MIR1826 (577715 downstream)																							TAGGAtttttttttttagatga	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33481145	33481146	+	IGR	INS	-	C	C	rs146417227	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33481145_33481146insC								SLC6A10P (584682 upstream) : MIR1826 (484362 downstream)																							GGAGATGGTGACTGCCCTCCAT	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33881797	33881798	+	IGR	INS	-	A	A	rs62027442		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33881797_33881798insA								SLC6A10P (985334 upstream) : MIR1826 (83710 downstream)																							gaatggaatcgaaggaatcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33895711	33895712	+	IGR	INS	-	TGG	TGG			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33895711_33895712insTGG								SLC6A10P (999248 upstream) : MIR1826 (69796 downstream)																							attccattcaatgattccattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33934022	33934023	+	IGR	INS	-	C	C	rs78524883	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33934022_33934023insC								None (None upstream) : MIR1826 (31485 downstream)																							CATACCAAAAACTTAAAATTTT	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35265857	35265858	+	IGR	INS	-	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35265857_35265858insG								LOC146481 (550890 upstream) : None (None downstream)																							taaaaactagacagaagcaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46463268	46463268	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46463268delC								None (None upstream) : ANKRD26P1 (39981 downstream)																							AAAATAACAACAATGAAATAA	0.154													5	4	---	---	---	---	
C16orf87	388272	broad.mit.edu	37	16	46841335	46841336	+	Intron	DEL	AA	-	-	rs113895696		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46841335_46841336delAA	uc002eek.1	-							NM_001001436	NP_001001436	Q6PH81	CP087_HUMAN	hypothetical protein LOC388272												0						tctcagaaggaaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49043859	49043859	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49043859delG								N4BP1 (399739 upstream) : CBLN1 (268352 downstream)																							GAAGCATGGAGGGAGAACAAT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51333782	51333782	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51333782delA								SALL1 (148599 upstream) : None (None downstream)																							tccaaaaaagaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54381270	54381271	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54381270_54381271insT								IRX3 (60892 upstream) : IRX5 (583840 downstream)																							ttctctcGttcttttttttttt	0.005													5	3	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57097658	57097658	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57097658delT	uc002ekk.1	+						NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_Intron|NLRC5_uc002eko.1_Intron|NLRC5_uc002ekq.1_Intron|NLRC5_uc002ekr.1_Intron	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				CCAAAATAACttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58445482	58445485	+	IGR	DEL	AGGA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58445482_58445485delAGGA								GINS3 (5435 upstream) : NDRG4 (52064 downstream)																							gaaggaagagaggaaggaaggaag	0.044													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59375751	59375751	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59375751delC								GOT2 (607505 upstream) : None (None downstream)																							tggatttctaccccagcacca	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60271310	60271311	+	IGR	DEL	AC	-	-	rs71388636		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60271310_60271311delAC								None (None upstream) : None (None downstream)																							TACAGAGcatacacacacacac	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60704034	60704034	+	IGR	DEL	A	-	-	rs68188841		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60704034delA								None (None upstream) : CDH8 (983201 downstream)																							ctgccataagaaaaaaaaaaa	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	67421654	67421654	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67421654delG								LRRC36 (2546 upstream) : TPPP3 (2060 downstream)																							TGTTAGGGGAGGGGCAGTGGC	0.527													4	2	---	---	---	---	
PDPR	55066	broad.mit.edu	37	16	70169972	70169974	+	Intron	DEL	AAA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70169972_70169974delAAA	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		actccatctcaaaaaaaaaaaaa	0.153													3	3	---	---	---	---	
CALB2	794	broad.mit.edu	37	16	71416057	71416064	+	Intron	DEL	AAGAAAAT	-	-	rs145128266	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									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													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74407695	74407695	+	IGR	DEL	T	-	-	rs11305054		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74407695delT								LOC283922 (5542 upstream) : CLEC18B (34836 downstream)																							GAGAACAATCttttttttttt	0.289													4	2	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74526264	74526264	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74526264delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						actctgtctcaaaaaaaaaaa	0.010													4	3	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76572958	76572958	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76572958delG	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						TGTTCGATAAGTGTATTTATT	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80010682	80010682	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80010682delA								MAF (376060 upstream) : DYNLRB2 (564172 downstream)																							cacttcttccaaaagtactCC	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84373367	84373367	+	IGR	DEL	G	-	-	rs35597059		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84373367delG								WFDC1 (9921 upstream) : ATP2C2 (28766 downstream)																							gctttgaaacggggggtaaca	0.060													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87597709	87597710	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87597709_87597710delTG								ZCCHC14 (72249 upstream) : JPH3 (37731 downstream)																							tgtgcgcatttgtgtgtgttgg	0.000													2	5	---	---	---	---	
JPH3	57338	broad.mit.edu	37	16	87654093	87654094	+	Intron	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87654093_87654094delGA	uc002fkd.2	+						JPH3_uc010vou.1_Intron	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		agaagagagggagagggggagg	0.322													4	3	---	---	---	---	
CBFA2T3	863	broad.mit.edu	37	16	89000193	89000193	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89000193delC	uc002fmm.1	-						CBFA2T3_uc002fml.1_Intron|CBFA2T3_uc010cif.1_Intron|CBFA2T3_uc002fmn.1_Intron	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16						cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0275)		ACGTCTGCGTCCCCACAGCCA	0.607			T	RUNX1	AML								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	89088336	89088337	+	IGR	DEL	AA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89088336_89088337delAA								CBFA2T3 (44935 upstream) : ACSF3 (71917 downstream)																							agactgtctcaaaaaaaaaaaa	0.050													3	3	---	---	---	---	
GLOD4	51031	broad.mit.edu	37	17	673935	673936	+	Intron	INS	-	T	T	rs79441857		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:673935_673936insT	uc002frv.2	-						GLOD4_uc002frt.2_Intron|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164	Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		acgcatctatgttttttttttt	0.000													3	3	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	716157	716158	+	Intron	INS	-	GT	GT	rs71865201		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:716157_716158insGT	uc002fsa.2	-						NXN_uc010vqd.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		tgtgactgtaggtgtgtgcgtg	0.000													4	2	---	---	---	---	
ABR	29	broad.mit.edu	37	17	1019977	1019978	+	Intron	INS	-	G	G	rs149515097	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1019977_1019978insG	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010cjq.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		atctactaaacgggggcagccc	0.059													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	1809942	1809942	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1809942delA								RPA1 (7094 upstream) : RTN4RL1 (28031 downstream)																							GTCTTTGTAGAAAAATAAATG	0.463													4	2	---	---	---	---	
C17orf87	388325	broad.mit.edu	37	17	5121327	5121327	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5121327delT	uc002gbh.2	-						uc002gbf.1_Intron|uc002gbg.1_Intron|C17orf87_uc010clb.1_Intron|C17orf87_uc002gbi.2_Intron	NM_207103	NP_996986	Q6UWF3	CQ087_HUMAN	hypothetical protein LOC388325							integral to membrane				ovary(1)	1						cccaccaacattttttttttt	0.000													3	3	---	---	---	---	
PITPNM3	83394	broad.mit.edu	37	17	6433205	6433206	+	Intron	INS	-	CC	CC	rs146034463	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6433205_6433206insCC	uc002gdd.3	-						PITPNM3_uc010cln.2_Intron	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1						phosphatidylinositol metabolic process	endomembrane system|integral to membrane	calcium ion binding|lipid binding|phosphatidylinositol transporter activity|receptor tyrosine kinase binding			ovary(2)|central_nervous_system(2)	4				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		TCCCCAGACATGTTGGGGCTGG	0.594													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7428179	7428180	+	IGR	DEL	CG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7428179_7428180delCG								POLR2A (10250 upstream) : TNFSF12 (24195 downstream)																							tagctgggcacggtggctcacg	0.000													4	2	---	---	---	---	
SHISA6	388336	broad.mit.edu	37	17	11385214	11385215	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11385214_11385215insA	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269	Q6ZSJ9	SHSA6_HUMAN	shisa homolog 6							integral to membrane				breast(1)	1						attgatgccataaaaaaatgcc	0.040													4	2	---	---	---	---	
MYOCD	93649	broad.mit.edu	37	17	12619681	12619682	+	Intron	DEL	AG	-	-	rs34311048		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12619681_12619682delAG	uc002gnn.2	+						MYOCD_uc002gno.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GACCCCTCTCAGGGGGCCACTG	0.505													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13304174	13304175	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13304174_13304175delAC								ELAC2 (382815 upstream) : HS3ST3A1 (94831 downstream)																							AATTGGGGATacacacacacac	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14747339	14747339	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14747339delA								HS3ST3B1 (497847 upstream) : PMP22 (385758 downstream)																							actccatctcaaaaaaaaaaG	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15707013	15707014	+	IGR	INS	-	AA	AA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15707013_15707014insAA								MEIS3P1 (13996 upstream) : ADORA2B (141217 downstream)																							aagtgtaattgaaaaaaaaaaa	0.069													3	3	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	16067232	16067233	+	Intron	INS	-	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16067232_16067233insC	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.2_Intron|NCOR1_uc002gps.1_Intron|NCOR1_uc010coz.1_Intron|NCOR1_uc010cpb.1_Intron|NCOR1_uc010cpa.1_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		atgattctgttttttctgatat	0.000													4	2	---	---	---	---	
C17orf76	388341	broad.mit.edu	37	17	16382533	16382533	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16382533delG	uc010cph.1	-						C17orf76_uc002gqh.2_Intron	NM_001113567	NP_001107039	Q8NAA5	CQ076_HUMAN	hypothetical protein LOC388341 isoform 1												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		ATACAGGACTGGTAGCTGGAA	0.507													4	2	---	---	---	---	
PEMT	10400	broad.mit.edu	37	17	17467687	17467688	+	Intron	INS	-	C	C	rs149983277	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17467687_17467688insC	uc002grj.2	-						PEMT_uc002grk.2_Intron|PEMT_uc002grl.2_Intron|PEMT_uc010vwx.1_Intron	NM_148173	NP_680478	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase						cell proliferation|phosphatidylcholine biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial membrane	phosphatidylethanolamine N-methyltransferase activity				0				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		CTGTTTCCAAGCCCTCTTCCCC	0.366													1	7	---	---	---	---	
TOM1L2	146691	broad.mit.edu	37	17	17760108	17760108	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17760108delC	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc002grv.3_Intron	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)					GATGAGCTGACCCTCTCTCCA	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18345812	18345812	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18345812delG								LOC339240 (17166 upstream) : LGALS9C (34287 downstream)																							AGGCTCCTGAGGCTCCCCGGC	0.617													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21226865	21226865	+	IGR	DEL	G	-	-	rs67907688		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21226865delG								MAP2K3 (8316 upstream) : KCNJ12 (52834 downstream)																							CGTCGGAGGTGGGGAAAAGGA	0.597													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21251747	21251749	+	IGR	DEL	CGT	-	-	rs58901223		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21251747_21251749delCGT								MAP2K3 (33198 upstream) : KCNJ12 (27950 downstream)																							GGTCGGGGGGCGTCCACCGCCCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21521488	21521489	+	IGR	INS	-	TC	TC	rs8079195	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21521488_21521489insTC								C17orf51 (43757 upstream) : FAM27L (303881 downstream)																							AATGTATATTTTTTTTCTAGAA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21551333	21551333	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21551333delT								C17orf51 (73602 upstream) : FAM27L (274037 downstream)																							TCCGAGGCAGTTTTATGGCAA	0.587													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21560553	21560556	+	IGR	DEL	ACCA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21560553_21560556delACCA								C17orf51 (82822 upstream) : FAM27L (264814 downstream)																							AGGTCTAAGTACCAACCATCATGC	0.446													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25308525	25308525	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25308525delA								None (None upstream) : WSB1 (312581 downstream)																							atacagttataaaaagaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27178892	27178892	+	IGR	DEL	A	-	-	rs35357029		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27178892delA								C17orf63 (9051 upstream) : ERAL1 (3151 downstream)																							actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35026267	35026268	+	IGR	INS	-	A	A	rs35654039		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35026267_35026268insA								MRM1 (60861 upstream) : LHX1 (268231 downstream)																							aacttcatctcaaaaaaaaaaa	0.144													3	4	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35676015	35676015	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35676015delA	uc002hnm.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTTCACTAGCAATCATATACT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36299091	36299091	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36299091delT								TBC1D3 (3993 upstream) : MRPL45 (153907 downstream)																							tttctttttcttttttttttt	0.174													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36818848	36818848	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36818848delT								SRCIN1 (56665 upstream) : C17orf96 (9113 downstream)																							TCTGATCttgttttttttttt	0.264													4	2	---	---	---	---	
LASP1	3927	broad.mit.edu	37	17	37070931	37070936	+	Intron	DEL	ACACAC	-	-	rs68023823		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37070931_37070936delACACAC	uc002hra.2	+						LASP1_uc010cvq.2_Intron|LASP1_uc010wdz.1_Intron	NM_006148	NP_006139	Q14847	LASP1_HUMAN	LIM and SH3 protein 1							cortical actin cytoskeleton	ion transmembrane transporter activity|SH3/SH2 adaptor activity|zinc ion binding			lung(1)	1						CGAGAGacagacacacacacacacac	0.427			T	MLL	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48240221	48240222	+	IGR	INS	-	GGAA	GGAA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48240221_48240222insGGAA								PPP1R9B (12344 upstream) : SGCA (3144 downstream)																							agagaagggagggagggaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52582808	52582809	+	IGR	INS	-	AAAC	AAAC	rs148258501	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52582808_52582809insAAAC								KIF2B (680235 upstream) : TOM1L1 (395243 downstream)																							tctgtctcacaaaacaaacaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53432543	53432544	+	IGR	DEL	TG	-	-	rs57969883	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53432543_53432544delTG								HLF (30117 upstream) : MMD (37431 downstream)																							aggcaagtAAtgtgtgtgtgtg	0.144													4	2	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60870365	60870367	+	Intron	DEL	CAC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60870365_60870367delCAC	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						ccacctccatcaccaccaccaca	0.000													4	6	---	---	---	---	
TANC2	26115	broad.mit.edu	37	17	61241491	61241491	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61241491delT	uc002jal.3	+							NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2						CATCAGCAGCttttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67917452	67917453	+	IGR	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67917452_67917453delTT								MAP2K6 (378990 upstream) : KCNJ16 (153973 downstream)																							CAATTACTGCTTTTTTTTTTTT	0.421													4	2	---	---	---	---	
CPSF4L	642843	broad.mit.edu	37	17	71255743	71255744	+	Intron	INS	-	ACT	ACT	rs144594533	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71255743_71255744insACT	uc010dfk.1	-							NM_001129885	NP_001123357	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor								RNA binding|zinc ion binding				0						CTGCTCTAGGGACTGGTTGGGC	0.540													3	3	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71384957	71384958	+	Intron	INS	-	TCCT	TCCT	rs140671690	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71384957_71384958insTCCT	uc010dfm.2	-						SDK2_uc002jjt.3_Intron|SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						ttccctccctctccttccttcc	0.005													4	2	---	---	---	---	
FDXR	2232	broad.mit.edu	37	17	72868621	72868622	+	Intron	DEL	CT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72868621_72868622delCT	uc002jly.2	-						FDXR_uc010wrj.1_Intron|FDXR_uc002jlw.2_5'UTR|FDXR_uc002jlx.2_Intron|FDXR_uc002jmc.2_Intron|FDXR_uc010wrk.1_Intron|FDXR_uc010wrl.1_Intron|FDXR_uc002jma.2_Intron|FDXR_uc010wrm.1_Intron|FDXR_uc002jlz.2_Intron|FDXR_uc002jmb.2_Intron	NM_024417	NP_077728	P22570	ADRO_HUMAN	ferredoxin reductase isoform 1 precursor						cholesterol metabolic process|electron transport chain|steroid biosynthetic process|transport	mitochondrial matrix	ferredoxin-NADP+ reductase activity|protein binding				0	all_lung(278;0.172)|Lung NSC(278;0.207)					CCTCTAACCCCTCTCTCTCTCC	0.545													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78614597	78614600	+	Intron	DEL	CTCC	-	-	rs112718811		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78614597_78614600delCTCC	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						TGAATGGGAACTCCCTCCCTTCTT	0.564													2	4	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80152185	80152186	+	Intron	INS	-	TT	TT	rs140430398		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80152185_80152186insTT	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GACTCAATGACttttttttttt	0.193													7	4	---	---	---	---	
LAMA1	284217	broad.mit.edu	37	18	7103818	7103818	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7103818delA	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor						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)	actccgtcttaaaaaaaaaaa	0.284													4	3	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8184326	8184327	+	Intron	INS	-	A	A	rs145231368	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8184326_8184327insA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				CTGCTGCAACTATGTAAAAGGA	0.381													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10133333	10133334	+	IGR	INS	-	TG	TG	rs148824892	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10133333_10133334insTG								VAPA (173316 upstream) : APCDD1 (321291 downstream)																							GCAGTGATTTCtgtgtgtgtgt	0.243													5	5	---	---	---	---	
GNAL	2774	broad.mit.edu	37	18	11771748	11771749	+	Intron	INS	-	T	T	rs147925621	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11771748_11771749insT	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron	NM_001142339	NP_001135811	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						gagtcgcactctgtcacccagg	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20685521	20685522	+	IGR	INS	-	T	T	rs146281866	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20685521_20685522insT								RBBP8 (79076 upstream) : CABLES1 (29006 downstream)																							GTTCTTACAGGTTCCTTACACA	0.317													3	3	---	---	---	---	
KCTD1	284252	broad.mit.edu	37	18	24063712	24063713	+	Intron	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24063712_24063713delTG	uc002kvw.2	-						KCTD1_uc010xbj.1_Intron|KCTD1_uc010xbk.1_Intron	NM_001136205	NP_001129677	Q719H9	KCTD1_HUMAN	potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			ACAACGGAGAtgtgtgtgtgtg	0.450													4	2	---	---	---	---	
B4GALT6	9331	broad.mit.edu	37	18	29209944	29209944	+	Intron	DEL	A	-	-	rs2595358		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29209944delA	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766	Q9UBX8	B4GT6_HUMAN	beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			AATGACCAGCAAAAAAAAAGG	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	29404670	29404671	+	IGR	INS	-	AA	AA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29404670_29404671insAA								MCART2 (63827 upstream) : KIAA1012 (4466 downstream)																							gaccctgtcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
KIAA1012	22878	broad.mit.edu	37	18	29439978	29439979	+	Intron	INS	-	A	A	rs79992437		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29439978_29439979insA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0						gactccgtctcaaaaaaaaaaa	0.124													5	3	---	---	---	---	
RPRD1A	55197	broad.mit.edu	37	18	33644334	33644334	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33644334delG	uc002kzf.1	-						RPRD1A_uc002kze.1_Intron|RPRD1A_uc002kzg.2_Intron|RPRD1A_uc010dmw.2_Intron|RPRD1A_uc010dmx.2_Intron	NM_018170	NP_060640	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2						aaagtcccgcggcgagtgcca	0.000													4	2	---	---	---	---	
SLC39A6	25800	broad.mit.edu	37	18	33695425	33695433	+	Intron	DEL	AACAACAAC	-	-	rs113587903		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33695425_33695433delAACAACAAC	uc010dmy.2	-						SLC39A6_uc002kzj.2_Intron	NM_012319	NP_036451	Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2						aaaaaaTTAAaacaacaacaacaacaaca	0.038													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35662275	35662276	+	IGR	INS	-	AGGTATAGAA	AGGTATAGAA	rs144591167	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35662275_35662276insAGGTATAGAA								CELF4 (516275 upstream) : None (None downstream)																							GAAAAGGAGTCAGACAAACTCT	0.446													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37438604	37438605	+	Intron	INS	-	GT	GT	rs143765235	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37438604_37438605insGT	uc010xck.1	-											Homo sapiens cDNA, FLJ99758.																		TGTGCATGTACgtgtgtgtgtg	0.233													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38233332	38233333	+	IGR	INS	-	A	A	rs149661084	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38233332_38233333insA								LOC647946 (853050 upstream) : KC6 (826905 downstream)																							TTCCTTTCCTGAAAAAAAAATT	0.361													2	4	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46761153	46761153	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46761153delA	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron|DYM_uc010dov.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						tgcacaatctaatcatatgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48991609	48991614	+	Intron	DEL	GTGTGT	-	-	rs111319023		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48991609_48991614delGTGTGT	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		GCAGGATGTCgtgtgtgtgtgtgtgt	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49768945	49768946	+	IGR	DEL	AC	-	-	rs34854787		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49768945_49768946delAC								None (None upstream) : DCC (97625 downstream)																							CCTCAAATAGacacacacacac	0.361													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50273337	50273339	+	Intron	DEL	GGA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50273337_50273339delGGA	uc002lfe.1	+							NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		aagtgtaaggggaggaggaggag	0.202													6	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50866426	50866447	+	Intron	DEL	ACACACACACACACACACACAT	-	-	rs66805812		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50866426_50866447delACACACACACACACACACACAT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTacacacacacacacacacacacacacacatacacacacac	0.275													4	3	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	56054652	56054652	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56054652delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						GTTTAAGATGTTTTTTTTTTT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62296706	62296707	+	IGR	INS	-	T	T	rs142246169	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62296706_62296707insT								C18orf20 (480446 upstream) : None (None downstream)																							tcctgccttccttccttccttc	0.188													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64614530	64614530	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64614530delA								CDH19 (343314 upstream) : DSEL (559289 downstream)																							ctagaactagaaataccattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	67928805	67928805	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67928805delG								RTTN (55843 upstream) : SOCS6 (27332 downstream)																							gggtgacagagggagatctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73843168	73843168	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73843168delC								C18orf62 (703579 upstream) : ZNF516 (228451 downstream)																							catctcaccacccccgcttta	0.000													2	4	---	---	---	---	
MBP	4155	broad.mit.edu	37	18	74805937	74805938	+	Intron	INS	-	T	T	rs74182685		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74805937_74805938insT	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)		tttttttcttcttttttttttt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75249608	75249608	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75249608delG								GALR1 (267514 upstream) : None (None downstream)																							actccatgctgggagaaccac	0.000													2	4	---	---	---	---	
SBNO2	22904	broad.mit.edu	37	19	1164372	1164372	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1164372delA	uc002lrk.3	-						SBNO2_uc010dse.2_Intron	NM_014963	NP_055778	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 isoform 1						macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent						0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAGATGCCAGGGGCAGTGG	0.348													6	3	---	---	---	---	
ADAMTSL5	339366	broad.mit.edu	37	19	1509662	1509665	+	Intron	DEL	GAGA	-	-	rs112785977	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1509662_1509665delGAGA	uc002ltd.2	-						ADAMTSL5_uc010dsl.2_Intron|ADAMTSL5_uc010xgq.1_Intron	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor							proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gaagggaagggagaaagggaagga	0.250													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3344919	3344920	+	IGR	INS	-	TGC	TGC	rs34770566		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3344919_3344920insTGC								CELF5 (47848 upstream) : NFIC (14696 downstream)																							ggcacctgatgtggaggaacag	0.000													4	3	---	---	---	---	
NFIC	4782	broad.mit.edu	37	19	3364158	3364158	+	5'Flank	DEL	A	-	-	rs5826816		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3364158delA	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_5'Flank|NFIC_uc010xhj.1_5'Flank	NM_205843	NP_995315	P08651	NFIC_HUMAN	nuclear factor I/C isoform 2						DNA replication|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|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		GAGTGCTTTGAAAAAAAAAAA	0.443													4	2	---	---	---	---	
RFX2	5990	broad.mit.edu	37	19	6070235	6070236	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6070235_6070236insT	uc002meb.2	-						RFX2_uc002mec.2_Intron|RFX2_uc010xiy.1_Intron	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6						gggatgggatgggatgggatgg	0.000													6	3	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153197	7153198	+	Intron	INS	-	CA	CA	rs140195352		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153197_7153198insCA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	aaacacacaaccacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	7949345	7949348	+	IGR	DEL	AAGG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7949345_7949348delAAGG								EVI5L (19484 upstream) : LRRC8E (4042 downstream)																							AAAGAAaagaaaggaaggaaggaa	0.049													3	3	---	---	---	---	
DOCK6	57572	broad.mit.edu	37	19	11365359	11365359	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11365359delA	uc002mqs.3	-							NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						ctttgtctcgaaaaaaaaaaa	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13101837	13101838	+	IGR	INS	-	CA	CA	rs137973398	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13101837_13101838insCA								DAND5 (16270 upstream) : NFIX (4746 downstream)																							acacacccacccacacacaccc	0.262													4	4	---	---	---	---	
ASF1B	55723	broad.mit.edu	37	19	14233668	14233668	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14233668delA	uc002mye.2	-							NM_018154	NP_060624	Q9NVP2	ASF1B_HUMAN	anti-silencing function 1B						cell differentiation|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus					0						GCAAGAGAGTAAGCAGGAGGT	0.562													4	2	---	---	---	---	
CLEC17A	388512	broad.mit.edu	37	19	14706562	14706564	+	Intron	DEL	TGT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14706562_14706564delTGT	uc010dzn.1	+						CLEC17A_uc002mzh.1_Intron|CLEC17A_uc010xnt.1_Intron|CLEC17A_uc010xnu.1_Intron|CLEC17A_uc010dzo.1_Intron			Q6ZS10	CL17A_HUMAN	SubName: Full=CLEC17A protein;							cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0						atagtgatggtgttgttggtatt	0.123													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16071769	16071769	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16071769delA								OR10H4 (11002 upstream) : LOC126536 (54675 downstream)																							CTTTGGCAGTAGAAAAGGCTC	0.438													4	2	---	---	---	---	
NWD1	284434	broad.mit.edu	37	19	16846774	16846775	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16846774_16846775insA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7						gactccaactcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20341611	20341612	+	IGR	DEL	GA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20341611_20341612delGA								ZNF486 (32627 upstream) : LOC284441 (26845 downstream)																							attgaacaatgagaacacttgg	0.000													4	2	---	---	---	---	
ZNF100	163227	broad.mit.edu	37	19	21926674	21926677	+	Intron	DEL	AAAG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21926674_21926677delAAAG	uc002nqi.2	-						ZNF100_uc002nqh.2_Intron	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						aaaaaaaaaaaaaGCCCAAAAAAC	0.304													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24551974	24551974	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24551974delT								LOC100101266 (205725 upstream) : None (None downstream)																							agaaagaagctttctgggaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27870563	27870563	+	IGR	DEL	T	-	-	rs111794544		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27870563delT								None (None upstream) : LOC148189 (410839 downstream)																							ggaaacactctttttgtagaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27871002	27871002	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27871002delT								None (None upstream) : LOC148189 (410400 downstream)																							ttctgaggaatttctttgtga	0.000													4	2	---	---	---	---	
CCDC123	84902	broad.mit.edu	37	19	33423088	33423089	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33423088_33423089insA	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron	NM_032816	NP_116205	Q96ST8	CEP89_HUMAN	coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)					ctccatctcacaaaaaaaaaaa	0.000													3	4	---	---	---	---	
TYROBP	7305	broad.mit.edu	37	19	36397636	36397637	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36397636_36397637insT	uc002ocm.2	-						TYROBP_uc002ocn.2_Intron	NM_003332	NP_003323	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein						axon guidance|cell junction assembly|cellular defense response|intracellular signal transduction|regulation of immune response	integral to plasma membrane|intracellular	identical protein binding|receptor signaling protein activity				0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			actcttcacgcttttttttttt	0.178													4	2	---	---	---	---	
SAMD4B	55095	broad.mit.edu	37	19	39868936	39868936	+	Intron	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39868936delG	uc002olb.2	+						SAMD4B_uc002ola.2_Intron	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B								protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			aggtttctaaggctaaaaatg	0.269													4	2	---	---	---	---	
AKT2	208	broad.mit.edu	37	19	40744160	40744161	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40744160_40744161insA	uc002onf.2	-						AKT2_uc010egs.2_Intron|AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc002one.2_Intron	NM_001626	NP_001617	P31751	AKT2_HUMAN	AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)			CAGAAGCTCATAAGTGACACAG	0.599			A		ovarian|pancreatic 								4	2	---	---	---	---	
ADCK4	79934	broad.mit.edu	37	19	41219782	41219782	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41219782delA	uc002oor.2	-						ADCK4_uc002ooq.1_Intron|ADCK4_uc002oos.2_Intron	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a							integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			actctgtctcaaaaaaaaaaa	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42469554	42469554	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42469554delT								RABAC1 (6026 upstream) : ATP1A3 (1182 downstream)																							cagatgcaacttttttttttt	0.000													3	3	---	---	---	---	
ZNF235	9310	broad.mit.edu	37	19	44757205	44757206	+	Intron	INS	-	AA	AA	rs35882358		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44757205_44757206insAA	uc010eji.2	-						ZNF235_uc002oyx.1_Intron			Q14590	ZN235_HUMAN	SubName: Full=Kruppel-associated box; Flags: Fragment;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)				aatttactaggaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45600224	45600225	+	Intron	DEL	AG	-	-	rs68128607		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45600224_45600225delAG	uc002pas.2	+											Homo sapiens leucine rich repeat containing 68, mRNA (cDNA clone IMAGE:5573062), partial cds.																		AGGGATTTGCAGGACAGAAAAC	0.584													7	6	---	---	---	---	
STRN4	29888	broad.mit.edu	37	19	47246510	47246511	+	Intron	DEL	CA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47246510_47246511delCA	uc002pfl.2	-						STRN4_uc002pfm.2_Intron|STRN4_uc010xyf.1_Intron|STRN4_uc010xyg.1_Intron|FKRP_uc002pfn.2_5'Flank|FKRP_uc002pfp.2_5'Flank	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1							cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		Tacacacactcacacacacaca	0.327													4	2	---	---	---	---	
PPFIA3	8541	broad.mit.edu	37	19	49644858	49644859	+	Intron	INS	-	GT	GT	rs147872140		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49644858_49644859insGT	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron|PPFIA3_uc002pmt.2_5'Flank	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		tgtgtgtatgagtgtgtgtgtg	0.198													4	5	---	---	---	---	
TSKS	60385	broad.mit.edu	37	19	50246343	50246343	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50246343delT	uc002ppm.2	-							NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate								protein binding			large_intestine(1)|skin(1)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GTACTAAGTGttttttttttt	0.239													4	3	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50791153	50791154	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50791153_50791154delAC	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		taacacacatacacacacacac	0.416													4	2	---	---	---	---	
KLK6	5653	broad.mit.edu	37	19	51463048	51463049	+	Intron	INS	-	GAG	GAG			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51463048_51463049insGAG	uc002pui.2	-						KLK6_uc010eoj.2_Intron|KLK6_uc002puh.2_Intron|KLK6_uc002puj.2_Intron|KLK6_uc010ycn.1_Intron|KLK6_uc002pul.2_Intron|KLK6_uc002pum.2_Intron	NM_001012964	NP_001012982	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform A						amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		gaagaggaggaggaagaggaga	0.000													8	5	---	---	---	---	
IGLON5	402665	broad.mit.edu	37	19	51822559	51822560	+	Intron	DEL	GT	-	-	rs35370241		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51822559_51822560delGT	uc002pwc.2	+							NM_001101372	NP_001094842	A6NGN9	IGLO5_HUMAN	IgLON family member 5 precursor							extracellular region					0						gtgtgtgtgcgtgtgtgtgtgt	0.446													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53470172	53470173	+	IGR	INS	-	TC	TC	rs139394812	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53470172_53470173insTC								ZNF321 (4058 upstream) : ZNF702P (1332 downstream)																							caatggcactatcggttcactg	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53524315	53524316	+	IGR	INS	-	T	T	rs141688476	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53524315_53524316insT								ZNF702P (27531 upstream) : ZNF160 (45552 downstream)																							gcctgtaaccccagcactttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54164329	54164329	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54164329delC								DPRX (24066 upstream) : MIR512-1 (5604 downstream)																							TTTCTCCTCGCCCCCCGGCTA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54892270	54892271	+	IGR	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54892270_54892271delTC								LAIR1 (10106 upstream) : TTYH1 (34364 downstream)																							gcacctctcttctctctctctc	0.000													4	2	---	---	---	---	
TTYH1	57348	broad.mit.edu	37	19	54929182	54929185	+	Intron	DEL	ACAC	-	-	rs67810488		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54929182_54929185delACAC	uc002qfq.2	+						TTYH1_uc010yey.1_Intron|TTYH1_uc002qfr.2_Intron|TTYH1_uc002qft.2_Intron|TTYH1_uc002qfu.1_5'Flank	NM_020659	NP_065710	Q9H313	TTYH1_HUMAN	tweety 1 isoform 1						cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CACACTTGGGacacacacacacac	0.466													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56030815	56030817	+	IGR	DEL	ATG	-	-	rs34819655		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56030815_56030817delATG								SSC5D (350 upstream) : SBK2 (10284 downstream)																							GGCGGTGGACatgatgatgatga	0.192													3	3	---	---	---	---	
U2AF2	11338	broad.mit.edu	37	19	56172866	56172871	+	Intron	DEL	ACACAC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56172866_56172871delACACAC	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		GGAGACTTGGacacacacacacacac	0.364													3	4	---	---	---	---	
ZNF835	90485	broad.mit.edu	37	19	57180098	57180099	+	Intron	INS	-	ACAGA	ACAGA	rs141479825	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57180098_57180099insACAGA	uc010ygo.1	-						ZNF835_uc010ygn.1_Intron	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4						ggtggggctggacagagcaact	0.054													5	3	---	---	---	---	
ZNF544	27300	broad.mit.edu	37	19	58753886	58753886	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58753886delT	uc010euo.2	+						ZNF544_uc010eun.1_Intron|ZNF544_uc010yhw.1_Intron|ZNF544_uc010yhx.1_Intron|ZNF544_uc010yhy.1_Intron|ZNF544_uc002qrt.3_Intron|ZNF544_uc002qru.3_Intron|ZNF544_uc002qrv.2_Intron	NM_014480	NP_055295	Q6NX49	ZN544_HUMAN	zinc finger protein 544						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		GTTGTTTCGCttttttttttt	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	145257	145258	+	IGR	INS	-	C	C	rs147530306	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:145257_145258insC								DEFB127 (5453 upstream) : DEFB128 (23269 downstream)																							atggtggcagggcctgtaatcc	0.000													2	4	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3622833	3622833	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3622833delT	uc002wim.2	+							NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						ttcttgtgtcttttacaccca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5011441	5011441	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5011441delC								SLC23A2 (20502 upstream) : C20orf30 (37689 downstream)																							cagctcacttcccaaattaag	0.010													4	2	---	---	---	---	
BTBD3	22903	broad.mit.edu	37	20	11873709	11873710	+	Intron	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11873709_11873710insT	uc002wny.2	+							NM_181443	NP_852108	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform b											ovary(2)|central_nervous_system(1)	3						AAAAATGTTCATTTTTTTTTTT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12006586	12006587	+	IGR	INS	-	T	T	rs143624710	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12006586_12006587insT								BTBD3 (99344 upstream) : SPTLC3 (983040 downstream)																							ctctgcctccctgagaATCTCT	0.188													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12061131	12061132	+	IGR	DEL	AC	-	-	rs35282318		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12061131_12061132delAC								BTBD3 (153889 upstream) : SPTLC3 (928495 downstream)																							CACCCCACCAacacacacacac	0.366													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16722714	16722715	+	IGR	INS	-	A	A	rs141628616	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16722714_16722715insA								SNRPB2 (677 upstream) : OTOR (6288 downstream)																							cttttagacttacgtagacagt	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	17852671	17852671	+	IGR	DEL	A	-	-	rs111247806		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17852671delA								BANF2 (136154 upstream) : SNX5 (69575 downstream)																							ctttctcaagaaaaaaaaaaa	0.239													3	3	---	---	---	---	
TMEM90B	79953	broad.mit.edu	37	20	24642124	24642127	+	Intron	DEL	GAAG	-	-	rs139131759		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24642124_24642127delGAAG	uc002wtw.1	+							NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						gagggaggaagaagggagggaggg	0.015													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25966194	25966195	+	IGR	INS	-	TG	TG	rs71332682		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25966194_25966195insTG								FAM182B (117408 upstream) : LOC100134868 (24240 downstream)																							ctgtatgACTCtgtgtgtgtgt	0.040													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26252699	26252700	+	IGR	INS	-	T	T	rs143639929		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26252699_26252700insT								MIR663 (63785 upstream) : None (None downstream)																							AGAAAGTGTCATCGATTTTTAC	0.441													6	6	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29617530	29617530	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29617530delT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						tactttgctcttgttttattg	0.000													8	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29628967	29628967	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628967delC	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TCTTGCTTTTCCTCTCTTtct	0.154													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29647652	29647653	+	Intron	INS	-	AGGG	AGGG	rs144300611	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29647652_29647653insAGGG	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						aggaaggaagtagggagggagg	0.000													5	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29648450	29648450	+	Intron	DEL	T	-	-	rs143554592		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648450delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						cagaactccctctcctgtttt	0.000													5	6	---	---	---	---	
HM13	81502	broad.mit.edu	37	20	30142180	30142181	+	Intron	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30142180_30142181insA	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwf.2_Intron|HM13_uc010gdu.2_Intron	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			agccccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31162590	31162591	+	Intron	INS	-	ACGG	ACGG	rs143125561	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31162590_31162591insACGG	uc002wxx.2	-											SubName: Full=LOC284804 protein; Flags: Fragment;																		AGGCCTAAGTCACGGGGTCCCC	0.703													4	2	---	---	---	---	
TP53INP2	58476	broad.mit.edu	37	20	33290617	33290617	+	5'Flank	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33290617delA	uc002xau.1	+							NM_021202	NP_067025	Q8IXH6	T53I2_HUMAN	tumor protein p53 inducible nuclear protein 2							nucleus					0						actccgtctcaaaaaaaaaaa	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36231842	36231845	+	IGR	DEL	TTTG	-	-	rs57438742		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36231842_36231845delTTTG								BLCAP (75539 upstream) : CTNNBL1 (90589 downstream)																							ccttcctttctttgtttcttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38739798	38739799	+	IGR	INS	-	T	T	rs138294541	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38739798_38739799insT								LOC339568 (886407 upstream) : MAFB (574720 downstream)																							CCTGACCTTACGCCTGTTGTGG	0.406													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41944593	41944593	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41944593delA								PTPRT (126036 upstream) : SFRS6 (141911 downstream)																							tctcacgtcgaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46606437	46606437	+	IGR	DEL	T	-	-	rs79933176		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46606437delT								SULF2 (191077 upstream) : LOC284749 (382217 downstream)																							ATAGATGCTGTTGAGACACTC	0.488													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52559918	52559919	+	IGR	DEL	TG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52559918_52559919delTG								SUMO1P1 (67670 upstream) : BCAS1 (160 downstream)																							TGCACACATTTGTGTGTGTGTG	0.302													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53298343	53298344	+	IGR	INS	-	TTC	TTC	rs113954719		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53298343_53298344insTTC								DOK5 (30634 upstream) : None (None downstream)																							ctccttcctttttttttttttt	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54755245	54755245	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54755245delC								CBLN4 (175233 upstream) : MC3R (68543 downstream)																							acacgttattcccaccagaat	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54766910	54766910	+	IGR	DEL	C	-	-	rs5842100		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54766910delC								CBLN4 (186898 upstream) : MC3R (56878 downstream)																							TTTTTTTTTTCCACAGACTGT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55192100	55192100	+	IGR	DEL	T	-	-	rs11475529		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55192100delT								C20orf107 (80526 upstream) : TFAP2C (12258 downstream)																							TTCCTTCCTCttttttttttt	0.274													4	5	---	---	---	---	
BMP7	655	broad.mit.edu	37	20	55791446	55791446	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55791446delA	uc010gip.1	-						BMP7_uc010giq.1_Intron|BMP7_uc002xyc.2_Intron	NM_001719	NP_001710	P18075	BMP7_HUMAN	bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			gaagtaaggcaagcttggaga	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59339199	59339200	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59339199_59339200delAC								MIR646 (455574 upstream) : CDH4 (488359 downstream)																							acacacctatacacacattcac	0.064													6	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59912387	59912389	+	Intron	DEL	ATA	-	-	rs146139681		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59912387_59912389delATA	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			gatggtgatgataatgatggtga	0.025													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60381631	60381632	+	Intron	INS	-	CA	CA	rs141897200	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60381631_60381632insCA	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ccacgcgcacgcacacacacat	0.396													1	5	---	---	---	---	
CABLES2	81928	broad.mit.edu	37	20	60973037	60973045	+	Intron	DEL	TGGCGGTGG	-	-	rs58871404	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60973037_60973045delTGGCGGTGG	uc002ycv.2	-							NM_031215	NP_112492	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2						cell cycle|cell division|regulation of cell cycle|regulation of cell division		cyclin-dependent protein kinase regulator activity			pancreas(1)	1	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			acagtggtgatggcggtggtggtgatgat	0.000													4	2	---	---	---	---	
CABLES2	81928	broad.mit.edu	37	20	60973071	60973073	+	Intron	DEL	GGT	-	-	rs113048661		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60973071_60973073delGGT	uc002ycv.2	-							NM_031215	NP_112492	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2						cell cycle|cell division|regulation of cell cycle|regulation of cell division		cyclin-dependent protein kinase regulator activity			pancreas(1)	1	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			tggttatggcggtggtggtggtg	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9832163	9832165	+	IGR	DEL	TTG	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9832163_9832165delTTG								None (None upstream) : None (None downstream)																							tttagtatacttgttgttgtgca	0.118													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10401098	10401099	+	IGR	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10401098_10401099delAC								None (None upstream) : TPTE (505644 downstream)																							caaaagaaatacacacacacac	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10602653	10602654	+	IGR	INS	-	A	A			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10602653_10602654insA								None (None upstream) : TPTE (304089 downstream)																							acctgtggcagaaaaaaaaaac	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10633109	10633109	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10633109delC								None (None upstream) : TPTE (273634 downstream)																							tccaaccccacatttccactt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10731178	10731179	+	IGR	DEL	AA	-	-	rs146936303		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10731178_10731179delAA								None (None upstream) : TPTE (175564 downstream)																							cagattctacaaaaaaagagag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10756906	10756915	+	IGR	DEL	AGAATCTATA	-	-	rs145320223		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10756906_10756915delAGAATCTATA								None (None upstream) : TPTE (149828 downstream)																							gtccgctagcagaatctataaGAATCTATA	0.014													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10793504	10793505	+	IGR	INS	-	TGGAA	TGGAA			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10793504_10793505insTGGAA								None (None upstream) : TPTE (113238 downstream)																							atataatggagtggagtggagt	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10837250	10837259	+	IGR	DEL	AATGGAATGC	-	-	rs149153731		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10837250_10837259delAATGGAATGC								None (None upstream) : TPTE (69484 downstream)																							aatggactcgaatggaatgcaatggaatgg	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10843980	10843987	+	IGR	DEL	AATAAAAA	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10843980_10843987delAATAAAAA								None (None upstream) : TPTE (62756 downstream)																							aattgaatggaataaaaaaatggaatgg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10851518	10851518	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10851518delA								None (None upstream) : TPTE (55225 downstream)																							aatggaatggaaaaggaatgg	0.000													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	11001893	11001895	+	Intron	DEL	AGT	-	-	rs148905557		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11001893_11001895delAGT	uc002yis.1	-									P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)		aacaaaactcagtagcgggagat	0.000													4	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11028703	11028704	+	Intron	INS	-	TG	TG	rs138520594	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11028703_11028704insTG	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)		cGAGTTTGTTTTGTTATTAAAT	0.144													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14359037	14359037	+	IGR	DEL	T	-	-	rs112182285		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14359037delT								None (None upstream) : C21orf99 (51450 downstream)																							gcgctcctaatttccacttgc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21662944	21662945	+	IGR	DEL	CA	-	-	rs5842805		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21662944_21662945delCA								None (None upstream) : C21orf131 (451969 downstream)																							aacacacatgcacacacacaca	0.243													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36271714	36271715	+	Intron	DEL	TC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36271714_36271715delTC	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tctctctctttctctctctctc	0.000			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36366136	36366137	+	Intron	DEL	AC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36366136_36366137delAC	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						acacacacagacacacacacac	0.173			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40292279	40292280	+	IGR	INS	-	TTCTTTC	TTCTTTC	rs139198056	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40292279_40292280insTTCTTTC								ETS2 (95403 upstream) : PSMG1 (255110 downstream)																							cctgtttttttttctttttttt	0.000													4	2	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45305708	45305715	+	Intron	DEL	GCAGGTGC	-	-	rs67407535		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45305708_45305715delGCAGGTGC	uc002zdv.2	+							NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		GTGAAGGTGTGCAGGTGCGCAGGTGCGC	0.644													3	3	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45357999	45358002	+	Intron	DEL	ACAC	-	-	rs8131264		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45357999_45358002delACAC	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		acacacacagacacacacacacac	0.299													4	2	---	---	---	---	
PCBP3	54039	broad.mit.edu	37	21	47294420	47294420	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47294420delT	uc002zhq.1	+						PCBP3_uc010gqb.2_Intron|PCBP3_uc002zhp.1_Intron|PCBP3_uc010gqc.1_Intron|PCBP3_uc002zhs.1_Intron|PCBP3_uc002zhr.1_Intron	NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		tcttcttttcttttttttttt	0.000													4	2	---	---	---	---	
C21orf57	54059	broad.mit.edu	37	21	47709946	47709947	+	Intron	DEL	TA	-	-	rs9975689		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47709946_47709947delTA	uc002ziv.2	+						C21orf57_uc002zit.1_Intron|C21orf57_uc002ziu.1_Intron|C21orf57_uc002ziw.2_Intron|C21orf57_uc002zix.2_Intron|C21orf57_uc010gqh.2_Intron|C21orf57_uc002ziy.2_Intron	NM_058181	NP_478061	P58557	YBEY_HUMAN	hypothetical protein LOC54059 isoform 1								metal ion binding|metalloendopeptidase activity				0	Breast(49;0.112)			Colorectal(79;0.236)		tgcagttttGTAtgtgtgtaag	0.035													4	2	---	---	---	---	
GGT3P	2679	broad.mit.edu	37	22	18771547	18771547	+	5'Flank	DEL	G	-	-	rs149629602		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18771547delG	uc010gri.1	-						GGT3P_uc011ago.1_Intron|GGT3P_uc011agp.1_Intron|GGT3P_uc002zob.1_Intron					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						TTTTTGttttgtttttttttt	0.204													4	4	---	---	---	---	
SMARCB1	6598	broad.mit.edu	37	22	24167050	24167050	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24167050delC	uc002zyb.2	+						SMARCB1_uc002zya.2_Intron|SMARCB1_uc002zyc.2_Intron|SMARCB1_uc002zyd.2_Intron	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin						cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding	p.?(3)		soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				CCCTGCCTTTCTGGTGTAGTC	0.572			D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				4	2	---	---	---	---	
C22orf45	646023	broad.mit.edu	37	22	24853065	24853065	+	Intron	DEL	T	-	-	rs144697561		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24853065delT	uc003aad.1	-											Homo sapiens hypothetical protein LOC646023, mRNA (cDNA clone IMAGE:5171383).												0						tcaataaCACttttttttttt	0.010													4	2	---	---	---	---	
TMEM211	255349	broad.mit.edu	37	22	25336690	25336691	+	5'Flank	INS	-	TCCT	TCCT			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25336690_25336691insTCCT	uc003abk.1	-							NM_001001663	NP_001001663	Q6ICI0	TM211_HUMAN	transmembrane protein 211							integral to membrane					0						ctttctttccttccttccttgc	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27363100	27363101	+	IGR	DEL	AG	-	-	rs34821678		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27363100_27363101delAG								MIAT (248151 upstream) : MN1 (781165 downstream)																							ACTAAGTTCAAGAGAGGGGTTG	0.337													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27405766	27405766	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27405766delG								MIAT (290817 upstream) : MN1 (738500 downstream)																							tgaaagtcatgggaggctctt	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27497454	27497457	+	IGR	DEL	TCCA	-	-	rs140527542		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27497454_27497457delTCCA								MIAT (382505 upstream) : MN1 (646809 downstream)																							CCTGCCTCTCtccatccatccatc	0.176													4	3	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28744923	28744923	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28744923delC	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						TAAAGTGGGTCCTGTGCATAA	0.418													4	2	---	---	---	---	
ZNRF3	84133	broad.mit.edu	37	22	29438754	29438755	+	Intron	INS	-	G	G	rs144703972	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29438754_29438755insG	uc003aeg.2	+						ZNRF3_uc003aeh.1_Intron	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1						ATTGGGGCACAGGGGGCAtttt	0.267													2	4	---	---	---	---	
AP1B1	162	broad.mit.edu	37	22	29741057	29741057	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29741057delT	uc003afj.2	-						AP1B1_uc003afi.2_Intron|AP1B1_uc003afk.2_Intron|AP1B1_uc003afl.2_Intron|AP1B1_uc011ako.1_Intron	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)|skin(1)	2						ACAAGTAttctttttttttga	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35339835	35339835	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35339835delG								None (None upstream) : ISX (122294 downstream)																							CATCTGGTTAGGGAAAATAAA	0.348													4	2	---	---	---	---	
APOBEC3D	140564	broad.mit.edu	37	22	39382946	39382946	+	Intron	DEL	G	-	-	rs112595223		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39382946delG	uc011aoe.1	+						APOBEC3A_uc011aoc.1_Intron|APOBEC3B_uc003awo.1_Intron|APOBEC3B_uc003awp.1_Intron|APOBEC3B_uc003awq.1_Intron|APOBEC3D_uc011aod.1_Intron|APOBEC3D_uc011aof.1_Intron	NM_152426	NP_689639	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)					GGCTGGGGACGGGGGGGGTCC	0.612													4	3	---	---	---	---	
TNRC6B	23112	broad.mit.edu	37	22	40528494	40528499	+	Intron	DEL	GAGGCG	-	-	rs57741755		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40528494_40528499delGAGGCG	uc003aym.2	+							NM_001024843	NP_001020014	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 3						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						caataaaggcgaggcgagggcgaggg	0.005													5	5	---	---	---	---	
L3MBTL2	83746	broad.mit.edu	37	22	41624856	41624856	+	Intron	DEL	A	-	-	rs139479		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41624856delA	uc003azo.2	+						L3MBTL2_uc003azn.2_Intron	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						tccatcgcacaaaaaaaaaaa	0.224													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43735761	43735761	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43735761delC	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron	NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				CTCCAACCCTCCCCCCACTCT	0.587													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44268806	44268806	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44268806delT								SULT4A1 (10428 upstream) : PNPLA5 (6753 downstream)																							ttttacagcgtttgactcttc	0.060													4	2	---	---	---	---	
PARVB	29780	broad.mit.edu	37	22	44541783	44541784	+	Intron	INS	-	T	T	rs35811915		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44541783_44541784insT	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				AAAAATTTCACTTTTTTTTTTT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44771141	44771141	+	IGR	DEL	A	-	-	rs34478273		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44771141delA								KIAA1644 (62410 upstream) : LDOC1L (117309 downstream)																							ggaacaagagaaaaaaaaaac	0.000													4	3	---	---	---	---	
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45172480	45172480	+	Intron	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45172480delC	uc003bfd.2	+						PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|ARHGAP8_uc003bfi.2_Intron|ARHGAP8_uc010gzv.2_Intron|ARHGAP8_uc003bfj.2_Intron|ARHGAP8_uc003bfk.2_Intron|PRR5-ARHGAP8_uc003bfg.1_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						tcttaataggctcctggagtt	0.254													4	2	---	---	---	---	
PHF21B	112885	broad.mit.edu	37	22	45279922	45279930	+	Intron	DEL	CACCACCAC	-	-	rs142141866	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45279922_45279930delCACCACCAC	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		ctgtgatcagcaccaccaccaccatcacc	0.010													3	3	---	---	---	---	
WNT7B	7477	broad.mit.edu	37	22	46338743	46338744	+	Intron	INS	-	TT	TT	rs9803093	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46338743_46338744insTT	uc003bgo.2	-						WNT7B_uc010haa.2_Intron	NM_058238	NP_478679	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		tgctgtgtgtgtgtgtgtgcgt	0.267													4	3	---	---	---	---	
WNT7B	7477	broad.mit.edu	37	22	46375610	46375612	+	5'Flank	DEL	ACA	-	-	rs148019771		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46375610_46375612delACA	uc003bgo.2	-							NM_058238	NP_478679	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		cacaccacacacaacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46378986	46378987	+	IGR	INS	-	GGAT	GGAT	rs140223755	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46378986_46378987insGGAT								WNT7B (5978 upstream) : LOC730668 (23509 downstream)																							tgtttaatacaggatggatgga	0.168													4	3	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47435356	47435356	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47435356delT	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TTAGTTACTCTTTAACCCCTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48709978	48709978	+	IGR	DEL	T	-	-	rs35127437		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48709978delT								None (None upstream) : FAM19A5 (175310 downstream)																							GTTGGATGGCTTGTTTTATCA	0.368													3	4	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	49058913	49058914	+	Intron	INS	-	TG	TG	rs148958992	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49058913_49058914insTG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		TGCTGGGCCCCTGGGTGTCTTA	0.535													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50082384	50082385	+	IGR	INS	-	G	G	rs148681603	by1000genomes	TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50082384_50082385insG								C22orf34 (31194 upstream) : BRD1 (84553 downstream)																							TGGTGCCTGGCGGGGCTCTTGA	0.569													4	2	---	---	---	---	
PLCXD1	55344	broad.mit.edu	37	X	203470	203470	+	Intron	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:203470delT	uc004cpc.2	+						PLCXD1_uc011mgx.1_Intron	NM_018390	NP_060860	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid metabolic process		phospholipase C 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)				gctatttatcttacttctgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	384828	384828	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:384828delA								PPP2R3B (37201 upstream) : SHOX (200251 downstream)																							ctccgtctccaaaaaaaaaaa	0.005													4	2	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2149856	2149857	+	Intron	INS	-	C	C			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2149856_2149857insC	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				ctctctcccttcctcttccttt	0.000													4	2	---	---	---	---	
MSL3	10943	broad.mit.edu	37	X	11782023	11782026	+	Frame_Shift_Del	DEL	CTTC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11782023_11782026delCTTC	uc004cuw.2	+	8	979_982	c.874_877delCTTC	c.(874-879)CTTCCAfs	p.L292fs	MSL3_uc004cuv.1_Frame_Shift_Del_p.L292fs|MSL3_uc004cux.2_Frame_Shift_Del_p.L233fs|MSL3_uc011mig.1_Frame_Shift_Del_p.L143fs|MSL3_uc011mih.1_Frame_Shift_Del_p.L280fs|MSL3_uc004cuy.2_Frame_Shift_Del_p.L126fs|MSL3_uc011mii.1_Frame_Shift_Del_p.L126fs	NM_078629	NP_523353	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	292_293					histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TAAATTTTTTCTTCCAATTAAGGA	0.377													36	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	12844932	12844932	+	IGR	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12844932delA								PRPS2 (2590 upstream) : TLR7 (40270 downstream)																							CGGGATTCTTACAGAAGCAGA	0.368													4	2	---	---	---	---	
RPS6KA3	6197	broad.mit.edu	37	X	20253005	20253005	+	Intron	DEL	A	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20253005delA	uc004czu.2	-						RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8						GAAGGCAGACAAAAAAAAAAA	0.313													9	4	---	---	---	---	
EIF2S3	1968	broad.mit.edu	37	X	24095044	24095045	+	3'UTR	DEL	TT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24095044_24095045delTT	uc004dbc.2	+	12						NM_001415	NP_001406	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1						GGTTAttctctttttttttttt	0.282													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61864624	61864624	+	IGR	DEL	G	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61864624delG								None (None upstream) : SPIN4 (702484 downstream)																							ttgtgaaaaaggaaatatctt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	93304425	93304426	+	IGR	INS	-	A	A	rs77708658		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93304425_93304426insA								FAM133A (337164 upstream) : None (None downstream)																							aaaaaaaaaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9932644	9932644	+	IGR	DEL	C	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9932644delC								TTTY22 (281790 upstream) : None (None downstream)																							accactatgactgccctggat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10008563	10008564	+	IGR	INS	-	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10008563_10008564insG								TTTY22 (357709 upstream) : None (None downstream)																							ttccaaggtcctcctttcatcc	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10042329	10042330	+	IGR	DEL	CT	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10042329_10042330delCT								TTTY22 (391475 upstream) : None (None downstream)																							agtctggaaactctattcttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10056505	10056506	+	IGR	INS	-	G	G			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10056505_10056506insG								TTTY22 (405651 upstream) : None (None downstream)																							atcaaaacaaagttcatctctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13457885	13457895	+	IGR	DEL	CTAGTAAATTC	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13457885_13457895delCTAGTAAATTC								None (None upstream) : None (None downstream)																							ccattccattctagtaaattccggtttattc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13628269	13628270	+	IGR	INS	-	T	T			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13628269_13628270insT								None (None upstream) : None (None downstream)																							cactttttcacttttttctgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13706007	13706007	+	IGR	DEL	T	-	-			TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13706007delT								None (None upstream) : None (None downstream)																							tggacacgaattgaatagaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28807588	28807589	+	IGR	INS	-	A	A	rs112875632		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28807588_28807589insA								None (None upstream) : None (None downstream)																							tggaatgtattgggtggaatgg	0.158													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59030478	59030479	+	IGR	INS	-	AAAC	AAAC	rs10578690		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59030478_59030479insAAAC								None (None upstream) : None (None downstream)																							caaaaaacaaaaaacaaacaaa	0.129													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59032254	59032255	+	IGR	INS	-	TT	TT	rs56224050		TCGA-66-2788-01A-01D-0983-08	TCGA-66-2788-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59032254_59032255insTT								None (None upstream) : None (None downstream)																							aaaaaaaaaaCGAGCTAAATGG	0.119													4	2	---	---	---	---	
