Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
ACOT7	11332	broad.mit.edu	37	1	6354951	6354951	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6354951T>C	uc001ams.2	-	7	989	c.832A>G	c.(832-834)ATT>GTT	p.I278V	ACOT7_uc010nzq.1_Missense_Mutation_p.I163V|ACOT7_uc001amt.2_Missense_Mutation_p.I268V|ACOT7_uc001amu.2_RNA|ACOT7_uc001amv.2_RNA|ACOT7_uc001amq.2_Missense_Mutation_p.I227V|ACOT7_uc001amr.2_Missense_Mutation_p.I248V	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb	278	Acyl coenzyme A hydrolase 2.					mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TGAAAATTAATGGCGTCCACG	0.542													9	37	---	---	---	---	PASS
ACOT7	11332	broad.mit.edu	37	1	6409851	6409851	+	Silent	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6409851T>A	uc001ams.2	-	2	406	c.249A>T	c.(247-249)GCA>GCT	p.A83A	ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Silent_p.A73A|ACOT7_uc001amu.2_RNA|ACOT7_uc001amv.2_RNA|ACOT7_uc001amq.2_Silent_p.A32A|ACOT7_uc001amr.2_Silent_p.A53A	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb	83	Acyl coenzyme A hydrolase 1.					mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TGATGGCGCCTGCCTCCTCGA	0.622													10	17	---	---	---	---	PASS
LUZP1	7798	broad.mit.edu	37	1	23418882	23418882	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23418882C>G	uc001bgk.2	-	4	2257	c.1873G>C	c.(1873-1875)GAA>CAA	p.E625Q	LUZP1_uc010odv.1_Missense_Mutation_p.E625Q|LUZP1_uc001bgl.2_Missense_Mutation_p.E625Q|LUZP1_uc001bgm.1_Missense_Mutation_p.E625Q	NM_033631	NP_361013	Q86V48	LUZP1_HUMAN	leucine zipper protein 1	625						nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TTAACCCCTTCTTTATGTGAG	0.468													34	115	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34158623	34158623	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34158623G>A	uc001bxn.1	-	25	3868	c.3839C>T	c.(3838-3840)TCG>TTG	p.S1280L	CSMD2_uc001bxm.1_Missense_Mutation_p.S1320L|CSMD2_uc001bxo.1_Missense_Mutation_p.S193L	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1280	CUB 8.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CACCTGCCCCGACACCTCTCC	0.572													61	67	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35351752	35351752	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35351752G>A	uc001byc.2	-	4	1521	c.1521C>T	c.(1519-1521)ATC>ATT	p.I507I		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	507					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				AGCCGGCCTGGATGGCCCGGA	0.692													5	5	---	---	---	---	PASS
CSF3R	1441	broad.mit.edu	37	1	36933539	36933539	+	Missense_Mutation	SNP	C	A	A	rs148104401	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36933539C>A	uc001caw.1	-	14	1926	c.1748G>T	c.(1747-1749)CGT>CTT	p.R583L	CSF3R_uc001cat.1_Missense_Mutation_p.R146L|CSF3R_uc009vvc.1_Missense_Mutation_p.R112L|CSF3R_uc001cau.1_5'UTR|CSF3R_uc001cav.1_Missense_Mutation_p.R583L|CSF3R_uc001cax.1_Missense_Mutation_p.R583L|CSF3R_uc001cay.1_Missense_Mutation_p.R583L	NM_000760	NP_000751	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform a	583	Fibronectin type-III 5.|Extracellular (Potential).				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GACAAAGCCACGGGAGGAGGC	0.637													11	13	---	---	---	---	PASS
ZC3H12A	80149	broad.mit.edu	37	1	37947224	37947224	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37947224G>T	uc001cbb.3	+	4	756	c.606G>T	c.(604-606)CTG>CTT	p.L202L	ZC3H12A_uc001cbc.1_5'UTR	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	202					angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGCGGGAACTGGAGAAGAAGA	0.597													5	80	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39833823	39833823	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39833823C>T	uc010oiu.1	+	14	8226	c.8095C>T	c.(8095-8097)CTC>TTC	p.L2699F	MACF1_uc010ois.1_Missense_Mutation_p.L2197F|MACF1_uc001cda.1_Missense_Mutation_p.L2105F|MACF1_uc001cdc.1_Missense_Mutation_p.L1284F|MACF1_uc001cdb.1_Missense_Mutation_p.L1284F	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	4264	LRR 15.				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTGACAGGAGCTCAATTTGGA	0.423													13	33	---	---	---	---	PASS
LEPR	3953	broad.mit.edu	37	1	66067350	66067350	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66067350G>T	uc001dci.2	+	9	1472	c.1270G>T	c.(1270-1272)GAA>TAA	p.E424*	LEPR_uc001dcg.2_Nonsense_Mutation_p.E424*|LEPR_uc001dch.2_Nonsense_Mutation_p.E424*|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Nonsense_Mutation_p.E424*|LEPR_uc001dck.2_Nonsense_Mutation_p.E424*	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1	424	Extracellular (Potential).|Ig-like.				energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TCGCTATGCTGAATTATATGT	0.353													7	11	---	---	---	---	PASS
MSH4	4438	broad.mit.edu	37	1	76342658	76342658	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76342658C>A	uc001dhd.1	+	10	1384	c.1343C>A	c.(1342-1344)GCT>GAT	p.A448D		NM_002440	NP_002431	O15457	MSH4_HUMAN	mutS homolog 4	448					chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5						TTATTAAGAGCTTACTATGGT	0.279								MMR					8	19	---	---	---	---	PASS
PRKACB	5567	broad.mit.edu	37	1	84663425	84663425	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84663425G>T	uc001djj.2	+	7	824	c.560G>T	c.(559-561)GGG>GTG	p.G187V	PRKACB_uc001djl.2_Missense_Mutation_p.G234V|PRKACB_uc010ort.1_Missense_Mutation_p.G194V|PRKACB_uc001djn.2_Missense_Mutation_p.G191V|PRKACB_uc010oru.1_Missense_Mutation_p.G175V|PRKACB_uc001djp.2_Missense_Mutation_p.G193V|PRKACB_uc001djq.2_Missense_Mutation_p.G157V|PRKACB_uc010orv.1_Missense_Mutation_p.G174V|PRKACB_uc001dji.2_Missense_Mutation_p.G187V|PRKACB_uc001djk.2_Missense_Mutation_p.G234V|PRKACB_uc009wcf.1_Missense_Mutation_p.G193V	NM_002731	NP_002722	P22694	KAPCB_HUMAN	cAMP-dependent protein kinase catalytic subunit	187	Protein kinase.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport	cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane	ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding			lung(2)|ovary(1)	3				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		ACAGACTTTGGGTTTGCCAAA	0.318													5	32	---	---	---	---	PASS
LRRC8D	55144	broad.mit.edu	37	1	90400188	90400188	+	Missense_Mutation	SNP	T	C	C	rs112842021		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90400188T>C	uc001dnm.2	+	3	1986	c.1561T>C	c.(1561-1563)TGC>CGC	p.C521R	LRRC8D_uc001dnn.2_Missense_Mutation_p.C521R	NM_001134479	NP_001127951	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member	521	LRR 1.					integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		GCTCCACCTCTGCCACTGCCC	0.453													36	53	---	---	---	---	PASS
PIAS3	10401	broad.mit.edu	37	1	145580518	145580518	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145580518C>G	uc001eoc.1	+	7	909	c.818C>G	c.(817-819)TCT>TGT	p.S273C	NBPF10_uc001emp.3_Intron|PIAS3_uc010oyy.1_3'UTR|PIAS3_uc001eod.1_5'UTR	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	273	PINIT.				positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TACTCCTTGTCTGTGTACCTG	0.512													31	43	---	---	---	---	PASS
HIST2H2BE	8349	broad.mit.edu	37	1	149858024	149858024	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149858024G>T	uc001etc.2	-	1	209	c.167C>A	c.(166-168)TCG>TAG	p.S56*	HIST2H2AC_uc001etd.2_5'Flank	NM_003528	NP_003519	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	56					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GGCCTTGGACGAGATGCCGGT	0.592													6	196	---	---	---	---	PASS
SELENBP1	8991	broad.mit.edu	37	1	151337409	151337409	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151337409G>C	uc001exx.2	-	11	1296	c.1249C>G	c.(1249-1251)CTC>GTC	p.L417V	SELENBP1_uc010pcy.1_Missense_Mutation_p.L459V|SELENBP1_uc001exy.2_Missense_Mutation_p.L314V|SELENBP1_uc001exz.2_Missense_Mutation_p.L314V|SELENBP1_uc010pcz.1_Missense_Mutation_p.L355V|SELENBP1_uc009wms.2_Missense_Mutation_p.L253V|SELENBP1_uc009wmt.2_Missense_Mutation_p.L314V|SELENBP1_uc001eya.2_Missense_Mutation_p.L353V|SELENBP1_uc009wmu.2_3'UTR	NM_003944	NP_003935	Q13228	SBP1_HUMAN	selenium binding protein 1	417					protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CACCTGATGAGATCAGGGTAA	0.572													4	23	---	---	---	---	PASS
FCRL3	115352	broad.mit.edu	37	1	157650786	157650786	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157650786G>A	uc001frb.2	-	12	2234	c.1942C>T	c.(1942-1944)CCA>TCA	p.P648S	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Missense_Mutation_p.P648S|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Missense_Mutation_p.P374S|FCRL3_uc001frc.1_Missense_Mutation_p.P648S	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	648	ITIM motif 1.|Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					CTGTACATTGGCTCCAGCTCC	0.587													4	49	---	---	---	---	PASS
FCRL1	115350	broad.mit.edu	37	1	157773754	157773754	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157773754C>A	uc001frg.2	-	3	313	c.200G>T	c.(199-201)AGC>ATC	p.S67I	FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Missense_Mutation_p.S67I|FCRL1_uc001fri.2_Missense_Mutation_p.S67I|FCRL1_uc001frj.2_RNA	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	67	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTTGGGGGAGCTGCTCCAGCC	0.562													35	34	---	---	---	---	PASS
APCS	325	broad.mit.edu	37	1	159557995	159557995	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159557995C>A	uc001ftv.2	+	2	265	c.169C>A	c.(169-171)CGA>AGA	p.R57R		NM_001639	NP_001630	P02743	SAMP_HUMAN	serum amyloid P component precursor	57	Pentaxin.				acute-phase response|chaperone-mediated protein complex assembly|protein folding	extracellular space	metal ion binding|sugar binding|unfolded protein binding			ovary(1)|breast(1)	2	all_hematologic(112;0.0429)					CTTGTGTTTTCGAGCCTATAG	0.428													4	68	---	---	---	---	PASS
CCDC19	25790	broad.mit.edu	37	1	159856431	159856431	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159856431C>T	uc001fui.2	-	6	655	c.637G>A	c.(637-639)GAG>AAG	p.E213K	CCDC19_uc009wtb.2_RNA|CCDC19_uc001fuj.2_RNA|CCDC19_uc001fuk.2_Missense_Mutation_p.E128K|CCDC19_uc001ful.2_Missense_Mutation_p.E128K|CCDC19_uc009wtc.1_Missense_Mutation_p.E213K	NM_012337	NP_036469	Q9UL16	CCD19_HUMAN	nasopharyngeal epithelium specific protein 1	213	Potential.					mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			TGCTGCTTCTCCAGGATTTGG	0.478													9	257	---	---	---	---	PASS
HSPA6	3310	broad.mit.edu	37	1	161495234	161495234	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161495234G>T	uc001gap.2	+	2	1446	c.786G>T	c.(784-786)CTG>CTT	p.L262L	HSPA6_uc001gaq.2_Silent_p.L262L	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	262					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AGCGTGCCCTGCGCAGGCTGC	0.632													7	9	---	---	---	---	PASS
KIFAP3	22920	broad.mit.edu	37	1	169993642	169993642	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169993642C>G	uc001ggv.2	-	9	1208	c.937G>C	c.(937-939)GAT>CAT	p.D313H	KIFAP3_uc010plx.1_Missense_Mutation_p.D15H	NM_014970	NP_055785	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	313					blood coagulation|plus-end-directed vesicle transport along microtubule|protein complex assembly|signal transduction	centrosome|condensed nuclear chromosome|cytosol|endoplasmic reticulum|kinesin II complex|spindle microtubule	kinesin binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTGTCCCGATCAAGGGCTTTC	0.358													5	25	---	---	---	---	PASS
MYOC	4653	broad.mit.edu	37	1	171605340	171605340	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171605340C>T	uc001ghu.2	-	3	1262	c.1240G>A	c.(1240-1242)GAA>AAA	p.E414K	MYOC_uc010pmk.1_Missense_Mutation_p.E356K	NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin precursor	414	Olfactomedin-like.		E -> K.		anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CAGGTTTGTTCGAGTTCCAGA	0.527													35	87	---	---	---	---	PASS
METTL13	51603	broad.mit.edu	37	1	171753518	171753518	+	Missense_Mutation	SNP	G	T	T	rs149343407	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171753518G>T	uc001ghz.2	+	2	1139	c.792G>T	c.(790-792)AGG>AGT	p.R264S	METTL13_uc001gia.2_Missense_Mutation_p.R178S|METTL13_uc001gib.2_Intron|METTL13_uc010pml.1_Missense_Mutation_p.R263S	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1	264							methyltransferase activity|protein binding			kidney(1)	1						GCAAGGCCAGGCTGGGGAGTG	0.677													7	21	---	---	---	---	PASS
TNN	63923	broad.mit.edu	37	1	175052998	175052998	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175052998C>T	uc001gkl.1	+	5	1274	c.1161C>T	c.(1159-1161)CCC>CCT	p.P387P	TNN_uc010pmx.1_Silent_p.P387P	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	387	Fibronectin type-III 2.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GATATGGCCCCATGACAGGAC	0.537													24	39	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175372563	175372563	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175372563C>T	uc001gkp.1	-	2	770	c.689G>A	c.(688-690)TGT>TAT	p.C230Y	TNR_uc009wwu.1_Missense_Mutation_p.C230Y|TNR_uc010pmz.1_Missense_Mutation_p.C230Y	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	230	Cys-rich.|EGF-like 2.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GAGTTCGGAACAGTCATCCCC	0.632													38	78	---	---	---	---	PASS
ASTN1	460	broad.mit.edu	37	1	176992713	176992713	+	Intron	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176992713G>A	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						GCTCCCTGCAGGGTGAGAGAA	0.542													9	19	---	---	---	---	PASS
ABL2	27	broad.mit.edu	37	1	179078459	179078459	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179078459C>A	uc001gmj.3	-	12	2230	c.1943G>T	c.(1942-1944)AGG>ATG	p.R648M	ABL2_uc010pnf.1_Missense_Mutation_p.R648M|ABL2_uc010png.1_Missense_Mutation_p.R627M|ABL2_uc010pnh.1_Missense_Mutation_p.R627M|ABL2_uc001gmg.3_Missense_Mutation_p.R633M|ABL2_uc001gmi.3_Missense_Mutation_p.R633M|ABL2_uc001gmh.3_Missense_Mutation_p.R612M|ABL2_uc010pne.1_Missense_Mutation_p.R612M	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b	648					axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GCCCCCCTTCCTATCCCTGGT	0.537			T	ETV6	AML								9	165	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181740495	181740495	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181740495T>C	uc001gow.2	+	36	5113	c.4948T>C	c.(4948-4950)TTT>CTT	p.F1650L	CACNA1E_uc009wxs.2_Missense_Mutation_p.F1538L|CACNA1E_uc001gox.1_Missense_Mutation_p.F876L|CACNA1E_uc009wxt.2_Missense_Mutation_p.F876L	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1650	Extracellular (Potential).|IV.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						CCGGAGTTTCTTTGGGTCCCT	0.473													3	12	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200946364	200946364	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200946364G>A	uc001gvs.1	-	31	4618	c.4301C>T	c.(4300-4302)GCC>GTC	p.A1434V	KIF21B_uc001gvr.1_Missense_Mutation_p.A1421V|KIF21B_uc009wzl.1_Missense_Mutation_p.A1434V|KIF21B_uc010ppn.1_Missense_Mutation_p.A1421V	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1434	WD 3.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						GATGCGGACGGCATTGCCCGA	0.632													29	79	---	---	---	---	PASS
PPP1R12B	4660	broad.mit.edu	37	1	202400696	202400696	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202400696G>T	uc001gya.1	+	8	1234	c.1090G>T	c.(1090-1092)GAG>TAG	p.E364*	PPP1R12B_uc001gxy.2_Nonsense_Mutation_p.E364*|PPP1R12B_uc009xad.1_Nonsense_Mutation_p.E170*|PPP1R12B_uc009xae.1_Nonsense_Mutation_p.E364*|PPP1R12B_uc001gxz.1_Nonsense_Mutation_p.E364*	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	364	Glu-rich.				regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			CAGCTCAGAGGAGGAGGAAGG	0.418													69	88	---	---	---	---	PASS
SPATA17	128153	broad.mit.edu	37	1	218036154	218036154	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218036154A>G	uc001hlh.1	+	10	1070	c.1044A>G	c.(1042-1044)TCA>TCG	p.S348S	SPATA17_uc001hli.2_Silent_p.S348S	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	348						cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		AGCTCTTCTCAAAGTATGGAA	0.284													43	52	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228456387	228456387	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228456387G>T	uc009xez.1	+	17	5062	c.5018G>T	c.(5017-5019)CGC>CTC	p.R1673L	OBSCN_uc001hsn.2_Missense_Mutation_p.R1673L|OBSCN_uc001hso.2_Missense_Mutation_p.R119L	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1673	Ig-like 17.			RV -> HM (in Ref. 1; CAC85750).	apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				TCGAAAGTGCGCGTGGAGGCC	0.687													41	44	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229596457	229596457	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229596457T>A	uc001htn.2	-	20	2837	c.2745A>T	c.(2743-2745)TTA>TTT	p.L915F		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	915					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TGGGCTGAGATAATAATTTGC	0.348													22	51	---	---	---	---	PASS
TAF5L	27097	broad.mit.edu	37	1	229730434	229730434	+	Silent	SNP	C	T	T	rs148664199		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229730434C>T	uc001htq.2	-	5	1546	c.1380G>A	c.(1378-1380)TCG>TCA	p.S460S		NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	460	WD 4.				histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				AAAGCCTCACCGAGTTCCCCT	0.582													21	113	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235840490	235840490	+	Splice_Site	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235840490T>A	uc001hxj.2	-	50	11116	c.10941_splice	c.e50-1	p.R3647_splice	LYST_uc001hxi.2_Splice_Site_p.R871_splice	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TAGCATAACCTGAAAGAAAAA	0.363									Chediak-Higashi_syndrome				21	23	---	---	---	---	PASS
GPR137B	7107	broad.mit.edu	37	1	236343287	236343287	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236343287G>A	uc001hxq.2	+	4	887	c.796G>A	c.(796-798)GTC>ATC	p.V266I	GPR137B_uc001hxr.1_Missense_Mutation_p.V48I|GPR137B_uc009xge.2_RNA	NM_003272	NP_003263	O60478	G137B_HUMAN	G protein-coupled receptor 137B	266	Extracellular (Potential).					integral to plasma membrane|membrane fraction					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			GAACAAGAGCGTCCATTCCTT	0.468													20	71	---	---	---	---	PASS
HNRNPU	3192	broad.mit.edu	37	1	245020153	245020153	+	Silent	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245020153T>A	uc001iaz.1	-	9	1838	c.1620A>T	c.(1618-1620)GCA>GCT	p.A540A	HNRNPU_uc001iaw.1_RNA|HNRNPU_uc001iax.1_RNA|HNRNPU_uc001iay.1_Silent_p.A264A|HNRNPU_uc001iba.1_Silent_p.A521A|HNRNPU_uc001ibb.1_Silent_p.A228A	NM_031844	NP_114032	Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U	540					CRD-mediated mRNA stabilization	catalytic step 2 spliceosome|cell surface|CRD-mediated mRNA stability complex|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	ATP binding|DNA binding|protein binding|RNA binding				0	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			TCTTAAAACCTGCCACCTATA	0.363													34	70	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247050612	247050612	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247050612T>C	uc001ibu.1	-	19	2380	c.2373A>G	c.(2371-2373)ACA>ACG	p.T791T	AHCTF1_uc001ibv.1_Silent_p.T800T|AHCTF1_uc009xgs.1_5'UTR	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	791	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TGGGAGTGTCTGTTTTGTTGG	0.353													44	40	---	---	---	---	PASS
OR2W5	441932	broad.mit.edu	37	1	247654714	247654714	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247654714C>T	uc001icz.1	+	1	285	c.285C>T	c.(283-285)CAC>CAT	p.H95H		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	95					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TCACCTACCACGGCTGTGTGG	0.557													42	36	---	---	---	---	PASS
OR2G2	81470	broad.mit.edu	37	1	247752503	247752503	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247752503A>T	uc010pyy.1	+	1	842	c.842A>T	c.(841-843)TAC>TTC	p.Y281F		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G,	281	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TCTCTCTTCTACACTGTGGTA	0.358													72	100	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112725	248112725	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112725T>A	uc001idt.1	+	1	566	c.566T>A	c.(565-567)ATG>AAG	p.M189K	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CTGGCCTGCATGGACACCTGG	0.468													16	33	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112726	248112726	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112726G>T	uc001idt.1	+	1	567	c.567G>T	c.(565-567)ATG>ATT	p.M189I	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGGCCTGCATGGACACCTGGG	0.473													16	32	---	---	---	---	PASS
DNMT3A	1788	broad.mit.edu	37	2	25467478	25467478	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25467478T>C	uc002rgc.2	-	14	1855	c.1598A>G	c.(1597-1599)TAC>TGC	p.Y533C	DNMT3A_uc002rgd.2_Missense_Mutation_p.Y533C|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.Y344C	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	533	Interaction with the PRC2/EED-EZH2 complex (By similarity).|ADD.				regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTAGGACTGGTAGCCGTCGTC	0.602			Mis|F|N|S		AML								15	3	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33525541	33525541	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33525541A>G	uc002ros.2	+	21	3262	c.3262A>G	c.(3262-3264)AAT>GAT	p.N1088D	LTBP1_uc002rot.2_Missense_Mutation_p.N762D|LTBP1_uc002rou.2_Missense_Mutation_p.N761D|LTBP1_uc002rov.2_Missense_Mutation_p.N708D|LTBP1_uc010ymz.1_Missense_Mutation_p.N761D|LTBP1_uc010yna.1_Missense_Mutation_p.N708D|LTBP1_uc010ynb.1_Missense_Mutation_p.N27D	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1087	EGF-like 9; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				TCAGCAAGGGAATCTATGTGT	0.488													39	23	---	---	---	---	PASS
DYNC2LI1	51626	broad.mit.edu	37	2	44016793	44016793	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44016793T>C	uc002rtk.2	+	5	349	c.253T>C	c.(253-255)TGG>CGG	p.W85R	DYNC2LI1_uc002rth.2_Missense_Mutation_p.W85R|DYNC2LI1_uc002rti.2_Missense_Mutation_p.W85R|DYNC2LI1_uc002rtj.2_Missense_Mutation_p.W85R|DYNC2LI1_uc002rtl.2_Missense_Mutation_p.W85R|DYNC2LI1_uc010ynz.1_5'UTR	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1	85						apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CGCTCACTTTTGGGAACTCGG	0.378													34	13	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48808748	48808748	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48808748C>T	uc010yol.1	+	1	1023	c.976C>T	c.(976-978)CCA>TCA	p.P326S	STON1_uc002rwo.3_Missense_Mutation_p.P326S|STON1_uc010fbm.2_Missense_Mutation_p.P326S|STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.P326S|STON1_uc002rwr.2_RNA|STON1_uc002rwq.2_Missense_Mutation_p.P326S	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	326					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACAGCTTGATCCATATTGTAG	0.378													7	265	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49210251	49210251	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49210251G>T	uc002rww.2	-	7	653	c.579C>A	c.(577-579)ACC>ACA	p.T193T	FSHR_uc002rwx.2_Silent_p.T193T|FSHR_uc010fbn.2_Silent_p.T167T|FSHR_uc010fbo.1_RNA	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	193	LRR 7.|Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	CATCTAGTTGGGTTCCATTGA	0.368									Gonadal_Dysgenesis_46_XX				11	72	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55576722	55576722	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55576722C>T	uc002ryv.2	-	9	1656	c.814G>A	c.(814-816)GAG>AAG	p.E272K	CCDC88A_uc010yoz.1_Missense_Mutation_p.E272K|CCDC88A_uc010ypa.1_Missense_Mutation_p.E272K|CCDC88A_uc010ypb.1_Missense_Mutation_p.E174K	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	272	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						AACAACTGCTCAGTCTTTTCC	0.328													11	23	---	---	---	---	PASS
CCDC85A	114800	broad.mit.edu	37	2	56603032	56603032	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56603032C>G	uc002rzn.2	+	5	2036	c.1534C>G	c.(1534-1536)CCT>GCT	p.P512A		NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	512										breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACATGCCACACCTTCCCAGCA	0.473													21	50	---	---	---	---	PASS
KIAA1841	84542	broad.mit.edu	37	2	61319611	61319611	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61319611G>T	uc002saw.3	+	11	1404	c.1101G>T	c.(1099-1101)TGG>TGT	p.W367C	KIAA1841_uc002sax.3_Missense_Mutation_p.W221C|KIAA1841_uc002say.2_Missense_Mutation_p.W367C	NM_001129993	NP_001123465	Q6NSI8	K1841_HUMAN	KIAA1841 protein isoform a	367											0			Epithelial(17;0.193)			ATAAGACATGGGATGTTCATG	0.284													8	384	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61459593	61459593	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61459593C>T	uc002sbe.2	-	58	7129	c.7107G>A	c.(7105-7107)GTG>GTA	p.V2369V	USP34_uc002sbf.2_Silent_p.V519V	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2369					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TTACCTGTCTCACAATTTGAT	0.308													81	149	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61459646	61459646	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61459646C>G	uc002sbe.2	-	58	7076	c.7054G>C	c.(7054-7056)GAT>CAT	p.D2352H	USP34_uc002sbf.2_Missense_Mutation_p.D502H	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2352					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CAGTCGTCATCAGCCATACGA	0.308													69	152	---	---	---	---	PASS
FAM161A	84140	broad.mit.edu	37	2	62065725	62065725	+	Intron	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62065725C>G	uc010ypo.1	-						FAM161A_uc002sbm.3_Missense_Mutation_p.D567H|FAM161A_uc002sbn.3_Intron|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Intron	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140						response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3						TGATGTGAGTCATAAGCCTTA	0.368													20	359	---	---	---	---	PASS
APLF	200558	broad.mit.edu	37	2	68772369	68772369	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68772369A>T	uc002sep.2	+	8	1384	c.1211A>T	c.(1210-1212)TAT>TTT	p.Y404F	APLF_uc002seq.1_RNA|APLF_uc010fdf.2_Missense_Mutation_p.Y380F|APLF_uc002ser.1_Missense_Mutation_p.Y135F	NM_173545	NP_775816	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	404					double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2						GATAGTGATTATGGAGGTGTA	0.413													21	38	---	---	---	---	PASS
ARHGAP25	9938	broad.mit.edu	37	2	69046265	69046265	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69046265G>T	uc002seu.2	+	9	1375	c.1011G>T	c.(1009-1011)CAG>CAT	p.Q337H	ARHGAP25_uc010fdg.2_Missense_Mutation_p.Q338H|ARHGAP25_uc010yql.1_Missense_Mutation_p.Q298H|ARHGAP25_uc002sev.2_Missense_Mutation_p.Q331H|ARHGAP25_uc002sew.2_Missense_Mutation_p.Q330H|ARHGAP25_uc002sex.2_Missense_Mutation_p.Q331H|ARHGAP25_uc002sey.2_Missense_Mutation_p.Q64H	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	337	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						GGACTCCTCAGATCCAAAGAG	0.498													8	341	---	---	---	---	PASS
DCTN1	1639	broad.mit.edu	37	2	74593698	74593698	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74593698G>A	uc002skx.2	-	22	2827	c.2516C>T	c.(2515-2517)GCT>GTT	p.A839V	DCTN1_uc002skt.1_5'Flank|DCTN1_uc002skv.2_Missense_Mutation_p.A705V|DCTN1_uc002sku.2_Missense_Mutation_p.A705V|DCTN1_uc002skw.1_Missense_Mutation_p.A815V|DCTN1_uc010ffd.2_Missense_Mutation_p.A819V|DCTN1_uc002sky.2_Missense_Mutation_p.A802V	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	839					cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5						CTGCAGCACAGCCACGACCCA	0.582													53	136	---	---	---	---	PASS
TMEM150A	129303	broad.mit.edu	37	2	85826823	85826823	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85826823C>A	uc002spw.1	-	6	1120	c.399G>T	c.(397-399)GTG>GTT	p.V133V	TMEM150A_uc002spx.1_Silent_p.V49V|TMEM150A_uc002spz.1_Silent_p.V80V|TMEM150A_uc002sqa.1_Silent_p.V49V|TMEM150A_uc002spy.1_Silent_p.V133V	NM_001031738	NP_001026908	Q86TG1	T150A_HUMAN	transmembrane protein 150A isoform 1	133	Extracellular (Potential).					integral to membrane|plasma membrane					0						TGGCATGATCCACCTGGGCCC	0.607													5	59	---	---	---	---	PASS
MRPL35	51318	broad.mit.edu	37	2	86426661	86426661	+	Intron	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86426661G>T	uc002srg.3	+						MRPL35_uc002srf.3_Intron	NM_016622	NP_057706	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35 isoform a						translation	mitochondrial ribosome	structural constituent of ribosome				0						CTTCAGGTCAGTGGAGAGCGA	0.527													13	62	---	---	---	---	PASS
EIF2AK3	9451	broad.mit.edu	37	2	88857340	88857340	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88857340T>C	uc002stc.3	-	17	3467	c.3265A>G	c.(3265-3267)AGA>GGA	p.R1089G		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	1089	Cytoplasmic (Potential).				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3						GACCTCTGTCTGAGCACTGTT	0.453													42	29	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89384807	89384807	+	RNA	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89384807C>T	uc010ytr.1	-	50		c.5333G>A			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		CTGGTGGATGCACCATAGATG	0.577													23	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89417018	89417018	+	RNA	SNP	C	T	T	rs77497402		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89417018C>T	uc010ytr.1	-	42		c.4584G>A			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		TGATACCAGCCTAAATCATTT	0.527													48	18	---	---	---	---	PASS
KIAA1310	55683	broad.mit.edu	37	2	97276805	97276805	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97276805C>T	uc002swn.3	-	10	1303	c.1157G>A	c.(1156-1158)AGA>AAA	p.R386K	KIAA1310_uc002swh.3_Missense_Mutation_p.R274K|KIAA1310_uc002swi.3_Missense_Mutation_p.R287K|KIAA1310_uc002swj.3_RNA|KIAA1310_uc002swk.3_Missense_Mutation_p.R299K|KIAA1310_uc010fhz.2_Missense_Mutation_p.R180K|KIAA1310_uc002swl.3_Missense_Mutation_p.R287K|KIAA1310_uc002swm.3_RNA|KIAA1310_uc010yur.1_Missense_Mutation_p.R180K|KIAA1310_uc002swp.1_Missense_Mutation_p.R287K|KIAA1310_uc002swq.1_Missense_Mutation_p.R158K|KIAA1310_uc010fhy.1_Missense_Mutation_p.R287K	NM_001115016	NP_001108488	Q9P2N6	K1310_HUMAN	hypothetical protein LOC55683 isoform a	386											0						TCTTACCCCTCTGGGGCCATC	0.512													49	70	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102452415	102452415	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102452415C>T	uc002tbg.2	+	9	803	c.748C>T	c.(748-750)CCT>TCT	p.P250S	MAP4K4_uc002tbc.2_Missense_Mutation_p.P250S|MAP4K4_uc002tbd.2_Missense_Mutation_p.P250S|MAP4K4_uc002tbe.2_Missense_Mutation_p.P250S|MAP4K4_uc002tbf.2_Missense_Mutation_p.P250S|MAP4K4_uc010yvy.1_Missense_Mutation_p.P250S|MAP4K4_uc002tbh.2_Missense_Mutation_p.P250S|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Missense_Mutation_p.P230S|MAP4K4_uc010fiw.1_Missense_Mutation_p.P92S|MAP4K4_uc002tbj.1_Missense_Mutation_p.P146S	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	250	Protein 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						CAGAAACCCTCCTCCCCGGCT	0.408													6	22	---	---	---	---	PASS
SLC9A4	389015	broad.mit.edu	37	2	103142717	103142717	+	Splice_Site	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103142717G>A	uc002tbz.3	+	11	2408	c.1951_splice	c.e11-1	p.A651_splice		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			skin(2)|central_nervous_system(1)	3						GCTACCCACAGGCTGGCACCA	0.418													36	72	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109384025	109384025	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109384025A>G	uc002tem.3	+	20	7156	c.7030A>G	c.(7030-7032)AAA>GAA	p.K2344E		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	2344	RanBD1 3.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						CAGATATGATAAAGATGTTGG	0.363													109	145	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116572495	116572495	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116572495G>A	uc002tla.1	+	20	2284	c.1827G>A	c.(1825-1827)CTG>CTA	p.L609L	DPP10_uc002tlb.1_Silent_p.L559L|DPP10_uc002tlc.1_Silent_p.L605L|DPP10_uc002tle.2_Silent_p.L613L|DPP10_uc002tlf.1_Silent_p.L602L	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	609	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TCCAGGGTCTGAAAATTTTGC	0.383													15	59	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125671847	125671847	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125671847A>C	uc002tno.2	+	24	4267	c.3903A>C	c.(3901-3903)AAA>AAC	p.K1301N	CNTNAP5_uc010flu.2_Missense_Mutation_p.K1302N	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1301	Cytoplasmic (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCGAGTGTAAACGGGAATATT	0.408													17	33	---	---	---	---	PASS
POLR2D	5433	broad.mit.edu	37	2	128610593	128610593	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128610593C>A	uc002tpj.2	-	2	215	c.160G>T	c.(160-162)GAA>TAA	p.E54*	POLR2D_uc002tpk.2_Nonsense_Mutation_p.E54*	NM_004805	NP_004796	O15514	RPB4_HUMAN	DNA directed RNA polymerase II polypeptide D	54					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA-directed RNA polymerase activity|nucleotide binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		AGCTCCTGTTCGTCCTCTGCA	0.418													9	68	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128707902	128707902	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128707902G>A	uc002tpp.2	-	16	2608	c.2476C>T	c.(2476-2478)CTA>TTA	p.L826L	SAP130_uc002tpn.2_Silent_p.L586L|SAP130_uc002tpo.2_Silent_p.L606L|SAP130_uc010fmd.2_Silent_p.L861L	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	826	Pro-rich.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CCAGGTGGTAGGTCACTTGTA	0.488													37	47	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128747236	128747236	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128747236C>G	uc002tpp.2	-	13	1892	c.1760G>C	c.(1759-1761)GGC>GCC	p.G587A	SAP130_uc002tpn.2_Missense_Mutation_p.G348A|SAP130_uc002tpo.2_Missense_Mutation_p.G332A|SAP130_uc010fmd.2_Missense_Mutation_p.G587A|SAP130_uc002tpq.1_Missense_Mutation_p.G560A	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	587					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TCCCTGTGTGCCAAGTGGTGC	0.567													22	42	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128913974	128913974	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128913974T>A	uc002tps.2	+	21	2423	c.2245T>A	c.(2245-2247)TCC>ACC	p.S749T	UGGT1_uc010fme.1_Missense_Mutation_p.S624T|UGGT1_uc002tpr.2_Missense_Mutation_p.S725T	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	749					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						AGGAATGTCCTCCAAGGAAAT	0.299													14	28	---	---	---	---	PASS
MGAT5	4249	broad.mit.edu	37	2	135180449	135180449	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135180449G>C	uc002ttv.1	+	13	1898	c.1753G>C	c.(1753-1755)GAG>CAG	p.E585Q		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	585	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		CAACAATCAGGAGGAAGTAGA	0.433													6	62	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141072507	141072507	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141072507G>T	uc002tvj.1	-	83	13774	c.12802C>A	c.(12802-12804)CTA>ATA	p.L4268I		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4268	Extracellular (Potential).|EGF-like 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TATTTACCTAGAACTGATGGT	0.353										TSP Lung(27;0.18)			15	22	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141081480	141081480	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141081480G>A	uc002tvj.1	-	81	13468	c.12496C>T	c.(12496-12498)CGT>TGT	p.R4166C		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4166	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGTTTATAACGATGAGATATC	0.244										TSP Lung(27;0.18)			6	13	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141533709	141533709	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141533709C>T	uc002tvj.1	-	33	6430	c.5458G>A	c.(5458-5460)GGG>AGG	p.G1820R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1820	Extracellular (Potential).|LDL-receptor class B 18.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGAACTACCCCAGAAGTCTTA	0.418										TSP Lung(27;0.18)			7	32	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152427088	152427088	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152427088T>C	uc010fnx.2	-	80	12129	c.11938A>G	c.(11938-11940)ATG>GTG	p.M3980V	NEB_uc002txr.2_Missense_Mutation_p.M403V	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3980					muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CCCGCCTTCATTTCATCCCAG	0.483													5	9	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166210793	166210793	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166210793A>G	uc002udc.2	+	17	3301	c.3011A>G	c.(3010-3012)CAG>CGG	p.Q1004R	SCN2A_uc002udd.2_Missense_Mutation_p.Q1004R|SCN2A_uc002ude.2_Missense_Mutation_p.Q1004R	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1004	II.				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	AATAATCTCCAGATTGCTGTG	0.383													27	75	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166870332	166870332	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166870332C>A	uc010zcz.1	-	18	3612	c.3594G>T	c.(3592-3594)AGG>AGT	p.R1198S	SCN1A_uc002udo.3_Missense_Mutation_p.R1078S|SCN1A_uc010fpk.2_Missense_Mutation_p.R1050S	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1209	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	GGAAACACGTCCTTCTCAGGT	0.398													13	19	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166870333	166870333	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166870333C>T	uc010zcz.1	-	18	3611	c.3593G>A	c.(3592-3594)AGG>AAG	p.R1198K	SCN1A_uc002udo.3_Missense_Mutation_p.R1078K|SCN1A_uc010fpk.2_Missense_Mutation_p.R1050K	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1209	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	GAAACACGTCCTTCTCAGGTT	0.398													13	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179605328	179605328	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179605328C>A	uc010zfh.1	-	46	12343	c.12119G>T	c.(12118-12120)GGG>GTG	p.G4040V	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Missense_Mutation_p.G3973V|TTN_uc010zfj.1_Missense_Mutation_p.G3848V|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	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)			TGGATAATTCCCTTCAGGTTC	0.388													15	71	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179654693	179654693	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179654693A>G	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron|TTN_uc010frg.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								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)			CAGCTCAAATATCTGTATTCA	0.313													11	24	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179665403	179665403	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179665403G>A	uc002und.2	-	4	527	c.302C>T	c.(301-303)ACA>ATA	p.T101I	TTN_uc010zfg.1_Missense_Mutation_p.T101I|TTN_uc010zfh.1_Missense_Mutation_p.T101I|TTN_uc010zfi.1_Missense_Mutation_p.T101I|TTN_uc010zfj.1_Missense_Mutation_p.T101I|TTN_uc002unb.2_Missense_Mutation_p.T101I			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	101							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)			GGGTGGTGCTGTCTCAGCTGC	0.498													20	40	---	---	---	---	PASS
COL3A1	1281	broad.mit.edu	37	2	189876412	189876412	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189876412G>T	uc002uqj.1	+	51	4430	c.4313G>T	c.(4312-4314)AGA>ATA	p.R1438I		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1438	Fibrillar collagen NC1.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)	AAGGCTGTGAGACTACCTATT	0.393													9	30	---	---	---	---	PASS
GLS	2744	broad.mit.edu	37	2	191795262	191795262	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191795262G>T	uc002usf.2	+	13	1789	c.1525G>T	c.(1525-1527)GGC>TGC	p.G509C	GLS_uc002use.2_Missense_Mutation_p.G509C|GLS_uc002usg.1_Missense_Mutation_p.G170C|GLS_uc002ush.2_Missense_Mutation_p.G170C|GLS_uc010zgi.1_Missense_Mutation_p.G80C|GLS_uc010zgj.1_Missense_Mutation_p.G14C	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor	509					cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GGATAAGATGGGCAACAGTGT	0.398													16	52	---	---	---	---	PASS
TRAK2	66008	broad.mit.edu	37	2	202250994	202250994	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202250994G>T	uc002uyb.3	-	14	2356	c.1910C>A	c.(1909-1911)CCA>CAA	p.P637Q		NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	637				Missing (in Ref. 2).		early endosome|plasma membrane	GABA receptor binding				0						CCCTGTTACTGGCTTGGATGT	0.418													4	26	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215843761	215843761	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215843761G>A	uc002vew.2	-	32	4964	c.4744C>T	c.(4744-4746)CCA>TCA	p.P1582S	ABCA12_uc002vev.2_Missense_Mutation_p.P1264S|ABCA12_uc010zjn.1_Missense_Mutation_p.P509S	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1582					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTTAAATTTGGACTCTAAGAG	0.458													12	38	---	---	---	---	PASS
RHBDD1	84236	broad.mit.edu	37	2	227773574	227773574	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227773574A>C	uc002voi.2	+	5	813	c.692A>C	c.(691-693)CAA>CCA	p.Q231P	RHBDD1_uc010fxc.2_Missense_Mutation_p.Q231P|RHBDD1_uc002voj.2_Missense_Mutation_p.Q62P	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1	231						integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		CCAGGACGGCAATACTACTTT	0.318													12	28	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228884383	228884383	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228884383G>T	uc002vpq.2	-	7	1234	c.1187C>A	c.(1186-1188)GCA>GAA	p.A396E	SPHKAP_uc002vpp.2_Missense_Mutation_p.A396E|SPHKAP_uc010zlx.1_Missense_Mutation_p.A396E	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	396						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CACGGATTCTGCTAAATTTGT	0.448													19	37	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228996713	228996713	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228996713T>C	uc002vpq.2	-	2	168	c.121A>G	c.(121-123)ATC>GTC	p.I41V	SPHKAP_uc002vpp.2_Missense_Mutation_p.I41V|SPHKAP_uc010zlx.1_Missense_Mutation_p.I41V	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	41						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CAGGCTGTGATGGAGTTCCCC	0.473													12	28	---	---	---	---	PASS
ALPP	250	broad.mit.edu	37	2	233245354	233245354	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233245354T>G	uc002vsq.2	+	8	1052	c.887T>G	c.(886-888)ATG>AGG	p.M296R	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	296						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CCTGGAGACATGAAATACGAG	0.627													4	36	---	---	---	---	PASS
UGT1A3	54659	broad.mit.edu	37	2	234638577	234638577	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234638577A>G	uc002vuy.2	+	1	805	c.805A>G	c.(805-807)ATC>GTC	p.I269V	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_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Missense_Mutation_p.I269V	NM_019093	NP_061966	P35503	UD13_HUMAN	UDP glycosyltransferase 1 family, polypeptide A3	269					flavonoid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(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;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CCCCAGGCCAATCATGCCCAA	0.507													31	78	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238277716	238277716	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238277716G>A	uc002vwl.2	-	10	4675	c.4390C>T	c.(4390-4392)CGA>TGA	p.R1464*	COL6A3_uc002vwo.2_Nonsense_Mutation_p.R1258*|COL6A3_uc010znj.1_Nonsense_Mutation_p.R857*	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1464	VWFA 8.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTGAGTCTTCGAACAATCCTG	0.473													5	33	---	---	---	---	PASS
FARP2	9855	broad.mit.edu	37	2	242407665	242407665	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242407665G>A	uc002wbi.1	+	18	2121	c.2004G>A	c.(2002-2004)AAG>AAA	p.K668K		NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	668	DH.				axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AGCTGCAGAAGGTCTGCTACT	0.552													28	48	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49688509	49688509	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49688509G>T	uc003cxe.3	+	4	2097	c.1983G>T	c.(1981-1983)GCG>GCT	p.A661A		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	661					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GTGGGGAGGCGGAGGTCAGTC	0.597													4	18	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108147433	108147433	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108147433T>A	uc003dxa.1	-	28	3725	c.3668A>T	c.(3667-3669)CAG>CTG	p.Q1223L		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1223	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CTTGACCTGCTGTAGATTTTC	0.483													30	85	---	---	---	---	PASS
DPPA2	151871	broad.mit.edu	37	3	109023411	109023411	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109023411C>A	uc003dxo.2	-	7	1012	c.765G>T	c.(763-765)AGG>AGT	p.R255S		NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	255						nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3						AAATCATCCTCCTGTGAGTGG	0.517													5	67	---	---	---	---	PASS
ABHD10	55347	broad.mit.edu	37	3	111698038	111698038	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111698038C>G	uc003dyk.3	+	1	211	c.130C>G	c.(130-132)CGG>GGG	p.R44G	ABHD10_uc011bhq.1_5'UTR	NM_018394	NP_060864	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10 precursor	44						mitochondrion	serine-type peptidase activity				0						GCGGGCGCCACGGTGGCTCCC	0.662													14	24	---	---	---	---	PASS
DTX3L	151636	broad.mit.edu	37	3	122288682	122288682	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122288682C>T	uc003efk.2	+	3	1835	c.1746C>T	c.(1744-1746)TGC>TGT	p.C582C	DTX3L_uc010hrj.2_Intron	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like	582	RING-type.				histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)	4				GBM - Glioblastoma multiforme(114;0.0459)		ATGAATTCTGCGCCCCTTGTA	0.453													7	155	---	---	---	---	PASS
SEMA5B	54437	broad.mit.edu	37	3	122645282	122645282	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122645282A>G	uc003efz.1	-	9	1397	c.1093T>C	c.(1093-1095)TTG>CTG	p.L365L	SEMA5B_uc011bju.1_Silent_p.L307L|SEMA5B_uc003ega.1_RNA|SEMA5B_uc003egb.1_Silent_p.L365L|SEMA5B_uc010hro.1_Silent_p.L307L|SEMA5B_uc010hrp.1_RNA	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1	365	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		TGCTCCGGCAAGTGGAAGGCA	0.602													11	18	---	---	---	---	PASS
ALG1L	200810	broad.mit.edu	37	3	125651529	125651529	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125651529C>A	uc003eig.1	-	3	288	c.124G>T	c.(124-126)GGA>TGA	p.G42*		NM_001015050	NP_001015050	Q6GMV1	ALG1L_HUMAN	asparagine-linked glycosylation 1-like	42							transferase activity, transferring glycosyl groups				0						AGGTTGTGTCCATCAAGAGTA	0.373													5	84	---	---	---	---	PASS
MRPL3	11222	broad.mit.edu	37	3	131198076	131198076	+	Intron	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131198076C>A	uc003eoh.2	-						MRPL3_uc011blo.1_Intron|MRPL3_uc011blp.1_Intron|SNORA58_uc003eoi.1_RNA	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3						translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						ACGAGTATGCCCTCCAAATTA	0.423													11	43	---	---	---	---	PASS
SOX14	8403	broad.mit.edu	37	3	137483975	137483975	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137483975G>C	uc003erm.1	+	1	397	c.349G>C	c.(349-351)GGC>CGC	p.G117R		NM_004189	NP_004180	O95416	SOX14_HUMAN	SRY-box 14	117					negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding				0						GGCCTCCGACGGCCTCCTGAG	0.692													15	6	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140281797	140281797	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140281797A>C	uc003etn.2	+	14	2547	c.2357A>C	c.(2356-2358)GAG>GCG	p.E786A		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	786	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						TTCAACTTGGAGGTGAGTGGG	0.552										HNSCC(16;0.037)			11	28	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906580	164906580	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906580C>A	uc003fej.3	-	2	2483	c.2039G>T	c.(2038-2040)CGA>CTA	p.R680L	SLITRK3_uc003fek.2_Missense_Mutation_p.R680L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	680	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						TCGACGCCTTCGGAGCACGTA	0.522										HNSCC(40;0.11)			48	36	---	---	---	---	PASS
GOLIM4	27333	broad.mit.edu	37	3	167758633	167758633	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167758633C>A	uc003ffe.2	-	7	969	c.625G>T	c.(625-627)GAG>TAG	p.E209*	GOLIM4_uc011bpe.1_Nonsense_Mutation_p.E209*|GOLIM4_uc011bpf.1_Intron|GOLIM4_uc011bpg.1_Intron	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	209	Potential.|Golgi targeting.|Lumenal (Potential).				transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						TGTTCATGCTCGGAGAGTAAA	0.413													4	106	---	---	---	---	PASS
SAMD7	344658	broad.mit.edu	37	3	169644749	169644749	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169644749C>G	uc003fgd.2	+	6	966	c.699C>G	c.(697-699)AGC>AGG	p.S233R	SAMD7_uc003fge.2_Missense_Mutation_p.S233R|SAMD7_uc011bpo.1_Missense_Mutation_p.S134R	NM_182610	NP_872416	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	233										skin(1)	1	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			AAGCACCCAGCAACCAGAAGT	0.483													75	86	---	---	---	---	PASS
PRKCI	5584	broad.mit.edu	37	3	170002300	170002300	+	Silent	SNP	G	A	A	rs146346249		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170002300G>A	uc003fgs.2	+	12	1357	c.1119G>A	c.(1117-1119)GGG>GGA	p.G373G		NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota	373	Protein kinase.				anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ATGAGCGAGGGATAATTTATA	0.318													20	41	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178917478	178917478	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178917478G>A	uc003fjk.2	+	3	510	c.353G>A	c.(352-354)GGT>GAT	p.G118D		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	118					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.G118D(6)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TTTATTAAAGGTTTTGCTATC	0.338		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			9	21	---	---	---	---	PASS
ACTL6A	86	broad.mit.edu	37	3	179287884	179287884	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179287884G>T	uc003fjw.2	+	3	305	c.132G>T	c.(130-132)GTG>GTT	p.V44V	ACTL6A_uc003fjx.2_Silent_p.V2V|ACTL6A_uc003fjy.2_Silent_p.V2V	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1	44					chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			TTGGTATGGTGGTAGAAAGAG	0.408													5	94	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515841	195515841	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515841G>A	uc011bto.1	-	2	3070	c.2610C>T	c.(2608-2610)GGC>GGT	p.G870G	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Silent_p.G752G	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	875	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)		GATGAAAGGTGCCGGGGACGA	0.592													9	18	---	---	---	---	PASS
RNF168	165918	broad.mit.edu	37	3	196199439	196199439	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196199439T>C	uc003fwq.2	-	6	1505	c.967A>G	c.(967-969)AAA>GAA	p.K323E	RNF168_uc010iah.2_Missense_Mutation_p.K156E|uc010iag.1_5'Flank	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	323					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		CATAACTCTTTCCCATGATTG	0.468													9	59	---	---	---	---	PASS
NCAPG	64151	broad.mit.edu	37	4	17826672	17826672	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17826672G>A	uc003gpp.2	+	10	1641	c.1465G>A	c.(1465-1467)GAA>AAA	p.E489K	NCAPG_uc011bxj.1_5'UTR	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G	489					cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)		AAGAAAGAAAGAACTCAAGGT	0.388													4	9	---	---	---	---	PASS
DHX15	1665	broad.mit.edu	37	4	24578074	24578074	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24578074G>C	uc003gqx.2	-	2	467	c.299C>G	c.(298-300)TCA>TGA	p.S100*		NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15	100					mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)				GGCATGCGTTGAATGAGCAGA	0.453													35	73	---	---	---	---	PASS
SLC34A2	10568	broad.mit.edu	37	4	25677904	25677904	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25677904T>A	uc003grr.2	+	13	1687	c.1606T>A	c.(1606-1608)TTC>ATC	p.F536I	SLC34A2_uc003grs.2_Missense_Mutation_p.F535I|SLC34A2_uc010iev.2_Missense_Mutation_p.F535I	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	536	Helical; Name=M7; (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)				CCTGATCATCTTCTTCTTCCT	0.607													52	85	---	---	---	---	PASS
PGM2	55276	broad.mit.edu	37	4	37857372	37857372	+	Intron	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37857372G>C	uc011byb.1	+						PGM2_uc011byc.1_Intron	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2						glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1						GGTATGATGTGGATGGCAGCT	0.463													16	29	---	---	---	---	PASS
UGDH	7358	broad.mit.edu	37	4	39511414	39511414	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39511414C>A	uc003guk.1	-	6	1093	c.777G>T	c.(775-777)CAG>CAT	p.Q259H	UGDH_uc011byp.1_Missense_Mutation_p.Q162H|UGDH_uc003gul.1_Missense_Mutation_p.Q192H	NM_003359	NP_003350	O60701	UGDH_HUMAN	UDP-glucose dehydrogenase	259					glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)	TTCCAATTCTCTGGTCCATTC	0.323													19	25	---	---	---	---	PASS
YIPF7	285525	broad.mit.edu	37	4	44631420	44631420	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44631420C>G	uc010ifx.1	-	4	515	c.498G>C	c.(496-498)CTG>CTC	p.L166L	YIPF7_uc010ify.1_3'UTR	NM_182592	NP_872398	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	166	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane					0						GACACATTACCAGAAGCAAGG	0.438													5	9	---	---	---	---	PASS
COX7B2	170712	broad.mit.edu	37	4	46736995	46736995	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46736995C>A	uc003gxf.2	-	3	395	c.215G>T	c.(214-216)AGA>ATA	p.R72I	COX7B2_uc010ige.2_RNA	NM_130902	NP_570972	Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2 precursor	72	Mitochondrial intermembrane (By similarity).					integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TGGGGTAACTCTGCCAACAGG	0.428													16	27	---	---	---	---	PASS
ATP10D	57205	broad.mit.edu	37	4	47548682	47548682	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47548682G>C	uc003gxk.1	+	10	1602	c.1438G>C	c.(1438-1440)GAA>CAA	p.E480Q	ATP10D_uc003gxl.1_5'UTR|ATP10D_uc003gxj.3_Missense_Mutation_p.E465Q	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	480	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						CTCTGAAGATGAAGATTTTAT	0.468													5	83	---	---	---	---	PASS
UGT2B4	7363	broad.mit.edu	37	4	70359570	70359570	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70359570A>G	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Intron	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						CTGATGGGGGAAAAAAAAAGA	0.368													11	15	---	---	---	---	PASS
EREG	2069	broad.mit.edu	37	4	75246733	75246733	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75246733C>G	uc003hie.1	+	3	323	c.157C>G	c.(157-159)CAG>GAG	p.Q53E	EREG_uc003hid.2_Missense_Mutation_p.Q47E	NM_001432	NP_001423	O14944	EREG_HUMAN	epiregulin preproprotein	53					angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)|skin(1)	2			Lung(101;0.196)			TTTTACAGTTCAGACAGAAGA	0.398													17	55	---	---	---	---	PASS
NAAA	27163	broad.mit.edu	37	4	76852392	76852392	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76852392C>T	uc003hjb.2	-	4	628	c.564G>A	c.(562-564)AAG>AAA	p.K188K	NAAA_uc003hja.2_Silent_p.K188K|NAAA_uc003hjc.3_Silent_p.K188K|NAAA_uc003hjd.3_RNA|NAAA_uc011cbq.1_Silent_p.K87K	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1	188					lipid metabolic process	lysosome	hydrolase activity			skin(1)	1						AAACTGTAAACTTGTGTGGGC	0.393													10	22	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104082412	104082412	+	Intron	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104082412T>C	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GTTCTTTCTATTGAGAAAAAC	0.308													9	5	---	---	---	---	PASS
QRFPR	84109	broad.mit.edu	37	4	122301679	122301679	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122301679C>A	uc010inj.1	-	1	503	c.124G>T	c.(124-126)GGA>TGA	p.G42*	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Nonsense_Mutation_p.G42*|QRFPR_uc010inl.1_Nonsense_Mutation_p.G42*	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	42	Extracellular (Potential).					plasma membrane	neuropeptide Y receptor activity				0						TTGGCGCGTCCCGGCAGCTCT	0.657													7	3	---	---	---	---	PASS
TRPC3	7222	broad.mit.edu	37	4	122825537	122825537	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122825537C>A	uc003ieg.2	-	8	2267	c.2193G>T	c.(2191-2193)ATG>ATT	p.M731I	TRPC3_uc010inr.2_Missense_Mutation_p.M603I|TRPC3_uc003ief.2_Missense_Mutation_p.M658I|TRPC3_uc011cgl.1_Missense_Mutation_p.M395I	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	646	Helical; (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						AAACGACCACCATAGTTACAT	0.328													8	15	---	---	---	---	PASS
TBC1D9	23158	broad.mit.edu	37	4	141592006	141592006	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141592006C>T	uc010ioj.2	-	7	1406	c.1134G>A	c.(1132-1134)ATG>ATA	p.M378I		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	378						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				ATAGGAAGGTCATCCTGTTTC	0.448													10	88	---	---	---	---	PASS
TMEM144	55314	broad.mit.edu	37	4	159136383	159136383	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159136383G>T	uc003ipx.2	+	4	670	c.150G>T	c.(148-150)TTG>TTT	p.L50F	TMEM144_uc010iqi.2_RNA	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	50	Helical; (Potential).					integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CCATATGGTTGGTTGCCTTGG	0.398													5	61	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187159519	187159519	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187159519G>T	uc003iyy.2	+	6	669	c.598G>T	c.(598-600)GGT>TGT	p.G200C	KLKB1_uc011clc.1_5'UTR|KLKB1_uc011cld.1_Missense_Mutation_p.G162C	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	200					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)		TTCAGAAATTGGTAATTGTAG	0.289													19	22	---	---	---	---	PASS
SLC9A3	6550	broad.mit.edu	37	5	485314	485314	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:485314C>G	uc003jbe.2	-	4	820	c.708G>C	c.(706-708)GCG>GCC	p.A236A	SLC9A3_uc011clx.1_Silent_p.A236A	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	236	Extracellular (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CACCTCCCAGCGCCACGAAAG	0.632													95	39	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9202306	9202306	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9202306G>C	uc003jek.2	-	9	1405	c.693C>G	c.(691-693)TTC>TTG	p.F231L		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	231	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						CTCGGAAAAAGAAGTAGGTAA	0.433													18	105	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13714594	13714594	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13714594C>A	uc003jfd.2	-	75	13087	c.13045G>T	c.(13045-13047)GAT>TAT	p.D4349Y	DNAH5_uc003jfc.2_Missense_Mutation_p.D517Y	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4349					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CGGGTCTCATCCCCTCCACCA	0.587									Kartagener_syndrome				11	123	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19591282	19591282	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19591282C>G	uc003jgc.2	-	6	1260	c.883G>C	c.(883-885)GCT>CCT	p.A295P	CDH18_uc003jgd.2_Missense_Mutation_p.A295P|CDH18_uc011cnm.1_Missense_Mutation_p.A295P	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	295	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CCAGTGTCAGCATCATTTGCC	0.403													18	37	---	---	---	---	PASS
OSMR	9180	broad.mit.edu	37	5	38919038	38919038	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38919038C>G	uc003jln.1	+	11	1826	c.1459C>G	c.(1459-1461)CCA>GCA	p.P487A	OSMR_uc011cpj.1_5'UTR	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	487	Fibronectin type-III 2.|Extracellular (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					CCATTCCATTCCAGCACCAGC	0.438													19	135	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41382017	41382017	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41382017C>T	uc003jmm.1	-	2	825	c.723G>A	c.(721-723)TCG>TCA	p.S241S		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	241					intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						ATATAAAAAACGATCCCTTCT	0.502													19	112	---	---	---	---	PASS
FAM169A	26049	broad.mit.edu	37	5	74101044	74101044	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74101044C>G	uc003kdm.2	-	7	779	c.736G>C	c.(736-738)GGA>CGA	p.G246R	FAM169A_uc010izm.2_Missense_Mutation_p.G186R|FAM169A_uc003kdl.2_Missense_Mutation_p.G64R	NM_015566	NP_056381	Q9Y6X4	F169A_HUMAN	hypothetical protein LOC26049	246											0						TACCAGTGTCCAACACCTTCA	0.383													16	8	---	---	---	---	PASS
FTMT	94033	broad.mit.edu	37	5	121187749	121187749	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121187749C>T	uc003kss.2	+	1	100	c.91C>T	c.(91-93)CGT>TGT	p.R31C		NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial precursor	31					cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GCTCCCGCTGCGTTGGGCCCC	0.766													8	1	---	---	---	---	PASS
HARS	3035	broad.mit.edu	37	5	140056476	140056476	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140056476G>T	uc003lgv.2	-	10	1039	c.957C>A	c.(955-957)TCC>TCA	p.S319S	HARS_uc003lgu.2_Silent_p.S250S|HARS_uc011czm.1_Silent_p.S279S|HARS_uc003lgw.2_Silent_p.S299S|HARS_uc011czn.1_Silent_p.S259S|HARS_uc010jfu.2_Silent_p.S319S|HARS_uc011czo.1_Silent_p.S245S|HARS_uc011czp.1_Silent_p.S205S|HARS_uc011czq.1_Silent_p.S209S	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	319					histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)	TCAGGTCAAAGGAGATCTGTG	0.552													5	82	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140594237	140594237	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140594237T>A	uc003lja.1	+	1	729	c.542T>A	c.(541-543)GTC>GAC	p.V181D		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	181	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TATTTTCGGGTCCTCACCCGC	0.498													7	34	---	---	---	---	PASS
PCDHGB3	56102	broad.mit.edu	37	5	140750236	140750236	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140750236G>A	uc003ljw.1	+	1	275	c.275G>A	c.(274-276)CGA>CAA	p.R92Q	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc011dat.1_Missense_Mutation_p.R92Q	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	92	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTATAGACCGAGAGGAGATT	0.443													15	164	---	---	---	---	PASS
HDAC3	8841	broad.mit.edu	37	5	141005343	141005343	+	Intron	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141005343G>A	uc003llf.2	-						HDAC3_uc003lle.1_Intron	NM_003883	NP_003874	O15379	HDAC3_HUMAN	histone deacetylase 3						anti-apoptosis|cellular lipid metabolic process|negative regulation of cell cycle|negative regulation of JNK cascade|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|spindle assembly|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|spindle microtubule|transcriptional repressor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription corepressor activity|transcription factor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	TTGGGGAGGAGAGGAGAAAGT	0.493													5	19	---	---	---	---	PASS
GLRA1	2741	broad.mit.edu	37	5	151239385	151239385	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151239385A>T	uc003lut.2	-	4	724	c.437T>A	c.(436-438)CTA>CAA	p.L146Q	GLRA1_uc003lur.2_Missense_Mutation_p.L146Q|GLRA1_uc003lus.2_Missense_Mutation_p.L63Q	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor	146	Extracellular (Probable).				muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GGAGATCCTTAGCAATTTGTT	0.527													26	32	---	---	---	---	PASS
GEMIN5	25929	broad.mit.edu	37	5	154316660	154316660	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154316660G>T	uc003lvx.3	-	2	335	c.252C>A	c.(250-252)ACC>ACA	p.T84T	GEMIN5_uc011ddk.1_Silent_p.T84T	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	84	WD 1.				ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CGTCGGAGCTGGTGGCACAGA	0.473													5	70	---	---	---	---	PASS
SGCD	6444	broad.mit.edu	37	5	156186285	156186285	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156186285C>A	uc003lwd.3	+	8	1230	c.754C>A	c.(754-756)CCT>ACT	p.P252T	SGCD_uc003lwc.3_Missense_Mutation_p.P253T	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3	252	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATCCTACACGCCTACAGGAAC	0.493													44	24	---	---	---	---	PASS
TIMD4	91937	broad.mit.edu	37	5	156381726	156381726	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381726G>A	uc003lwh.2	-	2	157	c.100C>T	c.(100-102)CAC>TAC	p.H34Y	TIMD4_uc010jii.2_Missense_Mutation_p.H34Y	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain	34	Ig-like V-type.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTCACCCGGTGACCCAAAACC	0.512													11	4	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160097495	160097495	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160097495C>T	uc003lym.1	-	7	1497	c.650G>A	c.(649-651)TGT>TAT	p.C217Y	ATP10B_uc003lyp.2_Missense_Mutation_p.C217Y|ATP10B_uc011deg.1_Missense_Mutation_p.C261Y|ATP10B_uc003lyo.2_Missense_Mutation_p.C189Y	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	217	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTCACGACACATCTTTGCTT	0.463													37	54	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167671566	167671566	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167671566C>A	uc010jjd.2	+	26	5635	c.5635C>A	c.(5635-5637)CTG>ATG	p.L1879M	ODZ2_uc003lzr.3_Missense_Mutation_p.L1649M|ODZ2_uc003lzt.3_Missense_Mutation_p.L1252M|ODZ2_uc010jje.2_Missense_Mutation_p.L1143M	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		CAGCAGCGGGCTGGCAGCTGT	0.577													29	14	---	---	---	---	PASS
FOXI1	2299	broad.mit.edu	37	5	169535450	169535450	+	Silent	SNP	G	T	T	rs56128152	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169535450G>T	uc003mai.3	+	2	1017	c.972G>T	c.(970-972)CCG>CCT	p.P324P	FOXI1_uc003maj.3_Silent_p.P229P	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	324					epidermal cell fate specification|otic placode formation|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTTCTCCCCGCTCACCAACC	0.622									Pendred_syndrome				15	12	---	---	---	---	PASS
F13A1	2162	broad.mit.edu	37	6	6224962	6224962	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6224962G>T	uc003mwv.2	-	7	1053	c.930C>A	c.(928-930)GTC>GTA	p.V310V	F13A1_uc011dib.1_Silent_p.V247V	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	310					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GGCCATACCGGACTGGATTCT	0.443													49	82	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7231198	7231198	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7231198G>T	uc003mxc.2	+	10	3256	c.2866G>T	c.(2866-2868)GCC>TCC	p.A956S	RREB1_uc003mxb.2_Missense_Mutation_p.A956S|RREB1_uc010jnx.2_Missense_Mutation_p.A956S	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	956					multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TCCCAGCGAAGCCAAGAAGCC	0.612													8	9	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25488823	25488823	+	Intron	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25488823C>G	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AGTAAGTTTTCTTTTCTTTAT	0.438													7	81	---	---	---	---	PASS
HIST1H3B	8358	broad.mit.edu	37	6	26032069	26032069	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26032069C>T	uc003nfs.1	-	1	220	c.220G>A	c.(220-222)GAA>AAA	p.E74K		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	74					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2						TGGGCGATTTCTCGCACCAGG	0.607													24	48	---	---	---	---	PASS
ZNF323	64288	broad.mit.edu	37	6	28297448	28297448	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28297448C>T	uc003nla.2	-	2	413	c.13G>A	c.(13-15)GAG>AAG	p.E5K	ZNF323_uc003nld.2_Missense_Mutation_p.E5K|ZNF323_uc010jra.2_Missense_Mutation_p.E5K|ZNF323_uc003nlb.2_Intron|ZNF323_uc010jrb.2_Intron|ZNF323_uc003nlc.2_Missense_Mutation_p.E5K	NM_001135216	NP_001128688	Q96LW9	ZN323_HUMAN	zinc finger protein 323	5					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						TACTGTTCCTCTGTTGAAGCC	0.423													23	40	---	---	---	---	PASS
OR14J1	442191	broad.mit.edu	37	6	29274902	29274902	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29274902G>A	uc011dln.1	+	1	436	c.436G>A	c.(436-438)GTG>ATG	p.V146M		NM_030946	NP_112208	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 5, subfamily U member	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						AGTGATAGCTGTGTGGATTGC	0.483													34	45	---	---	---	---	PASS
ZFP57	346171	broad.mit.edu	37	6	29643153	29643153	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29643153C>T	uc011dlw.1	-						ZFP57_uc003nnl.3_Intron	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog						DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)|skin(2)	5						CCCTGCTTGGCAATTCTTACC	0.493													30	52	---	---	---	---	PASS
STK19	8859	broad.mit.edu	37	6	31948290	31948290	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31948290C>T	uc003nyv.2	+	6	1006	c.878C>T	c.(877-879)CCT>CTT	p.P293L	STK19_uc003nyt.2_Missense_Mutation_p.P246L|STK19_uc011dox.1_Missense_Mutation_p.P250L|STK19_uc003nyw.2_Missense_Mutation_p.P289L|STK19_uc010jtn.1_RNA|C4A_uc011doy.1_5'Flank|C4A_uc011doz.1_5'Flank|C4A_uc011dpa.1_5'Flank	NM_032454	NP_115830	P49842	STK19_HUMAN	serine/threonine kinase 19 isoform 2	293						nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4						CTAGCTGTGCCTGGAGCTGGG	0.587													9	12	---	---	---	---	PASS
MEP1A	4224	broad.mit.edu	37	6	46787396	46787396	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46787396G>A	uc010jzh.1	+	7	553	c.511G>A	c.(511-513)GAC>AAC	p.D171N	MEP1A_uc011dwg.1_5'UTR|MEP1A_uc011dwh.1_Missense_Mutation_p.D199N|MEP1A_uc011dwi.1_Missense_Mutation_p.D71N	NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A alpha precursor	171	Extracellular (Potential).|Metalloprotease.				digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3			Lung(136;0.192)			GTCAAGGACGGACCGGGATGA	0.478													6	135	---	---	---	---	PASS
GPR116	221395	broad.mit.edu	37	6	46826157	46826157	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46826157G>A	uc003oyo.3	-	17	3772	c.3483C>T	c.(3481-3483)GTC>GTT	p.V1161V	GPR116_uc011dwj.1_Silent_p.V716V|GPR116_uc011dwk.1_Silent_p.V590V|GPR116_uc003oyp.3_Silent_p.V1019V|GPR116_uc003oyq.3_Silent_p.V1161V|GPR116_uc010jzi.1_Silent_p.V833V	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	1161	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			TGAGCCAACAGACATTCTTCC	0.547													15	19	---	---	---	---	PASS
TFAP2D	83741	broad.mit.edu	37	6	50740417	50740417	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50740417C>A	uc003paf.2	+	8	1711	c.1199C>A	c.(1198-1200)ACA>AAA	p.T400K	TFAP2D_uc011dwt.1_RNA	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	400	H-S-H (helix-span-helix), dimerization.						DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)					ACTTTCCAAACAGTTCTCAGT	0.458													16	33	---	---	---	---	PASS
GCLC	2729	broad.mit.edu	37	6	53372322	53372322	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53372322T>C	uc003pbw.1	-	9	1428	c.1040A>G	c.(1039-1041)GAC>GGC	p.D347G	GCLC_uc003pbv.1_Missense_Mutation_p.D71G	NM_001498	NP_001489	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	347					anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)	TATCGTCAAGTCGATGTCATT	0.383													14	45	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69785882	69785882	+	Intron	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69785882T>C	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)				CTGCTTTTTTTTTAGGGTACT	0.328													12	20	---	---	---	---	PASS
RIMS1	22999	broad.mit.edu	37	6	72974741	72974741	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72974741C>G	uc003pga.2	+	20	3257	c.3180C>G	c.(3178-3180)CAC>CAG	p.H1060Q	RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Missense_Mutation_p.H277Q|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_Intron|RIMS1_uc010kas.1_Intron	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1060					calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCAGTTCTCACTGGAATATTT	0.383													3	7	---	---	---	---	PASS
KHDC1	80759	broad.mit.edu	37	6	73951416	73951416	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73951416G>C	uc003pgo.2	-	5	1051	c.550C>G	c.(550-552)CTG>GTG	p.L184V	KHDC1_uc011dyl.1_Intron|KHDC1_uc003pgn.3_Missense_Mutation_p.L111V	NM_030568	NP_085045	Q4VXA5	KHDC1_HUMAN	KH homology domain containing 1	184						integral to membrane	RNA binding			skin(1)	1						TCGTTGGTCAGAGGCTGGCTT	0.567													6	65	---	---	---	---	PASS
CNR1	1268	broad.mit.edu	37	6	88854319	88854319	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88854319C>T	uc011dzq.1	-	2	4238	c.675G>A	c.(673-675)AAG>AAA	p.K225K	CNR1_uc010kbz.2_Silent_p.K225K|CNR1_uc011dzr.1_Silent_p.K225K|CNR1_uc011dzs.1_Silent_p.K225K|CNR1_uc003pmq.3_Silent_p.K225K|CNR1_uc011dzt.1_Silent_p.K225K|CNR1_uc010kca.2_Silent_p.K192K	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	225	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding			skin(2)	2		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TGACAATCCTCTTATAGGCCA	0.597													10	17	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	101103640	101103640	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101103640T>C	uc003pqk.2	-	17	3087	c.2758A>G	c.(2758-2760)ACT>GCT	p.T920A	ASCC3_uc011eai.1_Missense_Mutation_p.T822A	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	920					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)		TAAAGATAAGTGTAACTTATC	0.333													5	16	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112463333	112463333	+	Silent	SNP	G	A	A	rs35772073	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112463333G>A	uc003pvu.2	-	20	2964	c.2655C>T	c.(2653-2655)CTC>CTT	p.L885L	LAMA4_uc003pvv.2_Silent_p.L878L|LAMA4_uc003pvt.2_Silent_p.L878L	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	885	Laminin G-like 1.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TTTTGCTTCCGAGGTACAGGA	0.453													23	48	---	---	---	---	PASS
GJA1	2697	broad.mit.edu	37	6	121767995	121767995	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121767995T>A	uc003pyr.2	+	2	252	c.2T>A	c.(1-3)ATG>AAG	p.M1K	GJA1_uc011ebo.1_5'UTR|GJA1_uc011ebp.1_5'UTR	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	1					cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	CCAGGCAACATGGGTGACTGG	0.443													48	68	---	---	---	---	PASS
C6orf58	352999	broad.mit.edu	37	6	127901587	127901587	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127901587T>C	uc003qbh.2	+	3	578	c.566T>C	c.(565-567)TTT>TCT	p.F189S		NM_001010905	NP_001010905	Q6P5S2	CF058_HUMAN	hypothetical protein LOC352999 precursor	189						extracellular region					0				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		TGGAACACCTTTTACCAGGTT	0.378													7	17	---	---	---	---	PASS
L3MBTL3	84456	broad.mit.edu	37	6	130363886	130363886	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130363886T>A	uc003qbt.2	+	3	212	c.42T>A	c.(40-42)GAT>GAA	p.D14E	L3MBTL3_uc003qbu.2_Missense_Mutation_p.D14E	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a	14					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		AAGAGTTTGATGTGTTCAGTG	0.388													11	24	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144768768	144768768	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144768768C>T	uc003qkt.2	+	15	1845	c.1753C>T	c.(1753-1755)CAA>TAA	p.Q585*	UTRN_uc010khq.1_Nonsense_Mutation_p.Q585*	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	585	Interaction with SYNM.|Spectrin 4.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AATGAAGCGTCAAACATTGGA	0.388													23	59	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152642923	152642923	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152642923A>T	uc010kiw.2	-	83	16618	c.16016T>A	c.(16015-16017)GTT>GAT	p.V5339D	SYNE1_uc003qot.3_Missense_Mutation_p.V5268D|SYNE1_uc003qou.3_Missense_Mutation_p.V5339D|SYNE1_uc010kiz.2_Missense_Mutation_p.V1094D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5339	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CGTTTCCTGAACCCAACATTT	0.398										HNSCC(10;0.0054)			12	26	---	---	---	---	PASS
IGF2R	3482	broad.mit.edu	37	6	160491005	160491005	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160491005T>A	uc003qta.2	+	31	4506	c.4358T>A	c.(4357-4359)CTG>CAG	p.L1453Q		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	1453	10.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		ATAATTGTCCTGAAATACGTT	0.557													11	9	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165752791	165752791	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165752791C>T	uc003qun.2	-	21	2365	c.2124G>A	c.(2122-2124)AAG>AAA	p.K708K	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Silent_p.K638K|PDE10A_uc003quo.2_Silent_p.K718K	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	708					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)	CTTCATCCTTCTTGTCTCTGT	0.353													7	36	---	---	---	---	PASS
PAPOLB	56903	broad.mit.edu	37	7	4900374	4900374	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4900374C>A	uc003snk.2	-	1	1252	c.1068G>T	c.(1066-1068)AAG>AAT	p.K356N	RADIL_uc003sng.1_Intron|RADIL_uc011jwd.1_Intron|RADIL_uc003snj.1_Intron	NM_020144	NP_064529	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	355					mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		ACCACTCTGCCTTACTTAGCA	0.403													35	38	---	---	---	---	PASS
ISPD	729920	broad.mit.edu	37	7	16341084	16341084	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16341084T>C	uc010ktx.2	-	5	797	c.797A>G	c.(796-798)TAC>TGC	p.Y266C	ISPD_uc010kty.2_Missense_Mutation_p.Y216C	NM_001101426	NP_001094896	A4D126	ISPD_HUMAN	notch1-induced protein isoform a	266					isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1						ATCTCGTTTGTAGGTCACCTA	0.383										Multiple Myeloma(15;0.18)			16	11	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21892087	21892087	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21892087G>T	uc003svc.2	+	68	10951	c.10920G>T	c.(10918-10920)TTG>TTT	p.L3640F		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3640	AAA 5 (By similarity).				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						TTTATTAGTTGGTATTGACAA	0.294									Kartagener_syndrome				4	36	---	---	---	---	PASS
TXNDC3	51314	broad.mit.edu	37	7	37916617	37916617	+	Intron	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37916617A>T	uc003tfn.2	+							NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3						cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						AAGGTAGGGAATCAAGCATAA	0.274									Kartagener_syndrome				3	15	---	---	---	---	PASS
DBNL	28988	broad.mit.edu	37	7	44100498	44100498	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44100498G>A	uc003tjp.3	+	13	1374	c.1276G>A	c.(1276-1278)GTG>ATG	p.V426M	DBNL_uc003tjo.3_Missense_Mutation_p.V427M|DBNL_uc003tjr.3_Missense_Mutation_p.V299M|DBNL_uc003tjq.3_Missense_Mutation_p.V435M|DBNL_uc011kbm.1_Missense_Mutation_p.V402M|DBNL_uc011kbn.1_Missense_Mutation_p.V323M|DBNL_uc011kbo.1_Missense_Mutation_p.V327M|DBNL_uc011kbp.1_Missense_Mutation_p.V378M|DBNL_uc011kbq.1_Missense_Mutation_p.V351M|DBNL_uc011kbr.1_Missense_Mutation_p.V375M|DBNL_uc011kbs.1_Missense_Mutation_p.V331M	NM_001014436	NP_001014436	Q9UJU6	DBNL_HUMAN	drebrin-like isoform b	426	SH3.				activation of JUN kinase activity|cellular component disassembly involved in apoptosis|endocytosis|Rac protein signal transduction	cell cortex|cytoskeleton|cytosol|lamellipodium	actin binding|enzyme activator activity|identical protein binding			skin(1)	1						TGCCAACTACGTGGAGCTCAT	0.577													11	22	---	---	---	---	PASS
AEBP1	165	broad.mit.edu	37	7	44153224	44153224	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44153224C>A	uc003tkb.2	+	21	3146	c.2841C>A	c.(2839-2841)AAC>AAA	p.N947K	AEBP1_uc003tkc.3_Missense_Mutation_p.N522K|AEBP1_uc003tkd.2_Missense_Mutation_p.N197K	NM_001129	NP_001120	Q8IUX7	AEBP1_HUMAN	adipocyte enhancer binding protein 1 precursor	947	Interaction with PTEN (By similarity).|Required for transcriptional repression (By similarity).				cell adhesion|muscle organ development|proteolysis|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GAATCTTGAACCCGGGTGAGT	0.512													4	38	---	---	---	---	PASS
ADCY1	107	broad.mit.edu	37	7	45697428	45697428	+	Silent	SNP	C	T	T	rs142228376	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45697428C>T	uc003tne.3	+	6	1269	c.1251C>T	c.(1249-1251)GAC>GAT	p.D417D	ADCY1_uc003tnd.2_Silent_p.D192D	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	417	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGCAGTACGACGTGTGGTCCA	0.627													9	13	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57188613	57188613	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57188613G>T	uc010kzo.2	-	5	780	c.509C>A	c.(508-510)TCA>TAA	p.S170*		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	170					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			ATTGGAATTTGAAAATTTACC	0.299													11	20	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82579540	82579540	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82579540C>T	uc003uhx.2	-	6	10653	c.10364G>A	c.(10363-10365)CGG>CAG	p.R3455Q	PCLO_uc003uhv.2_Missense_Mutation_p.R3455Q|PCLO_uc010lec.2_Missense_Mutation_p.R420Q	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3386					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CACATAGCTCCGATCTGTGGC	0.428													28	38	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87053341	87053341	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87053341G>A	uc003uiv.1	-	17	2168	c.2092C>T	c.(2092-2094)CTG>TTG	p.L698L	ABCB4_uc003uiw.1_Silent_p.L698L|ABCB4_uc003uix.1_Silent_p.L698L	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	698	Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					AGGACCTTCAGAAAGGACACT	0.398													43	64	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92733928	92733928	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92733928T>G	uc003umf.2	-	3	1739	c.1483A>C	c.(1483-1485)AAT>CAT	p.N495H	SAMD9_uc003umg.2_Missense_Mutation_p.N495H	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	495						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AACCTGCCATTGCAGAAAATC	0.383													18	38	---	---	---	---	PASS
PON1	5444	broad.mit.edu	37	7	95025658	95025658	+	Missense_Mutation	SNP	C	G	G	rs146627952	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95025658C>G	uc011kih.1	-	1	30	c.5G>C	c.(4-6)GGG>GCG	p.G2A	PON3_uc003unt.2_Missense_Mutation_p.G2A|PON3_uc011kii.1_Missense_Mutation_p.G2A			P27169	PON1_HUMAN	SubName: Full=cDNA FLJ57644, highly similar to Serum paraoxonase/arylesterase 1 (EC 3.1.1.2);	2					aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)	CACGAGCTTCCCCATGGTCTC	0.701													16	34	---	---	---	---	PASS
OCM2	4951	broad.mit.edu	37	7	97619402	97619402	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97619402G>T	uc003upc.2	-	1	15	c.15C>A	c.(13-15)GAC>GAA	p.D5E		NM_006188	NP_006179	P0CE71	OCM2_HUMAN	oncomodulin-like	5							calcium ion binding				0						CACTGAGCACGTCCGTGATGC	0.557													14	44	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100346014	100346014	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100346014G>T	uc003uwj.2	+	11	1335	c.1170G>T	c.(1168-1170)GGG>GGT	p.G390G	ZAN_uc003uwk.2_Silent_p.G390G|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	390	MAM 3.|Extracellular (Potential).				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)			AGACTTCCGGGGATGGTGGAC	0.542													28	25	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100683043	100683043	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100683043C>A	uc003uxp.1	+	3	8399	c.8346C>A	c.(8344-8346)GTC>GTA	p.V2782V	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2782	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|45.					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)					GCATACCTGTCACCACTTCTA	0.473													65	197	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122047709	122047709	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122047709C>A	uc010lkp.2	-	19	2794	c.2631G>T	c.(2629-2631)GAG>GAT	p.E877D	CADPS2_uc011knx.1_Missense_Mutation_p.E252D|CADPS2_uc003vkg.3_Missense_Mutation_p.E571D|CADPS2_uc010lkq.2_Missense_Mutation_p.E871D	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	877	Interaction with DRD2.				exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						CCCAAAATTTCTCTGCATGTT	0.383													15	25	---	---	---	---	PASS
TAS2R16	50833	broad.mit.edu	37	7	122635373	122635373	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122635373T>C	uc003vkl.1	-	1	382	c.316A>G	c.(316-318)AAG>GAG	p.K106E		NM_016945	NP_058641	Q9NYV7	T2R16_HUMAN	taste receptor T2R16	106	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	endoplasmic reticulum|external side of plasma membrane|trans-Golgi network	bitter taste receptor activity|protein binding			ovary(1)|skin(1)	2						GAAGAGACCTTGATGCAGTAG	0.378													18	39	---	---	---	---	PASS
METTL2B	55798	broad.mit.edu	37	7	128141953	128141953	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128141953C>G	uc003vnf.2	+	9	1157	c.1120C>G	c.(1120-1122)CTG>GTG	p.L374V	METTL2B_uc003vng.2_Missense_Mutation_p.L309V|METTL2B_uc011kop.1_Missense_Mutation_p.L238V	NM_018396	NP_060866	Q6P1Q9	MTL2B_HUMAN	methyltransferase like 2B	374							methyltransferase activity			skin(1)	1						CAAGCCCCTTCTGTCCAGCAC	0.458													59	108	---	---	---	---	PASS
FAM71F1	84691	broad.mit.edu	37	7	128359064	128359064	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128359064C>G	uc003vno.1	+	3	667	c.614C>G	c.(613-615)ACC>AGC	p.T205S	FAM71F1_uc010llo.1_Missense_Mutation_p.T106S|FAM71F1_uc011koq.1_Missense_Mutation_p.T97S|FAM71F1_uc003vnm.1_RNA|FAM71F1_uc003vnn.1_Missense_Mutation_p.T106S|FAM71F1_uc010llp.1_RNA|FAM71F1_uc003vnp.1_Missense_Mutation_p.T205S	NM_032599	NP_115988	Q96KD3	F71F1_HUMAN	testes development-related NYD-SP18	205										skin(1)	1						TCCATCACCACCAAAGACCCT	0.507													34	74	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131864554	131864554	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131864554C>A	uc003vra.3	-	20	3995	c.3766G>T	c.(3766-3768)GTG>TTG	p.V1256L		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1256	Helical; (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GCAATGAGCACGGCCACGATG	0.622													6	11	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	132069983	132069983	+	Intron	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132069983A>C	uc003vra.3	-						PLXNA4_uc003vrc.2_Silent_p.T481T	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						GGAGTTCCAGAGTCACTGTTG	0.478													4	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142124548	142124548	+	Intron	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142124548C>A	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		CCGCACAGCACAGGAGCCCGA	0.607													13	71	---	---	---	---	PASS
PIP	5304	broad.mit.edu	37	7	142836604	142836604	+	Intron	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142836604T>G	uc003wcf.1	+							NM_002652	NP_002643	P12273	PIP_HUMAN	prolactin-induced protein precursor							extracellular region	actin binding			ovary(1)	1	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		GTCCCTGTCTTTTTCAGGAAC	0.498													7	111	---	---	---	---	PASS
ZNF746	155061	broad.mit.edu	37	7	149191588	149191588	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149191588G>A	uc003wfw.2	-	2	302	c.31C>T	c.(31-33)CCG>TCG	p.P11S	ZNF746_uc010lpi.2_Missense_Mutation_p.P11S	NM_152557	NP_689770	Q6NUN9	ZN746_HUMAN	zinc finger protein 746 isoform 2	11					negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|breast(1)	3	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ATCGTCCACGGAGAAATCTTT	0.547													21	53	---	---	---	---	PASS
GIMAP8	155038	broad.mit.edu	37	7	150171512	150171512	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150171512G>C	uc003whj.2	+	4	1425	c.1095G>C	c.(1093-1095)AGG>AGC	p.R365S		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	365						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TTCTTACCAGGAAAGAAGATT	0.383													46	85	---	---	---	---	PASS
ASB10	136371	broad.mit.edu	37	7	150878316	150878316	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150878316G>T	uc003wjm.1	-	3	1075	c.949C>A	c.(949-951)CGC>AGC	p.R317S	ASB10_uc003wjl.1_Missense_Mutation_p.R317S|ASB10_uc003wjn.1_Missense_Mutation_p.R257S	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	272	ANK 5.				intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCAGGCAGCGGGCGGTGGTG	0.677													3	14	---	---	---	---	PASS
GALNTL5	168391	broad.mit.edu	37	7	151699823	151699823	+	Missense_Mutation	SNP	G	T	T	rs149988530		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151699823G>T	uc003wkp.2	+	6	906	c.683G>T	c.(682-684)AGC>ATC	p.S228I	GALNTL5_uc003wkq.2_5'UTR|GALNTL5_uc003wkr.2_RNA|GALNTL5_uc003wks.2_RNA|GALNTL5_uc010lqf.2_Missense_Mutation_p.S117I	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	228	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		TTCCTGGACAGCCACTGTGAG	0.502													15	19	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157926395	157926395	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157926395C>T	uc003wno.2	-	9	1651	c.1530G>A	c.(1528-1530)GCG>GCA	p.A510A	PTPRN2_uc003wnp.2_Silent_p.A493A|PTPRN2_uc003wnq.2_Silent_p.A510A|PTPRN2_uc003wnr.2_Silent_p.A472A|PTPRN2_uc011kwa.1_Silent_p.A533A	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	510	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TGTAGCCCCGCGCCTCTTCCT	0.662													23	42	---	---	---	---	PASS
EPB49	2039	broad.mit.edu	37	8	21937755	21937755	+	Silent	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21937755G>C	uc011kyt.1	+	11	1129	c.900G>C	c.(898-900)CGG>CGC	p.R300R	EPB49_uc010ltl.2_Silent_p.R300R|EPB49_uc011kys.1_Silent_p.R260R|EPB49_uc010ltn.2_Silent_p.R275R|EPB49_uc011kyu.1_Silent_p.R300R|EPB49_uc011kyv.1_Silent_p.R300R|EPB49_uc010ltq.2_Silent_p.R300R	NM_001114136	NP_001107608	Q08495	DEMA_HUMAN	erythrocyte membrane protein band 4.9 isoform 1	300	Interaction with RASGRF2.				actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)		CCCTGAGCCGGGTAAGGTCTC	0.587													39	47	---	---	---	---	PASS
NRG1	3084	broad.mit.edu	37	8	32463185	32463185	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32463185C>A	uc003xiv.2	+	3	901	c.384C>A	c.(382-384)ACC>ACA	p.T128T	NRG1_uc003xip.2_Silent_p.T343T|NRG1_uc003xir.2_Silent_p.T128T|NRG1_uc010lvl.2_Silent_p.T128T|NRG1_uc010lvm.2_Silent_p.T128T|NRG1_uc010lvn.2_Silent_p.T128T|NRG1_uc003xis.2_Silent_p.T128T|NRG1_uc011lbf.1_Silent_p.T128T|NRG1_uc010lvo.2_Silent_p.T128T|NRG1_uc003xiu.2_Silent_p.T128T|NRG1_uc003xiw.2_Silent_p.T128T|NRG1_uc003xit.2_Silent_p.T128T|NRG1_uc010lvr.2_5'UTR|NRG1_uc010lvs.2_5'UTR|NRG1_uc010lvp.2_Silent_p.T94T|NRG1_uc010lvq.2_Silent_p.T94T|NRG1_uc003xix.2_Silent_p.T18T	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	128	Extracellular (Potential).|Ig-like C2-type.				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CCAATATCACCATCGTGGAAT	0.403													5	64	---	---	---	---	PASS
C8orf22	492307	broad.mit.edu	37	8	49985441	49985441	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49985441C>T	uc003xqq.3	+	2	235	c.52C>T	c.(52-54)CGA>TGA	p.R18*		NM_001007176	NP_001007177	Q8WWR9	PDPFL_HUMAN	hypothetical protein LOC492307	18											0		all_cancers(86;0.0452)|all_epithelial(80;0.000863)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				TCAGTATTATCGAAGTAAGTT	0.413													69	69	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52773466	52773466	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52773466C>G	uc003xqx.3	-	2	587	c.246G>C	c.(244-246)TTG>TTC	p.L82F	PCMTD1_uc003xqw.3_Missense_Mutation_p.L82F|PCMTD1_uc011ldn.1_Intron|PCMTD1_uc010lya.2_Intron|PCMTD1_uc011ldo.1_Missense_Mutation_p.L82F	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	82						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TAAGAAAAGACAATCCTGGTT	0.328													25	23	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69699678	69699678	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69699678G>C	uc010lyz.2	+	12	1247	c.1198G>C	c.(1198-1200)GAT>CAT	p.D400H	C8orf34_uc003xyb.2_Missense_Mutation_p.D375H	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	400					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)			TCTTTTGCAGGATGAATCCTT	0.348													8	22	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77776369	77776369	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77776369G>T	uc003yav.2	+	11	10671	c.10284G>T	c.(10282-10284)GAG>GAT	p.E3428D		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3424						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGCACAAAGAGAAAACAATCA	0.448										HNSCC(33;0.089)			53	55	---	---	---	---	PASS
ZFAND1	79752	broad.mit.edu	37	8	82630427	82630427	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82630427C>T	uc003ycj.1	-	2	102	c.88G>A	c.(88-90)GGA>AGA	p.G30R	ZFAND1_uc010lzx.1_Missense_Mutation_p.G30R|ZFAND1_uc003yck.1_5'UTR	NM_024699	NP_078975	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1	30	AN1-type 1.						zinc ion binding			ovary(1)	1						CAAAATATTCCTGAACAATCA	0.264													10	36	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885761	88885761	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885761C>A	uc003ydz.2	-	1	536	c.439G>T	c.(439-441)GTG>TTG	p.V147L		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	147										ovary(1)	1						GCAAGTCCCACGAAGCACAGC	0.542													43	28	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885967	88885967	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885967A>G	uc003ydz.2	-	1	330	c.233T>C	c.(232-234)CTG>CCG	p.L78P		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	78										ovary(1)	1						GGTATTCGCCAGTATGCGGTT	0.542													52	54	---	---	---	---	PASS
EIF3E	3646	broad.mit.edu	37	8	109226865	109226865	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109226865G>A	uc003ymu.2	-	10	1060	c.1032C>T	c.(1030-1032)TTC>TTT	p.F344F	EIF3E_uc003ymt.2_Silent_p.F295F|EIF3E_uc003ymv.2_Silent_p.F251F|EIF3E_uc010mci.1_Intron	NM_001568	NP_001559	P60228	EIF3E_HUMAN	eukaryotic translation initiation factor 3,	344	PCI.				negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			GGATGCGACAGAAAGTCTCAA	0.353													31	36	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113240998	113240998	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113240998G>A	uc003ynu.2	-	70	11110	c.10951C>T	c.(10951-10953)CTT>TTT	p.L3651F	CSMD3_uc003yns.2_Missense_Mutation_p.L2853F|CSMD3_uc003ynt.2_Missense_Mutation_p.L3611F|CSMD3_uc011lhx.1_Missense_Mutation_p.L3482F	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3651	Helical; (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TGTTTATAAAGATAAAATCCA	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			21	29	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113240999	113240999	+	Nonsense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113240999A>T	uc003ynu.2	-	70	11109	c.10950T>A	c.(10948-10950)TAT>TAA	p.Y3650*	CSMD3_uc003yns.2_Nonsense_Mutation_p.Y2852*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.Y3610*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.Y3481*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3650	Helical; (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GTTTATAAAGATAAAATCCAA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			23	28	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113564935	113564935	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113564935G>A	uc003ynu.2	-	26	4408	c.4249C>T	c.(4249-4251)CGT>TGT	p.R1417C	CSMD3_uc003yns.2_Missense_Mutation_p.R689C|CSMD3_uc003ynt.2_Missense_Mutation_p.R1377C|CSMD3_uc011lhx.1_Missense_Mutation_p.R1313C	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1417	Extracellular (Potential).|CUB 8.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CCTTTAAAACGACCTCCACAT	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			11	45	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113657329	113657329	+	Intron	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113657329G>C	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ATTTCATGAGGCAAATTACCT	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			10	16	---	---	---	---	PASS
ZHX2	22882	broad.mit.edu	37	8	123965654	123965654	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123965654A>G	uc003ypk.1	+	3	2471	c.1904A>G	c.(1903-1905)AAA>AGA	p.K635R		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	635	Homeobox 4.					cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GCAATTGCAAAAAGTCAAGAA	0.567													22	78	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131812772	131812772	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131812772G>T	uc003ytd.3	-	15	3216	c.2960C>A	c.(2959-2961)TCC>TAC	p.S987Y	ADCY8_uc010mds.2_Missense_Mutation_p.S856Y	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	987	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCCTGGGATGGAGGCAAACAT	0.493										HNSCC(32;0.087)			61	58	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139160773	139160773	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139160773A>T	uc003yuy.2	-	14	3609	c.3438T>A	c.(3436-3438)CAT>CAA	p.H1146Q	FAM135B_uc003yux.2_Missense_Mutation_p.H1047Q|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.H708Q|FAM135B_uc003yvb.2_Missense_Mutation_p.W674R	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1146										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CATCCAGGCCATGGACACAGA	0.348										HNSCC(54;0.14)			26	24	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139691922	139691922	+	Intron	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139691922G>A	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)			CAAGCAGCCTGAAAGTAGAAA	0.264										HNSCC(7;0.00092)			44	39	---	---	---	---	PASS
BAI1	575	broad.mit.edu	37	8	143624780	143624780	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143624780A>G	uc003ywm.2	+	28	4613	c.4430A>G	c.(4429-4431)TAT>TGT	p.Y1477C		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1477	Cytoplasmic (Potential).|Necessary for interaction with MAGI1.				axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AAGTCGCGGTATGCAGAACTG	0.632													13	19	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5770270	5770270	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5770270C>G	uc003zji.2	+	22	3464	c.3371C>G	c.(3370-3372)TCT>TGT	p.S1124C	KIAA1432_uc003zjl.3_Missense_Mutation_p.S1087C|ERMP1_uc011lme.1_Intron	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	1203						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		TCACCTTTATCTAATAAAGGT	0.393													9	65	---	---	---	---	PASS
TYRP1	7306	broad.mit.edu	37	9	12695754	12695754	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12695754G>T	uc003zkv.3	+	3	803	c.625G>T	c.(625-627)GGT>TGT	p.G209C		NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor	209	Lumenal, melanosome (Potential).				melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		GGAAAGCTTTGGTGAAGTGGA	0.433									Oculocutaneous_Albinism				4	47	---	---	---	---	PASS
BNC2	54796	broad.mit.edu	37	9	16436420	16436420	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16436420G>T	uc003zml.2	-	6	1912	c.1772C>A	c.(1771-1773)ACC>AAC	p.T591N	BNC2_uc011lmw.1_Missense_Mutation_p.T496N|BNC2_uc003zmm.2_Missense_Mutation_p.T549N|BNC2_uc003zmq.1_Missense_Mutation_p.T605N|BNC2_uc003zmr.1_Missense_Mutation_p.T628N|BNC2_uc003zmp.1_Missense_Mutation_p.T619N|BNC2_uc010mij.1_Missense_Mutation_p.T513N|BNC2_uc011lmv.1_Missense_Mutation_p.T417N|BNC2_uc003zmo.1_Missense_Mutation_p.T513N|BNC2_uc003zmj.2_Missense_Mutation_p.T356N|BNC2_uc003zmk.2_RNA|BNC2_uc003zmi.2_Missense_Mutation_p.T356N|BNC2_uc003zmn.1_Missense_Mutation_p.T356N	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	591	Pro-rich.				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)		GATGGGACTGGTTGGGAGGGA	0.527													44	25	---	---	---	---	PASS
KLHL9	55958	broad.mit.edu	37	9	21333994	21333994	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21333994C>T	uc003zoy.2	-	1	1436	c.865G>A	c.(865-867)GAT>AAT	p.D289N	KLHL9_uc003zow.2_Intron|KLHL9_uc003zox.2_RNA	NM_018847	NP_061335	Q9P2J3	KLHL9_HUMAN	kelch-like 9	289					cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|midbody				ovary(3)|skin(1)	4				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		GCAGTTCTATCTGACTGCATC	0.423													7	56	---	---	---	---	PASS
UBAP2	55833	broad.mit.edu	37	9	33923422	33923422	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33923422G>T	uc003ztq.1	-	25	2964	c.2851C>A	c.(2851-2853)CCC>ACC	p.P951T	UBAP2_uc011loc.1_Missense_Mutation_p.P860T|UBAP2_uc011lod.1_Missense_Mutation_p.P684T|UBAP2_uc011loe.1_Missense_Mutation_p.P706T|UBAP2_uc011lof.1_Missense_Mutation_p.P876T|UBAP2_uc003ztn.1_Missense_Mutation_p.P190T|UBAP2_uc003zto.1_Missense_Mutation_p.P190T|UBAP2_uc003ztp.1_Missense_Mutation_p.P190T	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	951										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		TGCTGGAAGGGAGGTGTGGGA	0.587													7	209	---	---	---	---	PASS
CREB3	10488	broad.mit.edu	37	9	35736623	35736623	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35736623G>A	uc003zxv.2	+	9	1469	c.1016G>A	c.(1015-1017)CGA>CAA	p.R339Q	CREB3_uc010mla.2_Missense_Mutation_p.R258Q	NM_006368	NP_006359	O43889	CREB3_HUMAN	cAMP responsive element binding protein 3	363	Lumenal (Potential).|Pro-rich.				chemotaxis|induction of positive chemotaxis|interspecies interaction between organisms|negative regulation of cell cycle|positive regulation of calcium ion transport|positive regulation of cell migration|positive regulation of transcription, DNA-dependent|reactivation of latent virus|regulation of cell proliferation	cytosol|endoplasmic reticulum|endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|integral to membrane|nucleus|nucleus	cAMP response element binding protein binding|CCR1 chemokine receptor binding|DNA binding|protein dimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity				0	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)	GBM - Glioblastoma multiforme(74;0.0285)		CCTCTCTGCCGAGGTCCCATC	0.582											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	126	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	119249690	119249690	+	Missense_Mutation	SNP	C	A	A	rs16933591	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119249690C>A	uc004bjs.1	-	20	3546	c.3445G>T	c.(3445-3447)GTC>TTC	p.V1149F	ASTN2_uc004bjr.1_Missense_Mutation_p.V1145F|ASTN2_uc004bjt.1_Missense_Mutation_p.V1098F|ASTN2_uc004bjp.1_Missense_Mutation_p.V242F|ASTN2_uc004bjq.1_Missense_Mutation_p.V201F|ASTN2_uc011lxr.1_Missense_Mutation_p.V201F|ASTN2_uc011lxs.1_Missense_Mutation_p.V201F|ASTN2_uc011lxt.1_Missense_Mutation_p.V201F|ASTN2_uc004bjo.1_5'UTR	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	1149	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						TAGATACTGACTTCAGGGACC	0.507													40	58	---	---	---	---	PASS
ZNF79	7633	broad.mit.edu	37	9	130197393	130197393	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130197393A>G	uc004bqw.3	+	3	544	c.130A>G	c.(130-132)ACG>GCG	p.T44A	ZNF79_uc011maf.1_Missense_Mutation_p.T20A|ZNF79_uc011mag.1_Missense_Mutation_p.T20A	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79	44	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						CAGCAGTGTGACGGTAGCTTT	0.512													39	18	---	---	---	---	PASS
MAN1B1	11253	broad.mit.edu	37	9	140002866	140002866	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140002866C>T	uc004cld.2	+	13	1958	c.1923C>T	c.(1921-1923)ATC>ATT	p.I641I	MAN1B1_uc011mep.1_3'UTR|MAN1B1_uc010ncc.2_RNA|MAN1B1_uc004clf.1_Silent_p.I314I|MAN1B1_uc004clg.1_RNA	NM_016219	NP_057303	Q9UKM7	MA1B1_HUMAN	alpha 1,2-mannosidase	641	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		ATTCTTCCATCAACAATGTCC	0.602													8	79	---	---	---	---	PASS
CACNA1B	774	broad.mit.edu	37	9	140773552	140773552	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140773552G>A	uc004cog.2	+	2	476	c.331G>A	c.(331-333)GTG>ATG	p.V111M	uc004cof.1_Intron	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	111	Helical; Name=S1 of repeat I; (Potential).|I.				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	CAACTGCATCGTGCTGGCCCT	0.647													5	39	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	12077311	12077311	+	Nonsense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12077311T>A	uc001ila.2	-	1	586	c.112A>T	c.(112-114)AAA>TAA	p.K38*	UPF2_uc001ilb.2_Nonsense_Mutation_p.K38*|UPF2_uc001ilc.2_Nonsense_Mutation_p.K38*|UPF2_uc009xiz.1_Nonsense_Mutation_p.K38*	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	38	Glu/Lys-rich.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				ATATCGTCTTTTGGCCTCTCC	0.453													49	52	---	---	---	---	PASS
ITGA8	8516	broad.mit.edu	37	10	15600177	15600177	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15600177G>A	uc001ioc.1	-	26	2662	c.2662C>T	c.(2662-2664)CCT>TCT	p.P888S	ITGA8_uc010qcb.1_Missense_Mutation_p.P873S	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	888	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						CTGAGCTCAGGGGTGTCCTCT	0.458													14	17	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16873262	16873262	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16873262G>A	uc001ioo.2	-	65	10569	c.10517C>T	c.(10516-10518)TCA>TTA	p.S3506L		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3506	CUB 26.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGAGGGTGATGAAGTCCAGAT	0.368													5	48	---	---	---	---	PASS
GPR158	57512	broad.mit.edu	37	10	25886869	25886869	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25886869G>A	uc001isj.2	+	11	2374	c.2314G>A	c.(2314-2316)GAG>AAG	p.E772K	GPR158_uc001isk.2_Missense_Mutation_p.E147K	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	772	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						GTGCTCTAAAGAGGACAAGGA	0.572													13	117	---	---	---	---	PASS
GAD2	2572	broad.mit.edu	37	10	26569943	26569943	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26569943A>T	uc001isp.2	+	12	1666	c.1163A>T	c.(1162-1164)AAC>ATC	p.N388I	GAD2_uc001isq.2_Missense_Mutation_p.N388I	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	388					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)	TTTAGGGCCAACTCTGTGACG	0.498													34	64	---	---	---	---	PASS
APBB1IP	54518	broad.mit.edu	37	10	26830582	26830582	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26830582G>A	uc001iss.2	+	11	1437	c.1116G>A	c.(1114-1116)ATG>ATA	p.M372I	APBB1IP_uc009xks.1_Missense_Mutation_p.M372I	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,	372	PH.				blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7						AGCATAAAATGAAATATAAAG	0.303													9	26	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30318360	30318360	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30318360C>T	uc001iux.2	-	2	776	c.717G>A	c.(715-717)GAG>GAA	p.E239E	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Silent_p.E101E|KIAA1462_uc009xle.1_Silent_p.E239E	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	239										ovary(4)	4						AACTCAGGCTCTCGGGGGAAA	0.458													34	68	---	---	---	---	PASS
ZNF37A	7587	broad.mit.edu	37	10	38407328	38407328	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38407328G>A	uc001izk.2	+	8	2068	c.1249G>A	c.(1249-1251)GGG>AGG	p.G417R	ZNF37A_uc001izl.2_Missense_Mutation_p.G417R|ZNF37A_uc001izm.2_Missense_Mutation_p.G417R	NM_001007094	NP_001007095	P17032	ZN37A_HUMAN	zinc finger protein 37a	417	C2H2-type 8.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1						TAATGAATGTGGGAAGTCATT	0.363													12	26	---	---	---	---	PASS
ZNF37A	7587	broad.mit.edu	37	10	38407329	38407329	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38407329G>T	uc001izk.2	+	8	2069	c.1250G>T	c.(1249-1251)GGG>GTG	p.G417V	ZNF37A_uc001izl.2_Missense_Mutation_p.G417V|ZNF37A_uc001izm.2_Missense_Mutation_p.G417V	NM_001007094	NP_001007095	P17032	ZN37A_HUMAN	zinc finger protein 37a	417	C2H2-type 8.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1						AATGAATGTGGGAAGTCATTC	0.368													13	25	---	---	---	---	PASS
C10orf72	196740	broad.mit.edu	37	10	50285339	50285339	+	Missense_Mutation	SNP	C	A	A	rs45489505	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50285339C>A	uc001jhf.2	-	4	588	c.559G>T	c.(559-561)GTG>TTG	p.V187L		NM_001031746	NP_001026916	Q8IW00	CJ072_HUMAN	hypothetical protein LOC196740 isoform 1	187	Helical; (Potential).					integral to membrane|plasma membrane					0						AGGATCCCCACGCAGCACACG	0.522													12	29	---	---	---	---	PASS
CHAT	1103	broad.mit.edu	37	10	50824633	50824633	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50824633C>T	uc001jhz.2	+	2	525	c.372C>T	c.(370-372)CCC>CCT	p.P124P	CHAT_uc001jhv.1_Silent_p.P6P|CHAT_uc001jhx.1_Silent_p.P6P|CHAT_uc001jhy.1_Silent_p.P6P|CHAT_uc001jia.2_Silent_p.P6P|CHAT_uc010qgs.1_Silent_p.P6P	NM_020549	NP_065574	P28329	CLAT_HUMAN	choline acetyltransferase isoform 2	124					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	CAAAAACTCCCAGCAGTGAGG	0.567													5	10	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55569209	55569209	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55569209T>C	uc010qhs.1	-	37	5011	c.4616A>G	c.(4615-4617)GAG>GGG	p.E1539G	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qht.1_Missense_Mutation_p.E1532G|PCDH15_uc010qhu.1_3'UTR	NM_001142769	NP_001136241	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-1 precursor	Error:Variant_position_missing_in_Q96QU1_after_alignment					equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				GTATGTAGGCTCAGCTGCTGG	0.398										HNSCC(58;0.16)			35	45	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55569211	55569211	+	Silent	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55569211A>T	uc010qhs.1	-	37	5009	c.4614T>A	c.(4612-4614)GCT>GCA	p.A1538A	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qht.1_Silent_p.A1531A|PCDH15_uc010qhu.1_3'UTR	NM_001142769	NP_001136241	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-1 precursor	Error:Variant_position_missing_in_Q96QU1_after_alignment					equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGTAGGCTCAGCTGCTGGTG	0.393										HNSCC(58;0.16)			38	49	---	---	---	---	PASS
DDIT4	54541	broad.mit.edu	37	10	74034808	74034808	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74034808C>G	uc001jsx.1	+	3	763	c.561C>G	c.(559-561)CCC>CCG	p.P187P		NM_019058	NP_061931	Q9NX09	DDIT4_HUMAN	RTP801	187					apoptosis					pancreas(1)	1						GACTCTGGCCCAAGATCCAGG	0.637											OREG0020262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	13	---	---	---	---	PASS
CDHR1	92211	broad.mit.edu	37	10	85973009	85973009	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85973009G>T	uc001kcv.2	+	16	1945	c.1945G>T	c.(1945-1947)GAC>TAC	p.D649Y	CDHR1_uc001kcw.2_Missense_Mutation_p.D649Y|CDHR1_uc009xst.2_Missense_Mutation_p.D353Y|CDHR1_uc001kcx.2_5'UTR	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	649	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1						ACCTGGAAGGGACTGCCTATG	0.577													24	61	---	---	---	---	PASS
WAPAL	23063	broad.mit.edu	37	10	88260398	88260398	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88260398G>C	uc001kdo.2	-	3	1044	c.602C>G	c.(601-603)GCT>GGT	p.A201G	WAPAL_uc001kdn.2_Missense_Mutation_p.A244G|WAPAL_uc009xsw.2_Missense_Mutation_p.A201G	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog	201	Mediates interaction with the cohesin complex.				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1						GATTTCAGAAGCCACTGTAGT	0.373													24	36	---	---	---	---	PASS
LIPA	3988	broad.mit.edu	37	10	91005508	91005508	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91005508G>T	uc001kga.3	-	3	322	c.154C>A	c.(154-156)CTA>ATA	p.L52I	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|LIPA_uc009xtq.2_Missense_Mutation_p.L52I	NM_000235	NP_000226	P38571	LICH_HUMAN	lipase A precursor	52					lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GTCTCAACTAGGTATTCCTCA	0.418													4	34	---	---	---	---	PASS
LBX1	10660	broad.mit.edu	37	10	102987414	102987414	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102987414G>A	uc001ksx.2	-	2	604	c.459C>T	c.(457-459)GCC>GCT	p.A153A	uc010qpy.1_5'Flank	NM_006562	NP_006553	P52954	LBX1_HUMAN	ladybird homeobox 1	153	Homeobox.				muscle organ development		sequence-specific DNA binding				0		Colorectal(252;0.234)		Epithelial(162;3.22e-09)|all cancers(201;1.79e-07)		GGTCGCGATCGGCGGGGGACA	0.582													10	68	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106960916	106960916	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106960916G>A	uc001kyi.1	+	16	2393	c.2166G>A	c.(2164-2166)AAG>AAA	p.K722K	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	722	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		AAATATTCAAGAAACGTAAGC	0.478													16	34	---	---	---	---	PASS
C10orf96	374355	broad.mit.edu	37	10	118084555	118084555	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118084555T>C	uc001lck.2	+	2	283	c.32T>C	c.(31-33)ATC>ACC	p.I11T		NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355	11										ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)		CAGCACATCATCTTCACCGAG	0.522													6	22	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118440730	118440730	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118440730G>A	uc001lct.2	-	9	1065	c.960C>T	c.(958-960)ACC>ACT	p.T320T	HSPA12A_uc001lcu.2_Silent_p.T237T	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	320							ATP binding			ovary(1)	1				all cancers(201;0.0158)		TCAGGTCTACGGTGCCACCGC	0.488													10	23	---	---	---	---	PASS
RGS10	6001	broad.mit.edu	37	10	121285580	121285580	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121285580T>C	uc001lee.2	-	2	195	c.195A>G	c.(193-195)GCA>GCG	p.A65A	RGS10_uc001lef.2_Silent_p.A59A|RGS10_uc001leg.2_Silent_p.A73A	NM_002925	NP_002916	O43665	RGS10_HUMAN	regulator of G-protein signaling 10 isoform b	65	RGS.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|protein binding|signal transducer activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)		AATCTTCACATGCTAGCCAAA	0.303													7	52	---	---	---	---	PASS
PWWP2B	170394	broad.mit.edu	37	10	134219163	134219163	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134219163G>A	uc001lll.3	+	2	1188	c.1159G>A	c.(1159-1161)GAG>AAG	p.E387K	PWWP2B_uc009ybe.2_Missense_Mutation_p.E387K	NM_138499	NP_612508	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2 isoform 1	387											0		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		AAGTTCGGGTGAGGACGATGA	0.667													7	40	---	---	---	---	PASS
NLRP6	171389	broad.mit.edu	37	11	278571	278571	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:278571T>C	uc010qvs.1	+	1	2	c.2T>C	c.(1-3)ATG>ACG	p.M1T	NLRP6_uc010qvt.1_Missense_Mutation_p.M1T	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	1	DAPIN.					cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGAGACCCCATGGACCAGCCA	0.647													24	20	---	---	---	---	PASS
SIGIRR	59307	broad.mit.edu	37	11	408162	408162	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:408162C>T	uc001lpd.2	-	4	581	c.251G>A	c.(250-252)GGG>GAG	p.G84E	SIGIRR_uc001lpf.2_Missense_Mutation_p.G84E|SIGIRR_uc001lpe.1_Missense_Mutation_p.G84E|SIGIRR_uc001lpg.2_Missense_Mutation_p.G84E	NM_001135054	NP_001128526	Q6IA17	SIGIR_HUMAN	single Ig IL-1R-related molecule	84	Ig-like C2-type.|Extracellular (Potential).				acute-phase response|innate immune response|negative regulation of chemokine biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity	integral to membrane	protein binding|transmembrane receptor activity				0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CACGTTGACCCCCAGGACACT	0.587													10	49	---	---	---	---	PASS
KRTAP5-6	440023	broad.mit.edu	37	11	1718593	1718593	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1718593T>G	uc001lua.2	+	1	169	c.118T>G	c.(118-120)TGC>GGC	p.C40G		NM_001012416	NP_001012416	Q6L8G9	KRA56_HUMAN	keratin associated protein 5-6	40	3.|6 X 4 AA repeats of C-C-X-P.					keratin filament					0		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCCCGTGTGCTGCTGTGTGCC	0.667													32	36	---	---	---	---	PASS
ART5	116969	broad.mit.edu	37	11	3660919	3660919	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3660919C>A	uc001lyb.1	-	2	1133	c.740G>T	c.(739-741)TGG>TTG	p.W247L	ART5_uc001lyc.1_Missense_Mutation_p.W247L|ART5_uc001lyd.2_Intron|ART5_uc009yea.2_Intron	NM_053017	NP_443750	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5 precursor	247						extracellular region	NAD(P)+-protein-arginine ADP-ribosyltransferase activity			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATTATAGCTCCAGAGAGTCAC	0.527													6	69	---	---	---	---	PASS
OR52E8	390079	broad.mit.edu	37	11	5878375	5878375	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5878375C>A	uc010qzr.1	-	1	558	c.558G>T	c.(556-558)GAG>GAT	p.E186D	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCCATGTGCTCACAATAAG	0.483													5	58	---	---	---	---	PASS
OR52E4	390081	broad.mit.edu	37	11	5905533	5905533	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5905533T>C	uc010qzs.1	+	1	11	c.11T>C	c.(10-12)ATC>ACC	p.I4T	TRIM5_uc001mbq.1_Intron	NM_001005165	NP_001005165	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E,	4	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGCCTTCTATCAATGACACC	0.428													23	29	---	---	---	---	PASS
OR52B2	255725	broad.mit.edu	37	11	6190722	6190722	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6190722C>A	uc010qzy.1	-	1	835	c.835G>T	c.(835-837)GCC>TCC	p.A279S		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	279	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAAAGATTGGCCAGCAAGATA	0.448													12	17	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6655522	6655522	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6655522C>T	uc001mem.1	-	3	2223	c.1813G>A	c.(1813-1815)GCG>ACG	p.A605T		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	605	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCACTATCCGCGTCTGTGGCT	0.572													13	14	---	---	---	---	PASS
HTATIP2	10553	broad.mit.edu	37	11	20398241	20398241	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20398241A>G	uc009yia.1	+	4	485	c.419A>G	c.(418-420)AAT>AGT	p.N140S	HTATIP2_uc009yib.1_Missense_Mutation_p.N140S|HTATIP2_uc001mpx.2_Missense_Mutation_p.N174S|HTATIP2_uc001mpz.2_Missense_Mutation_p.N140S	NM_006410	NP_006401	Q9BUP3	HTAI2_HUMAN	HIV-1 Tat interactive protein 2, 30kDa isoform	140					angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0						AAATCAAGCAATTTTTTATAT	0.363													11	34	---	---	---	---	PASS
OR4X2	119764	broad.mit.edu	37	11	48267476	48267476	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48267476T>C	uc001ngs.1	+	1	821	c.821T>C	c.(820-822)CTG>CCG	p.L274P		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	274	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ACCGCGATCCTGAACCCTGTC	0.478													21	45	---	---	---	---	PASS
OR4S1	256148	broad.mit.edu	37	11	48328071	48328071	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48328071C>G	uc010rhu.1	+	1	297	c.297C>G	c.(295-297)CTC>CTG	p.L99L		NM_001004725	NP_001004725	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S,	99	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGACCCAGCTCTTTTCTGCCC	0.493													3	49	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136005	55136005	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136005G>T	uc010rif.1	+	1	646	c.646G>T	c.(646-648)GCT>TCT	p.A216S		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	216	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						ATTGAAACTTGCTTGCACCAA	0.418													21	27	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587663	55587663	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587663C>T	uc010rin.1	+	1	558	c.558C>T	c.(556-558)CTC>CTT	p.L186L		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				CCTCACTACTCTCCCTTTCTT	0.408													19	58	---	---	---	---	PASS
ZFP91	80829	broad.mit.edu	37	11	58384716	58384716	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58384716G>A	uc001nmx.3	+	11	1418	c.1250G>A	c.(1249-1251)TGG>TAG	p.W417*	ZFP91_uc001nmy.3_Nonsense_Mutation_p.W416*|ZFP91-CNTF_uc010rkm.1_RNA	NM_053023	NP_444251	Q96JP5	ZFP91_HUMAN	zinc finger protein 91	417	C2H2-type 4.				activation of NF-kappaB-inducing kinase activity|protein K63-linked ubiquitination	nucleus	nucleic acid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TCTCTTAATTGGCACATGAAG	0.413													14	38	---	---	---	---	PASS
OR5A1	219982	broad.mit.edu	37	11	59211431	59211431	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59211431C>T	uc001nnx.1	+	1	790	c.790C>T	c.(790-792)CGA>TGA	p.R264*		NM_001004728	NP_001004728	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2						CGTGTACTTGCGACCCAGCTC	0.527													40	82	---	---	---	---	PASS
GANAB	23193	broad.mit.edu	37	11	62402444	62402444	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62402444T>A	uc001nub.2	-	5	442	c.409A>T	c.(409-411)AGT>TGT	p.S137C	GANAB_uc001nua.2_Missense_Mutation_p.S137C|GANAB_uc001nuc.2_Missense_Mutation_p.S40C|GANAB_uc010rma.1_Missense_Mutation_p.S23C|GANAB_uc010rmb.1_Missense_Mutation_p.S23C	NM_198334	NP_938148	Q14697	GANAB_HUMAN	neutral alpha-glucosidase AB isoform 2	137					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5						AACTCCACACTGTTCTCATCA	0.463													46	41	---	---	---	---	PASS
KDM2A	22992	broad.mit.edu	37	11	66983395	66983395	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66983395G>T	uc001ojw.2	+	8	1526	c.662G>T	c.(661-663)TGG>TTG	p.W221L	KDM2A_uc001ojx.2_RNA|KDM2A_uc001ojy.2_5'UTR	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	221	JmjC.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9						ACCTCTGTTTGGTATCACATC	0.428													6	164	---	---	---	---	PASS
MYEOV	26579	broad.mit.edu	37	11	69063118	69063118	+	Missense_Mutation	SNP	C	A	A	rs139486495		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69063118C>A	uc001oov.2	+	3	651	c.201C>A	c.(199-201)TTC>TTA	p.F67L	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.F67L|MYEOV_uc001oow.2_Missense_Mutation_p.F9L	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	67											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		CTGGACACTTCGTGGAGGGCT	0.582													4	50	---	---	---	---	PASS
PGM2L1	283209	broad.mit.edu	37	11	74062614	74062614	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74062614C>T	uc001ovb.1	-	6	859	c.563G>A	c.(562-564)TGG>TAG	p.W188*		NM_173582	NP_775853	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	188					glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)					ACCAGTTTCCCAGTAAACCTA	0.328													8	22	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78380545	78380545	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78380545T>A	uc001ozl.3	-	32	7308	c.6845A>T	c.(6844-6846)AAC>ATC	p.N2282I	ODZ4_uc001ozk.3_Missense_Mutation_p.N507I|ODZ4_uc009yvb.1_Missense_Mutation_p.N866I	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	2282	Extracellular (Potential).|YD 21.				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						GCCAGCCCGGTTGTAGGCCTT	0.592													22	48	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85415985	85415985	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85415985T>C	uc010rth.1	-	14	2466	c.2190A>G	c.(2188-2190)CTA>CTG	p.L730L	SYTL2_uc010rtg.1_Silent_p.L731L|SYTL2_uc010rti.1_Silent_p.L706L|SYTL2_uc010rtj.1_Silent_p.L698L|SYTL2_uc001pav.2_Silent_p.L172L|SYTL2_uc010rte.1_Silent_p.L132L|SYTL2_uc001pax.2_Silent_p.L172L|SYTL2_uc001paz.2_Silent_p.L51L|SYTL2_uc001pba.2_Silent_p.L115L|SYTL2_uc001pay.2_Silent_p.L161L|SYTL2_uc001paw.2_Silent_p.L132L|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_Silent_p.L1028L|SYTL2_uc001pbb.2_Silent_p.L1068L|SYTL2_uc001pbc.2_Silent_p.L1052L|SYTL2_uc010rtf.1_Silent_p.L548L	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	730	C2 1.				intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CCACCTCCCCTAGGAAACTAT	0.388													24	33	---	---	---	---	PASS
PICALM	8301	broad.mit.edu	37	11	85701428	85701428	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85701428T>C	uc001pbm.2	-	13	1559	c.1273A>G	c.(1273-1275)ACT>GCT	p.T425A	PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc010rtk.1_Intron|PICALM_uc001pbo.1_Missense_Mutation_p.T57A	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	425					clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				GCATCTACAGTAGCAGAGAAA	0.338			T	MLLT10|MLL	TALL|AML|								6	19	---	---	---	---	PASS
EED	8726	broad.mit.edu	37	11	85988171	85988171	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85988171C>A	uc001pbp.2	+	10	1573	c.1116C>A	c.(1114-1116)TTC>TTA	p.F372L	EED_uc010rtm.1_Missense_Mutation_p.F372L|EED_uc001pbq.2_Missense_Mutation_p.F372L|EED_uc001pbr.2_Missense_Mutation_p.F397L|EED_uc001pbs.2_Missense_Mutation_p.F292L|EED_uc010rtn.1_RNA	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a	372	Interaction with EZH2 (By similarity).|Required for interaction with the matrix protein MA of HIV-1.|WD 6.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				CTATGGATTTCTGGCAAAAGG	0.333													11	28	---	---	---	---	PASS
NAALAD2	10003	broad.mit.edu	37	11	89911209	89911209	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89911209G>A	uc001pdf.3	+	16	1891	c.1782G>A	c.(1780-1782)TTG>TTA	p.L594L	NAALAD2_uc009yvx.2_Silent_p.L561L|NAALAD2_uc009yvy.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	594	Extracellular (Potential).				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CAGAAGCTTTGAAAAACTATG	0.338													26	32	---	---	---	---	PASS
ANGPTL5	253935	broad.mit.edu	37	11	101762074	101762074	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101762074G>T	uc001pgl.2	-	9	1699	c.1103C>A	c.(1102-1104)TCA>TAA	p.S368*		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5 precursor	368	Fibrinogen C-terminal.				signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		CTTGACAGGTGAGTTGTTTTT	0.333													23	47	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108384542	108384542	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108384542C>A	uc001pkk.2	-	6	1803	c.1692G>T	c.(1690-1692)GTG>GTT	p.V564V	EXPH5_uc010rvy.1_Silent_p.V376V|EXPH5_uc010rvz.1_Silent_p.V408V|EXPH5_uc010rwa.1_Silent_p.V488V	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	564					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CATGTGATACCACCATGCTAT	0.438													4	31	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117351887	117351887	+	Splice_Site	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117351887A>T	uc001prh.1	-	13	2838	c.2836_splice	c.e13+1	p.E946_splice		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		AGGTGAAGGTACCTTGCACAG	0.627													6	23	---	---	---	---	PASS
KCNJ1	3758	broad.mit.edu	37	11	128709173	128709173	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128709173G>T	uc001qeo.1	-	2	1074	c.1023C>A	c.(1021-1023)TTC>TTA	p.F341L	KCNJ1_uc001qep.1_Missense_Mutation_p.F322L|KCNJ1_uc001qeq.1_Missense_Mutation_p.F322L|KCNJ1_uc001qer.1_Missense_Mutation_p.F322L|KCNJ1_uc001qes.1_Missense_Mutation_p.F322L	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	341	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)	TAAAGTTATGGAAATCCACTC	0.483													14	23	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	132016281	132016281	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132016281G>T	uc001qgp.2	+	2	937	c.273G>T	c.(271-273)CTG>CTT	p.L91L	NTM_uc001qgm.2_Silent_p.L91L|NTM_uc010sch.1_Silent_p.L82L|NTM_uc010sci.1_Silent_p.L91L|NTM_uc010scj.1_Silent_p.L50L|NTM_uc001qgo.2_Silent_p.L91L|NTM_uc001qgq.2_Silent_p.L91L	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1	91	Ig-like C2-type 1.				cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						TGGTCCTTCTGAGCAACACCC	0.567													22	43	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	132180054	132180054	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132180054A>C	uc001qgp.2	+	5	1374	c.710A>C	c.(709-711)CAA>CCA	p.Q237P	NTM_uc001qgm.2_Missense_Mutation_p.Q237P|NTM_uc010sch.1_Missense_Mutation_p.Q228P|NTM_uc010sci.1_Missense_Mutation_p.Q237P|NTM_uc010scj.1_Missense_Mutation_p.Q196P|NTM_uc001qgo.2_Missense_Mutation_p.Q237P|NTM_uc001qgq.2_Missense_Mutation_p.Q237P|NTM_uc001qgr.2_5'UTR	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1	237	Ig-like C2-type 3.				cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CCCGTGGGACAAAAGGGGACA	0.483													42	83	---	---	---	---	PASS
B3GAT1	27087	broad.mit.edu	37	11	134253897	134253897	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134253897C>T	uc001qhq.2	-	4	559	c.298G>A	c.(298-300)GCC>ACC	p.A100T	B3GAT1_uc001qhr.2_Missense_Mutation_p.A100T|B3GAT1_uc010scv.1_Missense_Mutation_p.A113T	NM_018644	NP_061114	Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	100	Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		GTCAGCTCGGCCTTCTGCACC	0.716													6	5	---	---	---	---	PASS
B4GALNT3	283358	broad.mit.edu	37	12	665894	665894	+	Silent	SNP	C	A	A	rs113571884		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:665894C>A	uc001qii.1	+	15	2242	c.2242C>A	c.(2242-2244)CGG>AGG	p.R748R	B4GALNT3_uc001qik.1_Silent_p.R297R	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	748	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GGTCGAGGCCCGGAACCTGCA	0.637													3	16	---	---	---	---	PASS
TULP3	7289	broad.mit.edu	37	12	3048522	3048522	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3048522T>A	uc010seh.1	+	11	1322	c.1241T>A	c.(1240-1242)TTC>TAC	p.F414Y	TULP3_uc009zec.1_Missense_Mutation_p.F141Y|TULP3_uc010seg.1_RNA|TULP3_uc001qlj.2_Missense_Mutation_p.F414Y|TULP3_uc010sei.1_Missense_Mutation_p.F238Y	NM_003324	NP_003315	O75386	TULP3_HUMAN	tubby like protein 3 isoform 1	414					G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GATGACGTGTTCACACTGGAT	0.433													54	77	---	---	---	---	PASS
CHD4	1108	broad.mit.edu	37	12	6696922	6696922	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6696922T>C	uc001qpo.2	-	24	3823	c.3659A>G	c.(3658-3660)AAA>AGA	p.K1220R	CHD4_uc001qpn.2_Missense_Mutation_p.K1213R|CHD4_uc001qpp.2_Missense_Mutation_p.K1217R	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1220					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						AGTGCCAAATTTGAGGATATC	0.493													24	32	---	---	---	---	PASS
CLEC1A	51267	broad.mit.edu	37	12	10224077	10224077	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10224077C>T	uc001qxb.2	-	6	782	c.698G>A	c.(697-699)AGC>AAC	p.S233N	CLEC1A_uc009zhf.2_Missense_Mutation_p.S145N|CLEC1A_uc001qxc.2_Missense_Mutation_p.S145N|CLEC1A_uc001qxd.2_Missense_Mutation_p.S190N|CLEC1A_uc010sgx.1_Missense_Mutation_p.S131N	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1	233	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2						ACAGTCTCTGCTTCTTGGGCT	0.383													33	83	---	---	---	---	PASS
CLEC7A	64581	broad.mit.edu	37	12	10271049	10271049	+	3'UTR	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10271049C>A	uc001qxg.2	-	6					CLEC7A_uc001qxe.3_RNA|CLEC7A_uc001qxf.2_3'UTR|CLEC7A_uc001qxh.2_3'UTR|CLEC7A_uc001qxi.2_3'UTR|CLEC7A_uc001qxj.2_3'UTR|CLEC7A_uc009zhg.1_RNA|CLEC7A_uc001qxk.1_RNA	NM_197947	NP_922938	Q9BXN2	CLC7A_HUMAN	dendritic cell-associated C-type lectin 1						carbohydrate mediated signaling|defense response to protozoan|inflammatory response|innate immune response|phagocytosis, recognition|T cell activation	cytoplasm|integral to membrane	metal ion binding|MHC protein binding|sugar binding			central_nervous_system(1)	1						CCTTCTCCACCCTTCCTCTTA	0.388													18	31	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546665	11546665	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546665C>G	uc010shk.1	-	3	382	c.347G>C	c.(346-348)GGA>GCA	p.G116A		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)			TTGTGGCTTTCCTGGAGGAGA	0.597													10	372	---	---	---	---	PASS
GPRC5A	9052	broad.mit.edu	37	12	13061863	13061863	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13061863G>T	uc001rba.2	+	2	1330	c.680G>T	c.(679-681)TGG>TTG	p.W227L	GPRC5A_uc001raz.2_Missense_Mutation_p.W227L	NM_003979	NP_003970	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, family C, group 5,	227	Helical; Name=6; (Potential).					cytoplasmic vesicle membrane|Golgi apparatus|integral to plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TGGGTGGCCTGGATCACCCTG	0.572													33	49	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13724888	13724888	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13724888G>C	uc001rbt.2	-	10	2200	c.2021C>G	c.(2020-2022)CCT>CGT	p.P674R		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	674	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GAAGTCATTAGGTCTCTGGAA	0.323													10	12	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21229461	21229461	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21229461G>T	uc010sil.1	+	15	2071	c.2006G>T	c.(2005-2007)GGA>GTA	p.G669V	LST-3TM12_uc010sim.1_Missense_Mutation_p.G608V|LST-3TM12_uc010sin.1_Missense_Mutation_p.G561V			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)					AACAGCTGTGGAGCACGAGGG	0.348													41	70	---	---	---	---	PASS
GYS2	2998	broad.mit.edu	37	12	21712602	21712602	+	Silent	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21712602G>C	uc001rfb.2	-	9	1467	c.1212C>G	c.(1210-1212)CTC>CTG	p.L404L		NM_021957	NP_068776	P54840	GYS2_HUMAN	glycogen synthase 2	404					glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2						ATGCATCATAGAGTTTTTTTC	0.279													4	12	---	---	---	---	PASS
PPFIBP1	8496	broad.mit.edu	37	12	27832534	27832534	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27832534C>A	uc001ric.1	+	19	2123	c.1746C>A	c.(1744-1746)TCC>TCA	p.S582S	PPFIBP1_uc010sjr.1_Silent_p.S413S|PPFIBP1_uc001rib.1_Silent_p.S576S|PPFIBP1_uc001ria.2_Silent_p.S551S|PPFIBP1_uc001rid.1_Silent_p.S429S|PPFIBP1_uc001rif.1_Silent_p.S89S	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	582					cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					CTCCAGATTCCAAAAAGAAAT	0.458													6	148	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	31282805	31282805	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31282805T>A	uc010sjy.1	-	24	3079	c.3079A>T	c.(3079-3081)AGT>TGT	p.S1027C						RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		GTAAGAGCACTGAGCCTGTAA	0.348													7	12	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49420600	49420600	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49420600A>C	uc001rta.3	-	48	15149	c.15149T>G	c.(15148-15150)CTG>CGG	p.L5050R		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	5050					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GTCCAGGTTCAGCAGACGGGC	0.622			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			6	54	---	---	---	---	PASS
ITGA5	3678	broad.mit.edu	37	12	54794636	54794636	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54794636G>A	uc001sga.2	-	25	2705	c.2637C>T	c.(2635-2637)GGC>GGT	p.G879G		NM_002205	NP_002196	P08648	ITA5_HUMAN	integrin alpha 5 precursor	879	Extracellular (Potential).				angiogenesis|axon guidance|blood coagulation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|wound healing, spreading of epidermal cells	alphav-beta3 integrin-vitronectin complex|integrin complex|ruffle	platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			ovary(2)	2						TCACCTCCAGGCCCTTTGGGT	0.572													12	19	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57110896	57110896	+	Intron	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57110896G>T	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Missense_Mutation_p.P1473H|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						CTTGGGGGAAGGAGGAGTCAC	0.632			T	BCL6	NHL								4	29	---	---	---	---	PASS
AGAP2	116986	broad.mit.edu	37	12	58135800	58135800	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58135800G>T	uc001spr.2	-	1	141	c.55C>A	c.(55-57)CAT>AAT	p.H19N	TSPAN31_uc001spt.2_5'Flank|TSPAN31_uc009zqb.2_5'Flank	NM_014770	NP_055585	Q99490	AGAP2_HUMAN	centaurin, gamma 1 isoform PIKE-S	Error:Variant_position_missing_in_Q99490_after_alignment					axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5						GCCACCTCATGTCGTCTGACT	0.587													22	46	---	---	---	---	PASS
LEMD3	23592	broad.mit.edu	37	12	65633948	65633948	+	Nonsense_Mutation	SNP	G	T	T	rs147072982	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65633948G>T	uc001ssl.1	+	8	2062	c.2056G>T	c.(2056-2058)GAA>TAA	p.E686*	LEMD3_uc009zqo.1_Nonsense_Mutation_p.E685*	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	686					negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		AGCCTGCCAGGAAAACAAAGA	0.328													13	29	---	---	---	---	PASS
HELB	92797	broad.mit.edu	37	12	66700214	66700214	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66700214A>T	uc001sti.2	+	3	725	c.697A>T	c.(697-699)ATA>TTA	p.I233L	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	233					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TAAATGGATCATAGGGTCAGG	0.358													18	35	---	---	---	---	PASS
PPFIA2	8499	broad.mit.edu	37	12	81769626	81769626	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81769626C>T	uc001szo.1	-	10	1241	c.1080G>A	c.(1078-1080)ATG>ATA	p.M360I	PPFIA2_uc010sue.1_Missense_Mutation_p.M260I|PPFIA2_uc010sug.1_RNA|PPFIA2_uc010suh.1_RNA|PPFIA2_uc010sui.1_RNA|PPFIA2_uc010suj.1_RNA|PPFIA2_uc009zsi.1_RNA	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2	286										ovary(3)|lung(2)|pancreas(1)	6						GTTTATCATTCATGTCATGTA	0.408													8	15	---	---	---	---	PASS
RASSF9	9182	broad.mit.edu	37	12	86199616	86199616	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86199616C>T	uc001taf.1	-	2	511	c.172G>A	c.(172-174)GAG>AAG	p.E58K		NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family	58	Ras-associating.				endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						TCATGTTCCTCAAGCAAAGCC	0.488													39	91	---	---	---	---	PASS
MYO1H	283446	broad.mit.edu	37	12	109849790	109849790	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109849790C>T	uc010sxn.1	+	13	1454	c.1454C>T	c.(1453-1455)ACC>ATC	p.T485I		NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H	Error:Variant_position_missing_in_B4DNW6_after_alignment						myosin complex	motor activity				0						CACTTCGAAACGTACATACTT	0.393													6	7	---	---	---	---	PASS
RNF10	9921	broad.mit.edu	37	12	121013583	121013583	+	Intron	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121013583G>T	uc001typ.3	+						RNF10_uc010szk.1_Intron|RNF10_uc001tyq.3_Intron	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTTTAACACTGGTATTTTTTA	0.438													6	152	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124401007	124401007	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124401007G>A	uc001uft.3	+	62	10397	c.10372G>A	c.(10372-10374)GCT>ACT	p.A3458T		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3458	AAA 5 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTTCCAGGTCGCTTCCTTTAA	0.507													44	76	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133327335	133327335	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133327335C>G	uc001ukx.2	-	3	808	c.741G>C	c.(739-741)GAG>GAC	p.E247D	ANKLE2_uc001uky.3_Missense_Mutation_p.E185D	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	247						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		TAGCAAATTTCTCAGCGTCTT	0.393													12	33	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38154048	38154048	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38154048G>T	uc001uwo.3	-	12	1728	c.1610C>A	c.(1609-1611)ACC>AAC	p.T537N	POSTN_uc010tet.1_Missense_Mutation_p.T65N|POSTN_uc001uwp.3_Missense_Mutation_p.T537N|POSTN_uc001uwr.2_Missense_Mutation_p.T537N|POSTN_uc001uwq.2_Missense_Mutation_p.T537N|POSTN_uc010teu.1_Missense_Mutation_p.T537N|POSTN_uc010tev.1_Missense_Mutation_p.T537N|POSTN_uc010tew.1_Missense_Mutation_p.T537N|POSTN_uc010tex.1_Missense_Mutation_p.T452N	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	537	FAS1 4.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		AGCATCATTGGTTGGCACAAA	0.408													14	29	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38357173	38357173	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38357173G>T	uc001uws.2	-	2	533	c.298C>A	c.(298-300)CTA>ATA	p.L100I	TRPC4_uc010abv.2_5'UTR|TRPC4_uc001uwt.2_Missense_Mutation_p.L100I|TRPC4_uc010tey.1_Missense_Mutation_p.L100I|TRPC4_uc010abw.2_Missense_Mutation_p.L100I|TRPC4_uc010abx.2_Missense_Mutation_p.L100I|TRPC4_uc010aby.2_Missense_Mutation_p.L100I	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	100	ANK 3.|Cytoplasmic (Potential).|Multimerization domain (By similarity).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		GCATGTAATAGAGCATCTCCA	0.264													11	20	---	---	---	---	PASS
PCDH8	5100	broad.mit.edu	37	13	53419706	53419706	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53419706C>G	uc001vhi.2	-	2	2896	c.2693G>C	c.(2692-2694)GGA>GCA	p.G898A	PCDH8_uc001vhj.2_Missense_Mutation_p.G801A	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	898	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		GAAGGAGTGTCCTTTCCACAC	0.587													11	29	---	---	---	---	PASS
DIAPH3	81624	broad.mit.edu	37	13	60590048	60590048	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60590048T>A	uc001vht.2	-	7	989	c.770A>T	c.(769-771)CAG>CTG	p.Q257L	DIAPH3_uc001vhu.2_5'Flank|DIAPH3_uc001vhw.1_Missense_Mutation_p.Q246L|DIAPH3_uc010aed.1_Missense_Mutation_p.Q211L|DIAPH3_uc010aee.1_Missense_Mutation_p.Q187L|uc001vhx.2_Intron|uc001vhy.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	257	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		TGTACATACCTGCGTATTCAT	0.313													4	6	---	---	---	---	PASS
UCHL3	7347	broad.mit.edu	37	13	76179926	76179926	+	Missense_Mutation	SNP	C	T	T	rs139878255		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76179926C>T	uc001vjq.2	+	9	701	c.671C>T	c.(670-672)GCG>GTG	p.A224V	UCHL3_uc001vjr.2_Missense_Mutation_p.A188V	NM_006002	NP_005993	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3	224	Interaction with ubiquitin.				ubiquitin-dependent protein catabolic process	cytoplasm	cysteine-type peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity				0				GBM - Glioblastoma multiforme(99;0.0125)		AGATTTAATGCGATTGCTCTT	0.338													5	21	---	---	---	---	PASS
FAM155A	728215	broad.mit.edu	37	13	107822900	107822900	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107822900C>T	uc001vql.2	-	3	1838	c.1322G>A	c.(1321-1323)GGA>GAA	p.G441E		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	441						integral to membrane	binding			skin(1)	1						AAAGCTCAGTCCGGCTGTGTT	0.527													15	25	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109704819	109704819	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109704819G>T	uc001vqt.1	+	25	3104	c.2978G>T	c.(2977-2979)AGT>ATT	p.S993I	MYO16_uc010agk.1_Missense_Mutation_p.S1015I|MYO16_uc001vqu.1_Missense_Mutation_p.S793I|MYO16_uc010tjh.1_Missense_Mutation_p.S505I	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	993	Myosin head-like 2.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CTAGAACTTAGTAAGGTAGGA	0.279													20	26	---	---	---	---	PASS
CARKD	55739	broad.mit.edu	37	13	111290867	111290867	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111290867G>C	uc001vrb.2	+	10	1050	c.1036G>C	c.(1036-1038)GAA>CAA	p.E346Q	CARKD_uc010tjj.1_Missense_Mutation_p.E328Q|CARKD_uc001vqz.2_RNA|CARKD_uc001vra.2_RNA|CARKD_uc010tjk.1_Missense_Mutation_p.E236Q|CARKD_uc010tjl.1_Missense_Mutation_p.E215Q|CARKD_uc001vrc.2_Nonstop_Mutation_p.*391S			Q8IW45	CARKD_HUMAN	RecName: Full=Carbohydrate kinase domain-containing protein; Flags: Precursor;	346										skin(1)	1						CAAGCTCTTTGAAACCTGAGC	0.617													3	32	---	---	---	---	PASS
ZNF828	283489	broad.mit.edu	37	13	115091162	115091162	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115091162C>A	uc010ahb.2	+	3	2174	c.1845C>A	c.(1843-1845)TCC>TCA	p.S615S	ZNF828_uc001vuv.2_Silent_p.S615S|ZNF828_uc010tko.1_Silent_p.S615S	NM_001164144	NP_001157616	Q96JM3	ZN828_HUMAN	zinc finger protein 828	615	Mediates localization to the chromosome and the spindle and negatively regulates chromosome alignment.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|protein localization to kinetochore|protein localization to microtubule|sister chromatid biorientation	condensed chromosome kinetochore|cytoplasm|nucleus|spindle	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_epithelial(44;0.122)|all_lung(25;0.123)	BRCA - Breast invasive adenocarcinoma(86;0.104)	OV - Ovarian serous cystadenocarcinoma(48;0.193)|Epithelial(10;0.197)		TATTTCCTTCCTCAAAGAAGC	0.373													6	140	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20216261	20216261	+	Silent	SNP	C	A	A	rs140842827	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20216261C>A	uc010tkt.1	+	1	675	c.675C>A	c.(673-675)ACC>ACA	p.T225T		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTGATCACCCTGAGAACAC	0.493													6	100	---	---	---	---	PASS
METT11D1	64745	broad.mit.edu	37	14	21464794	21464794	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21464794C>T	uc001vyn.2	+	13	1386	c.1189C>T	c.(1189-1191)CGC>TGC	p.R397C	METT11D1_uc001vym.2_Missense_Mutation_p.R397C|METT11D1_uc001vyo.2_Missense_Mutation_p.R397C|METT11D1_uc001vyp.2_Missense_Mutation_p.R239C|METT11D1_uc001vyq.2_Missense_Mutation_p.R239C|SLC39A2_uc001vyr.2_5'Flank|SLC39A2_uc001vys.2_5'Flank	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform	397					translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TAAACGGCCTCGCCATGTGCA	0.572													15	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22251234	22251234	+	Intron	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22251234C>A	uc010tmf.1	+											SubName: Full=Putative uncharacterized protein ENSP00000374943;																		GAGACCTGTCCTAATTATATT	0.393													6	31	---	---	---	---	PASS
LRP10	26020	broad.mit.edu	37	14	23345565	23345565	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23345565C>G	uc001whd.2	+	5	1961	c.1408C>G	c.(1408-1410)CGC>GGC	p.R470G	LRP10_uc001whe.2_Missense_Mutation_p.R346G	NM_014045	NP_054764	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein	470	Cytoplasmic (Potential).				endocytosis	coated pit|integral to membrane				central_nervous_system(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		CTATGCCATTCGCACCCAGGA	0.607													3	39	---	---	---	---	PASS
JPH4	84502	broad.mit.edu	37	14	24040344	24040344	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24040344G>T	uc001wkq.2	-	6	2514	c.1596C>A	c.(1594-1596)CTC>CTA	p.L532L	JPH4_uc010tnr.1_Silent_p.L197L|JPH4_uc001wkr.2_Silent_p.L532L	NM_032452	NP_115828	Q96JJ6	JPH4_HUMAN	junctophilin 4	532	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane				ovary(1)|pancreas(1)	2	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TGCAGCCTCCGAGGAGTGGGG	0.677													6	148	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33014470	33014470	+	Nonsense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33014470C>G	uc001wrq.2	+	4	781	c.611C>G	c.(610-612)TCA>TGA	p.S204*	AKAP6_uc010aml.2_Nonsense_Mutation_p.S201*	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	204					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTGGATGACTCAGGACAATTA	0.408													6	62	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64450532	64450532	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64450532A>G	uc001xgm.2	+	18	2309	c.2079A>G	c.(2077-2079)GAA>GAG	p.E693E	SYNE2_uc001xgl.2_Silent_p.E693E	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	693	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)		TATCTAAAGAAGAGAAAGCAA	0.284													7	19	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72138262	72138262	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72138262C>T	uc001xms.2	+	8	3030	c.2682C>T	c.(2680-2682)AGC>AGT	p.S894S	SIPA1L1_uc001xmt.2_Silent_p.S894S|SIPA1L1_uc001xmu.2_Silent_p.S894S|SIPA1L1_uc001xmv.2_Silent_p.S894S|SIPA1L1_uc010ttm.1_Silent_p.S369S	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	894					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)		AAACAAAGAGCGTGGTCTTCA	0.463													25	52	---	---	---	---	PASS
PPP4R4	57718	broad.mit.edu	37	14	94731818	94731818	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94731818A>G	uc001ycs.1	+							NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4						CAAGTAAGAAATAACTTCTTT	0.368													16	13	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102452390	102452390	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102452390C>A	uc001yks.2	+	8	1992	c.1828C>A	c.(1828-1830)CAG>AAG	p.Q610K		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	610	Interaction with DYNC1I2 (By similarity).|Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						CCAGCTGATCCAGCGCGTGAA	0.507													4	38	---	---	---	---	PASS
PPP1R13B	23368	broad.mit.edu	37	14	104251226	104251226	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104251226C>G	uc001yof.1	-	3	466	c.183G>C	c.(181-183)ATG>ATC	p.M61I	PPP1R13B_uc001yog.1_5'UTR	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1	61					apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				GTTCGTACATCATATGATCAA	0.388													4	51	---	---	---	---	PASS
OCA2	4948	broad.mit.edu	37	15	28230328	28230328	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28230328G>C	uc001zbh.3	-	13	1356	c.1246C>G	c.(1246-1248)CGG>GGG	p.R416G	OCA2_uc010ayv.2_Missense_Mutation_p.R392G	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	416	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CGGGAGAGCCGGTATGCCTGG	0.567									Oculocutaneous_Albinism				8	16	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34042220	34042220	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34042220G>A	uc001zhi.2	+	56	8310	c.8240G>A	c.(8239-8241)TGG>TAG	p.W2747*	RYR3_uc010bar.2_Nonsense_Mutation_p.W2747*	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2747	4.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CACAATATCTGGGCCAAGAAG	0.512													9	14	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44912449	44912449	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44912449T>G	uc001ztx.2	-	15	2804	c.2773A>C	c.(2773-2775)ATT>CTT	p.I925L	SPG11_uc010ueh.1_Missense_Mutation_p.I925L|SPG11_uc010uei.1_Missense_Mutation_p.I925L|SPG11_uc001ztz.1_Missense_Mutation_p.I84L	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	925	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTCTGGTTAATAACATCAACA	0.358													3	62	---	---	---	---	PASS
SQRDL	58472	broad.mit.edu	37	15	45954329	45954329	+	Intron	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45954329C>A	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		AGAAGGTAACCACTGAGGCCT	0.413													4	53	---	---	---	---	PASS
SHC4	399694	broad.mit.edu	37	15	49148318	49148318	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49148318C>A	uc001zxb.1	-	8	1503	c.1074G>T	c.(1072-1074)GAG>GAT	p.E358D	SHC4_uc010uey.1_Missense_Mutation_p.E115D|SHC4_uc010uez.1_Missense_Mutation_p.E72D	NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein	358	PID.				intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TATGCACCTCCTCACTGTGAA	0.438													5	78	---	---	---	---	PASS
MNS1	55329	broad.mit.edu	37	15	56739137	56739137	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56739137C>G	uc002adr.2	-	4	523	c.358G>C	c.(358-360)GAG>CAG	p.E120Q	MNS1_uc010bfo.2_5'UTR	NM_018365	NP_060835	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	120	Potential.|Glu-rich.				meiosis					ovary(1)	1				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		TCTCTAAGCTCAATGCTGTTT	0.254													5	18	---	---	---	---	PASS
IGDCC4	57722	broad.mit.edu	37	15	65684253	65684253	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65684253A>C	uc002aou.1	-	12	2399	c.2189T>G	c.(2188-2190)GTG>GGG	p.V730G	IGDCC4_uc002aot.1_Missense_Mutation_p.V318G	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member	730	Extracellular (Potential).|Fibronectin type-III 3.					integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3						GCCCTTCCACACTGCTGCATA	0.622													43	78	---	---	---	---	PASS
DIS3L	115752	broad.mit.edu	37	15	66621462	66621462	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66621462G>A	uc010ujm.1	+	13	2371	c.2356G>A	c.(2356-2358)GGT>AGT	p.G786S	DIS3L_uc002app.2_Missense_Mutation_p.G703S|DIS3L_uc010bho.2_Missense_Mutation_p.G652S	NM_001143688	NP_001137160	Q8TF46	DI3L1_HUMAN	DIS3 mitotic control homolog (S.	786					rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2						CCATCATTACGGTGAATCATA	0.433													15	25	---	---	---	---	PASS
SH2D7	646892	broad.mit.edu	37	15	78385066	78385066	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78385066C>A	uc010blb.1	+	1	140	c.140C>A	c.(139-141)GCC>GAC	p.A47D		NM_001101404	NP_001094874	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	47											0						CAGAACGGTGCCCTGCCTCCC	0.607													5	10	---	---	---	---	PASS
ZNF598	90850	broad.mit.edu	37	16	2049631	2049631	+	Missense_Mutation	SNP	G	A	A	rs144186452	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2049631G>A	uc002cof.1	-	11	1934	c.1919C>T	c.(1918-1920)CCG>CTG	p.P640L	ZNF598_uc002coe.1_Missense_Mutation_p.P4L	NM_178167	NP_835461	Q86UK7	ZN598_HUMAN	zinc finger protein 598	640	Pro-rich.					intracellular	zinc ion binding			lung(1)|breast(1)	2						AGCAGGGGCCGGGCCCTCCAT	0.711													6	8	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2812505	2812505	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2812505G>T	uc002crk.2	+	11	2525	c.1976G>T	c.(1975-1977)CGC>CTC	p.R659L	SRRM2_uc002crj.1_Missense_Mutation_p.R563L|SRRM2_uc002crl.1_Missense_Mutation_p.R659L|SRRM2_uc010bsu.1_Missense_Mutation_p.R563L	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	659	Arg-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						GGCCGCTCACGCTCCAGAACC	0.622													24	62	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2813279	2813279	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2813279C>T	uc002crk.2	+	11	3299	c.2750C>T	c.(2749-2751)CCC>CTC	p.P917L	SRRM2_uc002crj.1_Missense_Mutation_p.P821L|SRRM2_uc002crl.1_Missense_Mutation_p.P917L|SRRM2_uc010bsu.1_Missense_Mutation_p.P821L	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	917	Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						TCTCCACAACCCAAAGTGAAG	0.512													21	44	---	---	---	---	PASS
CLDN6	9074	broad.mit.edu	37	16	3066004	3066004	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3066004G>T	uc002csu.3	-	2	79	c.19C>A	c.(19-21)CAG>AAG	p.Q7K		NM_021195	NP_067018	P56747	CLD6_HUMAN	claudin 6	7	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CCCAGGATCTGCATTCCGGCA	0.602													7	17	---	---	---	---	PASS
DNASE1	1773	broad.mit.edu	37	16	3707119	3707119	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3707119C>T	uc002cvr.2	+							NM_005223	NP_005214	P24855	DNAS1_HUMAN	deoxyribonuclease I precursor						apoptosis|DNA catabolic process	extracellular region|nuclear envelope	actin binding|deoxyribonuclease I activity				0		Ovarian(90;0.0261)		Kidney(780;0.0556)	Dornase Alfa(DB00003)	GGAGGTGAGGCCCTCCCAGGG	0.637								Direct_reversal_of_damage					13	26	---	---	---	---	PASS
MKL2	57496	broad.mit.edu	37	16	14340860	14340860	+	Silent	SNP	C	T	T	rs148779363	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14340860C>T	uc010uza.1	+	12	1898	c.1743C>T	c.(1741-1743)ATC>ATT	p.I581I	MKL2_uc002dcg.2_Silent_p.I581I|MKL2_uc002dcj.2_5'Flank	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	570	Required for interaction with itself and with MKL1.|Potential.				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						AGAAGCAAATCGAAGAGCTGA	0.507													5	49	---	---	---	---	PASS
USP31	57478	broad.mit.edu	37	16	23079361	23079361	+	3'UTR	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23079361G>A	uc002dll.2	-	16					USP31_uc002dlk.2_3'UTR|USP31_uc010vca.1_3'UTR|USP31_uc010bxm.2_3'UTR	NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)		TTTGATTGCAGAAATATCACT	0.423													21	30	---	---	---	---	PASS
ERN2	10595	broad.mit.edu	37	16	23712343	23712343	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23712343G>T	uc002dma.3	-	12	1609	c.1440C>A	c.(1438-1440)GAC>GAA	p.D480E	ERN2_uc010bxp.2_Intron|ERN2_uc010bxq.1_Missense_Mutation_p.D288E	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	432	Helical; (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CTGCCAGCAGGTCTTGGGGTC	0.572													24	37	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24196462	24196462	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24196462G>T	uc002dmd.2	+	14	1761	c.1564G>T	c.(1564-1566)GTG>TTG	p.V522L	PRKCB_uc002dme.2_Missense_Mutation_p.V522L	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	522	Protein kinase.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	TGGGAAGTCCGTGGATTGGTG	0.458													28	34	---	---	---	---	PASS
ABCC11	85320	broad.mit.edu	37	16	48234333	48234333	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48234333G>A	uc002eff.1	-	14	2286	c.1936C>T	c.(1936-1938)CGC>TGC	p.R646C	ABCC11_uc002efg.1_Missense_Mutation_p.R646C|ABCC11_uc002efh.1_Missense_Mutation_p.R646C|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	646	ABC transporter 1.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				TAGACGGCGCGGGCCAGGCTG	0.582									Cerumen_Type				20	24	---	---	---	---	PASS
CES7	221223	broad.mit.edu	37	16	55883659	55883659	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55883659C>T	uc002eip.2	-	11	1449	c.1300G>A	c.(1300-1302)GAG>AAG	p.E434K	CES7_uc002eio.2_Intron|CES7_uc002eiq.2_Missense_Mutation_p.E195K|CES7_uc002eir.2_Missense_Mutation_p.E328K	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	434						extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		TGCCGAAACTCATAGAAGTAG	0.567													6	112	---	---	---	---	PASS
GPR114	221188	broad.mit.edu	37	16	57608715	57608715	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57608715C>T	uc002elx.3	+						GPR114_uc010vhr.1_Intron|GPR114_uc002ely.2_Intron	NM_153837	NP_722579	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1						GACACGTCACCCTCCCCTGCA	0.657													7	19	---	---	---	---	PASS
GAN	8139	broad.mit.edu	37	16	81397433	81397433	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81397433G>T	uc002fgo.2	+	7	1269	c.1121G>T	c.(1120-1122)GGG>GTG	p.G374V		NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin	374	Kelch 2.				cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)				GAGATAGATGGGATGCTGTAC	0.398													6	91	---	---	---	---	PASS
PLCG2	5336	broad.mit.edu	37	16	81957085	81957085	+	Intron	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81957085G>A	uc002fgt.2	+							NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						TGTTTTCCCTGAAAGCCTCAG	0.552													6	25	---	---	---	---	PASS
JPH3	57338	broad.mit.edu	37	16	87678227	87678227	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87678227G>A	uc002fkd.2	+	2	1000	c.746G>A	c.(745-747)GGC>GAC	p.G249D	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	249	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		AGCGAGGCGGGCATGAGCACC	0.672													4	71	---	---	---	---	PASS
SPIRE2	84501	broad.mit.edu	37	16	89936621	89936621	+	Missense_Mutation	SNP	C	T	T	rs144349271		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89936621C>T	uc002foz.1	+	15	2138	c.2086C>T	c.(2086-2088)CGC>TGC	p.R696C	SPIRE2_uc010ciw.1_Missense_Mutation_p.R648C|SPIRE2_uc002fpa.1_Missense_Mutation_p.R648C|SPIRE2_uc010cix.1_Missense_Mutation_p.R563C	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2	696					transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TACGCCACGACGCAGTCGCCA	0.607													8	2	---	---	---	---	PASS
VPS53	55275	broad.mit.edu	37	17	534816	534816	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:534816C>T	uc002frn.2	-	8	808	c.661G>A	c.(661-663)GAA>AAA	p.E221K	VPS53_uc002frk.2_5'UTR|VPS53_uc010cjo.1_Missense_Mutation_p.E221K|VPS53_uc002frl.2_RNA|VPS53_uc002frm.2_Missense_Mutation_p.E192K|VPS53_uc002fro.2_Missense_Mutation_p.E23K|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2	221					protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GGAAACGCTTCTTCAAAATCT	0.498													7	44	---	---	---	---	PASS
CTNS	1497	broad.mit.edu	37	17	3563244	3563244	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3563244G>A	uc002fwb.2	+	11	1538	c.945G>A	c.(943-945)CAG>CAA	p.Q315Q	CTNS_uc002fwa.2_Silent_p.Q315Q|CTNS_uc010ckj.2_Silent_p.Q315Q|CTNS_uc010vrv.1_Silent_p.Q168Q|CTNS_uc010vrw.1_Silent_p.Q207Q	NM_004937	NP_004928	O60931	CTNS_HUMAN	cystinosin isoform 2	315	Helical; (Potential).|PQ-loop 2.				ATP metabolic process|brain development|cognition|glutathione metabolic process	integral to membrane|late endosome|lysosomal membrane	L-cystine transmembrane transporter activity				0				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GCCTCCTGCAGATGTTCCTCC	0.627													6	9	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	A	A	rs28934576	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577120C>A	uc002gim.2	-	8	1012	c.818G>T	c.(817-819)CGT>CTT	p.R273L	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R273L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R141L|TP53_uc010cng.1_Missense_Mutation_p.R141L|TP53_uc002gii.1_Missense_Mutation_p.R141L|TP53_uc010cnh.1_Missense_Mutation_p.R273L|TP53_uc010cni.1_Missense_Mutation_p.R273L|TP53_uc002gij.2_Missense_Mutation_p.R273L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	273	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R273H(469)|p.R273C(394)|p.R273L(83)|p.R273P(24)|p.R273S(11)|p.R273G(9)|p.0?(7)|p.R273fs*72(3)|p.?(2)|p.R273fs*33(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273R(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)		GGCACAAACACGCACCTCAAA	0.542	R273H(NCIH1793_LUNG)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PANC1_PANCREAS)|R273H(NCIH508_LARGE_INTESTINE)|R273H(NCIH1975_LUNG)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(NCIH2405_LUNG)|R273H(HEC59_ENDOMETRIUM)|R273H(NCIH1155_LUNG)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(EN_ENDOMETRIUM)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(MDAMB468_BREAST)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW620_LARGE_INTESTINE)|R273H(SUIT2_PANCREAS)|R273H(SW480_LARGE_INTESTINE)|R273H(SKMEL30_SKIN)|R273H(OC314_OVARY)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)	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)			7	7	---	---	---	---	PASS
SLC6A4	6532	broad.mit.edu	37	17	28539890	28539890	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28539890A>G	uc002hey.3	-						SLC6A4_uc010csg.2_5'Flank	NM_001045	NP_001036	P31645	SC6A4_HUMAN	solute carrier family 6 member 4						response to toxin|serotonin uptake|thalamus development	cytosol|endomembrane system|endosome membrane|membrane raft	actin filament binding|Rab GTPase binding|serotonin transmembrane transporter activity|serotonin:sodium symporter activity			skin(3)|ovary(1)	4					Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Doxepin(DB01142)|Duloxetine(DB00476)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Minaprine(DB00805)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phentermine(DB00191)|Protriptyline(DB00344)|Sertraline(DB01104)|Sibutramine(DB01105)|Tegaserod(DB01079)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Zimelidine(DB04832)	GCATCTCTGGAGGGGAAAACC	0.572													6	5	---	---	---	---	PASS
CCL3	6348	broad.mit.edu	37	17	34416024	34416024	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34416024A>T	uc002hkv.2	-	3	375	c.273T>A	c.(271-273)AGT>AGA	p.S91R		NM_002983	NP_002974	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	91					cell-cell signaling|cellular calcium ion homeostasis|cellular component movement|cytoskeleton organization|exocytosis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|regulation of viral genome replication	extracellular space|soluble fraction	chemoattractant activity|chemokine activity|signal transducer activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCCCTCAGGCACTCAGCTCCA	0.627													21	23	---	---	---	---	PASS
SLC25A39	51629	broad.mit.edu	37	17	42398095	42398095	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42398095C>G	uc002ign.2	-	9	850	c.696G>C	c.(694-696)CTG>CTC	p.L232L	SLC25A39_uc002igm.2_Silent_p.L224L|SLC25A39_uc002igo.2_Silent_p.L224L|SLC25A39_uc010wiw.1_Silent_p.L209L|SLC25A39_uc010czu.2_Silent_p.L100L|SLC25A39_uc010wix.1_3'UTR|SLC25A39_uc010wiy.1_3'UTR	NM_001143780	NP_001137252	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39 isoform a	232	Helical; Name=4; (Potential).|Solcar 2.				heme biosynthetic process|transport	integral to membrane|mitochondrial inner membrane				upper_aerodigestive_tract(1)	1		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TGAACCAGTACAGGGCTTGGG	0.582													35	13	---	---	---	---	PASS
GRN	2896	broad.mit.edu	37	17	42429158	42429158	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42429158C>A	uc002igp.1	+	10	1393	c.1174C>A	c.(1174-1176)CCA>ACA	p.P392T	GRN_uc002igr.1_Missense_Mutation_p.P186T	NM_002087	NP_002078	P28799	GRN_HUMAN	granulin precursor	392					signal transduction	extracellular space	cytokine activity|growth factor activity			ovary(2)|central_nervous_system(2)|skin(1)	5		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CTGTCCAATCCCAGAGGTATA	0.582													4	22	---	---	---	---	PASS
TBX21	30009	broad.mit.edu	37	17	45822322	45822322	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45822322C>T	uc002ilv.1	+	6	1409	c.1198C>T	c.(1198-1200)CGA>TGA	p.R400*		NM_013351	NP_037483	Q9UL17	TBX21_HUMAN	T-box 21	400					lymphocyte migration|multicellular organismal development|positive regulation of transcription, DNA-dependent|response to virus	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0						GGCTGAGTTTCGAGCAGTCAG	0.652													10	24	---	---	---	---	PASS
TOM1L1	10040	broad.mit.edu	37	17	52981062	52981062	+	Intron	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52981062T>A	uc002iud.2	+						TOM1L1_uc002iub.2_Intron|TOM1L1_uc002iuc.2_Intron|TOM1L1_uc010dca.1_Intron|TOM1L1_uc010wnb.1_Intron|TOM1L1_uc010wnc.1_Intron|TOM1L1_uc010dbz.2_Intron|TOM1L1_uc010wnd.1_Intron	NM_005486	NP_005477	O75674	TM1L1_HUMAN	target of myb1-like 1						intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1						CAGCTTTTTCTTGGCAGAAAA	0.418													32	12	---	---	---	---	PASS
SFRS1	6426	broad.mit.edu	37	17	56083716	56083716	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56083716C>G	uc002ivi.2	-	2	576	c.367G>C	c.(367-369)GTG>CTG	p.V123L	SFRS1_uc002ivj.2_Missense_Mutation_p.V123L	NM_006924	NP_008855	Q07955	SRSF1_HUMAN	splicing factor, arginine/serine-rich 1 isoform	123	RRM 2.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA 5'-splice site recognition|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytoplasm|nuclear speck	nucleotide binding|RNA binding				0		Colorectal(1115;0.0691)		LUAD - Lung adenocarcinoma(1115;0.247)		GAGACAACCACTCTGTTTTCA	0.552													38	12	---	---	---	---	PASS
ERN1	2081	broad.mit.edu	37	17	62144022	62144022	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62144022C>T	uc002jdz.2	-							NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9						CCCCGAGCTCCCAACTCACGT	0.607													21	16	---	---	---	---	PASS
ACOX1	51	broad.mit.edu	37	17	73945424	73945424	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73945424C>A	uc002jqf.2	-	12	1892	c.1602G>T	c.(1600-1602)GTG>GTT	p.V534V	ACOX1_uc010wsq.1_Silent_p.V496V|ACOX1_uc002jqe.2_Silent_p.V534V|ACOX1_uc010wsr.1_Silent_p.V466V	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b	534				VV -> GL (in Ref. 1; AAA19113 and 2; AAA18595).	fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						GCTTAACTACCACATAGTGGC	0.358													5	110	---	---	---	---	PASS
SEC14L1	6397	broad.mit.edu	37	17	75205569	75205569	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75205569C>T	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_Intron|SEC14L1_uc010wtj.1_Intron|SEC14L1_uc002jtr.2_Intron	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						GTACGTCCTCCGCCTTCCTGC	0.597													13	5	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78319717	78319717	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78319717C>T	uc002jyh.1	+	4	2024	c.1801C>T	c.(1801-1803)CGG>TGG	p.R601W		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CAATCCATACCGGAAGCACTC	0.527													30	11	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2769684	2769684	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2769684A>G	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						GTTTGTTTATATGTACAGAGT	0.323													4	8	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	6983088	6983088	+	Intron	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6983088C>T	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)	GAAGCCACGTCGTTTCCTACC	0.488													10	31	---	---	---	---	PASS
PTPRM	5797	broad.mit.edu	37	18	8114782	8114782	+	Intron	SNP	G	A	A	rs139751751		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8114782G>A	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)				CTCTTTATTTGACACAGGAAA	0.308													6	16	---	---	---	---	PASS
NDUFV2	4729	broad.mit.edu	37	18	9122569	9122569	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9122569C>T	uc002knu.2	+	5	426	c.359C>T	c.(358-360)ACA>ATA	p.T120I		NM_021074	NP_066552	P19404	NDUV2_HUMAN	NADH dehydrogenase ubiquinone flavoprotein 2	120					cardiac muscle tissue development|mitochondrial electron transport, NADH to ubiquinone|nervous system development|transport	mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity			ovary(1)	1					NADH(DB00157)	ACTTTTTATACAATGTATAAT	0.363													9	63	---	---	---	---	PASS
ZNF521	25925	broad.mit.edu	37	18	22805745	22805745	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22805745G>T	uc002kvk.2	-	4	2384	c.2137C>A	c.(2137-2139)CTG>ATG	p.L713M	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Missense_Mutation_p.L713M|ZNF521_uc002kvl.2_Missense_Mutation_p.L493M	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	713	C2H2-type 16.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ATGTCCAGCAGGTGTTTCTGA	0.453			T	PAX5	ALL								5	75	---	---	---	---	PASS
CDH7	1005	broad.mit.edu	37	18	63477173	63477173	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63477173C>A	uc002ljz.2	+	3	769	c.444C>A	c.(442-444)GAC>GAA	p.D148E	CDH7_uc002lka.2_Missense_Mutation_p.D148E|CDH7_uc002lkb.2_Missense_Mutation_p.D148E	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	148	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				ATATCAACGACAATGAACCCA	0.507													4	71	---	---	---	---	PASS
CTDP1	9150	broad.mit.edu	37	18	77477810	77477810	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77477810G>T	uc002lnh.1	+	10	2358	c.2211G>T	c.(2209-2211)AGG>AGT	p.R737S	CTDP1_uc002lni.1_Missense_Mutation_p.R737S|CTDP1_uc010drd.1_Missense_Mutation_p.R737S	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	737					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		CCTCCGACAGGGAGAACAGCC	0.677													19	4	---	---	---	---	PASS
CCDC94	55702	broad.mit.edu	37	19	4254382	4254382	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4254382G>C	uc002lzv.3	+	4	334	c.301G>C	c.(301-303)GAG>CAG	p.E101Q		NM_018074	NP_060544	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	101											0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		CTACACCATGGAGCATGGAGC	0.403													22	36	---	---	---	---	PASS
TMEM146	257062	broad.mit.edu	37	19	5751819	5751819	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5751819C>T	uc002mda.2	+	12	1210	c.1149C>T	c.(1147-1149)CAC>CAT	p.H383H	TMEM146_uc010duj.1_Silent_p.H41H	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor	383	Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						CTGAACTCCACGTTGGAAAGT	0.378													14	28	---	---	---	---	PASS
PNPLA6	10908	broad.mit.edu	37	19	7625941	7625941	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7625941G>C	uc010xjq.1	+	32	4083	c.3888G>C	c.(3886-3888)GAG>GAC	p.E1296D	PNPLA6_uc002mgq.1_Missense_Mutation_p.E1248D|PNPLA6_uc010xjp.1_Missense_Mutation_p.E1221D|PNPLA6_uc002mgr.1_Missense_Mutation_p.E1248D|PNPLA6_uc002mgs.2_Missense_Mutation_p.E1286D|PNPLA6_uc002mgt.1_RNA	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	1287	Cytoplasmic (Potential).			E -> G (in Ref. 5; CAB43674).	cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						ACTTGGCAGAGATTGTGTCCC	0.642													4	8	---	---	---	---	PASS
CLEC4M	10332	broad.mit.edu	37	19	7828371	7828371	+	Intron	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7828371G>T	uc002mih.2	+						CLEC4M_uc010xjv.1_Intron|CLEC4M_uc002mhy.2_Intron|CLEC4M_uc010xjw.1_Intron|CLEC4M_uc010dvt.2_Intron|CLEC4M_uc010dvs.2_Intron|CLEC4M_uc010xjx.1_Intron|CLEC4M_uc002mhz.2_Intron|CLEC4M_uc002mic.2_Intron|CLEC4M_uc002mia.2_Intron	NM_001144910	NP_001138382	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M isoform						cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to plasma membrane	ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding			pancreas(1)	1						AGGTAGGCAAGAGTTAGGGAG	0.333													29	47	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9072086	9072086	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9072086A>G	uc002mkp.2	-	3	15564	c.15360T>C	c.(15358-15360)TCT>TCC	p.S5120S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5122	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CTGTGTTTATAGAAGGAAAAA	0.443													44	49	---	---	---	---	PASS
ZNF440	126070	broad.mit.edu	37	19	11943153	11943153	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11943153A>G	uc002msp.1	+	4	1318	c.1162A>G	c.(1162-1164)AGG>GGG	p.R388G		NM_152357	NP_689570	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	388	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATATCATGAAAGGACTCACAC	0.443													30	38	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30934940	30934940	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30934940C>T	uc002nsu.1	+	2	609	c.471C>T	c.(469-471)CCC>CCT	p.P157P	ZNF536_uc010edd.1_Silent_p.P157P	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	157					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					GCGAGAAGCCCTTCAAGTGCC	0.652													16	32	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232191	35232191	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35232191T>C	uc002nvu.3	+	4	1368	c.905T>C	c.(904-906)TTT>TCT	p.F302S	ZNF181_uc010xsa.1_Missense_Mutation_p.F301S|ZNF181_uc010xsb.1_Missense_Mutation_p.F301S|ZNF181_uc010xsc.1_Missense_Mutation_p.F237S	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	302	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GGGAAGGCCTTTAGCCATGTC	0.428													7	62	---	---	---	---	PASS
ZNF571	51276	broad.mit.edu	37	19	38055702	38055702	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38055702G>C	uc002ogt.2	-	4	1729	c.1628C>G	c.(1627-1629)TCA>TGA	p.S543*	uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF540_uc002ogq.2_Intron|ZNF571_uc002ogr.1_Intron|uc002ogs.1_5'Flank|ZNF571_uc010efp.2_Nonsense_Mutation_p.S543*	NM_016536	NP_057620	Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	543	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGTAAGGTGTGAGCCACGAAT	0.423													4	29	---	---	---	---	PASS
PPP1R14A	94274	broad.mit.edu	37	19	38742961	38742961	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38742961A>C	uc002ohq.2	-	3	493	c.300T>G	c.(298-300)TGT>TGG	p.C100W	PPP1R14A_uc010efv.2_Missense_Mutation_p.C73W	NM_033256	NP_150281	Q96A00	PP14A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	100	Inhibitory.				regulation of phosphorylation	cytoplasm	protein binding|protein phosphatase inhibitor activity				0	all_cancers(60;9.57e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGGTTTCCCACATGACTTCA	0.522													11	11	---	---	---	---	PASS
ZNF233	353355	broad.mit.edu	37	19	44771015	44771015	+	Intron	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44771015A>G	uc002oyz.1	+						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF233_uc002oyy.1_Intron	NM_181756	NP_861421	A6NK53	ZN233_HUMAN	zinc finger protein 233						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2		Prostate(69;0.0435)|all_neural(266;0.226)				TTTCTTTTTCACAGGCTATCA	0.353													14	82	---	---	---	---	PASS
GPR77	27202	broad.mit.edu	37	19	47844500	47844500	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47844500G>A	uc010ela.1	+	2	662	c.444G>A	c.(442-444)GCG>GCA	p.A148A	GPR77_uc002pgk.1_Silent_p.A148A	NM_018485	NP_060955	Q9P296	C5ARL_HUMAN	G protein-coupled receptor 77	148	Cytoplasmic (Potential).				chemotaxis	integral to membrane|plasma membrane	C5a anaphylatoxin receptor activity			ovary(1)	1		all_cancers(25;1.72e-06)|all_lung(116;2.15e-05)|all_epithelial(76;3.44e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.0652)|Ovarian(192;0.086)		all cancers(93;0.000129)|OV - Ovarian serous cystadenocarcinoma(262;0.000415)|Epithelial(262;0.0109)|GBM - Glioblastoma multiforme(486;0.0138)		TTCAGCGGGCGTGCGGGGTGC	0.677													50	30	---	---	---	---	PASS
GPR77	27202	broad.mit.edu	37	19	47844501	47844501	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47844501T>A	uc010ela.1	+	2	663	c.445T>A	c.(445-447)TGC>AGC	p.C149S	GPR77_uc002pgk.1_Missense_Mutation_p.C149S	NM_018485	NP_060955	Q9P296	C5ARL_HUMAN	G protein-coupled receptor 77	149	Cytoplasmic (Potential).				chemotaxis	integral to membrane|plasma membrane	C5a anaphylatoxin receptor activity			ovary(1)	1		all_cancers(25;1.72e-06)|all_lung(116;2.15e-05)|all_epithelial(76;3.44e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.0652)|Ovarian(192;0.086)		all cancers(93;0.000129)|OV - Ovarian serous cystadenocarcinoma(262;0.000415)|Epithelial(262;0.0109)|GBM - Glioblastoma multiforme(486;0.0138)		TCAGCGGGCGTGCGGGGTGCA	0.682													48	30	---	---	---	---	PASS
FPR2	2358	broad.mit.edu	37	19	52272195	52272195	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52272195G>C	uc002pxr.2	+	2	329	c.284G>C	c.(283-285)TGG>TCG	p.W95S	FPR2_uc002pxs.3_Missense_Mutation_p.W95S|FPR2_uc010epf.2_Missense_Mutation_p.W95S	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	95	Extracellular (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(3)|ovary(1)	4						CCTTTTGGCTGGTTCCTGTGT	0.473													57	44	---	---	---	---	PASS
ZNF28	7576	broad.mit.edu	37	19	53304795	53304795	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53304795C>T	uc002qad.2	-	4	423	c.303G>A	c.(301-303)TGG>TGA	p.W101*	ZNF28_uc002qac.2_Nonsense_Mutation_p.W48*|ZNF28_uc010eqe.2_Nonsense_Mutation_p.W47*	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	101					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CATCTTCTTTCCACTGAAACT	0.428													57	132	---	---	---	---	PASS
LILRB5	10990	broad.mit.edu	37	19	54758611	54758611	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54758611C>G	uc002qex.2	-	6	1353	c.1242G>C	c.(1240-1242)GAG>GAC	p.E414D	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.E405D|LILRB5_uc002qey.2_Missense_Mutation_p.E414D|LILRB5_uc002qez.2_Missense_Mutation_p.E314D|LILRB5_uc002qfa.1_Missense_Mutation_p.E304D|LILRB5_uc010yes.1_RNA	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	414	Ig-like C2-type 4.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGACCACGAGCTCCTGGGGGT	0.632													32	22	---	---	---	---	PASS
LILRB2	10288	broad.mit.edu	37	19	54782923	54782923	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54782923A>G	uc002qfb.2	-	6	965	c.699T>C	c.(697-699)CCT>CCC	p.P233P	LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.2_Silent_p.P233P|LILRB2_uc010erj.2_RNA|LILRB2_uc002qfc.2_Silent_p.P233P|LILRB2_uc010yet.1_Silent_p.P117P|LILRB2_uc010yeu.1_Intron	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,	233	Extracellular (Potential).|Ig-like C2-type 3.				cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity			skin(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGCCACGACAGGACCCGGCT	0.577													36	47	---	---	---	---	PASS
LILRA1	11024	broad.mit.edu	37	19	55106308	55106308	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106308C>T	uc002qgh.1	+	4	431	c.249C>T	c.(247-249)TTC>TTT	p.F83F	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Silent_p.F83F	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	83	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)		AGGGCCAGTTCCCCATCCCAT	0.567													7	129	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55143129	55143129	+	Silent	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55143129C>T	uc002qgj.2	+	5	589	c.249C>T	c.(247-249)TTC>TTT	p.F83F	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Silent_p.F83F|LILRB1_uc002qgk.2_Silent_p.F83F|LILRB1_uc002qgm.2_Silent_p.F83F|LILRB1_uc010erq.2_Silent_p.F83F|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	83	Ig-like C2-type 1.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		AGGGCCAGTTCCCCATCCCAT	0.567										HNSCC(37;0.09)			59	70	---	---	---	---	PASS
KIR2DS4	3809	broad.mit.edu	37	19	55351040	55351040	+	Missense_Mutation	SNP	G	A	A	rs3189418		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55351040G>A	uc002qhm.1	+	5	596	c.550G>A	c.(550-552)GAC>AAC	p.D184N	KIR2DS4_uc010yfj.1_Silent_p.P169P|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Silent_p.P176P|KIR2DS4_uc002qhn.1_Intron	NM_012314	NP_036446	P43632	KI2S4_HUMAN	killer cell immunoglobulin-like receptor, two	184	Extracellular (Potential).|Ig-like C2-type 2.					integral to plasma membrane	receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		ATTCCAGGCCGACTTTCCTCT	0.587													53	46	---	---	---	---	PASS
NLRP7	199713	broad.mit.edu	37	19	55451776	55451776	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55451776G>T	uc002qih.3	-	4	487	c.411C>A	c.(409-411)ACC>ACA	p.T137T	NLRP7_uc002qig.3_Silent_p.T137T|NLRP7_uc002qii.3_Silent_p.T137T|NLRP7_uc010esk.2_Silent_p.T137T|NLRP7_uc010esl.2_Silent_p.T165T	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	137							ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		CTTGCCAAAAGGTGTTCTTCC	0.453													218	208	---	---	---	---	PASS
TNNT1	7138	broad.mit.edu	37	19	55652325	55652325	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55652325G>A	uc002qjb.3	-	9	402	c.313C>T	c.(313-315)CGG>TGG	p.R105W	TNNT1_uc002qiz.3_Missense_Mutation_p.R35W|TNNT1_uc002qja.3_Missense_Mutation_p.R35W|TNNT1_uc002qjc.3_Missense_Mutation_p.R105W|TNNT1_uc002qje.3_Missense_Mutation_p.R94W|TNNT1_uc002qjd.3_Missense_Mutation_p.R94W|TNNT1_uc002qjf.2_Missense_Mutation_p.R101W	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a	105					muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		GACCGGCGCCGCTCCTGGGAA	0.607											OREG0025677	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	20	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56515098	56515098	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56515098A>T	uc002qmj.2	+	2	79	c.79A>T	c.(79-81)ACA>TCA	p.T27S	NLRP5_uc002qmi.2_Missense_Mutation_p.T27S	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	27						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CACTCTTTCCACAGGTCCTAC	0.418													48	34	---	---	---	---	PASS
ZNF772	400720	broad.mit.edu	37	19	57985799	57985799	+	Intron	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57985799G>A	uc002qot.2	-						ZNF547_uc002qpm.3_Intron|ZNF772_uc010ygy.1_Intron|ZNF772_uc010ygz.1_Intron|ZNF772_uc010yha.1_Intron|ZNF772_uc002qou.2_Intron	NM_001024596	NP_001019767	Q68DY9	ZN772_HUMAN	zinc finger protein 772 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		CCTGAAAGCAGAGAAATGCTG	0.448													11	41	---	---	---	---	PASS
SIRPG	55423	broad.mit.edu	37	20	1616857	1616857	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1616857G>C	uc002wfm.1	-	3	790	c.725C>G	c.(724-726)GCC>GGC	p.A242G	SIRPG_uc002wfn.1_Missense_Mutation_p.A242G|SIRPG_uc002wfo.1_Intron|uc002wfp.1_Intron	NM_018556	NP_061026	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma isoform 1	242	Extracellular (Potential).|Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|cell-cell signaling|intracellular signal transduction|leukocyte migration|negative regulation of cell proliferation|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to membrane|intracellular|plasma membrane	protein binding			ovary(1)	1						AGACAAGTTGGCAGTCCCACG	0.637													20	32	---	---	---	---	PASS
SIRPA	140885	broad.mit.edu	37	20	1915374	1915374	+	Nonsense_Mutation	SNP	G	T	T	rs141454528		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1915374G>T	uc002wfq.2	+	8	1600	c.1240G>T	c.(1240-1242)GAG>TAG	p.E414*	SIRPA_uc010zps.1_Nonsense_Mutation_p.E394*|SIRPA_uc002wfr.2_Nonsense_Mutation_p.E414*|SIRPA_uc002wfs.2_Nonsense_Mutation_p.E414*|SIRPA_uc002wft.2_Nonsense_Mutation_p.E414*	NM_001040022	NP_001035111	P78324	SHPS1_HUMAN	signal-regulatory protein alpha precursor	414	Cytoplasmic (Potential).				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GCATGAGCCCGAGAAGAATGC	0.338													51	59	---	---	---	---	PASS
SLC4A11	83959	broad.mit.edu	37	20	3218266	3218266	+	Silent	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3218266A>G	uc002wig.2	-	1	108	c.60T>C	c.(58-60)CAT>CAC	p.H20H	SLC4A11_uc010zqe.1_Intron|SLC4A11_uc002wih.2_Intron|SLC4A11_uc010zqf.1_Intron	NM_032034	NP_114423	Q8NBS3	S4A11_HUMAN	solute carrier family 4 member 11	20	Cytoplasmic (Potential).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1						CACCAGCCCCATGGACCAAGC	0.592													8	87	---	---	---	---	PASS
HSPA12B	116835	broad.mit.edu	37	20	3725561	3725561	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3725561C>A	uc002wjd.2	+	5	382	c.279C>A	c.(277-279)GGC>GGA	p.G93G	HSPA12B_uc010zqi.1_Silent_p.G93G|HSPA12B_uc002wje.2_Silent_p.G6G|HSPA12B_uc010zqj.1_5'UTR	NM_052970	NP_443202	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	93							ATP binding				0						AATGGGAGGGCGGAGACCCGG	0.532													25	37	---	---	---	---	PASS
PRNP	5621	broad.mit.edu	37	20	4680514	4680514	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4680514C>A	uc002wku.2	+	2	1011	c.648C>A	c.(646-648)ACC>ACA	p.T216T	PRNP_uc002wkv.2_Silent_p.T216T|PRNP_uc002wkw.2_Silent_p.T216T|PRNP_uc002wkx.2_Silent_p.T216T|PRNP_uc002wkt.1_Silent_p.T186T|PRNP_uc002wky.2_Silent_p.T216T|PRNP_uc010gbe.1_Silent_p.T216T	NM_001080122	NP_001073591	P04156	PRIO_HUMAN	prion protein preproprotein	216	Interaction with GRB2, ERI3 and SYN1 (By similarity).				axon guidance|cell cycle arrest|cellular copper ion homeostasis|metabolic process|negative regulation of activated T cell proliferation|negative regulation of calcineurin-NFAT signaling pathway|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-2 production|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell receptor signaling pathway|protein homooligomerization|response to oxidative stress	anchored to membrane|endoplasmic reticulum|extrinsic to membrane|Golgi apparatus|membrane raft|nucleus|plasma membrane	copper ion binding|identical protein binding|microtubule binding			central_nervous_system(1)	1					Tetracycline(DB00759)	TGTGTATCACCCAGTACGAGA	0.532													5	66	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20493389	20493389	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20493389G>C	uc002wrz.2	-	32	4767	c.4624C>G	c.(4624-4626)CTA>GTA	p.L1542V	RALGAPA2_uc010gcx.2_Missense_Mutation_p.L1246V|RALGAPA2_uc010zsg.1_Missense_Mutation_p.L990V|RALGAPA2_uc002wsa.1_Missense_Mutation_p.L314V	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1542					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GGTTCATTTAGATTTAGCTGT	0.413													32	120	---	---	---	---	PASS
TMEM90B	79953	broad.mit.edu	37	20	24523840	24523840	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24523840G>C	uc002wtw.1	+	2	740	c.107G>C	c.(106-108)AGA>ACA	p.R36T		NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B	36	Cytoplasmic (Potential).				response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						GCCGAGAGCAGAGATGGTCTG	0.562													5	90	---	---	---	---	PASS
ZNF337	26152	broad.mit.edu	37	20	25656728	25656728	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25656728G>A	uc002wva.2	-	4	1718	c.1196C>T	c.(1195-1197)TCA>TTA	p.S399L	uc002wuz.2_RNA|ZNF337_uc010ztg.1_Missense_Mutation_p.S367L|ZNF337_uc002wvb.2_Missense_Mutation_p.S399L|ZNF337_uc002wvc.2_Missense_Mutation_p.S399L	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	399					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTTCTCCCCTGAGTGTGTTCT	0.498													24	75	---	---	---	---	PASS
PLUNC	51297	broad.mit.edu	37	20	31825574	31825574	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31825574C>A	uc002wyv.2	+	2	127	c.57C>A	c.(55-57)GCC>GCA	p.A19A	PLUNC_uc002wyt.3_Silent_p.A19A|PLUNC_uc002wyu.3_Silent_p.A19A	NM_130852	NP_570913	Q9NP55	PLUNC_HUMAN	palate, lung and nasal epithelium associated	19					innate immune response	extracellular region	lipid binding				0						AGACCATGGCCCAGTTTGGAG	0.552													15	32	---	---	---	---	PASS
PLUNC	51297	broad.mit.edu	37	20	31825575	31825575	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31825575C>T	uc002wyv.2	+	2	128	c.58C>T	c.(58-60)CAG>TAG	p.Q20*	PLUNC_uc002wyt.3_Nonsense_Mutation_p.Q20*|PLUNC_uc002wyu.3_Nonsense_Mutation_p.Q20*	NM_130852	NP_570913	Q9NP55	PLUNC_HUMAN	palate, lung and nasal epithelium associated	20					innate immune response	extracellular region	lipid binding				0						GACCATGGCCCAGTTTGGAGG	0.547													17	32	---	---	---	---	PASS
CHMP4B	128866	broad.mit.edu	37	20	32439921	32439921	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32439921G>T	uc002xaa.2	+	4	678	c.522G>T	c.(520-522)GAG>GAT	p.E174D		NM_176812	NP_789782	Q9H444	CHM4B_HUMAN	chromatin modifying protein 4B	174	Potential.				cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2						TAGAACAGGAGGAACTAGACA	0.507													6	121	---	---	---	---	PASS
MYH7B	57644	broad.mit.edu	37	20	33575001	33575001	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33575001A>G	uc002xbi.1	+	14	1276	c.1184A>G	c.(1183-1185)TAT>TGT	p.Y395C		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	353	Myosin head-like.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)			TGTGCCTGCTATAAGATCGTG	0.607													36	68	---	---	---	---	PASS
FAM83D	81610	broad.mit.edu	37	20	37580566	37580566	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37580566T>C	uc002xjg.2	+	4	1292	c.1251T>C	c.(1249-1251)ATT>ATC	p.I417I		NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	387					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)				GAAAGGCCATTGACGCTGCCA	0.567													15	22	---	---	---	---	PASS
MATN4	8785	broad.mit.edu	37	20	43932922	43932922	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43932922C>A	uc002xnn.2	-	3	776	c.589G>T	c.(589-591)GAG>TAG	p.E197*	MATN4_uc002xno.2_Nonsense_Mutation_p.E197*|MATN4_uc002xnp.2_Nonsense_Mutation_p.E197*|MATN4_uc010zwr.1_Nonsense_Mutation_p.E145*|MATN4_uc002xnr.1_Nonsense_Mutation_p.E197*|RBPJL_uc002xns.2_5'Flank|RBPJL_uc002xnt.2_5'Flank	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	197	VWFA 1.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)				TCGAAGGACTCTACGAGGAAG	0.627													5	80	---	---	---	---	PASS
TNNC2	7125	broad.mit.edu	37	20	44453289	44453289	+	Intron	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44453289G>C	uc002xpr.2	-							NM_003279	NP_003270	P02585	TNNC2_HUMAN	fast skeletal muscle troponin C						muscle filament sliding|regulation of muscle contraction|skeletal muscle contraction	cytosol|troponin complex	calcium ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(115;0.0122)				TGCGAGGGAGGGCAGAGGGCA	0.612													6	20	---	---	---	---	PASS
SLC35C2	51006	broad.mit.edu	37	20	44986276	44986276	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44986276C>A	uc002xro.2	-	3	798	c.257G>T	c.(256-258)AGA>ATA	p.R86I	SLC35C2_uc002xrp.2_Missense_Mutation_p.R86I|SLC35C2_uc002xrq.2_Missense_Mutation_p.R86I|SLC35C2_uc002xrr.2_Missense_Mutation_p.R86I|SLC35C2_uc010zxn.1_5'UTR|SLC35C2_uc010zxo.1_5'UTR|SLC35C2_uc010zxp.1_Missense_Mutation_p.R115I	NM_173179	NP_775271	Q9NQQ7	S35C2_HUMAN	solute carrier family 35, member C2 isoform a	86					transport	integral to membrane				ovary(1)	1		Myeloproliferative disorder(115;0.0122)				GGGAGCCACTCTTCTGAGGTA	0.627													27	57	---	---	---	---	PASS
NCOA3	8202	broad.mit.edu	37	20	46254215	46254215	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46254215T>G	uc002xtk.2	+	5	552	c.347T>G	c.(346-348)CTT>CGT	p.L116R	NCOA3_uc010ght.1_Missense_Mutation_p.L116R|NCOA3_uc002xtl.2_Missense_Mutation_p.L116R|NCOA3_uc002xtm.2_Missense_Mutation_p.L116R|NCOA3_uc002xtn.2_Missense_Mutation_p.L116R|NCOA3_uc010zyc.1_5'Flank	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a	116	PAS.				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5						TTAGGACCGCTTTTACTTCAG	0.348													5	52	---	---	---	---	PASS
TSHZ2	128553	broad.mit.edu	37	20	51872343	51872343	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872343T>C	uc002xwo.2	+	2	3302	c.2346T>C	c.(2344-2346)TCT>TCC	p.S782S		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	782					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			AAGCACAATCTTGTATGTCCC	0.572													42	88	---	---	---	---	PASS
SPO11	23626	broad.mit.edu	37	20	55906898	55906898	+	Silent	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55906898T>C	uc002xye.2	+	2	234	c.141T>C	c.(139-141)GTT>GTC	p.V47V	SPO11_uc002xyf.2_Intron	NM_012444	NP_036576	Q9Y5K1	SPO11_HUMAN	meiotic recombination protein SPO11 isoform a	47					female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)			GTTCTGAGGTTCTTGCATCTA	0.328								Editing_and_processing_nucleases					7	152	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57768671	57768671	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57768671C>T	uc002yan.2	+	1	2597	c.2597C>T	c.(2596-2598)CCA>CTA	p.P866L		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	866						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					GGGGAGGTGCCAGGGGGCTCA	0.652													20	22	---	---	---	---	PASS
CDH26	60437	broad.mit.edu	37	20	58581786	58581786	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58581786A>G	uc002ybe.2	+	17	2539	c.2239A>G	c.(2239-2241)ATG>GTG	p.M747V	CDH26_uc002ybf.1_Missense_Mutation_p.M286V|CDH26_uc010zzy.1_RNA|CDH26_uc002ybg.2_Missense_Mutation_p.M238V|CDH26_uc002ybh.2_Missense_Mutation_p.M80V|CDH26_uc002ybi.2_Missense_Mutation_p.M39V	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	706	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AGATGCCACAATGCACAGACA	0.557													22	60	---	---	---	---	PASS
CDH4	1002	broad.mit.edu	37	20	60504842	60504842	+	Silent	SNP	G	A	A	rs151300553		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60504842G>A	uc002ybn.1	+	13	2195	c.2181G>A	c.(2179-2181)GCG>GCA	p.A727A	CDH4_uc002ybp.1_Silent_p.A653A	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	727	Extracellular (Potential).				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CAGTGGCAGCGGCTGGTCTGG	0.607													12	34	---	---	---	---	PASS
LAMA5	3911	broad.mit.edu	37	20	60885614	60885614	+	Silent	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60885614G>A	uc002ycq.2	-	76	10528	c.10461C>T	c.(10459-10461)TTC>TTT	p.F3487F		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	3487	Laminin G-like 4.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CACAGCCGCTGAACCCGACGG	0.682													25	23	---	---	---	---	PASS
SLCO4A1	28231	broad.mit.edu	37	20	61288084	61288084	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61288084C>T	uc002ydb.1	+	2	483	c.278C>T	c.(277-279)CCG>CTG	p.P93L	SLCO4A1_uc002ydc.1_RNA	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	93	Cytoplasmic (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)			GCCTTCGCACCGCCGTGCCTG	0.662													15	8	---	---	---	---	PASS
DIDO1	11083	broad.mit.edu	37	20	61525406	61525406	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61525406C>T	uc002ydr.1	-	12	2977	c.2713G>A	c.(2713-2715)GAG>AAG	p.E905K	DIDO1_uc002yds.1_Missense_Mutation_p.E905K|DIDO1_uc002ydt.1_Missense_Mutation_p.E905K|DIDO1_uc002ydu.1_Missense_Mutation_p.E905K	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	905					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					GGCACAGCCTCCGGCATCACC	0.502													36	116	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45861595	45861595	+	Silent	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45861595G>T	uc002zet.1	+	33	4620	c.4407G>T	c.(4405-4407)TCG>TCT	p.S1469S	TRPM2_uc002zeu.1_Silent_p.S1469S|TRPM2_uc002zew.1_Silent_p.S1469S|TRPM2_uc010gpt.1_Silent_p.S1519S|TRPM2_uc002zex.1_Silent_p.S1255S|TRPM2_uc002zey.1_Silent_p.S948S|TRPM2_uc011aff.1_Silent_p.S150S	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	1469	Nudix hydrolase.|Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CCTGCGACTCGGGGGCCTCCA	0.652													3	14	---	---	---	---	PASS
DGCR2	9993	broad.mit.edu	37	22	19055686	19055686	+	Silent	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19055686C>A	uc002zoq.1	-	3	503	c.255G>T	c.(253-255)CGG>CGT	p.R85R	DGCR2_uc002zor.1_5'UTR|DGCR2_uc011agr.1_Silent_p.R44R	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor	85	Extracellular (Potential).				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					CCCGCCCCTGCCGCGGATCCA	0.632													5	14	---	---	---	---	PASS
KLHL22	84861	broad.mit.edu	37	22	20812204	20812204	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20812204C>A	uc002zsl.1	-	5	1305	c.1196G>T	c.(1195-1197)AGG>ATG	p.R399M	KLHL22_uc011ahr.1_Missense_Mutation_p.R256M|KLHL22_uc002zsm.1_Missense_Mutation_p.R399M	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like	399	Kelch 2.				cell division	Cul3-RING ubiquitin ligase complex				lung(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GTAGATGTACCTGCCTACAAC	0.612													4	21	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23135349	23135349	+	RNA	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23135349G>T	uc011aim.1	+	251		c.11991G>T								Parts of antibodies, mostly variable regions.												0						CATGATTTATGATGTCAGTAA	0.552													29	427	---	---	---	---	PASS
SLC2A11	66035	broad.mit.edu	37	22	24225966	24225966	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24225966T>C	uc002zyn.3	+	9	1091	c.992T>C	c.(991-993)GTA>GCA	p.V331A	SLC2A11_uc002zyl.1_3'UTR|SLC2A11_uc002zym.3_Missense_Mutation_p.V338A|SLC2A11_uc002zyo.3_RNA|SLC2A11_uc011ajc.1_Intron|SLC2A11_uc002zyp.3_Missense_Mutation_p.V334A	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c	331	Helical; Name=8; (Potential).					integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						CAGTGTGTGGTAATCGAGAGG	0.612													6	72	---	---	---	---	PASS
RFPL2	10739	broad.mit.edu	37	22	32588926	32588926	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32588926C>A	uc003amg.3	-	4	1455	c.519G>T	c.(517-519)AAG>AAT	p.K173N	RFPL2_uc003ame.3_Missense_Mutation_p.K112N|RFPL2_uc003amf.3_Missense_Mutation_p.K83N|RFPL2_uc003amh.3_Missense_Mutation_p.K83N	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	173	B30.2/SPRY.						zinc ion binding			skin(1)	1						TCTGCAGAATCTTCTTCAGCT	0.512													50	135	---	---	---	---	PASS
MCM5	4174	broad.mit.edu	37	22	35796559	35796559	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35796559G>T	uc003anu.3	+	2	222	c.128G>T	c.(127-129)CGA>CTA	p.R43L	MCM5_uc010gwr.2_5'UTR|MCM5_uc003anv.3_Missense_Mutation_p.R43L	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	43					cell cycle checkpoint|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	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1						CGGCAGTACCGAGTGGGCACC	0.672													10	20	---	---	---	---	PASS
RASD2	23551	broad.mit.edu	37	22	35943063	35943063	+	Silent	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35943063C>G	uc003anx.2	+	2	412	c.207C>G	c.(205-207)CTC>CTG	p.L69L	RASD2_uc003any.2_Silent_p.L69L	NM_014310	NP_055125	Q96D21	RHES_HUMAN	RASD family, member 2 precursor	69					locomotory behavior|positive regulation of protein kinase B signaling cascade|positive regulation of protein sumoylation|regulation of cAMP-mediated signaling	intracellular|plasma membrane	G-protein beta-subunit binding|GTP binding|GTPase activity			lung(2)|skin(1)	3						TGTACCAGCTCGACATCCTGG	0.617													31	32	---	---	---	---	PASS
APOL5	80831	broad.mit.edu	37	22	36122449	36122449	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36122449G>C	uc003aof.2	+	3	334	c.334G>C	c.(334-336)GAG>CAG	p.E112Q		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	112					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0						GCACAAGTTTGAGCTAGAACA	0.458													6	66	---	---	---	---	PASS
CELSR1	9620	broad.mit.edu	37	22	46835291	46835291	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46835291C>G	uc003bhw.1	-	3	4201	c.4201G>C	c.(4201-4203)GAT>CAT	p.D1401H		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1401	Extracellular (Potential).				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GAGCGGGCATCCACCTCACAG	0.647													6	16	---	---	---	---	PASS
PLXNB2	23654	broad.mit.edu	37	22	50728775	50728775	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50728775G>A	uc003bkv.3	-	3	345	c.239C>T	c.(238-240)CCG>CTG	p.P80L		NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	80	Extracellular (Potential).|Sema.				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCGATGGGCGGCGTGCACTT	0.652													9	15	---	---	---	---	PASS
SHOX	6473	broad.mit.edu	37	X	601814	601814	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:601814T>C	uc004cph.1	+	5	1316	c.625T>C	c.(625-627)TTC>CTC	p.F209L	SHOX_uc004cpi.2_Missense_Mutation_p.F209L	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	209					skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACGGATGCCTTTCCAACAGGT	0.567													24	18	---	---	---	---	PASS
CSF2RA	1438	broad.mit.edu	37	X	1428351	1428351	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1428351G>C	uc010nct.2	+	14	1504	c.1182G>C	c.(1180-1182)TTG>TTC	p.L394F	CSF2RA_uc004cpq.2_3'UTR|CSF2RA_uc004cpn.2_Missense_Mutation_p.L394F|CSF2RA_uc004cpo.2_Missense_Mutation_p.L394F|CSF2RA_uc010ncu.2_RNA|CSF2RA_uc011mhc.1_Missense_Mutation_p.L261F|CSF2RA_uc004cpp.2_Missense_Mutation_p.D335H|CSF2RA_uc010ncv.2_Missense_Mutation_p.L428F|CSF2RA_uc004cpr.2_3'UTR	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain	394	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		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)			Sargramostim(DB00020)	AAGAGGTCTTGACCGTGAAGG	0.527													6	133	---	---	---	---	PASS
ASMT	438	broad.mit.edu	37	X	1743268	1743268	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1743268G>A	uc004cqd.2	+	4	496	c.351G>A	c.(349-351)TGG>TGA	p.W117*	ASMT_uc010ncy.2_Nonsense_Mutation_p.W117*|ASMT_uc004cqe.2_Nonsense_Mutation_p.W117*	NM_004043	NP_004034	P46597	HIOM_HUMAN	acetylserotonin O-methyltransferase	117					melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		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)				ACCGGTGCTGGGGCCACCTGG	0.662													9	80	---	---	---	---	PASS
MAGEB1	4112	broad.mit.edu	37	X	30269565	30269565	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30269565T>A	uc004dcc.2	+	4	1275	c.955T>A	c.(955-957)TCC>ACC	p.S319T	MAGEB1_uc004dcd.2_Missense_Mutation_p.S319T|MAGEB1_uc004dce.2_Missense_Mutation_p.S319T	NM_002363	NP_002354	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	319											0						CCAAGTCCGATCCAGTGTTAG	0.547													34	13	---	---	---	---	PASS
CXorf22	170063	broad.mit.edu	37	X	35969926	35969926	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35969926G>C	uc004ddj.2	+	6	951	c.892G>C	c.(892-894)GAT>CAT	p.D298H	CXorf22_uc010ngv.2_RNA	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	298										large_intestine(1)|lung(1)|ovary(1)	3						ACAGGGTACAGATATTCAACA	0.269													9	5	---	---	---	---	PASS
SUV39H1	6839	broad.mit.edu	37	X	48564683	48564683	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48564683C>T	uc004dkn.2	+	4	901	c.856C>T	c.(856-858)CGG>TGG	p.R286W	SUV39H1_uc011mmf.1_Missense_Mutation_p.R297W|SUV39H1_uc011mmg.1_RNA	NM_003173	NP_003164	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1	286	Mediates interaction with MECOM (By similarity).|SET.				cell cycle|cell differentiation|chromatin silencing at rDNA|interspecies interaction between organisms|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|chromosome, centromeric region|condensed nuclear chromosome|rDNA heterochromatin	chromatin binding|histone methyltransferase activity (H3-K9 specific)|protein N-terminus binding|zinc ion binding				0						GGCAGAGCGGCGGGGCCAGAT	0.592													5	21	---	---	---	---	PASS
MAGED2	10916	broad.mit.edu	37	X	54840805	54840805	+	Intron	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54840805G>T	uc004dtk.1	+						MAGED2_uc004dtl.1_Intron|MAGED2_uc004dtm.1_Intron|MAGED2_uc010nkc.1_Intron|MAGED2_uc004dtn.1_Intron|MAGED2_uc004dto.1_Intron|SNORA11_uc004dtp.1_RNA	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2											ovary(2)|breast(1)	3						CTTGCAGTGGGGTGTGCTCAG	0.527													4	30	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73963358	73963358	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73963358C>A	uc004eby.2	-	3	1651	c.1034G>T	c.(1033-1035)TGC>TTC	p.C345F		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	345					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						TCGCTTGGGGCAGGTAGTAAA	0.463													27	7	---	---	---	---	PASS
CXorf26	51260	broad.mit.edu	37	X	75397617	75397617	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75397617G>C	uc004ecl.1	+	6	779	c.576G>C	c.(574-576)GAG>GAC	p.E192D		NM_016500	NP_057584	Q9BVG4	CX026_HUMAN	hypothetical protein LOC51260	192											0						atggaggagagaaaggagctg	0.040													14	5	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91090495	91090495	+	5'UTR	SNP	G	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91090495G>T	uc004efk.1	+	1					PCDH11X_uc004efl.1_5'UTR|PCDH11X_uc004efo.1_5'UTR|PCDH11X_uc010nmv.1_5'UTR|PCDH11X_uc004efm.1_5'UTR|PCDH11X_uc004efn.1_5'UTR|PCDH11X_uc004efh.1_5'UTR|PCDH11X_uc004efj.1_5'UTR	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						TGTAACAAGTGTACCTGGTAT	0.468													22	12	---	---	---	---	PASS
DCX	1641	broad.mit.edu	37	X	110574147	110574147	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110574147C>T	uc004epd.2	-	5	1346	c.1174G>A	c.(1174-1176)GCA>ACA	p.A392T	DCX_uc011msv.1_Missense_Mutation_p.G392S|DCX_uc004epe.2_Missense_Mutation_p.A311T|DCX_uc004epf.2_Missense_Mutation_p.G311S|DCX_uc004epg.2_Missense_Mutation_p.A311T	NM_000555	NP_000546	O43602	DCX_HUMAN	doublecortin isoform a	392	Pro/Ser-rich.				axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4						TGGTCGTTACCTGAGTCAGCT	0.527													75	30	---	---	---	---	PASS
CXorf61	203413	broad.mit.edu	37	X	115593069	115593069	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115593069C>A	uc004eqj.1	-	2	301	c.181G>T	c.(181-183)GAC>TAC	p.D61Y		NM_001017978	NP_001017978	Q5H943	KKLC1_HUMAN	chromosome X open reading frame 61	61	Extracellular (Potential).					integral to membrane|plasma membrane					0						CGAGAGAGGTCGTAGACTGCA	0.418													26	8	---	---	---	---	PASS
NKAP	79576	broad.mit.edu	37	X	119064021	119064021	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119064021A>C	uc004esh.2	-	8	1198	c.1031T>G	c.(1030-1032)ATT>AGT	p.I344S	NKAP_uc004esg.2_Missense_Mutation_p.I231S	NM_024528	NP_078804	Q8N5F7	NKAP_HUMAN	NFKB activating protein	344	Necessary for interaction with HDAC3 and transcriptional repression.				negative regulation of transcription, DNA-dependent|Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding			ovary(2)	2						AAATGATGCAATTTCTTCACT	0.393													13	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	852254	852255	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:852254_852255delCA								FAM41C (40072 upstream) : FLJ39609 (698 downstream)																							ATCAGGTTGCCAGCACTTTTCA	0.530													4	2	---	---	---	---	
RER1	11079	broad.mit.edu	37	1	2332691	2332692	+	Intron	INS	-	CC	CC	rs148750749	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2332691_2332692insCC	uc001aje.1	+						RER1_uc001ajf.1_Intron	NM_007033	NP_008964	O15258	RER1_HUMAN	RER1 retention in endoplasmic reticulum 1						retrograde vesicle-mediated transport, Golgi to ER	integral to Golgi membrane					0	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.28e-37)|OV - Ovarian serous cystadenocarcinoma(86;8.29e-23)|GBM - Glioblastoma multiforme(42;4.71e-08)|Colorectal(212;4.73e-05)|COAD - Colon adenocarcinoma(227;0.00021)|Kidney(185;0.00116)|BRCA - Breast invasive adenocarcinoma(365;0.00459)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0182)|Lung(427;0.204)		tcctccctccttcctccctcct	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2468428	2468429	+	IGR	DEL	GT	-	-	rs113262362		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2468428_2468429delGT								HES5 (6744 upstream) : LOC115110 (12930 downstream)																							GCACCTGTGCGtgtgtgtgtgt	0.124													4	3	---	---	---	---	
NPHP4	261734	broad.mit.edu	37	1	5958904	5958905	+	Intron	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5958904_5958905delCA	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|NPHP4_uc009vlu.1_Intron	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CCcacacatgcacacacacaca	0.198													4	2	---	---	---	---	
THAP3	90326	broad.mit.edu	37	1	6693976	6693977	+	Intron	INS	-	A	A	rs3215503		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6693976_6693977insA	uc001aoe.1	+							NM_138350	NP_612359	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated								DNA binding|metal ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		gactcagtctgaaaaaaaaaaC	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9283352	9283360	+	IGR	DEL	TCATCTTCT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9283352_9283360delTCATCTTCT								MIR34A (71516 upstream) : H6PD (11503 downstream)																							ttcttcttcgtcatcttcttcatcttctt	0.000													6	3	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10751163	10751164	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10751163_10751164insT	uc001aro.2	-						CASZ1_uc001arp.1_Intron|CASZ1_uc009vmx.2_Intron	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		cctctctTTCCTTTTTTTTTTA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11460618	11460619	+	IGR	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11460618_11460619delTG								UBIAD1 (112128 upstream) : PTCHD2 (78676 downstream)																							GATTTAAGGTtgtgtgtgtgtg	0.168													4	2	---	---	---	---	
PTCHD2	57540	broad.mit.edu	37	1	11596339	11596339	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11596339delC	uc001ash.3	+							NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CCAGAGGGGTCCCGCAGGCAG	0.701													8	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11612086	11612087	+	IGR	DEL	AA	-	-	rs34827805		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11612086_11612087delAA								PTCHD2 (14447 upstream) : FBXO2 (96363 downstream)																							accctgtctcaaaaaaaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14745991	14745992	+	IGR	DEL	AG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14745991_14745992delAG								PRDM2 (594419 upstream) : KAZ (179221 downstream)																							TGGACTTACCAGAGTGTTAGGC	0.371													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16871463	16871464	+	IGR	INS	-	C	C	rs75135182		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16871463_16871464insC								CROCCL2 (52267 upstream) : NBPF1 (18948 downstream)																							TGCtttttttttttctttcttt	0.238													3	3	---	---	---	---	
PADI6	353238	broad.mit.edu	37	1	17699379	17699380	+	Intron	INS	-	AC	AC	rs150250586	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17699379_17699380insAC	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)	TCGGAGAGCAAACACAGGGGTC	0.569													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18190793	18190797	+	IGR	DEL	TCCCT	-	-	rs140303237	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18190793_18190797delTCCCT								ACTL8 (37237 upstream) : IGSF21 (243443 downstream)																							catccatccatcccttccatccatc	0.161													3	3	---	---	---	---	
AKR7A3	22977	broad.mit.edu	37	1	19610321	19610322	+	Intron	INS	-	C	C	rs138929566	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610321_19610322insC	uc001bbv.1	-							NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3						cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		tgagactctgtccccccaaaaa	0.139													4	7	---	---	---	---	
KIF17	57576	broad.mit.edu	37	1	21020596	21020597	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21020596_21020597insT	uc001bdr.3	-						KIF17_uc009vpx.2_Intron|KIF17_uc001bds.3_Intron	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		ccatcctgtccttttttttttt	0.010													4	2	---	---	---	---	
TCEA3	6920	broad.mit.edu	37	1	23719106	23719107	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23719106_23719107insA	uc001bgx.1	-						TCEA3_uc009vqm.1_Intron	NM_003196	NP_003187	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3						regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	nucleus	DNA binding|translation elongation factor activity|zinc ion binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		acatcatacacacacacacaca	0.020													4	2	---	---	---	---	
DHDDS	79947	broad.mit.edu	37	1	26773179	26773180	+	Intron	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26773179_26773180delGT	uc001bml.2	+						DHDDS_uc001bmk.2_Intron|DHDDS_uc001bmm.2_Intron|DHDDS_uc001bmn.2_Intron|DHDDS_uc010ofd.1_Intron	NM_205861	NP_995583	Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase isoform b								protein binding|transferase activity, transferring alkyl or aryl (other than methyl) groups			breast(3)	3		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		CACCAAATAAgtgtgtgtgtgt	0.351													3	3	---	---	---	---	
EPB41	2035	broad.mit.edu	37	1	29320677	29320677	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29320677delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		AAGTTGACAAttttttttttg	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29460062	29460062	+	IGR	DEL	A	-	-	rs12034124		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29460062delA								TMEM200B (9655 upstream) : SFRS4 (14189 downstream)																							aaagaaaaagaaaaaaaaaag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30196697	30196702	+	IGR	DEL	CAGCAT	-	-	rs72368977	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30196697_30196702delCAGCAT								PTPRU (543382 upstream) : MATN1 (987424 downstream)																							tcaccactaccagcatcaccaacatc	0.000													4	4	---	---	---	---	
RNF19B	127544	broad.mit.edu	37	1	33421366	33421366	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33421366delG	uc010oho.1	-						RNF19B_uc001bwm.3_Intron|RNF19B_uc010ohp.1_Intron	NM_153341	NP_699172	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B isoform a							integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				aaaaaaaaaagaaaagaaaaT	0.224													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34617415	34617416	+	Intron	INS	-	C	C	rs150297416	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34617415_34617416insC	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				cctccctccctccccccccttc	0.139													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	41992319	41992320	+	Intron	DEL	CA	-	-	rs117190127		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41992319_41992320delCA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ctcacacccccacactcacact	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	42602455	42602456	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42602455_42602456delCA								HIVEP3 (100859 upstream) : GUCA2B (16636 downstream)																							tccAGTTCTTCACTCTAGCATC	0.277													4	2	---	---	---	---	
CCDC30	728621	broad.mit.edu	37	1	43061998	43061999	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43061998_43061999insA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30												0						gaatatctgagaaaaatcccct	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43434811	43434811	+	Intron	DEL	T	-	-	rs67506605		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43434811delT	uc001cil.2	+											Homo sapiens cDNA FLJ32224 fis, clone PLACE6004336.																		AAAAGGGAGAttttttttttt	0.179													4	2	---	---	---	---	
JAK1	3716	broad.mit.edu	37	1	65326510	65326513	+	Intron	DEL	TGTG	-	-	rs71686880		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65326510_65326513delTGTG	uc001dbu.1	-						JAK1_uc009wam.1_Intron	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		CAGATGACTCtgtgtgtgtgtgtg	0.265			Mis		ALL								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83867324	83867324	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83867324delC								None (None upstream) : TTLL7 (467735 downstream)																							TAAAACACTTCCCAGAATATT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95413021	95413021	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95413021delA								CNN3 (20286 upstream) : ALG14 (35258 downstream)																							AAATTCCCTCAAAAAAACAGA	0.393													4	2	---	---	---	---	
GSTM2	2946	broad.mit.edu	37	1	110221775	110221775	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110221775delT	uc010ovt.1	+						GSTM2_uc009wfk.2_Intron	NM_001142368	NP_001135840	P28161	GSTM2_HUMAN	glutathione S-transferase mu 2 isoform 2						glutathione metabolic process|xenobiotic catabolic process	cytoplasm	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0122)|Colorectal(144;0.0129)|Epithelial(280;0.0146)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.047)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	CATCTTATGATTTTTTTTTTT	0.144													4	2	---	---	---	---	
MOV10	4343	broad.mit.edu	37	1	113225709	113225709	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113225709delT	uc001eck.2	+						MOV10_uc001ecl.2_Intron|MOV10_uc001ecn.2_Intron|MOV10_uc001ecm.2_Intron|MOV10_uc009wgj.1_Intron	NM_001130079	NP_001123551	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog						mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		gcctggctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115744343	115744343	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115744343delA								TSPAN2 (112228 upstream) : NGF (84194 downstream)																							ctaagcaagcaaaatgaatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116005817	116005820	+	IGR	DEL	AGGA	-	-	rs34578935		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116005817_116005820delAGGA								NGF (124960 upstream) : VANGL1 (178754 downstream)																							agagggagggaggaaggaaggaag	0.088													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121142796	121142797	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121142796_121142797insA								FCGR1B (206852 upstream) : LOC647121 (118113 downstream)																							gaaatgagatgaatgatgagat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142559278	142559279	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142559278_142559279insT								None (None upstream) : None (None downstream)																							ATATGTCATAGTTTTTTTCTAT	0.282													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142587613	142587613	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142587613delA								None (None upstream) : None (None downstream)																							gtcatcttttaaaaaaaatag	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144590644	144590644	+	Intron	DEL	A	-	-	rs139951242		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144590644delA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						tgcagatgagaaaaacagaaa	0.010													2	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144998136	144998136	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144998136delT	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)		ACATTGTACGTTTTGCTTTGT	0.174			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145262809	145262811	+	Intron	DEL	TTC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145262809_145262811delTTC	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)		TTCCTTTTTTTTCTTTCTTTTTA	0.369													4	4	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145622421	145622422	+	Intron	INS	-	TT	TT	rs150989367	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145622421_145622422insTT	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_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)		tttgttttttgtttttttttga	0.173													3	3	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148947071	148947072	+	Intron	DEL	AA	-	-	rs147156945		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148947071_148947072delAA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						tatctgagataagttaatttat	0.139													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149209072	149209081	+	IGR	DEL	GGGACTGGAT	-	-	rs67367254		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149209072_149209081delGGGACTGGAT								LOC645166 (256018 upstream) : LOC388692 (70395 downstream)																							TCATCAAACAGGGACTGGATCCTTGTCAAA	0.405													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149227513	149227514	+	IGR	INS	-	G	G	rs141540641		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149227513_149227514insG								LOC645166 (274459 upstream) : LOC388692 (51962 downstream)																							cagaggaaactactaaggtttg	0.030													4	2	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149285546	149285547	+	RNA	INS	-	A	A	rs144216017	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149285546_149285547insA	uc010pbf.1	+	1		c.6071_6072insA			LOC388692_uc001esg.3_5'Flank	NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						ttctgtctctcaaaaaaaaTGC	0.163													8	4	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149287128	149287129	+	RNA	DEL	CT	-	-	rs140343451		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149287128_149287129delCT	uc010pbf.1	+	1		c.7653_7654delCT			LOC388692_uc001esg.3_5'Flank	NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						GGGGACTGGCCTCTCTGCACGG	0.594													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149865853	149865853	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149865853delT								HIST2H2AB (6387 upstream) : BOLA1 (5302 downstream)																							tggatctctctttccacgtgg	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149912119	149912120	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149912119_149912120insA								MTMR11 (3328 upstream) : OTUD7B (113 downstream)																							TCGCTTGATAGAAAAAAAAAAA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	151704740	151704740	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151704740delA								C1orf230 (2658 upstream) : MRPL9 (27385 downstream)																							gcagaaagggaagacggggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153568694	153568695	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153568694_153568695delCA								S100A2 (30388 upstream) : S100A16 (10672 downstream)																							catgcacaagcacacacacaca	0.183													4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154728252	154728253	+	Intron	DEL	GA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154728252_154728253delGA	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			ggtggaggaggagagagagagg	0.059													9	6	---	---	---	---	
CD1D	912	broad.mit.edu	37	1	158152517	158152517	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158152517delG	uc001frr.2	+						CD1D_uc009wsr.1_3'UTR|CD1D_uc009wss.2_Intron|CD1D_uc009wst.1_3'UTR	NM_001766	NP_001757	P15813	CD1D_HUMAN	CD1D antigen precursor						antigen processing and presentation, endogenous lipid antigen via MHC class Ib|detection of bacterium|innate immune response|interspecies interaction between organisms|positive regulation of innate immune response|T cell selection	endosome membrane|integral to plasma membrane|lysosomal membrane	beta-2-microglobulin binding|exogenous lipid antigen binding|histone binding			ovary(1)	1	all_hematologic(112;0.0378)					TGAAAGTTGTGGGAGACTTCA	0.483													3	11	---	---	---	---	
SPTA1	6708	broad.mit.edu	37	1	158619725	158619725	+	Frame_Shift_Del	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158619725delG	uc001fst.1	-	25	3689	c.3490delC	c.(3490-3492)CGCfs	p.R1164fs		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1164	Spectrin 11.				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)					GAACCCCAGCGGGAATTCAAT	0.443													23	10	---	---	---	---	
CCDC19	25790	broad.mit.edu	37	1	159883964	159883965	+	Intron	INS	-	T	T	rs146265138	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159883964_159883965insT	uc001ful.2	-							NM_012337	NP_036469	Q9UL16	CCD19_HUMAN	nasopharyngeal epithelium specific protein 1							mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			CCCTCCTCCCATTTTTTTCCCC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	160698746	160698749	+	IGR	DEL	AGAA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160698746_160698749delAGAA								CD48 (17161 upstream) : SLAMF7 (10328 downstream)																							agagaaagagagaaagaaagaaag	0.083													2	4	---	---	---	---	
ITLN1	55600	broad.mit.edu	37	1	160850095	160850096	+	Intron	INS	-	A	A	rs141641663		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160850095_160850096insA	uc001fxc.2	-							NM_017625	NP_060095	Q8WWA0	ITLN1_HUMAN	intelectin precursor						positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction	anchored to membrane|brush border membrane|extracellular region|membrane raft	receptor binding|sugar binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)	7	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			aactccatctcaaaaaaaaaaa	0.005													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161427422	161427423	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161427422_161427423insA								C1orf192 (89758 upstream) : FCGR2A (47782 downstream)																							CCACGGTGGTGAAAAAAAAAAA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161587945	161587945	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161587945delA								HSPA7 (9604 upstream) : FCGR3B (5045 downstream)																							ccctgaacggagggaccagct	0.159													8	6	---	---	---	---	
OLFML2B	25903	broad.mit.edu	37	1	161974852	161974852	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161974852delC	uc001gbu.2	-						OLFML2B_uc010pkq.1_Intron	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			TCAAGTCCTGCCACCAAAACT	0.413													3	5	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162109623	162109623	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162109623delT	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			GCCGTCTTACttttttttttt	0.239													6	3	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165204660	165204661	+	Intron	DEL	CT	-	-	rs5778434		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165204660_165204661delCT	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)					cacacacacactcacactcaca	0.520													5	3	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165259679	165259680	+	Intron	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165259679_165259680delGT	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)					cattgccttcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
RXRG	6258	broad.mit.edu	37	1	165417270	165417271	+	5'Flank	DEL	AC	-	-	rs34340291		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165417270_165417271delAC	uc001gda.2	-						RXRG_uc001gdb.1_5'Flank	NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)	GGCTTGGGATACACACTCTCTG	0.475													0	9	---	---	---	---	
TMCO1	54499	broad.mit.edu	37	1	165788848	165788848	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165788848delC	uc001gdn.3	-									Q9UM00	TMCO1_HUMAN	Homo sapiens mRNA for putative membrane protein, complete cds.							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					ATGGGTGCAGCGGGAAAAGAC	0.438													21	14	---	---	---	---	
FAM78B	149297	broad.mit.edu	37	1	166101533	166101534	+	Intron	INS	-	CTAA	CTAA	rs139764906	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166101533_166101534insCTAA	uc001gdr.2	-						FAM78B_uc010plc.1_Intron	NM_001017961	NP_001017961	Q5VT40	FA78B_HUMAN	hypothetical protein LOC149297											central_nervous_system(1)|skin(1)	2	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					TCCCCTCTCCCCTAACCCTCGC	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	169042787	169042787	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169042787delG								MGC4473 (280667 upstream) : ATP1B1 (33160 downstream)																							ATTGTGTTTTGTTTGTCCACG	0.483													4	2	---	---	---	---	
NME7	29922	broad.mit.edu	37	1	169256356	169256357	+	Intron	INS	-	A	A	rs146291925	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169256356_169256357insA	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_3'UTR	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					AATCCACAAAGAAAAGACAAAT	0.342													4	6	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172291963	172291963	+	Intron	DEL	T	-	-	rs112152513		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172291963delT	uc001gie.2	+						DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						CTTTTCCTTCTTTTTTTTTTT	0.423													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174605666	174605666	+	Intron	DEL	A	-	-	rs34604603		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174605666delA	uc001gjx.2	+							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						actctacttcaaaaaaaaaaa	0.159													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176819228	176819228	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176819228delT								PAPPA2 (7260 upstream) : ASTN1 (7213 downstream)																							agagccaggatttggacccag	0.194													4	2	---	---	---	---	
RASAL2	9462	broad.mit.edu	37	1	178268642	178268643	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178268642_178268643insT	uc001glq.2	+						RASAL2_uc009wxb.2_Intron	NM_170692	NP_733793	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 2						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						tttcttttttctttttttttga	0.188													4	2	---	---	---	---	
C1orf49	84066	broad.mit.edu	37	1	178479880	178479880	+	5'Flank	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178479880delA	uc001glt.1	+						C1orf49_uc001glu.1_5'Flank|C1orf49_uc001glv.1_5'Flank|C1orf49_uc001glw.1_5'Flank	NM_032126	NP_115502	Q5T0J7	CA049_HUMAN	hypothetical protein LOC84066							microtubule cytoskeleton					0						CTTAAAACTGAAAAAAAAAAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178681813	178681844	+	IGR	DEL	AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA	-	-	rs71108077	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178681813_178681844delAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA								C1orf220 (163789 upstream) : RALGPS2 (12456 downstream)																							agaaagaaagagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag	0.091													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178682052	178682053	+	IGR	INS	-	A	A	rs138814017	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178682052_178682053insA								C1orf220 (164028 upstream) : RALGPS2 (12247 downstream)																							aagagagaaagaaaAAAGGACT	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184164702	184164702	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184164702delA								TSEN15 (121361 upstream) : C1orf21 (191448 downstream)																							ttaaaaagtcaaaaaaaatag	0.000													4	2	---	---	---	---	
CRB1	23418	broad.mit.edu	37	1	197258103	197258103	+	Intron	DEL	A	-	-	rs35227217		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197258103delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc001gty.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor						cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						tacataggttaaaaaaAAAAA	0.204													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198909985	198909986	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198909985_198909986insT								MIR181A1 (81703 upstream) : None (None downstream)																							ttaaacttttcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201103703	201103705	+	IGR	DEL	GAG	-	-	rs138628632		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201103703_201103705delGAG								CACNA1S (22009 upstream) : TMEM9 (196 downstream)																							CTAATCAGGTGAGGAGGACTTCC	0.571													4	2	---	---	---	---	
PKP1	5317	broad.mit.edu	37	1	201285278	201285281	+	Intron	DEL	GGAT	-	-	rs28411916	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201285278_201285281delGGAT	uc001gwd.2	+						PKP1_uc001gwe.2_Intron|PKP1_uc009wzm.2_Intron	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b						cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2						atggacggacggatggatggatgg	0.176													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	202067976	202067977	+	IGR	INS	-	T	T	rs34654089		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202067976_202067977insT								ELF3 (81670 upstream) : GPR37L1 (24052 downstream)																							ctctcacatacttttttttttt	0.000													5	4	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202346448	202346448	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202346448delT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GGGTAGTATCttttttttttt	0.204													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	202818522	202818523	+	IGR	DEL	AA	-	-	rs71729349		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202818522_202818523delAA								KDM5B (40973 upstream) : LOC148709 (12359 downstream)																							tggggcagacaaaagttatacg	0.064													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203000586	203000586	+	IGR	DEL	C	-	-	rs67932508		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203000586delC								TMEM183A (6611 upstream) : PPFIA4 (3026 downstream)																							ACACATGACACCCCCCCATTC	0.473													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	204013813	204013814	+	IGR	INS	-	AGGAAGGAAGG	AGGAAGGAAGG	rs150755445	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204013813_204013814insAGGAAGGAAGG								C1orf157 (3421 upstream) : SOX13 (28432 downstream)																							aggagggagaaaggaaggaagg	0.000													7	4	---	---	---	---	
PLEKHA6	22874	broad.mit.edu	37	1	204305692	204305693	+	Intron	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204305692_204305693delGT	uc001hau.2	-							NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3											ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			gtgtgtgagcgtgtgtgtgtgt	0.411													3	3	---	---	---	---	
RASSF5	83593	broad.mit.edu	37	1	206709018	206709019	+	Intron	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206709018_206709019delGT	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TGTTTTCAGGgtgtgtgtgtgt	0.312													4	3	---	---	---	---	
CD34	947	broad.mit.edu	37	1	208077989	208077989	+	Intron	DEL	T	-	-	rs11323111		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208077989delT	uc001hgw.1	-						CD34_uc001hgx.1_Intron|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a						cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						agtggatatCTTTTGTTTTAG	0.219													2	4	---	---	---	---	
TRAF3IP3	80342	broad.mit.edu	37	1	209944711	209944728	+	Intron	DEL	TGGAGGTGTGTGTGCAGG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209944711_209944728delTGGAGGTGTGTGTGCAGG	uc001hho.2	+						TRAF3IP3_uc001hhl.2_Intron|TRAF3IP3_uc001hhm.1_Intron|TRAF3IP3_uc001hhn.2_Intron|TRAF3IP3_uc009xcr.2_Intron	NM_025228	NP_079504	Q9Y228	T3JAM_HUMAN	TRAF3-interacting JNK-activating modulator							integral to membrane	protein binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CGTGTGCAGCTGGAGGTGTGTGTGCAGGTGGAAGTGTG	0.211													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	212103602	212103603	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212103602_212103603insT								LPGAT1 (99488 upstream) : INTS7 (11095 downstream)																							Ctttctttgccttttttttttt	0.243													4	2	---	---	---	---	
RPS6KC1	26750	broad.mit.edu	37	1	213228666	213228667	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213228666_213228667insT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc009xdh.2_Intron	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		atagtatgcacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213616301	213616302	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213616301_213616302insT								RPS6KC1 (169494 upstream) : PROX1 (544984 downstream)																							CTTTCTCAGGGTTTTTTTTTTT	0.475													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215157708	215157708	+	IGR	DEL	T	-	-	rs59594818		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215157708delT								CENPF (319796 upstream) : KCNK2 (21177 downstream)																							gcattttgcctctgccctaga	0.000													4	4	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	216756386	216756387	+	Intron	INS	-	A	A	rs147921883	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216756386_216756387insA	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	AGTGTTTGAAGAAAAAAAAAAC	0.361													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218083897	218083901	+	IGR	DEL	CTGAG	-	-	rs71560544		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218083897_218083901delCTGAG								SPATA17 (43395 upstream) : RRP15 (374728 downstream)																							GAAAAGACATCTGAGCTTGAGGGGG	0.488													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	220469697	220469698	+	IGR	DEL	AA	-	-	rs10570102		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220469697_220469698delAA								RAB3GAP2 (23854 upstream) : MARK1 (231870 downstream)																							CTCTGTGGAGAAGTTATTCCTC	0.510													1	6	---	---	---	---	
TAF5L	27097	broad.mit.edu	37	1	229731419	229731419	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229731419delT	uc001htq.2	-							NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CACTTCAAGAttttttttttt	0.219													4	2	---	---	---	---	
COG2	22796	broad.mit.edu	37	1	230828536	230828538	+	Intron	DEL	TTA	-	-	rs67968273		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230828536_230828538delTTA	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GTGTGTGTTGTTATTGTCGTTTT	0.325													4	4	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240264809	240264810	+	Intron	DEL	TG	-	-	rs149465557	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240264809_240264810delTG	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			tgtgtgtgtatgtgtgtgtgtg	0.144													4	2	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240415936	240415936	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240415936delG	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyf.1_Intron|FMN2_uc010pyg.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ttattctgacggggggggtgg	0.000													4	2	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242026725	242026726	+	Intron	INS	-	A	A	rs151293012	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242026725_242026726insA	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAAAAAAAAACAAAAAAAGCGT	0.337								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
SDCCAG8	10806	broad.mit.edu	37	1	243643906	243643906	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243643906delA	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		gatgggtgggatggatggatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244245399	244245400	+	IGR	INS	-	G	G	rs142999527	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244245399_244245400insG								ZNF238 (24623 upstream) : C1orf100 (270537 downstream)																							AAAGTCCTCGTCCTTCTTTCAA	0.381													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4517831	4517833	+	IGR	DEL	GAG	-	-	rs112813492		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4517831_4517833delGAG								ALLC (767573 upstream) : None (None downstream)																							ggaggagaacgaggaggaggagg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6458434	6458434	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6458434delG								LOC400940 (330070 upstream) : CMPK2 (522069 downstream)																							aatccagtcagaaaaaaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12154609	12154609	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12154609delT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		ATATGATTCATTTTCCTAGTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15865924	15865925	+	IGR	INS	-	G	G	rs144010326	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15865924_15865925insG								DDX1 (94700 upstream) : MYCNOS (214095 downstream)																							GATTGTGAAGAGGGGGTCtgta	0.327													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22386012	22386013	+	IGR	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22386012_22386013delGT								None (None upstream) : None (None downstream)																							GTAAAGCAGCgtgtgtgtgtgt	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23434915	23434915	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23434915delG								None (None upstream) : KLHL29 (320540 downstream)																							GAGGCTGCCTGGAAGTCACTG	0.458													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31337142	31337142	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31337142delA	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					AACAAGTGGGAAAAAAAAAAA	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48636159	48636160	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48636159_48636160insA								FOXN2 (29725 upstream) : KLRAQ1 (31748 downstream)																							gcctacattagaaaaaaaaaaa	0.000													5	3	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48851599	48851602	+	Intron	DEL	ATAG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48851599_48851602delATAG	uc010yol.1	+						STON1-GTF2A1L_uc002rwp.1_Intron|GTF2A1L_uc002rws.1_Intron|GTF2A1L_uc010yom.1_Intron|GTF2A1L_uc002rwt.2_Intron	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			gtgctttgatatagatagatagat	0.005													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49144463	49144463	+	IGR	DEL	T	-	-	rs75906108		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49144463delT								LHCGR (161583 upstream) : FSHR (45190 downstream)																							atgcctctcatttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	50144551	50144551	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50144551delT								FSHR (762921 upstream) : NRXN1 (1093 downstream)																							TCCTTGATGCttttttttttt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51330237	51330238	+	IGR	INS	-	AAAC	AAAC	rs147671910	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51330237_51330238insAAAC								NRXN1 (70563 upstream) : None (None downstream)																							ccctgtctctaaaacaaacaaa	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	55298328	55298328	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55298328delA								RTN4 (20594 upstream) : C2orf63 (101359 downstream)																							ACTGGCCACCAGGGGGTCTCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60259244	60259245	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60259244_60259245delAC								None (None upstream) : BCL11A (419058 downstream)																							ccaaagtaaaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60939374	60939375	+	IGR	INS	-	T	T	rs35097330		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60939374_60939375insT								BCL11A (158741 upstream) : PAPOLG (44008 downstream)																							ATTATTTTACCttttttttttt	0.035													7	5	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61414640	61414643	+	3'UTR	DEL	CAAT	-	-	rs146849510		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61414640_61414643delCAAT	uc002sbe.2	-	80					USP34_uc002sbd.2_3'UTR	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CACAGAATAGCAATCAATCAATCA	0.309													1	11	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61563255	61563256	+	Intron	DEL	TG	-	-	rs5831604		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61563255_61563256delTG	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			CAAAACAAATTGTGTGTGTGTG	0.203													3	3	---	---	---	---	
COMMD1	150684	broad.mit.edu	37	2	62346243	62346243	+	Intron	DEL	A	-	-	rs34874144		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62346243delA	uc002sbp.2	+						uc002sbr.2_Intron	NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			agaggggctcaaatccagaat	0.000													4	6	---	---	---	---	
ACTR2	10097	broad.mit.edu	37	2	65462304	65462305	+	Intron	DEL	GT	-	-	rs72218070		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65462304_65462305delGT	uc002sdq.2	+						ACTR2_uc010yqf.1_Intron|ACTR2_uc002sdp.2_Intron|ACTR2_uc010yqg.1_Intron	NM_005722	NP_005713	P61160	ARP2_HUMAN	actin-related protein 2 isoform b						cellular component movement	Arp2/3 protein complex|cell projection|cytoplasm	actin binding|ATP binding				0						TGTGTGAGAGgtgtgtgtgtgt	0.252													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65975417	65975418	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65975417_65975418insT	uc010fcy.1	+						uc010fcz.1_Intron					Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		tccttccttccttcctttcttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67978790	67978791	+	IGR	INS	-	TGTG	TGTG	rs145633866	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67978790_67978791insTGTG								ETAA1 (341257 upstream) : C1D (290542 downstream)																							atgtacatgcatgtgtgtgtgt	0.376													4	2	---	---	---	---	
ANTXR1	84168	broad.mit.edu	37	2	69436193	69436194	+	Intron	INS	-	TGAG	TGAG	rs144767370	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69436193_69436194insTGAG	uc002sfg.2	+							NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor						actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						tgctaccacgTTGTTTTATTAA	0.173									Familial_Infantile_Hemangioma				3	3	---	---	---	---	
NFU1	27247	broad.mit.edu	37	2	69650554	69650555	+	Intron	INS	-	T	T	rs141049329	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69650554_69650555insT	uc002sfk.2	-						NFU1_uc002sfj.2_Intron|NFU1_uc002sfl.2_Intron|NFU1_uc002sfm.2_Intron|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Intron	NM_001002755	NP_001002755	Q9UMS0	NFU1_HUMAN	HIRA interacting protein 5 isoform 2						iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0						aacaggccTTATTTTTTTTTTA	0.129													5	5	---	---	---	---	
ADD2	119	broad.mit.edu	37	2	70974561	70974561	+	Intron	DEL	T	-	-	rs34719997		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70974561delT	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3						TGCTCTCCCATCATGCCATGT	0.493													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72011661	72011661	+	IGR	DEL	A	-	-	rs72156201		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72011661delA								DYSF (97769 upstream) : CYP26B1 (344706 downstream)																							accctgtctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75860958	75860961	+	IGR	DEL	TCAT	-	-	rs10609102		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75860958_75860961delTCAT								FAM176A (64110 upstream) : MRPL19 (12948 downstream)																							GCGTTAATACTCATTCATACCTCA	0.309													9	4	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77158602	77158602	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77158602delT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CCTTTAATCCTGAGTGTGGGA	0.473													4	2	---	---	---	---	
REG1A	5967	broad.mit.edu	37	2	79348504	79348504	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79348504delT	uc002snz.2	+						REG1A_uc010ffx.1_Intron|REG1A_uc010ysd.1_Intron	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor						positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						ATTCATTCTGTTTTTTTTCCC	0.418													46	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85180643	85180643	+	IGR	DEL	A	-	-	rs112105164		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85180643delA								TMSB10 (46844 upstream) : KCMF1 (17588 downstream)																							actccgtctcaaaaaaaaaaa	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85909202	85909202	+	IGR	DEL	T	-	-	rs72266075		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85909202delT								SFTPB (13828 upstream) : GNLY (12212 downstream)																							gtcaggagtgttttttttttt	0.209													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89870543	89870547	+	IGR	DEL	CCAAA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89870543_89870547delCCAAA								FLJ40330 (764418 upstream) : None (None downstream)																							ccgttccattccaaaccattccatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89879529	89879543	+	IGR	DEL	TTTAATAAAAGCGAG	-	-	rs147496846	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89879529_89879543delTTTAATAAAAGCGAG								FLJ40330 (773404 upstream) : None (None downstream)																							tggaaaggaatttaataaaagcgagtggaatggaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91738373	91738375	+	IGR	DEL	TCA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738373_91738375delTCA								None (None upstream) : LOC654342 (66817 downstream)																							tcatttcatctcatcatttcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95406567	95406568	+	IGR	INS	-	AC	AC	rs35447196		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95406567_95406568insAC								None (None upstream) : ANKRD20B (20107 downstream)																							cctacacacagacacacacaca	0.252													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95930098	95930099	+	IGR	DEL	CA	-	-	rs36034926		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95930098_95930099delCA								ZNF2 (80036 upstream) : PROM2 (10102 downstream)																							CCCTTCCATCcacacacacaca	0.228													3	3	---	---	---	---	
DUSP2	1844	broad.mit.edu	37	2	96810459	96810459	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96810459delG	uc002svk.3	-							NM_004418	NP_004409	Q05923	DUS2_HUMAN	dual specificity phosphatase 2						endoderm formation|inactivation of MAPK activity|regulation of apoptosis	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity			breast(1)	1		Ovarian(717;0.0228)				AGTCCGCGGCGGGGAGAGAGG	0.612													4	2	---	---	---	---	
FAM178B	51252	broad.mit.edu	37	2	97544083	97544084	+	Intron	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97544083_97544084insC	uc002sxl.3	-						FAM178B_uc002sxi.3_Intron|FAM178B_uc002sxk.3_Intron|FAM178B_uc002sxj.3_Intron	NM_001122646	NP_001116118	Q8IXR5	F178B_HUMAN	hypothetical protein LOC51252 isoform A												0						ATCCCAGCCAACCCCCGCCGCT	0.653													5	3	---	---	---	---	
TXNDC9	10190	broad.mit.edu	37	2	99944254	99944255	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99944254_99944255insT	uc002szz.2	-						TXNDC9_uc010yvp.1_Intron|TXNDC9_uc002taa.1_Intron	NM_005783	NP_005774	O14530	TXND9_HUMAN	thioredoxin domain containing 9						cell redox homeostasis		protein binding				0						gtttgtttttgttttttttttt	0.114													4	2	---	---	---	---	
EIF5B	9669	broad.mit.edu	37	2	99999545	99999545	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99999545delT	uc002tab.2	+							NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3						ttgtgtatagttttttttttt	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101861415	101861415	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101861415delC								TBC1D8 (93569 upstream) : C2orf29 (7930 downstream)																							agtgcattgacggcatcgcgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102141054	102141054	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102141054delA								RFX8 (49889 upstream) : MAP4K4 (173434 downstream)																							AGAAGTCATGAAATAAGGCAA	0.348													4	2	---	---	---	---	
EDAR	10913	broad.mit.edu	37	2	109556046	109556048	+	Intron	DEL	GGA	-	-	rs66548467		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109556046_109556048delGGA	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						gtgagggctgggaggaggagaac	0.202													4	2	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116153057	116153058	+	Intron	DEL	AA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116153057_116153058delAA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						CGTCAATGCTAAACAGCCTCCA	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118456448	118456449	+	IGR	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118456448_118456449delCT								None (None upstream) : DDX18 (115806 downstream)																							GCCCCCACCCctctctctctct	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118634063	118634063	+	IGR	DEL	T	-	-	rs34450378		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118634063delT								DDX18 (44110 upstream) : CCDC93 (39086 downstream)																							ctccaggctattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120045734	120045735	+	IGR	INS	-	T	T	rs67363258		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120045734_120045735insT								STEAP3 (22509 upstream) : C2orf76 (14285 downstream)																							ttatacttcaattttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120173331	120173332	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120173331_120173332delCA								DBI (43211 upstream) : TMEM37 (16114 downstream)																							AGATCTCCAGCACACACACACA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126576920	126576921	+	IGR	DEL	GT	-	-	rs10597712		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126576920_126576921delGT								CNTNAP5 (904059 upstream) : GYPC (836763 downstream)																							AATAGGAACAgtgtgtgtgtgt	0.173													4	3	---	---	---	---	
ARHGEF4	50649	broad.mit.edu	37	2	131769517	131769517	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131769517delG	uc002tsa.1	+						ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Intron|ARHGEF4_uc010fmx.1_Intron	NM_015320	NP_056135	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor 4 isoform						apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		gttggattctggataataaag	0.000													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132982902	132982902	+	Intron	DEL	A	-	-	rs76618316		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132982902delA	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						atcttcccataaaaactagag	0.000													4	4	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133016372	133016372	+	5'Flank	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133016372delC	uc002ttj.3	-						MIR663B_hsa-mir-663b|MI0006336_5'Flank	NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						ccgaggtgggcagatcacctg	0.065													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133062601	133062604	+	Intron	DEL	CTCA	-	-	rs4063334	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133062601_133062604delCTCA	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AGCGCTTGGGCTCAGTTTGGGGAG	0.583													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133101571	133101572	+	IGR	INS	-	T	T	rs140120478	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133101571_133101572insT								NCRNA00164 (86029 upstream) : GPR39 (72575 downstream)																							attaatcaaactttttttttct	0.010													3	3	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137878187	137878188	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137878187_137878188delTT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATCTCTTTGCTTATATCTTGAA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161735521	161735521	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161735521delA								RBMS1 (385203 upstream) : TANK (257945 downstream)																							CACTTGGGATAAAGTTTAACA	0.234													4	2	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166911317	166911317	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166911317delT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	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)	AGTAACAGTGTTTTTTCATAG	0.274													4	3	---	---	---	---	
PRKRA	8575	broad.mit.edu	37	2	179296248	179296249	+	3'UTR	INS	-	ACA	ACA	rs145339215	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179296248_179296249insACA	uc002umf.2	-	8					PRKRA_uc002umc.2_3'UTR|PRKRA_uc002umd.2_3'UTR|PRKRA_uc002ume.2_3'UTR|PRKRA_uc002umg.2_3'UTR|uc002umb.1_Intron	NM_003690	NP_003681	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double						immune response|negative regulation of cell proliferation|production of siRNA involved in RNA interference|response to virus	perinuclear region of cytoplasm	double-stranded RNA binding|enzyme activator activity|protein homodimerization activity			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			AAATCTTATTCACAATGGCTAA	0.282													6	3	---	---	---	---	
PDE1A	5136	broad.mit.edu	37	2	183298204	183298205	+	Intron	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183298204_183298205delAC	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)			gttcaagtctacagcccttgat	0.074													4	2	---	---	---	---	
MFSD6	54842	broad.mit.edu	37	2	191294298	191294298	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191294298delC	uc002urz.2	+							NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane				ovary(2)	2						aggtgatcctcccaaagtgct	0.000													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210598185	210598188	+	3'UTR	DEL	CACA	-	-	rs112861196		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210598185_210598188delCACA	uc002vde.1	+	15					MAP2_uc002vdd.1_3'UTR|MAP2_uc002vdf.1_3'UTR|MAP2_uc002vdg.1_3'UTR|MAP2_uc002vdh.1_3'UTR|MAP2_uc002vdi.1_3'UTR	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TGACCTTCTCcacacacacacaca	0.328													5	4	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	215243353	215243353	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215243353delC	uc002veq.2	+						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)		ccctggagctccccctaaggg	0.144													3	3	---	---	---	---	
TMEM169	92691	broad.mit.edu	37	2	216953831	216953831	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216953831delG	uc010zjr.1	+						TMEM169_uc010zjs.1_Intron|TMEM169_uc002vfw.2_Intron|TMEM169_uc002vfv.3_Intron	NM_001142310	NP_001135782	Q96HH4	TM169_HUMAN	transmembrane protein 169							integral to membrane				ovary(1)	1		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATTATGGGTTGGAGAAAGCAG	0.403													4	2	---	---	---	---	
RUFY4	285180	broad.mit.edu	37	2	218953652	218953653	+	Intron	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218953652_218953653delCT	uc002vgw.2	+						RUFY4_uc002vgy.1_Intron|RUFY4_uc010fvl.1_Intron	NM_198483	NP_940885	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4								metal ion binding			pancreas(1)	1		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ctctccaatcctctctctctct	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228507821	228507821	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228507821delT								C2orf83 (9785 upstream) : SLC19A3 (42106 downstream)																							GTGCCTGCTCTTTTCCCCCCC	0.318													4	2	---	---	---	---	
FBXO36	130888	broad.mit.edu	37	2	230806318	230806318	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230806318delA	uc002vqa.2	+						FBXO36_uc002vpz.2_Intron|FBXO36_uc002vqb.2_Intron|FBXO36_uc010fxi.1_Intron|FBXO36_uc002vqc.2_Intron	NM_174899	NP_777559	Q8NEA4	FBX36_HUMAN	F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		AGGAGAGGCGAAAAAAAAAAA	0.403													4	2	---	---	---	---	
GPR55	9290	broad.mit.edu	37	2	231778343	231778344	+	Intron	INS	-	A	A	rs150899907	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231778343_231778344insA	uc002vrg.2	-						GPR55_uc002vrf.2_Intron|GPR55_uc010fxs.1_Intron	NM_005683	NP_005674	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55						activation of phospholipase C activity|bone resorption|negative regulation of osteoclast differentiation|positive regulation of ERK1 and ERK2 cascade|positive regulation of Rho protein signal transduction	integral to plasma membrane	cannabinoid receptor activity			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		TGTGTAGGAGTAACTGGTCCTA	0.480													0	6	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237262822	237262823	+	Intron	INS	-	TG	TG	rs150397641	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237262822_237262823insTG	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1						ACATGCGTGTATGTCTGTGGTC	0.302													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238384530	238384531	+	IGR	INS	-	AC	AC	rs149024783	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238384530_238384531insAC								COL6A3 (61680 upstream) : MLPH (10522 downstream)																							TTGACACACAAACACGCGCGTG	0.510													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239833378	239833379	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239833378_239833379delAC								TWIST2 (1141 upstream) : HDAC4 (136486 downstream)																							AAGcacacagacacacacacac	0.272													3	3	---	---	---	---	
LOC728323	728323	broad.mit.edu	37	2	243084121	243084122	+	Intron	INS	-	CA	CA			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:243084121_243084122insCA	uc010zpd.1	+						LOC728323_uc010zpe.1_Intron|LOC728323_uc010zpf.1_Intron|LOC728323_uc010zpg.1_Intron	NR_024437				Homo sapiens cDNA FLJ60027 complete cds, moderately similar to F-box only protein 25.												0						CTTCTGTCTTTcacacacacac	0.262													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	12021000	12021001	+	IGR	INS	-	AAC	AAC	rs148121957	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12021000_12021001insAAC								C3orf31 (132648 upstream) : SYN2 (24861 downstream)																							ctctgtctcaaaacaactaaaa	0.000													4	4	---	---	---	---	
RPL32	6161	broad.mit.edu	37	3	12880015	12880016	+	Intron	INS	-	G	G	rs145621003	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12880015_12880016insG	uc003bxl.2	-						RPL32_uc003bxm.2_Intron|RPL32_uc003bxn.2_Intron	NM_001007074	NP_001007075	P62910	RL32_HUMAN	ribosomal protein L32						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome			ovary(1)	1						AGTTTCCTCCTGTTCTCCATCT	0.490													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	12888072	12888072	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12888072delA								RPL32 (4991 upstream) : IQSEC1 (50647 downstream)																							tccagaccctagaatggtaga	0.000													4	2	---	---	---	---	
NUP210	23225	broad.mit.edu	37	3	13374226	13374227	+	Intron	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13374226_13374227delCA	uc003bxv.1	-							NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)					gaccctatctcaCACACACACA	0.233													4	2	---	---	---	---	
GRIP2	80852	broad.mit.edu	37	3	14555758	14555759	+	Intron	INS	-	AGTT	AGTT	rs138623401	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14555758_14555759insAGTT	uc011avi.1	-						GRIP2_uc010heh.2_5'Flank|GRIP2_uc011avh.1_Intron	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2						synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1						CAGTTTCTCTCAGAGAGTGGCA	0.351													5	3	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25552632	25552633	+	Intron	INS	-	T	T	rs141184320	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25552632_25552633insT	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	gttttggtttgtttttttttga	0.050													2	6	---	---	---	---	
ZCWPW2	152098	broad.mit.edu	37	3	28516252	28516252	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28516252delC	uc003ceh.2	+						ZCWPW2_uc003cei.2_Intron|ZCWPW2_uc010hfo.2_Intron	NM_001040432	NP_001035522	Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2								zinc ion binding			ovary(2)	2						taattatcttcctcttgggta	0.005													1	5	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54286912	54286913	+	Intron	DEL	AC	-	-	rs10575283		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54286912_54286913delAC	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		CCCCCGGGAAACACATAGTCCA	0.490													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75991116	75991121	+	IGR	DEL	CTCTCT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75991116_75991121delCTCTCT								ZNF717 (156446 upstream) : None (None downstream)																							ATAAACAGCCCTCTCTCTCTCTCTGT	0.374													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90347069	90347070	+	IGR	DEL	GC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90347069_90347070delGC								EPHA3 (815787 upstream) : None (None downstream)																							aggcctcaaagcactccaaata	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94629980	94629981	+	IGR	INS	-	A	A	rs76668304		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94629980_94629981insA								NSUN3 (784350 upstream) : LOC255025 (27126 downstream)																							gactcagtctcaaaaaaaaaaa	0.149													7	4	---	---	---	---	
NIT2	56954	broad.mit.edu	37	3	100060889	100060889	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100060889delA	uc003dtv.2	+						NIT2_uc011bha.1_Intron	NM_020202	NP_064587	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2						nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1						actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	102248368	102248368	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102248368delA								ZPLD1 (49683 upstream) : None (None downstream)																							AGGTTTATCCAAAAAAAAAAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105817054	105817054	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105817054delA								CBLB (228788 upstream) : LOC100302640 (738606 downstream)																							gcctctggagaaaaaaaagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109224798	109224799	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109224798_109224799delAC								FLJ25363 (10784 upstream) : None (None downstream)																							aaaacaaacaacacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109810090	109810101	+	IGR	DEL	ACACACACACAC	-	-	rs72396928		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109810090_109810101delACACACACACAC								FLJ25363 (596076 upstream) : PVRL3 (980764 downstream)																							AGCTCAATAGacacacacacacacacacacac	0.184													6	3	---	---	---	---	
ZDHHC23	254887	broad.mit.edu	37	3	113674207	113674208	+	Intron	DEL	GT	-	-	rs71971721		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113674207_113674208delGT	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2						TCACTTATTCgtgtgtgtgtgt	0.337													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	113951669	113951669	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113951669delG	uc003ebe.1	+											Homo sapiens cDNA FLJ35583 fis, clone SPLEN2006701.																		GCCCTGTGAAGCTCAGAGGCA	0.642													11	6	---	---	---	---	
IGSF11	152404	broad.mit.edu	37	3	118749942	118749942	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118749942delA	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0						cgtctctactaaaaatacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	119818400	119818400	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119818400delT	uc003edp.2	+											Homo sapiens cDNA clone IMAGE:4827879.																		ctggttgcccttttttttttt	0.000													3	3	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123102551	123102552	+	Intron	INS	-	A	A	rs72587294	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123102551_123102552insA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		CTCAGCTAGGGGGTTTAAACTA	0.495													5	6	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123112201	123112201	+	Intron	DEL	C	-	-	rs111486728		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123112201delC	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		gagttcaaaaccagcctgagc	0.005													4	3	---	---	---	---	
UROC1	131669	broad.mit.edu	37	3	126214826	126214826	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126214826delG	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)		CCTCACCTTTGGGCAGTCTTC	0.647													5	9	---	---	---	---	
CHCHD6	84303	broad.mit.edu	37	3	126436628	126436629	+	Intron	INS	-	TT	TT	rs140248664	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126436628_126436629insTT	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719	Q9BRQ6	CHCH6_HUMAN	coiled-coil-helix-coiled-coil-helix domain												0						GTGTGTGTGTGTGGCTTAGATT	0.535													3	4	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	128046135	128046135	+	Intron	DEL	C	-	-	rs112559050		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128046135delC	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						CTTTTCCCATCCCCCCCCCCC	0.443													6	4	---	---	---	---	
SRPRB	58477	broad.mit.edu	37	3	133527169	133527169	+	Intron	DEL	G	-	-	rs7650925		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133527169delG	uc003epx.1	+							NM_021203	NP_067026	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, beta							endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1						CTTTATTGTTGTTTTTTTTTA	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135387313	135387313	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135387313delG								EPHB1 (408008 upstream) : PPP2R3A (297254 downstream)																							TCTCTTTTTTGGTCCATTTTC	0.438													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136108529	136108530	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136108529_136108530delTT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						atctggttaatttttgtatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137772409	137772409	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137772409delA								CLDN18 (19915 upstream) : DZIP1L (8425 downstream)																							actccatctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
PRR23C	389152	broad.mit.edu	37	3	138766166	138766166	+	5'Flank	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138766166delG	uc011bmt.1	-							NM_001134657	NP_001128129	Q6ZRP0	PR23C_HUMAN	proline rich 23C											skin(1)	1						TGTGTTGGATGGTGGCCCTGC	0.637													4	2	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143105858	143105858	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143105858delT	uc003evn.2	-							NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						gatttttgtattttcagtaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144241285	144241285	+	IGR	DEL	A	-	-	rs111948516		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144241285delA								C3orf58 (530076 upstream) : None (None downstream)																							agaaaggtagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144430543	144430543	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144430543delA								C3orf58 (719334 upstream) : None (None downstream)																							caataacagtaagggtcttca	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147431594	147431595	+	IGR	INS	-	T	T	rs142856841	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147431594_147431595insT								ZIC1 (297090 upstream) : AGTR1 (984063 downstream)																							TTCTCAGAATATTTTTTTTTTC	0.332													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151182621	151182622	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151182621_151182622insA								IGSF10 (6124 upstream) : AADACL2 (269082 downstream)																							cataatgcaggaaaaggaggta	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154373314	154373315	+	IGR	INS	-	AC	AC	rs141777793	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154373314_154373315insAC								GPR149 (225810 upstream) : MME (368598 downstream)																							ACTGAACTAATacacacacaca	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155074136	155074137	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155074136_155074137insA								MME (172618 upstream) : PLCH1 (123534 downstream)																							acaaaaaatacaaaaaaattag	0.000													4	2	---	---	---	---	
C3orf33	285315	broad.mit.edu	37	3	155503840	155503840	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155503840delA	uc003fal.1	-						C3orf33_uc003fam.1_Intron	NM_173657	NP_775928	Q96NB5	Q96NB5_HUMAN	hypothetical protein LOC285315								hydrolase activity, acting on ester bonds|nucleic acid binding				0			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			aggaaaaaggaaaaggaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157334073	157334074	+	IGR	DEL	GT	-	-	rs71965785		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157334073_157334074delGT								C3orf55 (15054 upstream) : SHOX2 (479727 downstream)																							gcgtgcatgcgtgtgtgtgtgt	0.317													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161146872	161146873	+	IGR	DEL	AT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161146872_161146873delAT								C3orf57 (57001 upstream) : OTOL1 (67723 downstream)																							TGGTGAAAAGATATATATATAT	0.342													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163791273	163791274	+	IGR	INS	-	TA	TA	rs137910963		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163791273_163791274insTA								None (None upstream) : MIR1263 (97985 downstream)																							ctgacttcaataaAAAAAAAAA	0.094													3	5	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169002360	169002361	+	Intron	DEL	CA	-	-	rs59802264	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169002360_169002361delCA	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						TATATGAGCGcacacacacaca	0.213													4	3	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173846625	173846626	+	Intron	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173846625_173846626delTC	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			GTCCTGATTATCAATCACCCTC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176518719	176518720	+	IGR	INS	-	AA	AA			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176518719_176518720insAA								NAALADL2 (995293 upstream) : TBL1XR1 (219823 downstream)																							ctagcctagacaacagagccag	0.000													8	5	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178512189	178512190	+	Intron	INS	-	A	A	rs150906670	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178512189_178512190insA	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			AAGCACCATCTAAAAAAAAAGG	0.490													4	2	---	---	---	---	
ZMAT3	64393	broad.mit.edu	37	3	178791794	178791795	+	5'Flank	DEL	AA	-	-	rs35562604		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178791794_178791795delAA	uc003fjg.2	-						ZMAT3_uc010hxa.2_5'Flank|ZMAT3_uc003fji.2_5'Flank	NM_022470	NP_071915	Q9HA38	ZMAT3_HUMAN	p53 target zinc finger protein isoform 1						apoptosis|protein transport|regulation of growth|response to DNA damage stimulus|transmembrane transport	nucleolus	RNA binding|zinc ion binding			ovary(2)	2	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			TTTGCGGTTGAAAAAAAAAAAa	0.188													4	2	---	---	---	---	
EIF4G1	1981	broad.mit.edu	37	3	184043926	184043929	+	Intron	DEL	ACAC	-	-	rs112208190		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184043926_184043929delACAC	uc003fnp.2	+						EIF4G1_uc003fnt.2_Intron|EIF4G1_uc003fnq.2_Intron|EIF4G1_uc003fnr.2_Intron|EIF4G1_uc010hxx.2_Intron|EIF4G1_uc003fns.2_Intron|EIF4G1_uc010hxy.2_Intron|EIF4G1_uc003fnv.3_Intron|EIF4G1_uc003fnu.3_Intron|EIF4G1_uc003fnw.2_Intron|EIF4G1_uc003fnx.2_Intron|EIF4G1_uc003fny.3_Intron|EIF4G1_uc003foa.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4						insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTTTGGCAAacacacacacacac	0.250													4	2	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184730453	184730453	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184730453delA	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			tttctcatttaaaaaaaaaaa	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184900714	184900714	+	RNA	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184900714delA	uc003fpe.2	+	6		c.1133delA								Homo sapiens hypothetical LOC339926, mRNA (cDNA clone IMAGE:4838153).																		actttggaacaaaaggacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186464213	186464213	+	IGR	DEL	T	-	-	rs11329782		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186464213delT								KNG1 (2472 upstream) : EIF4A2 (37148 downstream)																							AGCAGCTATATTTTAAAACTC	0.443													2	5	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187952825	187952829	+	Intron	DEL	AAAGG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187952825_187952829delAAAGG	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)		GGACAAGAATAAAGGAAGGAAAGGA	0.278			T	HMGA2|MLL|C12orf9	lipoma|leukemia								7	5	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187956164	187956164	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187956164delT	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)		ctttatgaacttttttttttt	0.000			T	HMGA2|MLL|C12orf9	lipoma|leukemia								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189892564	189892564	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189892564delT								LEPREL1 (52338 upstream) : CLDN1 (130939 downstream)																							tctttcttccttttttttttg	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191639508	191639509	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191639508_191639509insT								PYDC2 (460265 upstream) : FGF12 (220175 downstream)																							cttagtaacagttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191850828	191850829	+	IGR	INS	-	TG	TG	rs147740439	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191850828_191850829insTG								PYDC2 (671585 upstream) : FGF12 (8855 downstream)																							acatgcacacacgcacacacac	0.104													7	4	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	191920923	191920924	+	Intron	DEL	TG	-	-	rs112395553		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191920923_191920924delTG	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ATTAAATATTtgtgtgtgtgtg	0.218													4	2	---	---	---	---	
ATP13A5	344905	broad.mit.edu	37	3	193021974	193021974	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193021974delG	uc011bsq.1	-							NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GTGAAGAAGAGGAAGGAGTTA	0.433													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195473757	195473758	+	3'UTR	DEL	GT	-	-	rs71634711		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-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													2	4	---	---	---	---	
LOC348840	348840	broad.mit.edu	37	3	197795180	197795180	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197795180delT	uc003fyx.3	-						LOC348840_uc010iat.2_Intron	NR_003291				Homo sapiens hypothetical protein LOC348840, mRNA (cDNA clone IMAGE:5167648), partial cds.												0						taacagagcattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197846146	197846161	+	IGR	DEL	ATATAGAAATTGGGAT	-	-	rs112902539		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197846146_197846161delATATAGAAATTGGGAT								LOC348840 (38604 upstream) : FAM157A (33076 downstream)																							atatagagagatatagaaattgggataaaaaattat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3583672	3583673	+	Intron	INS	-	GA	GA	rs148829881	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3583672_3583673insGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		CCTGCAAGTCTGATTCTTCTGT	0.614													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4737338	4737339	+	IGR	INS	-	T	T	rs34741165		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4737338_4737339insT								STX18 (193563 upstream) : MSX1 (124053 downstream)																							ACTCTTGCTCATTTTTTTTTTT	0.351													3	3	---	---	---	---	
WDR1	9948	broad.mit.edu	37	4	10091125	10091125	+	Intron	DEL	C	-	-	rs3836719		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10091125delC	uc003gmf.2	-						WDR1_uc003gmg.2_Intron|WDR1_uc003gmh.1_Intron|WDR1_uc011bwu.1_Intron	NM_017491	NP_059830	O75083	WDR1_HUMAN	WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CCAGGGGCGACTCTGTTACTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10397632	10397632	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10397632delC								WDR1 (279059 upstream) : ZNF518B (43873 downstream)																							gagaggggtaccccagggatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24228706	24228706	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24228706delT								PPARGC1A (337006 upstream) : MIR573 (293109 downstream)																							ctaacacttcttttttttttt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26559328	26559328	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26559328delC								CCKAR (67286 upstream) : TBC1D19 (26218 downstream)																							CAAACTCTTGCCCTATCAGGA	0.204													4	2	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39241884	39241885	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39241884_39241885insT	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						attCACTCTTATTTTTTTTTCA	0.198													4	2	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39827205	39827205	+	Intron	DEL	T	-	-	rs72009420		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39827205delT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						ATCTAAAATCttttttttttt	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42308086	42308091	+	IGR	DEL	GTGTGT	-	-	rs35010640		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42308086_42308091delGTGTGT								BEND4 (153191 upstream) : SHISA3 (91765 downstream)																							GGGGACATTAgtgtgtgtgtgtgtgt	0.432													4	2	---	---	---	---	
SLAIN2	57606	broad.mit.edu	37	4	48362170	48362171	+	Intron	INS	-	A	A	rs34874508		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48362170_48362171insA	uc003gya.3	+							NM_020846	NP_065897	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2							centrosome					0						gactctgtctcaaaaaaaaaaa	0.139													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49101790	49101791	+	IGR	INS	-	G	G	rs62641954		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49101790_49101791insG								CWH43 (37697 upstream) : None (None downstream)																							ccattccattcggttgattcca	0.000													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49218022	49218022	+	IGR	DEL	A	-	-	rs78904448		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49218022delA								CWH43 (153929 upstream) : None (None downstream)																							aattccccagaaaaaataaca	0.000													4	4	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54588112	54588113	+	Intron	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54588112_54588113delTG	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)	CAtgtgtgcatgtgtgtgtgtg	0.376			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62723443	62723446	+	Intron	DEL	TCTC	-	-	rs3065828		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62723443_62723446delTCTC	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hcs.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						ctttctttcttctctctttctttc	0.015													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72819988	72819988	+	IGR	DEL	G	-	-	rs143381474		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72819988delG								GC (150230 upstream) : NPFFR2 (77533 downstream)																							GAAtttttttgtttgtttgtt	0.234													4	4	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79123877	79123877	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79123877delC	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						Tctggatccacctctgggatt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	81087205	81087208	+	IGR	DEL	CCTC	-	-	rs76920241		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81087205_81087208delCCTC								ANTXR2 (92728 upstream) : PRDM8 (18231 downstream)																							ttccttctttcctccctccctccc	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82671432	82671433	+	IGR	INS	-	CTTCTA	CTTCTA	rs143781492	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82671432_82671433insCTTCTA								RASGEF1B (278371 upstream) : HNRNPD (603034 downstream)																							tctttacattccttctactacc	0.030													1	6	---	---	---	---	
GPRIN3	285513	broad.mit.edu	37	4	90195177	90195177	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90195177delA	uc003hsm.1	-							NM_198281	NP_938022	Q6ZVF9	GRIN3_HUMAN	G protein-regulated inducer of neurite outgrowth											ovary(3)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		gcagatgtctaaacaaatgat	0.060													4	2	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94133496	94133496	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94133496delT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc010ikz.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						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)	AAACAATATATTTTTTTCATT	0.279													3	4	---	---	---	---	
BMPR1B	658	broad.mit.edu	37	4	95978404	95978404	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95978404delT	uc003htm.3	+							NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		GATGTTTCACttttttttttt	0.204													4	2	---	---	---	---	
METAP1	23173	broad.mit.edu	37	4	99960737	99960737	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99960737delT	uc003huf.3	+						METAP1_uc003hug.2_Intron	NM_015143	NP_055958	P53582	AMPM1_HUMAN	methionyl aminopeptidase 1						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)		CCAGCCATGCttttttttttt	0.184													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104940859	104940860	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104940859_104940860insA								TACR3 (299886 upstream) : CXXC4 (452485 downstream)																							ATGCTAATTAGAAAAAAAAAAC	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109286193	109286196	+	IGR	DEL	AGAG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109286193_109286196delAGAG								LEF1 (196615 upstream) : LOC285456 (173150 downstream)																							AAGGGgagaaagagagagagagag	0.245													3	3	---	---	---	---	
CASP6	839	broad.mit.edu	37	4	110623483	110623483	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110623483delT	uc003hzn.1	-						CASP6_uc003hzo.1_Intron	NM_001226	NP_001217	P55212	CASP6_HUMAN	caspase 6 isoform alpha preproprotein						cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis	cytosol|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		CGTTTCGttcttttttttttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	112920468	112920472	+	IGR	DEL	GGGAG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112920468_112920472delGGGAG								None (None upstream) : C4orf32 (146081 downstream)																							aggaaggaaagggaggggaggggag	0.049													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120324739	120324753	+	Intron	DEL	TTCTGGTGCAAGAGA	-	-	rs70944868		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120324739_120324753delTTCTGGTGCAAGAGA	uc003icx.1	+											Homo sapiens cDNA FLJ40382 fis, clone TESTI2035775.																		TCCTGCCACCTTCTGGTGCAAGAGACCTGAAAGTG	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	123015143	123015143	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123015143delT								TRPC3 (142234 upstream) : KIAA1109 (76615 downstream)																							TTTAGTGATCTGGGGAAGCAG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125932173	125932174	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125932173_125932174insA								ANKRD50 (298286 upstream) : FAT4 (305393 downstream)																							CATTAGTAAGGAAAAAAAAAAA	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126123576	126123577	+	IGR	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126123576_126123577insG								ANKRD50 (489689 upstream) : FAT4 (113990 downstream)																							cccagctacccggaggctgagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129230502	129230502	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129230502delA								PGRMC2 (21554 upstream) : PHF17 (500277 downstream)																							TGTTTATTTGAAGGCAATCCA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139493034	139493034	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139493034delC								SLC7A11 (329531 upstream) : CCRN4L (443909 downstream)																							tcctggaatacctcctaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	146368812	146368813	+	IGR	DEL	GA	-	-	rs111907063		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146368812_146368813delGA								OTUD4 (267980 upstream) : SMAD1 (34138 downstream)																							AAAAGAGAGCGAGAGAGAGAGA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	150184812	150184812	+	IGR	DEL	G	-	-	rs140758690	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150184812delG								NR3C2 (821169 upstream) : DCLK2 (815268 downstream)																							GAAGGCAGGCGGGGAAGAAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154568395	154568395	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154568395delG								KIAA0922 (10535 upstream) : TLR2 (37046 downstream)																							tgttgcatttgggattcagtc	0.095													4	2	---	---	---	---	
DCHS2	54798	broad.mit.edu	37	4	155289071	155289072	+	Intron	INS	-	GCTCTGA	GCTCTGA	rs138147942	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155289071_155289072insGCTCTGA	uc003inw.2	-						DCHS2_uc003inx.2_Intron	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACGGCTGTCCTGCTCTGAGCTC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158852346	158852346	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158852346delT								LOC340017 (355051 upstream) : FAM198B (193387 downstream)																							agaaatttgctttaacatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166543630	166543630	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166543630delA								CPE (124149 upstream) : TLL1 (250780 downstream)																							GGCGAGAGGGAAAAAAAAAGG	0.313													4	2	---	---	---	---	
GALNTL6	442117	broad.mit.edu	37	4	173063063	173063064	+	Intron	DEL	CC	-	-	rs33969520		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173063063_173063064delCC	uc003isv.2	+							NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						cacacacacacCCCCCACACTC	0.267													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180955839	180955839	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180955839delG								None (None upstream) : None (None downstream)																							ttggaagggagggagggagga	0.109													2	4	---	---	---	---	
RWDD4A	201965	broad.mit.edu	37	4	184574560	184574560	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184574560delA	uc003ivt.1	-						RWDD4A_uc003ivu.1_Intron|RWDD4A_uc003ivv.1_Intron|RWDD4A_uc011ckl.1_Intron	NM_152682	NP_689895	Q6NW29	RWDD4_HUMAN	RWD domain containing 4A												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;7.35e-27)|Epithelial(43;1.49e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.76e-10)|GBM - Glioblastoma multiforme(59;5.54e-06)|Colorectal(24;7.92e-06)|STAD - Stomach adenocarcinoma(60;2.35e-05)|COAD - Colon adenocarcinoma(29;6.26e-05)|LUSC - Lung squamous cell carcinoma(40;0.00935)|READ - Rectum adenocarcinoma(43;0.166)		tgtctctattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184760203	184760204	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184760203_184760204delCA								C4orf41 (125459 upstream) : STOX2 (66305 downstream)																							ggtacacatgcacacacacaca	0.089													3	3	---	---	---	---	
SORBS2	8470	broad.mit.edu	37	4	186748260	186748265	+	Intron	DEL	CATCGC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186748260_186748265delCATCGC	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		tcatcaccatcatcgccatcatcatc	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	187488014	187488015	+	IGR	DEL	TG	-	-	rs10610652		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187488014_187488015delTG								MTNR1A (11477 upstream) : FAT1 (20923 downstream)																							cgtgtgtgtctgtgtgtgtgtg	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190557091	190557091	+	IGR	DEL	C	-	-	rs113963324		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190557091delC								None (None upstream) : FRG1 (304883 downstream)																							atatcaagaaccccgtcaCCA	0.095													4	3	---	---	---	---	
CEP72	55722	broad.mit.edu	37	5	649980	649981	+	Intron	INS	-	TG	TG	rs142053577		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:649980_649981insTG	uc003jbf.2	+							NM_018140	NP_060610	Q9P209	CEP72_HUMAN	centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			TGAGGCGTGACTGAGGTGTGGA	0.594													8	4	---	---	---	---	
TPPP	11076	broad.mit.edu	37	5	684711	684712	+	Intron	INS	-	G	G	rs144240746	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:684711_684712insG	uc003jbh.3	-							NM_007030	NP_008961	O94811	TPPP_HUMAN	tubulin polymerization promoting protein						microtubule bundle formation|microtubule polymerization|positive regulation of protein polymerization	nucleus|perinuclear region of cytoplasm|soluble fraction	calcium ion binding|microtubule binding				0		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		TTCTAGGACCTGGAGCCCTGCC	0.639													4	2	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	804071	804071	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:804071delA	uc011cma.1	-						ZDHHC11_uc010itc.2_Intron|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)			ttaggaccagaaaaaaaaaaa	0.000													4	3	---	---	---	---	
SLC6A19	340024	broad.mit.edu	37	5	1205036	1205037	+	Intron	DEL	AG	-	-	rs10545401		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1205036_1205037delAG	uc003jbw.3	+							NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19						cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GAGAGAAAAAAGGGGAAGCTTA	0.505													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2325094	2325099	+	IGR	DEL	GTGTGT	-	-	rs5865418		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2325094_2325099delGTGTGT								IRX4 (442214 upstream) : IRX2 (421182 downstream)																							gcacgtgtgcgtgtgtgcatgtgtga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4013381	4013382	+	IGR	INS	-	C	C	rs148319706	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4013381_4013382insC								IRX1 (411865 upstream) : None (None downstream)																							AAAGACAGCAGCCCCCTCCCTC	0.663													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4053233	4053234	+	IGR	INS	-	T	T	rs138714668	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4053233_4053234insT								IRX1 (451717 upstream) : LOC340094 (981238 downstream)																							caagagactgatttcaataact	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4296511	4296516	+	IGR	DEL	TGTGTG	-	-	rs72081453		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4296511_4296516delTGTGTG								IRX1 (694995 upstream) : LOC340094 (737956 downstream)																							GTGAAAAGGTtgtgtgtgtgtgtgtg	0.374													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4438465	4438465	+	IGR	DEL	G	-	-	rs70963784		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4438465delG								IRX1 (836949 upstream) : LOC340094 (596007 downstream)																							ggaagaggaaggaggaggagg	0.060													5	5	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5312562	5312562	+	Intron	DEL	T	-	-	rs66575720		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5312562delT	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						gttgttgttattttttttttt	0.149													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6116395	6116396	+	IGR	INS	-	GT	GT	rs141647340	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6116395_6116396insGT								KIAA0947 (626058 upstream) : FLJ33360 (194158 downstream)																							GTACTAATAGCgtgtgtgtgtg	0.198													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6682094	6682095	+	IGR	DEL	GT	-	-	rs112622178	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6682094_6682095delGT								SRD5A1 (12421 upstream) : PAPD7 (32623 downstream)																							tgtgtggggggtgtgtgtgtgt	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6944006	6944012	+	IGR	DEL	TACACGA	-	-	rs11279914		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6944006_6944012delTACACGA								PAPD7 (186845 upstream) : ADCY2 (452331 downstream)																							GGAATGCGTCTACACGATATTGTTTCA	0.498													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8262379	8262393	+	IGR	DEL	ACTGTTGGATGTGAT	-	-	rs59587116		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8262379_8262393delACTGTTGGATGTGAT								MTRR (361146 upstream) : SEMA5A (772745 downstream)																							agggtggagcactgttggatgtgataaatgctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8690207	8690208	+	IGR	INS	-	AAC	AAC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8690207_8690208insAAC								MTRR (788974 upstream) : SEMA5A (344930 downstream)																							acaaacaaacaaaaaaaacaaa	0.124													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8903785	8903785	+	IGR	DEL	G	-	-	rs150816561		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8903785delG								None (None upstream) : SEMA5A (131353 downstream)																							TCCTGATTTTGTGCATTCGAT	0.458													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	9942064	9942066	+	IGR	DEL	CTT	-	-	rs72254945		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9942064_9942066delCTT								LOC285692 (38128 upstream) : FAM173B (284372 downstream)																							TATCTCTGGCCTTCTCCACAAAT	0.207													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10269486	10269486	+	IGR	DEL	A	-	-	rs71744072		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10269486delA								CCT5 (2986 upstream) : CMBL (8222 downstream)																							accctgactcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13262535	13262547	+	IGR	DEL	AGCATTGTGATGA	-	-	rs6148918		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13262535_13262547delAGCATTGTGATGA								None (None upstream) : DNAH5 (427890 downstream)																							ctgatccTTCAGCATTGTGATGAAGCAACACTG	0.061													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13328991	13328992	+	IGR	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13328991_13328992delTT								None (None upstream) : DNAH5 (361445 downstream)																							caggacagactttatcaatacg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13379339	13379340	+	IGR	INS	-	TCTCTCCCTC	TCTCTCCCTC	rs151097160	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13379339_13379340insTCTCTCCCTC								None (None upstream) : DNAH5 (311097 downstream)																							aggaaccagaatctctccctct	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15077525	15077525	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15077525delT								ANKH (205638 upstream) : FBXL7 (422780 downstream)																							ggccaagtgatttttttgcca	0.000													4	2	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15769845	15769846	+	Intron	INS	-	A	A	rs56743583		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15769845_15769846insA	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						ttctggacacgaaaaaaaaaaa	0.035													6	3	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16734915	16734915	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16734915delA	uc003jft.3	-						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						actctgtctcaaaaaaaaaaa	0.224													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17619552	17619552	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17619552delT								BASP1 (342617 upstream) : None (None downstream)																							acccagctaattttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18074425	18074425	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18074425delA								BASP1 (797490 upstream) : None (None downstream)																							TTATCACTTCAAAACAGCAAT	0.274													4	2	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19831105	19831105	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19831105delA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					gagtacatataaacacaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20117139	20117140	+	IGR	INS	-	GT	GT	rs143909104	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20117139_20117140insGT								CDH18 (128832 upstream) : None (None downstream)																							tgtgtgtgtgagtgtgtgtgtg	0.238													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20371146	20371146	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20371146delA								CDH18 (382839 upstream) : GUSBP1 (970796 downstream)																							actctgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28051505	28051506	+	IGR	INS	-	A	A	rs149352902	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28051505_28051506insA								None (None upstream) : None (None downstream)																							tatgacaacataaaaaaaaatc	0.025													5	3	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31242967	31242967	+	Intron	DEL	A	-	-	rs143490918		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31242967delA	uc003jhe.1	+						CDH6_uc003jhc.1_Intron|CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						cgcctctactaaaaaaaaaaa	0.090													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31555429	31555429	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31555429delA								C5orf22 (265 upstream) : PDZD2 (84088 downstream)																							ccaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZFR	51663	broad.mit.edu	37	5	32402268	32402268	+	Intron	DEL	A	-	-	rs11323186		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32402268delA	uc003jhr.1	-							NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		atagaggcggacagtgagacg	0.139													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32571141	32571142	+	IGR	INS	-	AACTTACC	AACTTACC	rs138675326	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32571141_32571142insAACTTACC								ZFR (126297 upstream) : SUB1 (14463 downstream)																							CACTCTAGTGGAATTTCTATTT	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34541474	34541474	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34541474delA								C1QTNF3 (498157 upstream) : RAI14 (114959 downstream)																							CCTAGGAGGTAAGGGGGAAAG	0.483													4	2	---	---	---	---	
AGXT2	64902	broad.mit.edu	37	5	35008059	35008060	+	Intron	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35008059_35008060delTC	uc003jjf.2	-						AGXT2_uc003jje.1_Intron|AGXT2_uc011com.1_Intron	NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor						glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)	tctcttgctttctctctctctc	0.000													4	2	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	36928091	36928091	+	Intron	DEL	T	-	-	rs72171938		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36928091delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			gcTGCAGTGATTTTTTTTTTT	0.075													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	37905675	37905676	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37905675_37905676insT								GDNF (65893 upstream) : EGFLAM (352857 downstream)																							agacatttttcttttttttttg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38815863	38815866	+	Intron	DEL	CACA	-	-	rs145433189		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38815863_38815866delCACA	uc003jlk.1	-											full-length cDNA clone CS0DI053YO12 of Placenta Cot 25-normalized of Homo sapiens (human).																		CTCCTCTGACcacacacacacaca	0.221													3	4	---	---	---	---	
OSMR	9180	broad.mit.edu	37	5	38859839	38859842	+	Intron	DEL	TTTG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38859839_38859842delTTTG	uc003jln.1	+						OSMR_uc003jlm.1_Intron	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor						cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					tgagaatgtatttgtttgtgtttt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39947737	39947738	+	IGR	DEL	AC	-	-	rs34755185		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39947737_39947738delAC								DAB2 (522402 upstream) : PTGER4 (732294 downstream)																							acacacacagacacacacacTA	0.277													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40486797	40486797	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40486797delC								None (None upstream) : PTGER4 (193235 downstream)																							GTTAAAATCACCTGGTCCAAC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42903783	42903784	+	IGR	DEL	AC	-	-	rs35404690		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42903783_42903784delAC								SEPP1 (77785 upstream) : C5orf39 (135399 downstream)																							ccacccacagacacacacacac	0.193													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43049558	43049559	+	IGR	DEL	AA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43049558_43049559delAA								LOC153684 (4188 upstream) : ZNF131 (71426 downstream)																							aggttgaatgaaaaaaaaaaaa	0.000													3	3	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43220395	43220396	+	Intron	INS	-	T	T	rs35094149		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43220395_43220396insT	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						gtgggtatcTCttttttttttt	0.005													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	45093622	45093623	+	IGR	INS	-	AC	AC	rs140815952	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45093622_45093623insAC								MRPS30 (278008 upstream) : HCN1 (165730 downstream)																							AGTCCTCAAATacacacacaca	0.327													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46116427	46116428	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46116427_46116428insT								HCN1 (420207 upstream) : None (None downstream)																							gttgtagagtctttttttttgt	0.000													4	2	---	---	---	---	
UTP15	84135	broad.mit.edu	37	5	72875092	72875092	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72875092delT	uc003kcw.1	+						UTP15_uc011cso.1_Intron|UTP15_uc011csp.1_Intron|UTP15_uc010ize.1_Intron	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,						rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GTTTTAAGGATTTTTTTTTTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84506381	84506381	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84506381delT								EDIL3 (825770 upstream) : None (None downstream)																							CTGCTCCTCATTTTATTTGCA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	86176737	86176737	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86176737delC								COX7C (260156 upstream) : RASA1 (387414 downstream)																							agtgtttgcacaggccagtag	0.124													4	2	---	---	---	---	
C5orf36	285600	broad.mit.edu	37	5	93578284	93578284	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93578284delT	uc011cuk.1	-						C5orf36_uc003kkn.2_Intron	NM_001145678	NP_001139150	Q8IV33	K0825_HUMAN	hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)		ccttccttcctttttttcttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120772851	120772851	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120772851delC								PRR16 (749889 upstream) : FTMT (414799 downstream)																							atcttatgatccacccacctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123181135	123181135	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123181135delG								CSNK1G3 (228673 upstream) : ZNF608 (791475 downstream)																							TTTAGCAGGTGGAAGGCTTTT	0.498													4	2	---	---	---	---	
CSNK1A1	1452	broad.mit.edu	37	5	148889380	148889381	+	Intron	DEL	AG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148889380_148889381delAG	uc003lqx.1	-						CSNK1A1_uc011dcb.1_Intron|CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883	P48729	KC1A_HUMAN	casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		ctgggattacaggtgtgagcca	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164180768	164180768	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164180768delG								None (None upstream) : None (None downstream)																							GAAACATGCTGGACAATATTG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177590863	177590864	+	IGR	INS	-	AAAAAG	AAAAAG			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177590863_177590864insAAAAAG								NHP2 (9902 upstream) : GMCL1L (20647 downstream)																							gggaaaagagaaaaaagaaaag	0.198													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8668157	8668158	+	Intron	INS	-	AA	AA	rs151113092	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8668157_8668158insAA	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																		AAGATAGAATGAAAAAAAAAAG	0.391													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8750771	8750771	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8750771delA								HULC (96694 upstream) : None (None downstream)																							aatgttaagcaatctgtccaa	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	10341748	10341749	+	IGR	INS	-	A	A	rs77470581		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10341748_10341749insA								None (None upstream) : TFAP2A (55168 downstream)																							aactctgtctcaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14011987	14011987	+	IGR	DEL	G	-	-	rs34294517		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14011987delG								RNF182 (31754 upstream) : CD83 (105878 downstream)																							aaaagccagtgggggtacttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15946910	15946910	+	IGR	DEL	T	-	-	rs35166896		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15946910delT								DTNBP1 (283639 upstream) : MYLIP (182407 downstream)																							gcttggttaattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20033299	20033299	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20033299delC								ID4 (192385 upstream) : MBOAT1 (67636 downstream)																							atggaccaatcagcaggatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21514540	21514540	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21514540delT								CDKAL1 (281908 upstream) : SOX4 (79432 downstream)																							AAGCTCAATCttttttttttc	0.343													4	4	---	---	---	---	
KIAA0319	9856	broad.mit.edu	37	6	24613919	24613920	+	Intron	DEL	AC	-	-	rs67311961	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24613919_24613920delAC	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						AAAAAAAAAAACAAAATGAGGG	0.317													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26493449	26493449	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26493449delA								BTN2A1 (23584 upstream) : BTN1A1 (8046 downstream)																							ctctgtctccaaaaaaaaaaa	0.090													4	2	---	---	---	---	
HLA-B	3106	broad.mit.edu	37	6	31319837	31319838	+	Intron	INS	-	GGA	GGA	rs34934531		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31319837_31319838insGGA	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron			P01889	1B07_HUMAN	SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CCCttagaactggtccagggtt	0.233									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				4	2	---	---	---	---	
MSH5	4439	broad.mit.edu	37	6	31721511	31721511	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31721511delT	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron|MSH5_uc011dof.1_Intron|MSH5_uc003nwy.1_5'Flank	NM_172166	NP_751898	O43196	MSH5_HUMAN	mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3						TTCTACCCtcttttttttttt	0.234								Direct_reversal_of_damage|MMR					6	3	---	---	---	---	
HLA-DPB1	3115	broad.mit.edu	37	6	33047686	33047687	+	Intron	DEL	AA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33047686_33047687delAA	uc003ocu.1	+						HLA-DPA1_uc003oct.1_Intron|HLA-DPB1_uc011dqn.1_Intron|HLA-DPB1_uc011dqo.1_Intron|HLA-DPB1_uc011dqp.1_Intron|HLA-DPB1_uc011dqq.1_5'Flank	NM_002121	NP_002112	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex				ovary(1)	1						AAAAACTGCCAAAAAAAATTAC	0.401													6	3	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34078892	34078893	+	Intron	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34078892_34078893delAC	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc010jvk.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	caggccacatacacacacacac	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	36914594	36914594	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36914594delT								C6orf89 (17856 upstream) : PI16 (7615 downstream)																							CCAGTGCCCCTGTCCCTCAGA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48541515	48541516	+	IGR	INS	-	TG	TG	rs151020735	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48541515_48541516insTG								C6orf138 (462572 upstream) : MUT (857478 downstream)																							ATACCTTTTTTTGTGTGTGTGT	0.203													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57211816	57211819	+	Intron	DEL	TGTT	-	-	rs10577577		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57211816_57211819delTGTT	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)		TGCTTGCTTCTGTTTGTTTATCTC	0.446													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57242864	57242865	+	Intron	INS	-	T	T	rs114712589		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57242864_57242865insT	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)		tcttcttcttcttttttttttt	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57322786	57322812	+	Intron	DEL	ACTCATATTTAGGTTGTGGCATATCAC	-	-	rs67472830		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57322786_57322812delACTCATATTTAGGTTGTGGCATATCAC	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)		GCTTCTGCTTACTCATATTTAGGTTGTGGCATATCACAAAGTGTCTT	0.304													6	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57400245	57400246	+	Intron	INS	-	TG	TG	rs72127011		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57400245_57400246insTG	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)		tgattatattctgtgtgtgtgt	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415913	57415914	+	Intron	INS	-	T	T	rs146932610	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415913_57415914insT	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)		cttatttaagcttagaaattca	0.069													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57417082	57417091	+	Intron	DEL	TTGGCAAATG	-	-	rs140389069		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57417082_57417091delTTGGCAAATG	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)		aaagcaaatattggcaaatgggatctaatt	0.000													2	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57476812	57476813	+	Intron	INS	-	A	A	rs149122632		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57476812_57476813insA	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)		agaaagtcaggaggatatagaa	0.000													2	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57499788	57499789	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57499788_57499789insT	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)		GATTATTAGAGTAAGAGTGGGA	0.149													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57554978	57554979	+	IGR	INS	-	AC	AC	rs146629400		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57554978_57554979insAC								PRIM2 (41603 upstream) : GUSBL2 (691180 downstream)																							ctgctatgggtagtttctcccg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	61900769	61900769	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:61900769delA								None (None upstream) : KHDRBS2 (489096 downstream)																							ctgctcaatcaaaagaaaggt	0.000													5	3	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71181292	71181295	+	Intron	DEL	ATCA	-	-	rs112799880		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71181292_71181295delATCA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfk.2_Intron|FAM135A_uc003pfl.2_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						gagggagaggatcaatcaggaaga	0.000													2	4	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74521475	74521475	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74521475delA	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						ACAATGGATGAAGGTGATAAC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82679990	82679991	+	IGR	INS	-	GGCTGTGGCA	GGCTGTGGCA	rs144206920	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82679990_82679991insGGCTGTGGCA								FAM46A (217562 upstream) : IBTK (199965 downstream)																							aaaaccacacgggctgtggcag	0.000													4	3	---	---	---	---	
C6orf165	154313	broad.mit.edu	37	6	88118444	88118445	+	Intron	INS	-	AT	AT	rs150716423	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88118444_88118445insAT	uc003plv.2	+						C6orf165_uc003plw.2_Intron|C6orf165_uc010kbv.1_Intron|C6orf165_uc003plu.1_Intron	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1											central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		CCACTAAAAACAGGACTAATTT	0.302													4	3	---	---	---	---	
FYN	2534	broad.mit.edu	37	6	112046252	112046263	+	Intron	DEL	AGGAATAGCATT	-	-	rs138527406		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112046252_112046263delAGGAATAGCATT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	TTCAGTCAGCAGGAATAGCATTAGGAAAAGGA	0.387													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114164712	114164713	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114164712_114164713insT								None (None upstream) : MARCKS (13814 downstream)																							gcTGGATGAGATTTTTTTTTTT	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	122407728	122407729	+	IGR	DEL	GA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122407728_122407729delGA								GJA1 (636856 upstream) : HSF2 (312967 downstream)																							caaatctcatgagatagtgtgc	0.000													4	2	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128424267	128424267	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128424267delG	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		agagtggagcggcagagaagg	0.000													4	2	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136903402	136903403	+	Intron	DEL	GT	-	-	rs71673773		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136903402_136903403delGT	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)		gtgtgtatacgtgtgtgtgtgt	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	144597319	144597319	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144597319delT								STX11 (84244 upstream) : UTRN (10171 downstream)																							ttcttttgggttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	161298083	161298083	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161298083delG								PLG (123738 upstream) : MAP3K4 (114739 downstream)																							ctgtgggactggggcacatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165510844	165510844	+	IGR	DEL	G	-	-	rs9459290	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165510844delG								None (None upstream) : C6orf118 (182311 downstream)																							taagagggatgttttttttcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169173000	169173000	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169173000delT								SMOC2 (104329 upstream) : THBS2 (442876 downstream)																							cctcatttccttctaagccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169275522	169275522	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169275522delG								SMOC2 (206851 upstream) : THBS2 (340354 downstream)																							TGTGAACAGTGGTGACGGAGT	0.597													4	2	---	---	---	---	
THBS2	7058	broad.mit.edu	37	6	169636313	169636316	+	Intron	DEL	CACT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169636313_169636316delCACT	uc003qwt.2	-							NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		ACACCATCCACACTCACTCCCCAT	0.270													3	3	---	---	---	---	
GET4	51608	broad.mit.edu	37	7	916840	916841	+	Intron	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:916840_916841delCT	uc003sjl.1	+						GET4_uc003sjj.1_Intron	NM_015949	NP_057033	Q7L5D6	GET4_HUMAN	hypothetical protein LOC51608						tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	protein binding				0						CTTGGtctcgctctctctctct	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2666946	2666947	+	IGR	INS	-	AGA	AGA	rs150172686	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2666946_2666947insAGA								IQCE (12579 upstream) : TTYH3 (4656 downstream)																							gagtgaggaagaggagggaggg	0.000													4	2	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	5985001	5985001	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-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	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9068307	9068307	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9068307delT								NXPH1 (275715 upstream) : PER4 (605593 downstream)																							TGCAAAAAGATAATGAAAAGA	0.338													4	2	---	---	---	---	
ABCB5	340273	broad.mit.edu	37	7	20795082	20795082	+	Frame_Shift_Del	DEL	G	-	-	rs61999295	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20795082delG	uc003suw.3	+	19	2820	c.2274delG	c.(2272-2274)ACGfs	p.T758fs	ABCB5_uc010kuh.2_Frame_Shift_Del_p.T1203fs	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	758	Cytoplasmic (Potential).|ABC transporter 2.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						AAGCCAGGACGGGAAGGACAT	0.448													25	13	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26342092	26342095	+	Intron	DEL	CTCC	-	-	rs35323038		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26342092_26342095delCTCC	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						TTCACATGGTCTCCCTCTGTGTGC	0.574													4	2	---	---	---	---	
CPVL	54504	broad.mit.edu	37	7	29150069	29150069	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29150069delA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2						CTTCAGGCAGAGGGTAGTGGC	0.493													4	2	---	---	---	---	
C7orf41	222166	broad.mit.edu	37	7	30177489	30177490	+	Intron	INS	-	TCAT	TCAT			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30177489_30177490insTCAT	uc011kab.1	+						C7orf41_uc010kvr.1_Intron|C7orf41_uc003tar.1_Intron	NM_152793	NP_690006	Q8N3F0	CG041_HUMAN	hypothetical protein LOC222166												0						GTATTTCCACATCATTCattca	0.188													4	2	---	---	---	---	
CRHR2	1395	broad.mit.edu	37	7	30734513	30734514	+	Intron	INS	-	GAG	GAG	rs148999651	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30734513_30734514insGAG	uc003tbp.2	-						CRHR2_uc010kvz.1_Intron|CRHR2_uc003tbq.1_Intron|CRHR2_uc003tbr.1_Intron|CRHR2_uc010kwa.1_Intron|uc010kwb.1_Intron	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4						gaggggatgatgaggagagaag	0.000													2	5	---	---	---	---	
INMT	11185	broad.mit.edu	37	7	30759327	30759330	+	Intron	DEL	CATC	-	-	rs10259272		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30759327_30759330delCATC	uc010kwc.1	+									O95050	INMT_HUMAN	Homo sapiens indolethylamine N-methyltransferase (INMT) mRNA, INMT-1 allele, complete cds.							cytoplasm	amine N-methyltransferase activity				0						atccatcattcatccatccatcca	0.020													4	3	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37387295	37387295	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37387295delT	uc003tfk.1	-						ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						atgtaaaccctttttttcctt	0.080													4	2	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39317269	39317270	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39317269_39317270insA	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						GTGCTTTGGTTAACTTTCCCTT	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41994902	41994904	+	IGR	DEL	TTC	-	-	rs72044361		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41994902_41994904delTTC								LOC285954 (175928 upstream) : GLI3 (5646 downstream)																							CAGCAGAATGTTCTTCTCCCCTT	0.473													4	5	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48460798	48460798	+	Intron	DEL	C	-	-	rs34693576		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48460798delC	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						ttttctctctctttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56076139	56076140	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56076139_56076140insA								GBAS (8268 upstream) : PSPH (2606 downstream)																							acaacaacaacaaaaaaaacaa	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57414935	57414936	+	IGR	INS	-	C	C	rs147304156	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57414935_57414936insC								ZNF479 (207364 upstream) : ZNF716 (94947 downstream)																							ggaaagaggaacaaggggcctc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	58037731	58037731	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:58037731delG								ZNF716 (504466 upstream) : None (None downstream)																							aagtttctcagattgcttatg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61080835	61080835	+	IGR	DEL	G	-	-	rs139305348	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61080835delG								None (None upstream) : None (None downstream)																							ttcctttgatggagcagtttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65193044	65193045	+	Intron	DEL	TG	-	-	rs138251817		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65193044_65193045delTG	uc003tud.1	-						uc003tuf.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		GACAACAGTTtgtgtgtgtgtg	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65275129	65275132	+	IGR	DEL	AGTT	-	-	rs3981804		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65275129_65275132delAGTT								CCT6P1 (46468 upstream) : VKORC1L1 (63125 downstream)																							ctctttaaacagttagctctcaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65277108	65277109	+	IGR	INS	-	G	G	rs143366985	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65277108_65277109insG								CCT6P1 (48447 upstream) : VKORC1L1 (61148 downstream)																							ttagtagagacgggtttctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65277688	65277689	+	IGR	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65277688_65277689delTT								CCT6P1 (49027 upstream) : VKORC1L1 (60568 downstream)																							CAAACTCCAGttttgttttttg	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65286885	65286888	+	IGR	DEL	TTCT	-	-	rs77662069		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65286885_65286888delTTCT								CCT6P1 (58224 upstream) : VKORC1L1 (51369 downstream)																							AAATTAGGGCTTCTTTATCATGAA	0.221													4	2	---	---	---	---	
ASL	435	broad.mit.edu	37	7	65557448	65557449	+	Intron	INS	-	A	A	rs77144805		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65557448_65557449insA	uc003tuo.2	+						ASL_uc003tup.2_Intron|ASL_uc003tur.2_Intron|ASL_uc003tuq.2_Intron	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1						arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)	gtgtcaaaaagaaaaaaaaaaa	0.262													10	5	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70054386	70054386	+	Intron	DEL	A	-	-	rs113964353		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70054386delA	uc003tvw.3	+						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)		ACCCCCTGGGAAAAAAAATGA	0.323													5	3	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73177324	73177324	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73177324delC	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						ttctctcttgccccccccttc	0.000													4	4	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73232895	73232895	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73232895delT	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						cctttcttccttttttttttt	0.000													6	3	---	---	---	---	
ZP3	7784	broad.mit.edu	37	7	76065050	76065050	+	Intron	DEL	T	-	-	rs71751281		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76065050delT	uc003ufd.3	+						ZP3_uc003ufc.3_Intron|ZP3_uc003ufe.2_Intron	NM_001110354	NP_001103824	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0						ACCACCAGCAttttttttttt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82167785	82167786	+	IGR	INS	-	GA	GA	rs139322952	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82167785_82167786insGA								CACNA2D1 (94754 upstream) : PCLO (215535 downstream)																							agggagagggggagagagagag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	83315448	83315449	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83315448_83315449delAC								SEMA3E (37124 upstream) : SEMA3A (272216 downstream)																							cgtctctactacacacacacac	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84372322	84372323	+	IGR	INS	-	TG	TG	rs139098925	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84372322_84372323insTG								SEMA3A (548105 upstream) : SEMA3D (252551 downstream)																							tttggggtttttgtgtgtgtgt	0.000													3	4	---	---	---	---	
DYNC1I1	1780	broad.mit.edu	37	7	95689547	95689547	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95689547delA	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			CCTGTGGCACAAATCCATCAT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96975128	96975128	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96975128delA								ACN9 (164055 upstream) : TAC1 (386143 downstream)																							cgtctcaaggaaaaaaaaaaa	0.219													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98177516	98177523	+	IGR	DEL	CTACTTAC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98177516_98177523delCTACTTAC								BAIAP2L1 (147089 upstream) : NPTX2 (69074 downstream)																							gcctacctatctacttacctacctacct	0.000													4	2	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98558383	98558384	+	Intron	DEL	TG	-	-	rs35384186		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98558383_98558384delTG	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			cctggctttttgtgtgtgtgtg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101395437	101395437	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101395437delA								MYL10 (122861 upstream) : CUX1 (63855 downstream)																							ccctgtctctaaaaaaaaaaa	0.000													6	3	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103592313	103592313	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103592313delT	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)		agacacagggttttgccatgt	0.000													4	2	---	---	---	---	
ATXN7L1	222255	broad.mit.edu	37	7	105459892	105459892	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105459892delA	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1												0						TTTGGGatttaaaaaaaaaaa	0.398													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	110271028	110271029	+	IGR	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110271028_110271029delCT								EIF3IP1 (670758 upstream) : IMMP2L (32081 downstream)																							AATCTCATTCctctctctctct	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118859231	118859231	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118859231delG								ANKRD7 (976449 upstream) : None (None downstream)																							ctctttctgtggaggctggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	126008696	126008696	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126008696delC								None (None upstream) : GRM8 (69956 downstream)																							GAGAGCTGTGCCCCCCCtttt	0.164													4	2	---	---	---	---	
NRF1	4899	broad.mit.edu	37	7	129345781	129345782	+	Intron	DEL	GA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129345781_129345782delGA	uc003voz.2	+						NRF1_uc003vpa.2_Intron|NRF1_uc011kpa.1_Intron|NRF1_uc003vpb.2_Intron	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1						generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1						atccgagagtgagagagagaga	0.149													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132131465	132131465	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132131465delA	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						gtatcctcacaaaaaccccac	0.060													4	2	---	---	---	---	
STRA8	346673	broad.mit.edu	37	7	134939561	134939562	+	Intron	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134939561_134939562insG	uc011kpx.1	+							NM_182489	NP_872295	Q7Z7C7	STRA8_HUMAN	STRA8						DNA replication|regulation of transcription, DNA-dependent	cytoplasm|nucleus					0						ACCAGAACTGTGGGGGCATTCT	0.545													4	2	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139538205	139538205	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139538205delT	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron|TBXAS1_uc011kqx.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					TGCCTGGTGCTTTCTTCCTGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141074179	141074180	+	IGR	DEL	CA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141074179_141074180delCA								MRPS33 (359398 upstream) : AGK (176898 downstream)																							cacacacatgcacacacacaca	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142461985	142461986	+	Intron	INS	-	T	T	rs140493997	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142461985_142461986insT	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		CCACCTTCACCTCTGTCCCAAG	0.540													4	2	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	144049976	144049979	+	Intron	DEL	AGAG	-	-	rs5888130		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144049976_144049979delAGAG	uc003wec.1	-						ARHGEF5_uc003wek.2_5'Flank|ARHGEF5_uc003wel.2_5'Flank					SubName: Full=Seven transmembrane helix receptor;												0						TGATGAGAAAagagagagagagag	0.407													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146937754	146937755	+	Intron	DEL	CT	-	-	rs67573457		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146937754_146937755delCT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTGCAGGAGACTCTGCAGTTAC	0.480										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147129900	147129900	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147129900delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			atcacctccctacagaggcct	0.000										HNSCC(39;0.1)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150115623	150115623	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150115623delT								LOC728743 (6066 upstream) : GIMAP8 (32339 downstream)																							taattaaaacttttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150607557	150607557	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150607557delT								ABP1 (49178 upstream) : KCNH2 (34493 downstream)																							ggtgtgtgtgtggtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152582308	152582309	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152582308_152582309insT								ACTR3B (29845 upstream) : None (None downstream)																							GCAGGGAGAAGTTATCGTCACG	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152610542	152610542	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152610542delT								ACTR3B (58079 upstream) : DPP6 (973877 downstream)																							TTTGCCACCGTTTTTTTTTTT	0.413													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153909071	153909074	+	Intron	DEL	CCTC	-	-	rs66945988		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153909071_153909074delCCTC	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CCTGCCCCTTCCTCCCTCATCTCA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155683981	155683981	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155683981delG								SHH (79014 upstream) : C7orf4 (649204 downstream)																							tggtagtactggggtggagtt	0.000													4	2	---	---	---	---	
DNAJB6	10049	broad.mit.edu	37	7	157172500	157172509	+	Intron	DEL	TTTTTTTTTT	-	-	rs113947571		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157172500_157172509delTTTTTTTTTT	uc003wnk.2	+						DNAJB6_uc003wnj.2_Intron|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_Intron|uc003wnm.1_5'Flank	NM_058246	NP_490647	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		CAGAAATGCCtttttttttttttttttttt	0.062													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157541142	157541143	+	Intron	INS	-	G	G	rs139745517	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157541142_157541143insG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCCTGAGCTGTGGGGTGTCTGG	0.609													4	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4310739	4310740	+	Intron	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4310739_4310740delAC	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)		acacacagagacacacacacac	0.332													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6011001	6011002	+	IGR	INS	-	G	G	rs146661110	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6011001_6011002insG								None (None upstream) : MCPH1 (253119 downstream)																							cggaacaatcaccagctctctg	0.000													0	7	---	---	---	---	
MCPH1	79648	broad.mit.edu	37	8	6459044	6459045	+	Intron	DEL	AC	-	-	rs35349503		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6459044_6459045delAC	uc003wqi.2	+							NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		ATCATATGGGacacacacacac	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8401902	8401902	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8401902delA								SGK223 (162645 upstream) : CLDN23 (157764 downstream)																							TTACCTCCCCACCTGATTTCA	0.488													4	2	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12070093	12070094	+	Intron	INS	-	GA	GA			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12070093_12070094insGA	uc011kxp.1	+						uc003wvm.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						GCCCTGACTATgagagagagag	0.297													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13066255	13066256	+	Intron	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13066255_13066256delAC	uc003wwm.2	-						DLC1_uc003wwl.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						atacacacagacacacacacac	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15204969	15204970	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15204969_15204970delAC								SGCZ (109177 upstream) : TUSC3 (192760 downstream)																							gtttaaacatacacacaCATGC	0.059													4	2	---	---	---	---	
ZDHHC2	51201	broad.mit.edu	37	8	17057146	17057147	+	Intron	INS	-	CTC	CTC	rs150638210	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17057146_17057147insCTC	uc003wxe.2	+							NM_016353	NP_057437	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		ttcttcttcttctcctcctcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	17326366	17326367	+	IGR	INS	-	A	A	rs145235456	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17326366_17326367insA								MTMR7 (55326 upstream) : SLC7A2 (28233 downstream)																							GGGACCATGAGAAAAAAAAAGA	0.297													1	5	---	---	---	---	
PSD3	23362	broad.mit.edu	37	8	18855284	18855285	+	Intron	DEL	TT	-	-	rs148916351		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18855284_18855285delTT	uc003wza.2	-							NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		cccggtgcacttaccttccttc	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18925487	18925487	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18925487delG								PSD3 (54291 upstream) : SH2D4A (245720 downstream)																							TCAGGCACATGGGAAGTGATT	0.483													4	2	---	---	---	---	
SH2D4A	63898	broad.mit.edu	37	8	19184159	19184160	+	Intron	INS	-	TGTGTGTA	TGTGTGTA	rs150724704	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19184159_19184160insTGTGTGTA	uc003wzb.2	+						SH2D4A_uc011kym.1_Intron|SH2D4A_uc003wzc.2_Intron	NM_022071	NP_071354	Q9H788	SH24A_HUMAN	SH2 domain containing 4A							cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)		CCCACATCgtgtgtgtgtatgt	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20859369	20859369	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20859369delG								LZTS1 (746566 upstream) : GFRA2 (690161 downstream)																							CACACGAGGAGGGGGTGCAGG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23654271	23654271	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23654271delA								NKX2-6 (90349 upstream) : STC1 (45163 downstream)																							ctctatctttaaaaaaaaaaa	0.189													3	3	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27773933	27773934	+	Intron	INS	-	AT	AT	rs145079746	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27773933_27773934insAT	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		tatgtgcaaacgtgtacacatg	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29242548	29242548	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29242548delT								DUSP4 (34363 upstream) : C8orf75 (336230 downstream)																							attcactctattttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30631653	30631654	+	IGR	INS	-	G	G	rs138966548	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30631653_30631654insG								UBXN8 (7135 upstream) : PPP2CB (11473 downstream)																							tccgcagggctgggaggcctca	0.000													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	31847452	31847452	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31847452delT	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TAGCAAGCAATTTCTCATAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	34372032	34372035	+	IGR	DEL	ACAG	-	-	rs143812310	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34372032_34372035delACAG								DUSP26 (914593 upstream) : UNC5D (720940 downstream)																							acacacacacacagacacacacTT	0.348													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36507211	36507211	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36507211delA								UNC5D (855031 upstream) : KCNU1 (134631 downstream)																							tttcaaacttaaaaaaaaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40213005	40213006	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40213005_40213006delAC								C8orf4 (200184 upstream) : ZMAT4 (175110 downstream)																							GCACAAATAGACACACACACAC	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40242062	40242062	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40242062delG								C8orf4 (229241 upstream) : ZMAT4 (146054 downstream)																							gatggtgaatggggccacaag	0.000													4	2	---	---	---	---	
GINS4	84296	broad.mit.edu	37	8	41392258	41392258	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41392258delT	uc003xnx.2	+						GINS4_uc003xny.2_Intron	NM_032336	NP_115712	Q9BRT9	SLD5_HUMAN	GINS complex subunit 4						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			ACACAGGGTCttttttttttt	0.035													4	2	---	---	---	---	
ANK1	286	broad.mit.edu	37	8	41689173	41689177	+	Intron	DEL	AGAAG	-	-	rs141382085	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41689173_41689177delAGAAG	uc003xom.2	-							NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9						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)			aaaaaaaaaaagaagaagaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42004238	42004239	+	IGR	DEL	TT	-	-	rs71548561		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42004238_42004239delTT								MYST3 (94733 upstream) : AP3M2 (6225 downstream)																							TCTTCAAGTCtttttttttttt	0.193													6	3	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48177227	48177227	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48177227delT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				TGAGAttttcttttttttttt	0.229													3	3	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51301639	51301639	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51301639delA	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GTTCTCGTGCAATTGCAGAAG	0.473													3	6	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51504394	51504394	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51504394delT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				CCCTCCTACCTTAAGTCCCTC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54204040	54204041	+	IGR	INS	-	ACAC	ACAC	rs145236546	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54204040_54204041insACAC								OPRK1 (39846 upstream) : ATP6V1H (424075 downstream)																							catacacatatacacacacaca	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60595836	60595837	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60595836_60595837insT								TOX (564069 upstream) : CA8 (505586 downstream)																							ttaggtatttatttttagcaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61368398	61368398	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61368398delC								CA8 (174444 upstream) : RAB2A (61161 downstream)																							GAGACACTCACCTTTCTTACA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61387905	61387908	+	IGR	DEL	TTCT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61387905_61387908delTTCT								CA8 (193951 upstream) : RAB2A (41651 downstream)																							tctcctcctcttctttctccttac	0.005													4	3	---	---	---	---	
CHD7	55636	broad.mit.edu	37	8	61748948	61748948	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61748948delG	uc003xue.2	+							NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7						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)			GGGCTAGAATGGGGGAAGTGC	0.363													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61945613	61945620	+	IGR	DEL	AGAAAGAT	-	-	rs60907426		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61945613_61945620delAGAAAGAT								CHD7 (166150 upstream) : CLVS1 (254905 downstream)																							agaaaaagaaagaaagatagaaagaaag	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71845672	71845672	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71845672delT								XKR9 (197496 upstream) : EYA1 (263998 downstream)																							GGAAGAACAGTTTTTTTTTTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80664829	80664830	+	IGR	INS	-	AAC	AAC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80664829_80664830insAAC								STMN2 (86435 upstream) : HEY1 (11416 downstream)																							agaagaagaagaacaataacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81280624	81280624	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81280624delT								TPD52 (196788 upstream) : ZBTB10 (117230 downstream)																							AAGATTTTAATTTTTTTTTTT	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	95123642	95123643	+	IGR	INS	-	TG	TG	rs147099569	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95123642_95123643insTG								PDP1 (185348 upstream) : CDH17 (15751 downstream)																							GAATGCTCACTTGCCCTCAATG	0.411													3	3	---	---	---	---	
RAD54B	25788	broad.mit.edu	37	8	95482999	95482999	+	Intron	DEL	A	-	-	rs111820750		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95482999delA	uc003ygk.2	-						RAD54B_uc003ygl.1_Intron|RAD54B_uc003ygn.1_Intron	NM_012415	NP_036547	O95073	FSBP_HUMAN	RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			gaaaacaaagaaaaaaaaaaa	0.000								Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96584966	96584966	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96584966delT								C8orf37 (303529 upstream) : GDF6 (569594 downstream)																							cagaaaaccctgtgtccttgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96621564	96621565	+	IGR	DEL	TC	-	-	rs72239058		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96621564_96621565delTC								C8orf37 (340127 upstream) : GDF6 (532995 downstream)																							TTCCTTCCTTtctctctctctc	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96976325	96976325	+	IGR	DEL	T	-	-	rs35354881		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96976325delT								C8orf37 (694888 upstream) : GDF6 (178235 downstream)																							AGGGCAGttcttttttttttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97076352	97076352	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97076352delT								C8orf37 (794915 upstream) : GDF6 (78208 downstream)																							CTTATTTATGTTTACAACAGA	0.318													4	2	---	---	---	---	
C8orf47	203111	broad.mit.edu	37	8	99094156	99094156	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99094156delA	uc003yih.1	+							NM_173549	NP_775820	Q6P6B1	CH047_HUMAN	hypothetical protein LOC203111												0	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			aacttcgtctaaaaaaaaaaa	0.174													4	2	---	---	---	---	
C8orf47	203111	broad.mit.edu	37	8	99098016	99098016	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99098016delC	uc003yih.1	+							NM_173549	NP_775820	Q6P6B1	CH047_HUMAN	hypothetical protein LOC203111												0	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			TTTCCTGAGTCCTCCAGGCTT	0.552													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99721597	99721598	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99721597_99721598insA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		ccacaaaaaggaaaaaaaaagA	0.015													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102999127	102999128	+	Intron	INS	-	A	A	rs148401873	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102999127_102999128insA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			GGGTTGATAAGAATGTGAGGGG	0.490													3	3	---	---	---	---	
BAALC	79870	broad.mit.edu	37	8	104210078	104210078	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104210078delC	uc003yld.2	+						BAALC_uc003yle.2_Intron|uc003ylf.2_Intron	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			gaaggatatgccccatgatcc	0.015													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104952275	104952275	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104952275delA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_Intron	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			aaactgttccaacccctgccc	0.000										HNSCC(12;0.0054)			4	2	---	---	---	---	
ANGPT1	284	broad.mit.edu	37	8	108412790	108412790	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108412790delT	uc003ymn.2	-						ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			CAtttctttcttttttttttt	0.199													4	2	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110464254	110464254	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110464254delT	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AATCAGGTCATTTTTTTTTTG	0.279										HNSCC(38;0.096)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110767755	110767755	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110767755delT								SYBU (63735 upstream) : KCNV1 (211480 downstream)																							ttgattgtccttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111637151	111637151	+	IGR	DEL	T	-	-	rs150606555		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111637151delT								KCNV1 (649075 upstream) : None (None downstream)																							ctttccttgcttTTTTTTTTT	0.169													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112770100	112770100	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112770100delG								None (None upstream) : CSMD3 (465061 downstream)																							CAGCAAGAATGGTATAAGAAC	0.259													4	2	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119244871	119244874	+	Intron	DEL	CTTT	-	-	rs66945456		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119244871_119244874delCTTT	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146	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)			TGCATAGCTCCTTTCTTTCCTCCT	0.397													3	6	---	---	---	---	
DEPDC6	64798	broad.mit.edu	37	8	121046503	121046504	+	Intron	INS	-	AC	AC	rs144178343	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121046503_121046504insAC	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GCAAAGCATGTacacacacaca	0.347													4	4	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121558709	121558710	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121558709_121558710insT	uc010mdg.2	-							NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			TTTCCATTCTCttttttttgtt	0.163													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122253617	122253618	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122253617_122253618insA								SNTB1 (429308 upstream) : HAS2 (371653 downstream)																							GTTTATAAGACAAAAAAAAAAT	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123126146	123126146	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123126146delT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																		GGAGGCAATGTTTAAGTGGca	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124682446	124682446	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124682446delC								KLHL38 (17256 upstream) : ANXA13 (10589 downstream)																							tcctcctcctcctccccacct	0.154													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125809317	125809318	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125809317_125809318insA								MTSS1 (68587 upstream) : LOC157381 (142566 downstream)																							cacacacacacacacacacaca	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127144018	127144019	+	IGR	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127144018_127144019delTC								TRIB1 (693376 upstream) : FAM84B (420668 downstream)																							caaaggtatttctctctctctc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136753756	136753757	+	IGR	INS	-	A	A	rs75274130		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136753756_136753757insA								KHDRBS3 (93910 upstream) : None (None downstream)																							gactttgtctcaaaaaaaaaGG	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138311226	138311227	+	IGR	INS	-	G	G	rs137997336	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138311226_138311227insG								None (None upstream) : FAM135B (831041 downstream)																							AGAATACCCAAGGGGGGTCTCA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140311990	140311993	+	IGR	DEL	TGTT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140311990_140311993delTGTT								COL22A1 (385754 upstream) : KCNK9 (301089 downstream)																							AAGTTCTGGCTGTTTGTTTGTTTG	0.235													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141046321	141046321	+	Intron	DEL	A	-	-	rs10707510		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141046321delA	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						cgacttctttaaaaaaaaaaa	0.095													3	5	---	---	---	---	
EIF2C2	27161	broad.mit.edu	37	8	141562827	141562828	+	Intron	INS	-	CG	CG	rs142096576	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141562827_141562828insCG	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			acgcacatgcacgcgcgcgcgc	0.149													2	4	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	141952725	141952726	+	Intron	DEL	GC	-	-	rs35792894		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141952725_141952726delGC	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)			ATGAgtgcgtgcgtgtgtgtgt	0.248													4	2	---	---	---	---	
FLJ43860	389690	broad.mit.edu	37	8	142505989	142505990	+	Intron	INS	-	CACC	CACC	rs144475176	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142505989_142505990insCACC	uc003ywi.2	-						FLJ43860_uc011ljs.1_5'Flank|FLJ43860_uc010meu.1_5'Flank	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			ataaatttattcacccacccac	0.045													3	4	---	---	---	---	
HEATR7A	727957	broad.mit.edu	37	8	145266630	145266630	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145266630delA	uc003zbk.3	+						HEATR7A_uc003zbh.3_Intron|HEATR7A_uc003zbi.3_Intron|HEATR7A_uc011lla.1_Intron|HEATR7A_uc010mft.2_Intron	NM_032450	NP_115826	Q8NDA8	HTR7A_HUMAN	HEAT repeat containing 7A isoform 1								binding				0						attccatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	146136328	146136328	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146136328delC								COMMD5 (9482 upstream) : ZNF16 (19418 downstream)																							TGCTGCAGGACCCTTTGGTAT	0.473													4	2	---	---	---	---	
C8orf33	65265	broad.mit.edu	37	8	146281196	146281197	+	3'UTR	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146281196_146281197delTC	uc003zfc.3	+	5					C8orf33_uc003zfd.2_RNA	NM_023080	NP_075568	Q9H7E9	CH033_HUMAN	hypothetical protein LOC65265												0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)		ctctctctcttctctctctctc	0.000													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	10574203	10574204	+	Intron	INS	-	TA	TA	rs147806465		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10574203_10574204insTA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ATAGAtgtgtgtgtgtgtgtgc	0.267										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16301471	16301471	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16301471delC								C9orf93 (329576 upstream) : BNC2 (108031 downstream)																							tctgataggaccatgctgcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19796499	19796499	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19796499delT								SLC24A2 (7691 upstream) : MLLT3 (548469 downstream)																							ctctttcttgtttactccttt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19988396	19988396	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19988396delA								SLC24A2 (199588 upstream) : MLLT3 (356572 downstream)																							TCCAGTTCACAAGGCTTTTAA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26642439	26642439	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26642439delC								TUSC1 (963583 upstream) : C9orf82 (198245 downstream)																							GTGCTAAACACCTAAACTGTA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47199410	47199410	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47199410delA								KGFLP1 (451025 upstream) : None (None downstream)																							Aataatattgaacatatagat	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66826477	66826477	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66826477delA								LOC442421 (323450 upstream) : AQP7P1 (427790 downstream)																							agagttgaacattccttttca	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66843172	66843172	+	IGR	DEL	G	-	-	rs113243134		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66843172delG								LOC442421 (340145 upstream) : AQP7P1 (411095 downstream)																							tggtggaaaaggagatatctt	0.000													3	8	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67289313	67289314	+	RNA	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67289313_67289314insT	uc004aen.1	-	1		c.179_180insA			AQP7P1_uc004aeo.1_RNA|AQP7P1_uc004aep.1_RNA					Homo sapiens cDNA FLJ46364 fis, clone TESTI4051015.												0						AGCTATCCCTGTGTCCCCAGTC	0.614													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67337092	67337092	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67337092delT								AQP7P1 (47600 upstream) : FAM27B (455838 downstream)																							ataaaaatgcttcaacaagca	0.005													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68375419	68375420	+	IGR	INS	-	C	C	rs138387266	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68375419_68375420insC								FAM27B (581230 upstream) : MIR1299 (626819 downstream)																							aaacaaacaaaaaaaaaaaaaa	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68414977	68414978	+	IGR	DEL	AG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414977_68414978delAG								FAM27B (620788 upstream) : MIR1299 (587261 downstream)																							gaaaaagaaaagaaagaaaaga	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68989452	68989452	+	IGR	DEL	G	-	-	rs71498602		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68989452delG								None (None upstream) : MIR1299 (12787 downstream)																							ggctgcaggaggggcgtccac	0.000													5	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69643067	69643067	+	Intron	DEL	C	-	-	rs145420014		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69643067delC	uc004afu.3	-											Homo sapiens aquaporin 7 pseudogene 2, mRNA (cDNA clone IMAGE:30406582).																		TCTCttttttctttttttttt	0.100													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69982826	69982827	+	IGR	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69982826_69982827delCT								LOC100133920 (317877 upstream) : FOXD4L5 (192882 downstream)																							gtttgaaacactctttttccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	71208228	71208229	+	IGR	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71208228_71208229insC								C9orf71 (52445 upstream) : PIP5K1B (112387 downstream)																							gatgttggtgacctttggatgg	0.000													4	2	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72834534	72834534	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72834534delC	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron|uc004ahq.1_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						GCAGTGCAGTCAAAGGTGCTA	0.403													4	2	---	---	---	---	
C9orf57	138240	broad.mit.edu	37	9	74671829	74671829	+	Intron	DEL	T	-	-	rs67006603		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74671829delT	uc004aip.2	-						C9orf57_uc011lsd.1_Intron	NM_001128618	NP_001122090	Q5W0N0	CI057_HUMAN	hypothetical protein LOC138240							integral to membrane					0						ATATGTATACttttttttttt	0.204													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76323979	76323980	+	IGR	INS	-	T	T	rs112359930		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76323979_76323980insT								ANXA1 (538672 upstream) : RORB (788272 downstream)																							catgctgagcattttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78274627	78274627	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78274627delA								OSTF1 (512514 upstream) : PCSK5 (230933 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78899452	78899452	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78899452delT								PCSK5 (91114 upstream) : RFK (100981 downstream)																							tttttttgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	80980522	80980522	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80980522delA								PSAT1 (35515 upstream) : None (None downstream)																							CACGGTGCATAAGCAGCTCTG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83178253	83178253	+	IGR	DEL	A	-	-	rs66609866		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83178253delA								TLE4 (836596 upstream) : None (None downstream)																							AGTTGGACAGAAAAAAAAGAC	0.209													6	4	---	---	---	---	
UBQLN1	29979	broad.mit.edu	37	9	86324502	86324503	+	5'Flank	INS	-	GT	GT	rs142545107	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86324502_86324503insGT	uc004amv.2	-						UBQLN1_uc004amw.2_5'Flank|uc004amx.2_Intron	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						caacaaataccgtgtgtgtgtg	0.015													7	4	---	---	---	---	
SLC28A3	64078	broad.mit.edu	37	9	86924432	86924432	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86924432delT	uc010mpz.2	-						SLC28A3_uc011lsy.1_Intron|SLC28A3_uc004anu.1_Intron|SLC28A3_uc010mqb.2_Intron	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						agtgagactcttatctcaaaa	0.119													4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90692650	90692651	+	IGR	INS	-	G	G	rs150894278	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90692650_90692651insG								CDK20 (102983 upstream) : SPIN1 (310189 downstream)																							ctctggaggctggaagtccaac	0.050													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90708456	90708456	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90708456delT								CDK20 (118789 upstream) : SPIN1 (294384 downstream)																							AAAATGTGAAttttttttttt	0.214													3	4	---	---	---	---	
SHC3	53358	broad.mit.edu	37	9	91674670	91674670	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91674670delG	uc004aqg.2	-							NM_016848	NP_058544	Q92529	SHC3_HUMAN	src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4						ggtggaggatggtggtggagg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91868143	91868144	+	IGR	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91868143_91868144delGT								SHC3 (74461 upstream) : CKS2 (57969 downstream)																							GTAGTGTGGGgtgtgtgtgtgt	0.158													4	3	---	---	---	---	
SYK	6850	broad.mit.edu	37	9	93589439	93589439	+	Intron	DEL	T	-	-	rs113349852		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93589439delT	uc004aqz.2	+						SYK_uc004aqy.2_Intron|SYK_uc004ara.2_Intron|SYK_uc004arb.2_Intron|SYK_uc004arc.2_5'Flank	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1						cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						ACCAAGTTCATTTTTGGTAAA	0.408			T	ETV6|ITK	MDS|peripheral T-cell lymphoma								5	4	---	---	---	---	
AUH	549	broad.mit.edu	37	9	94109318	94109318	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94109318delT	uc004arf.3	-						AUH_uc004arg.3_Intron|AUH_uc011ltu.1_Intron	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0						ctgagccccattttttgtttt	0.000													4	2	---	---	---	---	
FAM120A	23196	broad.mit.edu	37	9	96284924	96284924	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96284924delT	uc004atw.2	+						FAM120A_uc004atv.2_Intron|FAM120A_uc004atx.2_Intron|FAM120A_uc004aty.2_Intron|FAM120A_uc004atz.2_Intron|FAM120A_uc010mrf.1_Intron	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0						GAAGACTGAGTTTTTTTCCAC	0.318													4	2	---	---	---	---	
PTPDC1	138639	broad.mit.edu	37	9	96791307	96791308	+	5'Flank	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96791307_96791308insT	uc004auf.1	+						PTPDC1_uc004aug.1_5'Flank	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1								protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1						CAATCCATTACttttttttttt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102388879	102388882	+	Intron	DEL	CACA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102388879_102388882delCACA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																		CTCTCTCTCTcacacacacacaca	0.314													4	2	---	---	---	---	
GRIN3A	116443	broad.mit.edu	37	9	104399375	104399375	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104399375delT	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)	ACACTGGACAttttttttttc	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	106089413	106089413	+	5'Flank	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106089413delT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																		ACTTCATGTCTTAGGCCAGAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	108704744	108704744	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108704744delT								TMEM38B (167300 upstream) : ZNF462 (920634 downstream)																							acctctgtcattatttcctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109391624	109391624	+	Intron	DEL	A	-	-	rs111608141		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109391624delA	uc004bcy.1	+											Homo sapiens cDNA FLJ36044 fis, clone TESTI2017584.																		actccgtagtaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110271814	110271815	+	IGR	INS	-	GTGT	GTGT	rs140793634	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110271814_110271815insGTGT								KLF4 (19767 upstream) : None (None downstream)																							ACCAACTCTGGgtgtgtgtgtg	0.218													3	3	---	---	---	---	
COL27A1	85301	broad.mit.edu	37	9	117000078	117000078	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117000078delA	uc011lxl.1	+						COL27A1_uc004bii.2_Intron	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						agggatggggaaagacttgct	0.313													14	10	---	---	---	---	
DEC1	50514	broad.mit.edu	37	9	117932385	117932386	+	Intron	INS	-	TTGT	TTGT	rs143972072	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117932385_117932386insTTGT	uc004bjk.1	+							NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1						agtttttttgcttgtttgtttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	119181704	119181705	+	IGR	DEL	CC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119181704_119181705delCC								PAPPA (17105 upstream) : ASTN2 (5802 downstream)																							TGGGCAGAGGCCAATTAAAAAG	0.490													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119214111	119214112	+	Intron	INS	-	TCTG	TCTG	rs145839727	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119214111_119214112insTCTG	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|ASTN2_uc004bjo.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						TATGCAAATGATCTGAGTGTAT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120812815	120812815	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120812815delT								TLR4 (333051 upstream) : None (None downstream)																							TCTAAAATGGTTTTTTTTTTT	0.269													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122959738	122959738	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122959738delC								DBC1 (827999 upstream) : MIR147 (47519 downstream)																							CCCTGCACTGCCCCCCAACCT	0.333													2	5	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	123971039	123971039	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123971039delT	uc004bld.1	+							NM_198252	NP_937895	P06396	GELS_HUMAN	gelsolin isoform b						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						gggaggattattactaatgag	0.114													4	2	---	---	---	---	
GOLGA1	2800	broad.mit.edu	37	9	127644493	127644494	+	Intron	INS	-	CA	CA	rs140546216	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127644493_127644494insCA	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97							Golgi cisterna membrane				ovary(1)	1						AAGCACTCTGCCACACACACAC	0.559													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	131995367	131995368	+	IGR	INS	-	TCCA	TCCA	rs12003676		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131995367_131995368insTCCA								IER5L (54827 upstream) : C9orf106 (87927 downstream)																							ccatccatctgtccatccatcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132192020	132192020	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132192020delA								C9orf106 (107138 upstream) : C9orf50 (182486 downstream)																							tgcaattaacaaaaagtctga	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137383014	137383014	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137383014delA								RXRA (50583 upstream) : COL5A1 (150638 downstream)																							ctctgtctctaaaaaaaaaaa	0.189													4	2	---	---	---	---	
OLFM1	10439	broad.mit.edu	37	9	137993796	137993796	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137993796delT	uc010nar.2	+						OLFM1_uc004cfl.3_Intron	NM_014279	NP_055094	Q99784	NOE1_HUMAN	olfactomedin related ER localized protein						nervous system development	endoplasmic reticulum lumen	protein binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		CCTTAGTTTCTTTTTTTTCCC	0.323													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	620483	620484	+	Intron	INS	-	GCAC	GCAC	rs138911643	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:620483_620484insGCAC	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)		ATCGTGGTGGGGCACCCTGATA	0.470													4	2	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1049094	1049094	+	Intron	DEL	T	-	-	rs75545687		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1049094delT	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		atgacagagattttttttctg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3357105	3357106	+	IGR	INS	-	A	A	rs140602943		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3357105_3357106insA								PITRM1 (142102 upstream) : KLF6 (461083 downstream)																							AGTGAGGGAAGGGACAGTGACT	0.554													5	3	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6223298	6223300	+	Intron	DEL	CAG	-	-	rs112548832		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6223298_6223300delCAG	uc010qaw.1	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron	NM_001145443	NP_001138915	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						atgtttatatcagcattattcac	0.000													6	3	---	---	---	---	
ITIH2	3698	broad.mit.edu	37	10	7781092	7781092	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7781092delC	uc001ijs.2	+							NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3						CTTTGCCTTTCCATTGACAAC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10770080	10770080	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10770080delT								None (None upstream) : SFTA1P (56322 downstream)																							atgagaatgattttttttttc	0.000													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11325868	11325869	+	Intron	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11325868_11325869delTG	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_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						gatggatgactgtgtggtaggt	0.000													4	2	---	---	---	---	
NSUN6	221078	broad.mit.edu	37	10	18928303	18928304	+	Intron	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18928303_18928304insC	uc010qcp.1	-							NM_182543	NP_872349	Q8TEA1	NSUN6_HUMAN	NOL1/NOP2/Sun domain family, member 6								methyltransferase activity|RNA binding			ovary(2)	2						tgcgcctgtagccccagctact	0.000													4	2	---	---	---	---	
SPAG6	9576	broad.mit.edu	37	10	22634784	22634785	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22634784_22634785insT	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_Intron	NM_012443	NP_036575	O75602	SPAG6_HUMAN	sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1						GCCCCCCGCGCACTGAGTCCCC	0.673													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	23660796	23660796	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23660796delA								C10orf67 (27024 upstream) : OTUD1 (67402 downstream)																							aggagaactgaaaacatatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	25934101	25934101	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25934101delA								GPR158 (42946 upstream) : MYO3A (288901 downstream)																							aggaacttagaaaaggccgat	0.000													4	2	---	---	---	---	
MYO3A	53904	broad.mit.edu	37	10	26466061	26466061	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26466061delG	uc001isn.2	+						MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						GGTATAGAGAGGGGGGCTGGC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29158012	29158012	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29158012delT								BAMBI (186144 upstream) : LYZL1 (419978 downstream)																							agttaagggattttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30849971	30849971	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30849971delT								MAP3K8 (99210 upstream) : LYZL2 (50738 downstream)																							ttcACTGCAATTTttttttcg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38872763	38872777	+	IGR	DEL	ACTAGAATGGTATAA	-	-	rs34767063		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38872763_38872777delACTAGAATGGTATAA								LOC399744 (131683 upstream) : None (None downstream)																							aatggaatggactagaatggtataaaatggaatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38939448	38939450	+	IGR	DEL	AAT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38939448_38939450delAAT								LOC399744 (198368 upstream) : None (None downstream)																							TCTTACCAACAATATTTGATTCA	0.222													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39128615	39128619	+	IGR	DEL	GAACC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39128615_39128619delGAACC								LOC399744 (387535 upstream) : None (None downstream)																							gaatggaatggaaccaaatgaaatg	0.000													15	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42647155	42647155	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42647155delC								None (None upstream) : LOC441666 (180160 downstream)																							gtagaacaaaccgaaaaatag	0.065													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54351318	54351319	+	IGR	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54351318_54351319delTG								DKK1 (273902 upstream) : MBL2 (173822 downstream)																							cctaacacactgtgtgtgtgtg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58971729	58971732	+	IGR	DEL	AGAG	-	-	rs71020964		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58971729_58971732delAGAG								ZWINT (850695 upstream) : IPMK (983886 downstream)																							ctgtcctaacagagggaggattca	0.000													3	4	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	62262587	62262588	+	Intron	INS	-	GAAG	GAAG	rs143061409	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62262587_62262588insGAAG	uc010qih.1	-						ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_001149	NP_001140	Q12955	ANK3_HUMAN	ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						aagaaaagaaagaaggagtaag	0.000													6	3	---	---	---	---	
MIR606	693191	broad.mit.edu	37	10	77312184	77312184	+	5'Flank	DEL	C	-	-	rs1367290		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312184delC	hsa-mir-606|MI0003619	+																							0						ttttttttttcccccccctct	0.000													3	3	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	77762262	77762262	+	Intron	DEL	T	-	-	rs150760335		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77762262delT	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					ttcctacatctgtaaaatggg	0.055													2	4	---	---	---	---	
POLR3A	11128	broad.mit.edu	37	10	79761561	79761561	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79761561delT	uc001jzn.2	-							NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			gcccagctaattttttttttt	0.030													4	2	---	---	---	---	
SH2D4B	387694	broad.mit.edu	37	10	82313470	82313470	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82313470delC	uc001kck.1	+						SH2D4B_uc001kcl.1_Intron	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)			GCGTGACCAGCCCCATGTCTG	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	92715106	92715107	+	IGR	INS	-	A	A	rs149789770	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92715106_92715107insA								ANKRD1 (34074 upstream) : NUDT9P1 (196654 downstream)																							gctggggtgtgaaaaaaactcc	0.000													2	5	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97202281	97202283	+	5'Flank	DEL	CCG	-	-	rs143343438		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97202281_97202283delCCG	uc001kkp.2	-						SORBS1_uc001kko.2_5'Flank|SORBS1_uc001kkq.2_5'Flank|SORBS1_uc001kkr.2_5'Flank|SORBS1_uc001kks.2_5'Flank|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		caccccccccccgcacccttact	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102648515	102648516	+	IGR	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102648515_102648516delAC								PAX2 (58818 upstream) : FAM178A (23810 downstream)																							TTCCACTGCTACACTGGAGCTA	0.475													4	2	---	---	---	---	
ACTR1A	10121	broad.mit.edu	37	10	104239318	104239319	+	3'UTR	DEL	CC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104239318_104239319delCC	uc001kvv.2	-	11					ACTR1A_uc010qqn.1_3'UTR|ACTR1A_uc010qqo.1_3'UTR	NM_005736	NP_005727	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		TTGGACCACTCCTAGGAGTCAG	0.589													4	2	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108735169	108735169	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108735169delT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GGTGTCAGCATTTTATCGGGC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112854305	112854305	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112854305delG								ADRA2A (13645 upstream) : None (None downstream)																							TCTCTCTTCTGGCAATAGCCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113654490	113654490	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113654490delA								ADRA2A (813830 upstream) : GPAM (255132 downstream)																							atgatgacagaaaaaaaaaat	0.000													4	2	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114818454	114818455	+	Intron	DEL	TG	-	-	rs112952265		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114818454_114818455delTG	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GGTCGTGAGCtgtgtgtgtgtg	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115299571	115299585	+	IGR	DEL	TTCTCTTCTCTTCTC	-	-	rs11267643		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115299571_115299585delTTCTCTTCTCTTCTC								TCF7L2 (372137 upstream) : HABP2 (13193 downstream)																							TCTCcttcttttctcttctcttctcttctcttctc	0.237													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124316901	124316904	+	IGR	DEL	GTCT	-	-	rs143124673		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124316901_124316904delGTCT								HTRA1 (42477 upstream) : DMBT1 (3277 downstream)																							TGTCCCCCTCGTCTGTCTGTCAGG	0.618													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125182780	125182780	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125182780delC	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																		TGATGCCTTTCCCCAACAGAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	127245438	127245438	+	IGR	DEL	A	-	-	rs111353948		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127245438delA								CTBP2 (395814 upstream) : LOC100169752 (17502 downstream)																							CTGAAGAGTTAAAAAAAAAAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	131180744	131180744	+	IGR	DEL	T	-	-	rs113680930		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131180744delT								None (None upstream) : MGMT (84710 downstream)																							GTTGGGTTTCTTTTTTTTTTT	0.418													3	3	---	---	---	---	
SAA3P	6290	broad.mit.edu	37	11	18136938	18136939	+	Intron	INS	-	TG	TG	rs148532042	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18136938_18136939insTG	uc001mnt.2	-							NR_026576				Homo sapiens truncated serum amyloid A3 precursor (SAA3) mRNA, complete cds.												0						atcttggggtttgtgtgtgtgt	0.010											OREG0020820	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
PRMT3	10196	broad.mit.edu	37	11	20499101	20499102	+	Intron	INS	-	A	A	rs148599172	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20499101_20499102insA	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3 isoform 1								zinc ion binding				0						gattccgtctcaaaaaaaaaaG	0.178													2	4	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21091685	21091685	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21091685delG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						TTTTTTTTTTGAAGTAGCCTA	0.408													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21198343	21198343	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21198343delG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						ctgataatatggGTTCTTGAT	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	21915858	21915858	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21915858delC								NELL1 (318631 upstream) : ANO5 (298864 downstream)																							TTTCCAAACTCCACCACTGTT	0.418													4	2	---	---	---	---	
MPPED2	744	broad.mit.edu	37	11	30516608	30516609	+	Intron	DEL	TG	-	-	rs147181484		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30516608_30516609delTG	uc001msr.2	-						MPPED2_uc001msq.3_Intron|MPPED2_uc009yji.2_Intron	NM_001584	NP_001575	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2						nervous system development		hydrolase activity|metal ion binding			skin(1)	1						gaGGCATGACTGTATATATCTA	0.203													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32922104	32922105	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32922104_32922105insA	uc001mty.2	+							NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					gactccatcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35577909	35577910	+	IGR	INS	-	T	T	rs148974392	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35577909_35577910insT								PAMR1 (26061 upstream) : FJX1 (61825 downstream)																							CCCATAGAGAATTTTTTTTTTG	0.441													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35658811	35658811	+	IGR	DEL	A	-	-	rs111255086		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35658811delA								FJX1 (16392 upstream) : TRIM44 (25542 downstream)																							actacaattcaaaaaaAAAAG	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35911630	35911630	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35911630delT								TRIM44 (80700 upstream) : LDLRAD3 (53982 downstream)																							AGTAAAATAATTAGGTTCGAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39267222	39267223	+	IGR	INS	-	GT	GT	rs146906877	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39267222_39267223insGT								None (None upstream) : LRRC4C (868530 downstream)																							TTTTAGTTtgcgtgtgtgtgtg	0.238													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41538107	41538108	+	IGR	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41538107_41538108delTT								LRRC4C (56784 upstream) : None (None downstream)																							Attttcttcctttttttttttt	0.158													4	2	---	---	---	---	
HSD17B12	51144	broad.mit.edu	37	11	43728240	43728241	+	Intron	DEL	GT	-	-	rs111500311		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43728240_43728241delGT	uc001mxq.3	+						HSD17B12_uc001mxp.2_Intron	NM_016142	NP_057226	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0						GAATGAAGGGgtgtgtgtgtgt	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44788090	44788090	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44788090delC								CD82 (146777 upstream) : TSPAN18 (93789 downstream)																							GGACGTTTCTCCATCAGGGGA	0.498													4	2	---	---	---	---	
CRY2	1408	broad.mit.edu	37	11	45898219	45898219	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45898219delC	uc010rgn.1	+						CRY2_uc009ykw.2_Intron|CRY2_uc010rgo.1_Intron	NM_021117	NP_066940	Q49AN0	CRY2_HUMAN	cryptochrome 2 (photolyase-like) isoform 1						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	blue light photoreceptor activity|damaged DNA binding|DNA photolyase activity|nucleotide binding|protein binding|single-stranded DNA binding			central_nervous_system(1)	1						CTCTTCCCCTCCCCCGCGGGC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	46416244	46416245	+	IGR	INS	-	T	T	rs112441668		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46416244_46416245insT								CHRM4 (8137 upstream) : AMBRA1 (1719 downstream)																							CTCAAATCCACttttttttttt	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48378345	48378346	+	IGR	INS	-	G	G	rs139358861	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48378345_48378346insG								OR4C45 (4346 upstream) : OR4A47 (131999 downstream)																							aaggtatttttaatgtagatag	0.089													1	5	---	---	---	---	
CPSF7	79869	broad.mit.edu	37	11	61172344	61172344	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61172344delT	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron	NM_001136040	NP_001129512	Q8N684	CPSF7_HUMAN	pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						TGTCTGACACTAGAAGTGGTG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	62002332	62002333	+	IGR	DEL	TA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62002332_62002333delTA								SCGB2A1 (20921 upstream) : SCGB1D2 (7391 downstream)																							gaaattgtggtatatatatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	63553430	63553431	+	IGR	INS	-	AG	AG			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63553430_63553431insAG								C11orf95 (17317 upstream) : C11orf84 (27492 downstream)																							gaaaaaaagaaagagagagaga	0.000													4	2	---	---	---	---	
CLCF1	23529	broad.mit.edu	37	11	67139219	67139219	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67139219delG	uc001okq.2	-						LOC100130987_uc010rpo.1_Intron|CLCF1_uc010rpp.1_Intron	NM_013246	NP_037378	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1 precursor						B cell differentiation|cytokine-mediated signaling pathway|JAK-STAT cascade|negative regulation of neuron apoptosis|positive regulation of astrocyte differentiation|positive regulation of B cell proliferation|positive regulation of immunoglobulin production|positive regulation of isotype switching to IgE isotypes|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	ciliary neurotrophic factor receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity				0			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			AGAGGGGCGTGGGGGGGGAGG	0.622											OREG0021129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71121302	71121303	+	Intron	INS	-	AAT	AAT	rs143570512	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71121302_71121303insAAT	uc001oqj.1	-											Homo sapiens cDNA FLJ42102 fis, clone TESOP2006746.																		ttctaatttgCAGAGCCTGAGA	0.277													3	3	---	---	---	---	
UVRAG	7405	broad.mit.edu	37	11	75814581	75814582	+	Intron	INS	-	T	T	rs34483800		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75814581_75814582insT	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6						TGCTGTTTTGGTTTTTTTTTTT	0.317													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	75954233	75954234	+	IGR	INS	-	A	A	rs145996582	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75954233_75954234insA								WNT11 (32430 upstream) : PRKRIR (106770 downstream)																							GATGCAGGTGGCAGAGCCCAGG	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76015298	76015298	+	IGR	DEL	A	-	-	rs34751721		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76015298delA								WNT11 (93495 upstream) : PRKRIR (45706 downstream)																							actccatctcaaaaaaaaaaa	0.109													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102114423	102114426	+	IGR	DEL	AAAG	-	-	rs111903349		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102114423_102114426delAAAG								YAP1 (10269 upstream) : BIRC3 (73768 downstream)																							agaaagagaaaaagaaagaaagaa	0.034													4	3	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103167468	103167469	+	Intron	INS	-	T	T	rs78927606		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103167468_103167469insT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ttttctggatcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	103420866	103420867	+	IGR	DEL	TT	-	-	rs34519514		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103420866_103420867delTT								DYNC2H1 (70275 upstream) : PDGFD (357048 downstream)																							ACTCCTGTGATTTTTTTTTTTT	0.416													4	2	---	---	---	---	
RAB39	54734	broad.mit.edu	37	11	107808030	107808030	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107808030delA	uc001pjt.2	+							NM_017516	NP_059986	Q14964	RB39A_HUMAN	RAB39, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0				BRCA - Breast invasive adenocarcinoma(274;3.04e-05)|Epithelial(105;8.56e-05)|all cancers(92;0.00179)		ccagctaattaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116303034	116303034	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116303034delT								CADM1 (927793 upstream) : BUD13 (315854 downstream)																							AGCACCAGCCTCAGGAAAATG	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116421690	116421690	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116421690delG								None (None upstream) : BUD13 (197198 downstream)																							AAAGGAGAATGGATCCCATTA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118802917	118802917	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118802917delA								BCL9L (21304 upstream) : UPK2 (24109 downstream)																							accctgtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119409304	119409305	+	IGR	INS	-	T	T	rs146107155	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119409304_119409305insT								THY1 (115058 upstream) : PVRL1 (99503 downstream)																							tccactcttagttcccacagga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122279296	122279297	+	IGR	INS	-	CA	CA	rs147659639	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122279296_122279297insCA								LOC399959 (40829 upstream) : UBASH3B (247101 downstream)																							GTTTCATTTTTcacacacacac	0.248													5	4	---	---	---	---	
C11orf45	219833	broad.mit.edu	37	11	128770193	128770193	+	3'UTR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128770193delC	uc001qeu.2	-	4					KCNJ5_uc001qet.2_Intron|KCNJ5_uc009zck.2_Intron|C11orf45_uc009zcl.2_3'UTR|C11orf45_uc001qev.2_3'UTR	NM_145013	NP_659450	Q8TAV5	CK045_HUMAN	hypothetical protein LOC219833 precursor							extracellular region					0	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)		ACATGAAACACCATTTAATCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129626532	129626532	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129626532delG								BARX2 (304359 upstream) : TMEM45B (59209 downstream)																							ggatgaagatggaaatcgtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	153965	153965	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:153965delT								FAM138D (4553 upstream) : IQSEC3 (22238 downstream)																							tCCttcttccttttttttttt	0.010													6	4	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	983320	983321	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:983320_983321insA	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			tgactcatctcaaaaaaaaaaa	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5316836	5316836	+	IGR	DEL	A	-	-	rs111404540		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5316836delA								KCNA5 (160888 upstream) : NTF3 (224444 downstream)																							AGAGGCTGACaaaaaaaaaaa	0.403													3	3	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	6012813	6012814	+	Intron	INS	-	TG	TG	rs143239619	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6012813_6012814insTG	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						ATGTGCAAAGAtgtgtgtgtgt	0.337													1	5	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	8976514	8976514	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8976514delG	uc001quz.3	+							NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						ACTAAAACCTGGGGAAACCGC	0.502													22	13	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11218761	11218762	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11218761_11218762delTT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						GAATCTGGTGTTTCTAAAGAAT	0.317										HNSCC(22;0.051)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15406180	15406181	+	IGR	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15406180_15406181delTG								RERG (31876 upstream) : PTPRO (69306 downstream)																							AAAGAGAGATtgtgtgtgtgtg	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19073163	19073163	+	IGR	DEL	T	-	-	rs34876958		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19073163delT								CAPZA3 (181042 upstream) : PLEKHA5 (209485 downstream)																							GTTCTTTATATTTATGTAGGA	0.159													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	20100267	20100267	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20100267delT								AEBP2 (425094 upstream) : PDE3A (421930 downstream)																							tttctttTTCTTTTTTTTTTA	0.114													3	3	---	---	---	---	
ST8SIA1	6489	broad.mit.edu	37	12	22413100	22413100	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22413100delT	uc001rfo.3	-						ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025	Q92185	SIA8A_HUMAN	alpha-2,8-sialyltransferase 1						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3						tttttcttccttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	26431921	26431922	+	IGR	INS	-	A	A	rs149503945	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26431921_26431922insA								SSPN (26068 upstream) : ITPR2 (56365 downstream)																							ggttctgtctcaaaaaaaaaac	0.000													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31562360	31562360	+	Intron	DEL	A	-	-	rs111670680		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31562360delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						AGTATCAAAGAAAAAAAAAAA	0.254													10	5	---	---	---	---	
CNTN1	1272	broad.mit.edu	37	12	41085780	41085781	+	5'Flank	INS	-	A	A	rs71945408		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41085780_41085781insA	uc001rmm.1	+						CNTN1_uc009zjy.1_5'Flank|CNTN1_uc001rmn.1_5'Flank	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)				ATGGAAACTTTAAAAAAAAACC	0.342													4	2	---	---	---	---	
SP7	121340	broad.mit.edu	37	12	53730229	53730229	+	5'Flank	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53730229delG	uc001sct.2	-						SP7_uc001scu.2_5'Flank|SP7_uc001scv.2_5'Flank	NM_152860	NP_690599	Q8TDD2	SP7_HUMAN	osterix						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TAGAGATCCAGGGGGGGGATG	0.418													4	2	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54502164	54502165	+	Intron	INS	-	C	C	rs57897003		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54502164_54502165insC	uc001sey.2	+							NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						acacacacacacaccaccacac	0.347													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	75092357	75092358	+	IGR	DEL	CT	-	-	rs68128503		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75092357_75092358delCT								ATXN7L3B (157134 upstream) : KCNC2 (341539 downstream)																							GGGGTCTGGACTCTCTCTCTCT	0.431													3	3	---	---	---	---	
UTP20	27340	broad.mit.edu	37	12	101760737	101760738	+	Intron	INS	-	CT	CT	rs149954080	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101760737_101760738insCT	uc001tia.1	+							NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						CCCATGAGTCCCTCTGAACTAC	0.248													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106608351	106608351	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106608351delA								NUAK1 (74540 upstream) : CKAP4 (23309 downstream)																							actctgtctcaaaaaaaaaaa	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108663892	108663892	+	IGR	DEL	A	-	-	rs35432494		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108663892delA								WSCD2 (19581 upstream) : CMKLR1 (17930 downstream)																							gcactcccttaaaaaaaaaaa	0.065													4	2	---	---	---	---	
SVOP	55530	broad.mit.edu	37	12	109337649	109337651	+	Intron	DEL	TCT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109337649_109337651delTCT	uc010sxh.1	-							NM_018711	NP_061181	Q8N4V2	SVOP_HUMAN	SV2 related protein							cell junction|integral to membrane|synaptic vesicle membrane	ion transmembrane transporter activity				0						ttcctcttcctcttcttcttctt	0.000													4	2	---	---	---	---	
MYL2	4633	broad.mit.edu	37	12	111358113	111358113	+	Intron	DEL	T	-	-	rs3216816		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111358113delT	uc001try.3	-						MYL2_uc001trx.3_5'Flank	NM_000432	NP_000423	P10916	MLRV_HUMAN	slow cardiac myosin regulatory light chain 2						cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	cytosol|myosin complex|sarcomere	actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle			ovary(1)	1						AACTCTCTTATTTTGTGTTTG	0.463													4	2	---	---	---	---	
PTPN11	5781	broad.mit.edu	37	12	112868409	112868409	+	Intron	DEL	T	-	-	rs112147637		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112868409delT	uc001ttx.2	+						PTPN11_uc001ttw.1_Intron	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						attacaaaacttttttttttt	0.000			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				4	2	---	---	---	---	
TMED2	10959	broad.mit.edu	37	12	124078510	124078511	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124078510_124078511delTT	uc001ufg.2	+							NM_006815	NP_006806	Q15363	TMED2_HUMAN	coated vesicle membrane protein precursor						protein transport|vesicle-mediated transport	COPI coated vesicle membrane|ER-Golgi intermediate compartment|integral to membrane|microsome|zymogen granule membrane	protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		acctggctaatttttttttttt	0.000													4	3	---	---	---	---	
ATP6V0A2	23545	broad.mit.edu	37	12	124205737	124205738	+	Intron	INS	-	TGTTT	TGTTT	rs142454152	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124205737_124205738insTGTTT	uc001ufr.2	+						ATP6V0A2_uc001ufq.1_Intron	NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		ATGAATCTAGGtgttttgtttt	0.312													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126837168	126837168	+	IGR	DEL	T	-	-	rs11334588		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126837168delT								TMEM132B (693579 upstream) : LOC100128554 (89859 downstream)																							GTACAAATCATTTTTTTTTTA	0.289													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128645507	128645507	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128645507delA								None (None upstream) : TMEM132C (253784 downstream)																							TTGCAATCTGAAGGACTCCAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	129258480	129258480	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129258480delA								TMEM132C (66017 upstream) : SLC15A4 (19259 downstream)																							atatgccaccaaactcagcta	0.000													4	2	---	---	---	---	
GLT1D1	144423	broad.mit.edu	37	12	129455983	129455994	+	Intron	DEL	CTCCCTTCCTCT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129455983_129455994delCTCCCTTCCTCT	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270	Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		ctcctcctccctcccttcctctctccctccat	0.061													6	3	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	131115501	131115501	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131115501delA	uc001uim.2	-									O15034	RIMB2_HUMAN	RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		acaagtggggaaaaaaaaaag	0.000													2	4	---	---	---	---	
DKFZp686A1627	266695	broad.mit.edu	37	13	19647028	19647029	+	Intron	INS	-	CCCTGGC	CCCTGGC	rs143958908	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19647028_19647029insCCCTGGC	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0						CTGACACTTGGCCCTGGCTCAG	0.574													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22696216	22696217	+	Intron	INS	-	GCGCGC	GCGCGC	rs141900109	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22696216_22696217insGCGCGC	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		TTGCTTtgtgtgcgcgcgcgcg	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	28335923	28335923	+	IGR	DEL	A	-	-	rs67150743		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28335923delA								POLR1D (94376 upstream) : GSX1 (30857 downstream)																							ctccaaaaataaaaaaaaaaa	0.129													4	2	---	---	---	---	
PAN3	255967	broad.mit.edu	37	13	28725652	28725652	+	Intron	DEL	A	-	-	rs34007586		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28725652delA	uc010tdo.1	+							NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		actctgtctcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31096873	31096874	+	Intron	INS	-	T	T	rs113846977		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31096873_31096874insT	uc001usz.2	-							NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		GTCTAAAAGTCttttttttttt	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31679886	31679886	+	IGR	DEL	T	-	-	rs34656008		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31679886delT								C13orf26 (130735 upstream) : HSPH1 (30879 downstream)																							CAAGGTTCCATTTCTTTCTGC	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35435139	35435139	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35435139delA								RFC3 (894445 upstream) : NBEA (81317 downstream)																							cctcctggagaaaaaaaacca	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43020057	43020057	+	IGR	DEL	A	-	-	rs35587382		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43020057delA								AKAP11 (122655 upstream) : TNFSF11 (116815 downstream)																							gccatgtaagatgtgtctctt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44790377	44790378	+	IGR	INS	-	G	G	rs139711148	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44790377_44790378insG								LOC121838 (185779 upstream) : SERP2 (157600 downstream)																							ggtttcagtatgaagttaagga	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57627741	57627741	+	IGR	DEL	T	-	-	rs138560946	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57627741delT								None (None upstream) : PRR20C (87311 downstream)																							TGAATGCTTGTTTTGTACATG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61327137	61327137	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61327137delG								TDRD3 (179125 upstream) : PCDH20 (656684 downstream)																							catggtgggtggaatatcaga	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75765750	75765751	+	IGR	INS	-	A	A	rs149205804	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75765750_75765751insA								None (None upstream) : LOC647288 (46139 downstream)																							atgctgaggggaaaaaaatatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82414384	82414386	+	IGR	DEL	GAT	-	-	rs147760851		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82414384_82414386delGAT								None (None upstream) : None (None downstream)																							accttatgtggatgatagcaggc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85005776	85005777	+	IGR	INS	-	A	A	rs9546681		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85005776_85005777insA								SLITRK1 (549248 upstream) : None (None downstream)																							acaacaacaacaaaaaaaaaaa	0.252													4	2	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95714740	95714741	+	Intron	INS	-	CA	CA	rs141058174	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95714740_95714741insCA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	TTATTAAATATcacacacacac	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105059697	105059697	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105059697delA								None (None upstream) : None (None downstream)																							aatagactggaaaaaaaaatg	0.000													5	3	---	---	---	---	
TNFSF13B	10673	broad.mit.edu	37	13	108930935	108930942	+	Intron	DEL	CTCCCCTT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108930935_108930942delCTCCCCTT	uc001vqr.2	+						TNFSF13B_uc010agj.2_Intron	NM_006573	NP_006564	Q9Y275	TN13B_HUMAN	tumor necrosis factor superfamily, member 13b						cell proliferation|immune response|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity|tumor necrosis factor receptor binding				0	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)			tctcctcctcctccccttctcttcctcc	0.120													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110822276	110822277	+	Intron	INS	-	A	A	rs150774157	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110822276_110822277insA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			aggaaggaaggagggagggagg	0.218													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112220461	112220462	+	IGR	INS	-	A	A	rs142834846		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112220461_112220462insA								C13orf16 (223868 upstream) : SOX1 (501451 downstream)																							TGGACCTTGTCGCCCCCACACT	0.525													5	4	---	---	---	---	
GRTP1	79774	broad.mit.edu	37	13	113986608	113986609	+	Intron	INS	-	CA	CA	rs146797859	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113986608_113986609insCA	uc001vtn.2	-						GRTP1_uc010tkb.1_Intron|GRTP1_uc010tkc.1_Intron	NM_024719	NP_078995	Q5TC63	GRTP1_HUMAN	growth hormone regulated TBC protein 1							intracellular	Rab GTPase activator activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0314)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0978)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			cacacacacaccacacgtgcac	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114025814	114025814	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114025814delC								GRTP1 (7351 upstream) : ADPRHL1 (50446 downstream)																							cctcctgagaccccctccctc	0.005													11	5	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114772790	114772791	+	Intron	INS	-	CA	CA	rs71105229		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114772790_114772791insCA	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			acccttctcccctcctgccctg	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19016097	19016097	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19016097delA								None (None upstream) : OR11H12 (361497 downstream)																							caaaggcctcaaagcgtttca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19448765	19448766	+	IGR	INS	-	AG	AG			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19448765_19448766insAG								OR11H12 (70193 upstream) : POTEG (104599 downstream)																							caaaaaaaaaaaaaaagaaaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20113546	20113546	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20113546delA								P704P (93274 upstream) : OR4Q3 (102041 downstream)																							tgcagccttgacctcctgggc	0.000													7	5	---	---	---	---	
CHD8	57680	broad.mit.edu	37	14	21881555	21881555	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21881555delT	uc001was.1	-						CHD8_uc001war.1_Intron	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8						ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		tacctaaaccttttttttttt	0.000													2	4	---	---	---	---	
NYNRIN	57523	broad.mit.edu	37	14	24867763	24867763	+	5'Flank	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24867763delT	uc001wpf.3	+							NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523						DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						CTACTCTACCTTAACCCTTTC	0.637													4	2	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25500132	25500132	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25500132delA	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		GAATGAAAAGAAAAAAAAAAA	0.303													4	3	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31643643	31643644	+	Intron	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31643643_31643644insG	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		accagctacttgggaggctgag	0.000													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34236686	34236686	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34236686delA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.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)		TCTACAGAGGAAAAAAAAAGA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35829629	35829630	+	IGR	INS	-	AC	AC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35829629_35829630insAC								KIAA0391 (42956 upstream) : NFKBIA (41087 downstream)																							TGTGTGTGAATacacacacaca	0.114													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37548048	37548048	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37548048delT	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		ATTATTTTCCTTTTTTTTTTT	0.323													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	48597155	48597155	+	IGR	DEL	T	-	-	rs113910235		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48597155delT								MDGA2 (453167 upstream) : None (None downstream)																							TCTTTCTTTCtttttttttta	0.244													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51660735	51660735	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51660735delA								TRIM9 (98313 upstream) : TMX1 (46151 downstream)																							TACATGAAAGAAAAAAAAATA	0.408													3	4	---	---	---	---	
NID2	22795	broad.mit.edu	37	14	52520416	52520416	+	Frame_Shift_Del	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52520416delG	uc001wzo.2	-	5	1544	c.1310delC	c.(1309-1311)CCAfs	p.P437fs	NID2_uc010tqs.1_Frame_Shift_Del_p.P437fs|NID2_uc010tqt.1_Frame_Shift_Del_p.P437fs|NID2_uc001wzp.2_Frame_Shift_Del_p.P437fs	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	437						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)					AGGATGAGCTGGGGGAACATC	0.547													46	26	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53989649	53989650	+	IGR	INS	-	A	A	rs147823436	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53989649_53989650insA								DDHD1 (369603 upstream) : BMP4 (426807 downstream)																							agaacttaaagaaaaaaaaaTA	0.144													3	3	---	---	---	---	
OTX2	5015	broad.mit.edu	37	14	57271594	57271595	+	Intron	INS	-	A	A	rs150120068	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57271594_57271595insA	uc001xcp.2	-						OTX2_uc010aou.2_Intron|OTX2_uc001xcq.2_Intron	NM_172337	NP_758840	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform b						axon guidance|forebrain development|midbrain development|positive regulation of embryonic development|positive regulation of gastrulation|primitive streak formation|protein complex assembly|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway	growth cone|nucleus|protein complex	eukaryotic initiation factor 4E binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					TGGAGGAAGTCACGCCTCTTGG	0.495													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	58008459	58008460	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58008459_58008460insT								C14orf105 (47883 upstream) : SLC35F4 (22180 downstream)																							ggattcattgattttttttgaa	0.000													4	2	---	---	---	---	
SIX1	6495	broad.mit.edu	37	14	61117303	61117304	+	5'Flank	DEL	GT	-	-	rs144852302		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61117303_61117304delGT	uc001xfb.3	-							NM_005982	NP_005973	Q15475	SIX1_HUMAN	SIX homeobox 1						branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		AAATAAAGAGgtgtgtgtgtgt	0.361													4	2	---	---	---	---	
HSPA2	3306	broad.mit.edu	37	14	65009534	65009535	+	3'UTR	INS	-	T	T	rs148978517	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65009534_65009535insT	uc001xhj.2	+	2					HSPA2_uc001xhk.3_3'UTR	NM_021979	NP_068814	P54652	HSP72_HUMAN	heat shock 70kDa protein 2						response to unfolded protein|spermatid development	cell surface	ATP binding|unfolded protein binding			skin(1)	1				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CTCTCTCTCTCTTTTTTTTTGT	0.411													3	7	---	---	---	---	
COQ6	51004	broad.mit.edu	37	14	74421547	74421549	+	Intron	DEL	AAA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74421547_74421549delAAA	uc001xph.2	+						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)		attccgtctcaaaaaaaaaaaaa	0.128													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77028885	77028887	+	IGR	DEL	GAA	-	-	rs34805815		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77028885_77028887delGAA								ESRRB (60707 upstream) : VASH1 (199348 downstream)																							AGTGATCAAGGAAGAAGGAGAGC	0.567													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82252335	82252335	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82252335delT								SEL1L (252130 upstream) : None (None downstream)																							actttcatcattttccagctc	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85404395	85404397	+	IGR	DEL	AGG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85404395_85404397delAGG								None (None upstream) : FLRT2 (592091 downstream)																							aagaaggagaaggaggaggagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88617819	88617820	+	IGR	DEL	GT	-	-	rs2896082		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88617819_88617820delGT								GPR65 (139405 upstream) : KCNK10 (28634 downstream)																							cacctaaaaggtgtgtgtgtgt	0.000													6	3	---	---	---	---	
SPATA7	55812	broad.mit.edu	37	14	88892994	88892995	+	Frame_Shift_Ins	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88892994_88892995insA	uc001xwq.2	+	6	942_943	c.791_792insA	c.(790-792)AGAfs	p.R264fs	SPATA7_uc001xwr.2_Frame_Shift_Ins_p.R232fs|SPATA7_uc001xws.2_Frame_Shift_Ins_p.R200fs|SPATA7_uc001xwt.2_Frame_Shift_Ins_p.R158fs|SPATA7_uc001xwu.2_5'Flank	NM_018418	NP_060888	Q9P0W8	SPAT7_HUMAN	spermatogenesis-associated protein 7 isoform a	264					response to stimulus|visual perception					ovary(1)	1						CCTGCCAAAAGAAAAAAGGATT	0.366													34	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	91328800	91328805	+	IGR	DEL	CTTCTT	-	-	rs80353457	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91328800_91328805delCTTCTT								TTC7B (46039 upstream) : RPS6KA5 (8362 downstream)																							cctcctcctccttcttcttcttcttc	0.000													5	3	---	---	---	---	
PRIMA1	145270	broad.mit.edu	37	14	94233576	94233579	+	Intron	DEL	CTAA	-	-	rs71896124		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94233576_94233579delCTAA	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		aagccctgggctaactaactatct	0.147													4	3	---	---	---	---	
SERPINA4	5267	broad.mit.edu	37	14	95035205	95035205	+	Intron	DEL	A	-	-	rs146839707		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95035205delA	uc001ydk.2	+						SERPINA4_uc010avd.2_Intron|SERPINA4_uc001ydl.2_Intron	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)|skin(1)	4				COAD - Colon adenocarcinoma(157;0.211)		actccatctcaaaaaaaaaaa	0.189													4	3	---	---	---	---	
C14orf139	79686	broad.mit.edu	37	14	95874114	95874115	+	3'UTR	DEL	AC	-	-	rs71707189		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95874114_95874115delAC	uc001yeh.3	-	1						NR_026779				RecName: Full=Uncharacterized protein C14orf139;												0						acacacacagacacacacacac	0.312													4	2	---	---	---	---	
PAPOLA	10914	broad.mit.edu	37	14	96984036	96984037	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96984036_96984037delTT	uc001yfq.2	+						PAPOLA_uc001yfo.2_Intron|PAPOLA_uc001yfp.2_Intron|PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021	P51003	PAPOA_HUMAN	poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		CAGCAAATGCtttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99059602	99059604	+	IGR	DEL	CTT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99059602_99059604delCTT								C14orf64 (615141 upstream) : C14orf177 (118346 downstream)																							ctgcgggctccttcttcttcttc	0.182													5	3	---	---	---	---	
SETD3	84193	broad.mit.edu	37	14	99941540	99941540	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99941540delA	uc001ygc.2	-						SETD3_uc001ygd.2_Intron|SETD3_uc001ygf.2_Intron	NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a						peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				TCTGGATTCTAAAACCAAGGA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101578715	101578715	+	IGR	DEL	C	-	-	rs34483509		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101578715delC								MIR656 (45577 upstream) : DIO3OS (439845 downstream)																							CCCAGGTCTGCCCCCTTTTCC	0.667													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	103205590	103205590	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103205590delT								RCOR1 (8678 upstream) : TRAF3 (38226 downstream)																							GCCCTTAGGCTTTCCTGGGAC	0.622													4	2	---	---	---	---	
TRAF3	7187	broad.mit.edu	37	14	103269435	103269435	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103269435delG	uc001ymc.1	+						TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1						apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		cctccccccaggtccctccca	0.090													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20006717	20006718	+	IGR	DEL	GA	-	-	rs61999499		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20006717_20006718delGA								None (None upstream) : GOLGA6L6 (730376 downstream)																							cagattctacgaagagagtgtt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23513706	23513707	+	IGR	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23513706_23513707insC								GOLGA8E (65283 upstream) : MKRN3 (296747 downstream)																							GTCTCAAAGCACCCCCCcacac	0.396													4	3	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	26814765	26814765	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26814765delT	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	gttttccatatttagacttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27818764	27818764	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27818764delT								GABRG3 (40630 upstream) : OCA2 (181261 downstream)																							TCTTCAGTTCTCCTTTGAGAT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28752014	28752014	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28752014delT								GOLGA8G (114843 upstream) : WHAMML2 (230715 downstream)																							GGTTGCTTCATCTAGGAGAAG	0.478													13	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30465339	30465344	+	IGR	DEL	TGTGTC	-	-	rs150380443		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30465339_30465344delTGTGTC								FAM7A3 (41393 upstream) : DKFZP434L187 (22895 downstream)																							gtgtgtggtgtgtgtctgtgtggtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30815889	30815889	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30815889delC								CHRFAM7A (130025 upstream) : FAM7A2 (48869 downstream)																							gcagctttctcaaggaccccc	0.204													4	2	---	---	---	---	
CHRM5	1133	broad.mit.edu	37	15	34310863	34310864	+	Intron	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34310863_34310864insC	uc001zhk.1	+						AVEN_uc001zhj.2_Intron|CHRM5_uc001zhl.1_Intron	NM_012125	NP_036257	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5						cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)	cttccacagaatggaaagggac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	34663372	34663373	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34663372_34663373insA								LPCAT4 (3977 upstream) : GOLGA8A (7899 downstream)																							ccttctcttcccccacttccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40367431	40367432	+	IGR	INS	-	G	G	rs72288077		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40367431_40367432insG								SRP14 (36042 upstream) : BMF (12662 downstream)																							cacagtgcagtgggggctgaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40617717	40617717	+	RNA	DEL	T	-	-	rs3214686		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40617717delT	uc001zlf.1	+	1		c.1037delT								Homo sapiens cDNA FLJ41776 fis, clone IMR322013053.																		TGTTTTTATCTTTTTTTTTTT	0.448													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45082391	45082391	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45082391delT								TRIM69 (22366 upstream) : C15orf43 (166512 downstream)																							TAATTGTTACTTTGATGTGAT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46790782	46790782	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46790782delA								SQRDL (807304 upstream) : SEMA6D (685621 downstream)																							CTTCTATTTTAATTTTTTTTG	0.199													4	2	---	---	---	---	
MYO5C	55930	broad.mit.edu	37	15	52546910	52546910	+	Intron	DEL	A	-	-	rs11328196		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52546910delA	uc010bff.2	-						MYO5C_uc010uga.1_Intron|MYO5C_uc010ugb.1_Intron	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		GAACAAAAGCAAAAAAAAAAA	0.279													7	4	---	---	---	---	
FAM63B	54629	broad.mit.edu	37	15	59143180	59143181	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59143180_59143181insT	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1						CCAAttttttgtttttttttca	0.163													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62388187	62388187	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62388187delA								C2CD4A (25078 upstream) : C2CD4B (67550 downstream)																							TATGATGCATAAAATAACTGG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62432734	62432734	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62432734delG								C2CD4A (69625 upstream) : C2CD4B (23003 downstream)																							CTGCCCTCAAGGGGGAAGGAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63187012	63187013	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63187012_63187013insA								TLN2 (50185 upstream) : TPM1 (147825 downstream)																							gattacatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TPM1	7168	broad.mit.edu	37	15	63340989	63340990	+	Intron	INS	-	G	G	rs148517607	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63340989_63340990insG	uc002alg.2	+						TPM1_uc002alh.2_Intron|TPM1_uc010bgn.2_Intron|TPM1_uc002ali.2_Intron|TPM1_uc002alj.2_Intron|TPM1_uc002alk.2_Intron|TPM1_uc002all.2_Intron|TPM1_uc002alm.2_Intron|TPM1_uc010uie.1_Intron|TPM1_uc002alp.2_Intron|uc002alq.1_Frame_Shift_Ins_p.A61fs|uc010bgo.2_Intron|TPM1_uc010uif.1_Intron|TPM1_uc002alr.2_Intron|TPM1_uc002als.2_Intron|TPM1_uc010uig.1_Intron|TPM1_uc002alt.2_Intron|TPM1_uc010bgp.2_Intron	NM_001018005	NP_001018005	P09493	TPM1_HUMAN	tropomyosin 1 alpha chain isoform 1						cardiac muscle contraction|cellular component movement|cellular response to reactive oxygen species|muscle filament sliding|negative regulation of cell migration|positive regulation of ATPase activity|positive regulation of cell adhesion|positive regulation of heart rate by epinephrine|positive regulation of stress fiber assembly|regulation of muscle contraction|ruffle organization|sarcomere organization|ventricular cardiac muscle tissue morphogenesis|wound healing	bleb|cytosol|muscle thin filament tropomyosin|ruffle membrane|stress fiber	actin binding|structural constituent of cytoskeleton|structural constituent of muscle				0						GCTTCCCCCCCCGCAGGCCCCG	0.748													3	3	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64200805	64200806	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64200805_64200806insA	uc002amr.2	-						DAPK2_uc010uim.1_RNA	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		TTCCTCTGGAGAAAAAAAAGAG	0.579													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77392205	77392205	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77392205delT								TSPAN3 (28692 upstream) : SGK269 (8266 downstream)																							gcatatactgttgcctctgtc	0.224													4	2	---	---	---	---	
SGK269	79834	broad.mit.edu	37	15	77538476	77538476	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77538476delG	uc002bcm.2	-							NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member						cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		tcagcctctcgagtagctggg	0.000													1	5	---	---	---	---	
LINGO1	84894	broad.mit.edu	37	15	77955634	77955634	+	Intron	DEL	G	-	-	rs11292034		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77955634delG	uc002bcu.1	-							NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A						negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2						GGTCGGGGGTGGGGAGGCTTC	0.562													3	3	---	---	---	---	
ADAMTS7	11173	broad.mit.edu	37	15	79089665	79089665	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79089665delC	uc002bej.3	-						ADAMTS7_uc010und.1_Intron|ADAMTS7_uc002bek.1_Intron	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GAAACTGAGGCCAAGAAGCAT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79536184	79536187	+	IGR	DEL	TCTA	-	-	rs141700431		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79536184_79536187delTCTA								MIR184 (33971 upstream) : ANKRD34C (38959 downstream)																							TAAGGAGGACTCTATCTACCCTGG	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	80318308	80318308	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80318308delA								BCL2A1 (54665 upstream) : ZFAND6 (33713 downstream)																							aaagaaaaggaaaaaaaaagc	0.000													4	2	---	---	---	---	
EFTUD1	79631	broad.mit.edu	37	15	82530088	82530088	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82530088delA	uc002bgt.1	-						EFTUD1_uc002bgu.1_Intron	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain						mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1						cccaaaaaggaaaaaaaaaaa	0.000													6	3	---	---	---	---	
C15orf40	123207	broad.mit.edu	37	15	83679511	83679511	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83679511delA	uc010uoo.1	-						C15orf40_uc010uon.1_Intron|C15orf40_uc002bjm.2_Intron|C15orf40_uc010uop.1_Intron|C15orf40_uc010uoq.1_Intron|C15orf40_uc010uor.1_Intron	NM_001160115	NP_001153587	Q8WUR7	CO040_HUMAN	hypothetical protein LOC123207 isoform d											skin(1)	1						GAAAGGGAGGAAAAAAAAATA	0.229											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
BNC1	646	broad.mit.edu	37	15	83938181	83938182	+	Intron	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83938181_83938182delGT	uc002bjt.1	-						BNC1_uc010uos.1_Intron	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1						epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TGGGAAGTGCGTGTGTGTGTGT	0.470													4	3	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85463935	85463936	+	Intron	DEL	GT	-	-	rs67647514	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85463935_85463936delGT	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			tctccaaggggtgtgtgtgtgt	0.025													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	86820549	86820550	+	Intron	INS	-	TG	TG	rs145717362	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86820549_86820550insTG	uc002blz.1	+						AGBL1_uc002bma.1_Intron|AGBL1_uc002bmb.1_Intron	NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						gtgtgtgtgtatgtgtgtgtgt	0.317													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90511457	90511457	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90511457delA								AP3S2 (55235 upstream) : ZNF710 (33295 downstream)																							aagagggaagaagaagaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90686999	90686999	+	IGR	DEL	A	-	-	rs10553548		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90686999delA								IDH2 (41291 upstream) : SEMA4B (41153 downstream)																							CCCATCCTAGAAAAAAAAAAA	0.333													4	2	---	---	---	---	
SEMA4B	10509	broad.mit.edu	37	15	90737764	90737765	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90737764_90737765insA	uc002boy.2	+							NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			aacaccatctcaaaaaaaaaac	0.020													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91010776	91010776	+	Frame_Shift_Del	DEL	T	-	-	rs1505936	byFrequency	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91010776delT	uc002bpl.1	+	18	2231	c.2130delT	c.(2128-2130)CCTfs	p.P710fs		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	710	WW.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGGatgaacctccaaattttg	0.323													49	52	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92256328	92256329	+	IGR	INS	-	T	T	rs149680864	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92256328_92256329insT								SV2B (417680 upstream) : SLCO3A1 (140609 downstream)																							ttatttgtggatttttgattga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93364181	93364183	+	IGR	DEL	TTG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93364181_93364183delTTG								FAM174B (86877 upstream) : CHD2 (65250 downstream)																							TTAAAAATACTTGTTGAtttttc	0.227													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93424434	93424435	+	IGR	DEL	GT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93424434_93424435delGT								FAM174B (147130 upstream) : CHD2 (4998 downstream)																							TATTTTGTGGGTGTGTGTGTGT	0.371													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96864333	96864333	+	Intron	DEL	A	-	-	rs112943129		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96864333delA	uc010bol.1	-						uc002bto.1_Intron					Homo sapiens cDNA FLJ10010 fis, clone HEMBA1000302.																		GGATTCATTTAAAAAAAAAAA	0.458													3	3	---	---	---	---	
ARRDC4	91947	broad.mit.edu	37	15	98485044	98485044	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98485044delG	uc002bui.3	+							NM_183376	NP_899232	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4						signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			gagaggccaaggtgaatggat	0.000													4	2	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99339406	99339407	+	Intron	DEL	TG	-	-	rs147778931		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99339406_99339407delTG	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	GTGTGGGCACTGTGCTGGGGGA	0.564													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101342465	101342465	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101342465delC								ASB7 (150563 upstream) : ALDH1A3 (77544 downstream)																							TAAAAAGCCTCCCCCAGGGAA	0.542													4	2	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	102017473	102017474	+	Intron	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102017473_102017474delTG	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)			tctgtgtgtctgtgtgtgtgtg	0.144													4	2	---	---	---	---	
C16orf73	254528	broad.mit.edu	37	16	1925559	1925559	+	Intron	DEL	T	-	-	rs111720551		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1925559delT	uc010uvr.1	-							NM_001163560	NP_001157032	Q8N635	CP073_HUMAN	hypothetical protein LOC254528 isoform 1						meiosis	cytoplasm					0						aagttttgtatttttttgtag	0.000													4	5	---	---	---	---	
DCI	1632	broad.mit.edu	37	16	2290218	2290219	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2290218_2290219insT	uc002cpr.2	-						DCI_uc002cps.2_Intron	NM_001919	NP_001910	P42126	ECI1_HUMAN	dodecenoyl-Coenzyme A delta isomerase precursor						fatty acid beta-oxidation	mitochondrial matrix	dodecenoyl-CoA delta-isomerase activity				0						Cttattttttatttttattttt	0.248													8	7	---	---	---	---	
PRSS22	64063	broad.mit.edu	37	16	2903343	2903343	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2903343delG	uc002cry.1	-						PRSS22_uc002crz.1_Intron	NM_022119	NP_071402	Q9GZN4	BSSP4_HUMAN	protease, serine, 22 precursor						proteolysis	extracellular region	serine-type endopeptidase activity			central_nervous_system(1)	1						GCAGAGAGGAGGCGAGGTTAG	0.706													4	2	---	---	---	---	
CLEC16A	23274	broad.mit.edu	37	16	11064866	11064867	+	Intron	DEL	TT	-	-	rs71404430		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11064866_11064867delTT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2						ATTGGCAACATTTTTTTTTTTT	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11499971	11499971	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11499971delC								C16orf75 (54354 upstream) : LITAF (141611 downstream)																							gtccctgtcacccaaatatcg	0.000											OREG0023614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12643346	12643351	+	Intron	DEL	ACACAT	-	-	rs66691443		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12643346_12643351delACACAT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GAAGATCCTCACACATACAAAGATGT	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12717897	12717898	+	IGR	INS	-	AA	AA	rs145149353	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12717897_12717898insAA								SNX29 (49752 upstream) : CPPED1 (35759 downstream)																							TGCCTCAGGATAGTTAACTTTC	0.426													4	3	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15859086	15859089	+	Intron	DEL	TGGG	-	-	rs36176100		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15859086_15859089delTGGG	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						ggtagatgaatgggtgaatgatgg	0.000			T	CBFB	AML								4	4	---	---	---	---	
ABCC1	4363	broad.mit.edu	37	16	16188380	16188381	+	Intron	INS	-	T	T	rs141071863	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16188380_16188381insT	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	ttttctttttcttttttttgag	0.198													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18327267	18327268	+	IGR	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18327267_18327268delTC								XYLT1 (762529 upstream) : NOMO2 (183915 downstream)																							cttctttctttctctctctctc	0.257													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20006525	20006525	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20006525delG								GPRC5B (109693 upstream) : GPR139 (36518 downstream)																							CTCACATCCTGGGGAAAATTG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26310829	26310829	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26310829delA								HS3ST4 (161821 upstream) : C16orf82 (767390 downstream)																							CAAGTTTGGCAAAAAAAAAAA	0.433													4	2	---	---	---	---	
ITGAM	3684	broad.mit.edu	37	16	31334357	31334358	+	Intron	DEL	GA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31334357_31334358delGA	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron|ITGAM_uc010cam.1_Intron|ITGAM_uc010can.2_Intron|ITGAM_uc002ebs.1_Intron|ITGAM_uc010vfj.1_5'Flank	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						ggtgggggaggagagagagaga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32535345	32535345	+	IGR	DEL	T	-	-	rs111821255		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32535345delT								HERC2P4 (371471 upstream) : TP53TG3B (149496 downstream)																							cagcttcatcttggaatattc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32843772	32843773	+	IGR	INS	-	T	T	rs145188849	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32843772_32843773insT								TP53TG3B (154894 upstream) : SLC6A10P (45024 downstream)																							TCACACCTGTGTTTTTTTCCAC	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33384184	33384185	+	IGR	INS	-	T	T	rs142955157		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33384184_33384185insT								SLC6A10P (487721 upstream) : MIR1826 (581323 downstream)																							ttctttctttcttttttttttt	0.124													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33538280	33538282	+	IGR	DEL	ATT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33538280_33538282delATT								SLC6A10P (641817 upstream) : MIR1826 (427226 downstream)																							TCAACAGCTCATTATTCCATTCT	0.394													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33569432	33569432	+	IGR	DEL	G	-	-	rs113882576		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33569432delG								SLC6A10P (672969 upstream) : MIR1826 (396076 downstream)																							GCCAGCCAGAGGCATCAGATG	0.458													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33585718	33585718	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33585718delT								SLC6A10P (689255 upstream) : MIR1826 (379790 downstream)																							CGACAATGTATTTTAAAATAT	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33779214	33779218	+	IGR	DEL	CCCTC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33779214_33779218delCCCTC								SLC6A10P (882751 upstream) : MIR1826 (186290 downstream)																							cctctccctgccctcccctcccctc	0.512													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33849613	33849613	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33849613delG								SLC6A10P (953150 upstream) : MIR1826 (115895 downstream)																							AGAAAATGAAGGGTATCTTTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33970764	33970765	+	IGR	INS	-	G	G	rs138031341		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33970764_33970765insG								MIR1826 (5172 upstream) : UBE2MP1 (433037 downstream)																							cggggttgtttgtttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35266912	35266912	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35266912delT								LOC146481 (551945 upstream) : None (None downstream)																							ttgtgatgtgtgcattcaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46435678	46435680	+	IGR	DEL	ATC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46435678_46435680delATC								None (None upstream) : ANKRD26P1 (67569 downstream)																							atcaaatggaatcatcatcgaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49376258	49376259	+	IGR	INS	-	C	C	rs143803459	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49376258_49376259insC								CBLN1 (60543 upstream) : C16orf78 (31549 downstream)																							GGAGGCACTGACCCCCCGAGGC	0.629													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50054213	50054229	+	IGR	DEL	AAGTGAGACTCCATCTC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50054213_50054229delAAGTGAGACTCCATCTC								ZNF423 (193295 upstream) : TMEM188 (4960 downstream)																							ctgggtgacaaagtgagactccatctcaaaaaaaaaa	0.000													3	4	---	---	---	---	
HEATR3	55027	broad.mit.edu	37	16	50123311	50123312	+	Intron	DEL	GA	-	-	rs10585363		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50123311_50123312delGA	uc002efw.2	+						HEATR3_uc002efx.2_Intron	NM_182922	NP_891552	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3								binding			ovary(1)|skin(1)	2						TTGGTAGTCTGAATTGGCCTTG	0.465													4	3	---	---	---	---	
ADCY7	113	broad.mit.edu	37	16	50326324	50326324	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50326324delC	uc002egd.1	+						ADCY7_uc002egb.1_Intron|ADCY7_uc002egc.1_Intron	NM_001114	NP_001105	P51828	ADCY7_HUMAN	adenylate cyclase 7						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)	CCTTAGCACGCATGCCCCTCG	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51377204	51377204	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51377204delC								SALL1 (192021 upstream) : None (None downstream)																							GTCTTAGCTTCCAGGGAGAGA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52315643	52315646	+	IGR	DEL	CGCA	-	-	rs67863857		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52315643_52315646delCGCA								None (None upstream) : TOX3 (156272 downstream)																							cgcgcgcgcgcgcacacacacaca	0.000													2	6	---	---	---	---	
MMP2	4313	broad.mit.edu	37	16	55531252	55531253	+	Intron	INS	-	A	A	rs140337904	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55531252_55531253insA	uc002ehz.3	+						MMP2_uc010vhd.1_Intron|MMP2_uc010ccc.2_Intron|MMP2_uc002eia.3_Intron	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a						angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)	ttttctagaagaaaaaaagtct	0.208													4	2	---	---	---	---	
SLC12A3	6559	broad.mit.edu	37	16	56904753	56904753	+	Intron	DEL	T	-	-	rs71882529		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56904753delT	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	ttttcttttcttttttttttt	0.294													6	3	---	---	---	---	
CETP	1071	broad.mit.edu	37	16	57015336	57015347	+	Intron	DEL	CTGCCAGGAAGA	-	-	rs67188110		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57015336_57015347delCTGCCAGGAAGA	uc002eki.2	+						CETP_uc002ekj.2_Intron	NM_000078	NP_000069	P11597	CETP_HUMAN	cholesteryl ester transfer protein, plasma						cholesterol homeostasis|cholesterol metabolic process|high-density lipoprotein particle remodeling|lipoprotein metabolic process|low-density lipoprotein particle remodeling|phosphatidylcholine metabolic process|phospholipid homeostasis|receptor-mediated endocytosis|regulation of cholesterol efflux|triglyceride homeostasis|triglyceride metabolic process|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle|vesicle	cholesterol binding|cholesterol transporter activity|phosphatidylcholine binding|phospholipid transporter activity|triglyceride binding			central_nervous_system(1)|skin(1)	2						GAATGGAGGGCTGCCAGGAAGAAGGGCCTGGC	0.575													3	5	---	---	---	---	
CPNE2	221184	broad.mit.edu	37	16	57125969	57125969	+	5'Flank	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57125969delA	uc002eks.1	+						CPNE2_uc010cct.1_5'Flank	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II											central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)				TTTGCTATTGAAAAAAAAAAG	0.507													1	6	---	---	---	---	
CX3CL1	6376	broad.mit.edu	37	16	57410420	57410423	+	Intron	DEL	ATGG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57410420_57410423delATGG	uc002eli.2	+							NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1 precursor						cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity				0						agatggatgaatggatggatggat	0.191													4	2	---	---	---	---	
CCDC113	29070	broad.mit.edu	37	16	58312702	58312703	+	Intron	INS	-	TTTTG	TTTTG	rs142772910	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58312702_58312703insTTTTG	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1							protein complex					0						AAGGATGATTTGTTTTTTTTGA	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58723730	58723730	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58723730delG								SLC38A7 (5056 upstream) : GOT2 (17305 downstream)																							gtcaaatggtggggttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59285971	59285971	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59285971delG								GOT2 (517725 upstream) : None (None downstream)																							GCAATGCAAAGATTTAAAAAA	0.219													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60521705	60521705	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60521705delA								None (None upstream) : None (None downstream)																							ttaagacgggaaaatgctaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65781607	65781608	+	IGR	INS	-	ACAC	ACAC	rs138620442	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65781607_65781608insACAC								LOC283867 (171404 upstream) : CDH5 (618917 downstream)																							TCTacaaacaaacacacacaca	0.163													3	3	---	---	---	---	
BEAN	146227	broad.mit.edu	37	16	66501074	66501074	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66501074delT	uc002eoq.2	+						BEAN_uc002eop.1_Intron	NM_001136106	NP_001129578	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with Nedd4						cell death	integral to membrane					0						tgacatgttcttacgctaaag	0.000													4	2	---	---	---	---	
TMCO7	79613	broad.mit.edu	37	16	69056606	69056607	+	Intron	INS	-	A	A	rs141293512	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69056606_69056607insA	uc002ewi.3	+							NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		gaccctgtctcaaaaaaaaaat	0.104													6	3	---	---	---	---	
CYB5B	80777	broad.mit.edu	37	16	69459258	69459259	+	Intron	INS	-	T	T	rs55771560		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69459258_69459259insT	uc002exg.1	+						CYB5B_uc002exf.2_Intron|CYB5B_uc010cfl.1_Intron	NM_030579	NP_085056	O43169	CYB5B_HUMAN	cytochrome b5 outer mitochondrial membrane						electron transport chain|transport	integral to membrane|mitochondrial outer membrane	heme binding				0		Ovarian(137;0.101)				TGCCTCCACTGTTTTTTTTTCC	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71353977	71353981	+	IGR	DEL	GCATG	-	-	rs72437812		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71353977_71353981delGCATG								FTSJD1 (30464 upstream) : CALB2 (38645 downstream)																							CACAGCCACAGCATGGTATAGAAAA	0.132													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79756932	79756934	+	IGR	DEL	TGG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79756932_79756934delTGG								MAF (122310 upstream) : DYNLRB2 (817920 downstream)																							atgatggtgatggtggtggtggt	0.000													7	5	---	---	---	---	
C16orf61	56942	broad.mit.edu	37	16	81027303	81027307	+	Intron	DEL	TAGAG	-	-	rs149221836		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81027303_81027307delTAGAG	uc002ffu.2	-						C16orf61_uc002ffv.2_Intron	NM_020188	NP_064573	Q9NRP2	CP061_HUMAN	hypothetical protein LOC56942												0						aagctaactctagagtaaagactat	0.093													4	2	---	---	---	---	
KIAA0513	9764	broad.mit.edu	37	16	85091376	85091376	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85091376delT	uc002fiu.2	+						KIAA0513_uc002fis.3_Intron|KIAA0513_uc010voj.1_Intron|KIAA0513_uc002fit.2_Intron	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764							cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)		tttgtttttgttttttttttt	0.468													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88213483	88213483	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88213483delG								BANP (102560 upstream) : ZNF469 (280396 downstream)																							atgggagggaggaagtacagg	0.000													1	8	---	---	---	---	
CDH15	1013	broad.mit.edu	37	16	89248044	89248045	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89248044_89248045insA	uc002fmt.2	+						CDH15_uc010cij.1_Intron	NM_004933	NP_004924	P55291	CAD15_HUMAN	cadherin 15 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0261)		gaccctctctcaaaaaaaaaag	0.005													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89509838	89509839	+	Intron	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89509838_89509839insC	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron|uc002fnh.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ctttAAAAAAAACACACACAGA	0.262													5	3	---	---	---	---	
RPL13	6137	broad.mit.edu	37	16	89624622	89624623	+	5'Flank	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89624622_89624623insT	uc002fnm.1	+						RPL13_uc010vpj.1_5'Flank|RPL13_uc002fnn.1_5'Flank|RPL13_uc002fno.1_5'Flank	NM_000977	NP_000968	P26373	RL13_HUMAN	ribosomal protein L13						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		CTCGGTAATTGttttttttttg	0.257													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6464046	6464047	+	IGR	INS	-	CT	CT			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6464046_6464047insCT								PITPNM3 (4169 upstream) : KIAA0753 (17599 downstream)																							tcctcctcctccttctcctcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21327654	21327655	+	IGR	DEL	AC	-	-	rs5819767		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21327654_21327655delAC								KCNJ12 (4475 upstream) : C17orf51 (103917 downstream)																							GCCCGCCCCAACCCCCAGCCCC	0.604													4	2	---	---	---	---	
NOS2	4843	broad.mit.edu	37	17	26126816	26126817	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26126816_26126817insA	uc002gzu.2	-						NOS2_uc010crh.1_Intron|NOS2_uc010wab.1_Intron	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A						arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)	aggctgTTTCCAAAAAAAAAAA	0.025													5	3	---	---	---	---	
CPD	1362	broad.mit.edu	37	17	28721920	28721921	+	Intron	DEL	TG	-	-	rs72122663		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28721920_28721921delTG	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2						CAtgtgtgtatgtgtgtgtgtg	0.356													3	3	---	---	---	---	
CPD	1362	broad.mit.edu	37	17	28754685	28754685	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28754685delT	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2						GAGTATCCTGTTACTGCTCTT	0.323													4	2	---	---	---	---	
PSMD11	5717	broad.mit.edu	37	17	30777924	30777925	+	Intron	INS	-	T	T	rs9899540	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30777924_30777925insT	uc010cta.1	+						PSMD11_uc010wbz.1_Intron|PSMD11_uc002hhm.2_Intron	NM_002815	NP_002806	O00231	PSD11_HUMAN	proteasome 26S non-ATPase subunit 11						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|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	proteasome complex	protein binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			gttaaaaaaaattttttttttt	0.000													4	2	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	35978526	35978527	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35978526_35978527insT	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				CACAAAATTCAttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	40209968	40209969	+	IGR	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40209968_40209969insG								NKIRAS2 (32314 upstream) : DHX58 (43453 downstream)																							ctcaaaaaaaagaaaaaagaat	0.277													4	2	---	---	---	---	
DHX8	1659	broad.mit.edu	37	17	41585987	41585988	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41585987_41585988delTT	uc002idu.1	+						DHX8_uc010wif.1_Intron|DHX8_uc010wig.1_Intron	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8							catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TATGCAAGTCtttttttttttt	0.238													4	2	---	---	---	---	
CDK5RAP3	80279	broad.mit.edu	37	17	46056812	46056812	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46056812delG	uc002imr.2	+						CDK5RAP3_uc010wlc.1_Intron|CDK5RAP3_uc002imq.1_Intron|CDK5RAP3_uc002imu.2_Intron|CDK5RAP3_uc002ims.2_Intron|CDK5RAP3_uc002imv.2_Intron|CDK5RAP3_uc002imw.2_Intron|CDK5RAP3_uc002imx.2_Intron	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3						brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						gtcccgaggtgggagcagacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46523510	46523510	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46523510delA								SKAP1 (15916 upstream) : HOXB1 (83297 downstream)																							TCCACTTTTCACCAAAGGTCC	0.348													4	2	---	---	---	---	
HOXB13	10481	broad.mit.edu	37	17	46804808	46804809	+	Intron	INS	-	AC	AC	rs139887310	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46804808_46804809insAC	uc002ioa.2	-						hsa-mir-3185|MI0014227_5'Flank	NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13						angiogenesis|epidermis development|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						tacatgcgcatacacacacaca	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48026282	48026283	+	IGR	INS	-	GT	GT	rs147308847	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48026282_48026283insGT								TAC4 (100903 upstream) : DLX4 (20279 downstream)																							GGAGGTGGGAGGGGGCAGAGGG	0.629													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48497809	48497809	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48497809delA								LRRC59 (22977 upstream) : ACSF2 (5710 downstream)																							agacaatatgaggggtggtct	0.000													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50128376	50128377	+	Intron	INS	-	GAAG	GAAG	rs11867660	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50128376_50128377insGAAG	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			aaggaaggaacgaaggaaggaa	0.050													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51835280	51835280	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51835280delA								None (None upstream) : KIF2B (64959 downstream)																							TGCAATTTTTAAAGCCTCAAA	0.418													4	4	---	---	---	---	
STXBP4	252983	broad.mit.edu	37	17	53087611	53087612	+	Intron	DEL	AT	-	-	rs10562786		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53087611_53087612delAT	uc002iuf.1	+						STXBP4_uc010dcc.1_Intron|STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1						AGACAATGTCatatatatatat	0.203													4	2	---	---	---	---	
C17orf67	339210	broad.mit.edu	37	17	54887513	54887514	+	Intron	INS	-	CA	CA	rs140946760	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54887513_54887514insCA	uc010dci.2	-						C17orf67_uc002iuq.2_Intron	NM_001085430	NP_001078899	Q0P5P2	CQ067_HUMAN	hypothetical protein LOC339210 precursor							extracellular region					0	Breast(9;2.49e-06)					cgcacacccctcacacccccac	0.000													1	5	---	---	---	---	
CUEDC1	404093	broad.mit.edu	37	17	55952055	55952055	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55952055delC	uc002ivd.1	-						CUEDC1_uc002ive.1_Intron	NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1											skin(2)	2						GAGAAGGCAGCCGAGGGCCGG	0.657													4	2	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60870870	60870872	+	Intron	DEL	CAC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60870870_60870872delCAC	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						ccacctccatcaccaccaccacc	0.000													4	3	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63656695	63656696	+	Intron	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63656695_63656696delCT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			caggttctcactctgttgccca	0.000													0	6	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64738846	64738847	+	Frame_Shift_Ins	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64738846_64738847insC	uc002jfp.1	+	13	1536_1537	c.1492_1493insC	c.(1492-1494)TTCfs	p.F498fs	PRKCA_uc002jfo.1_Frame_Shift_Ins_p.F369fs	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	498	Protein kinase.				activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	GACCAGGACCTTCTGTGGGACT	0.475													22	39	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66365681	66365681	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66365681delA	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			actctgtctcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69738516	69738517	+	IGR	INS	-	AT	AT	rs58338059		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69738516_69738517insAT								None (None upstream) : SOX9 (378644 downstream)																							cacacacatacacacacacaca	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70528388	70528388	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70528388delT	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																		GTTGTTGTGGttttttttttt	0.214													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	71046602	71046602	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71046602delT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						gtgaactgacttttttttttt	0.070													4	2	---	---	---	---	
C17orf54	283982	broad.mit.edu	37	17	71745586	71745587	+	3'UTR	INS	-	AT	AT	rs145301031		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71745586_71745587insAT	uc010dfo.2	-	4						NR_027146				SubName: Full=C17orf54 protein; Flags: Fragment;												0						AGGCGAGTCACATGTGAATAAG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75786285	75786285	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75786285delG								SEPT9 (289609 upstream) : FLJ45079 (88824 downstream)																							TAGTTTCTGTGGGCTTCGTCA	0.488													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80898098	80898099	+	Intron	DEL	CA	-	-	rs116354865	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80898098_80898099delCA	uc002kfz.2	+						TBCD_uc002kfy.1_Intron|TBCD_uc002kgc.2_Intron|TBCD_uc002kgd.2_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			tgcacgcgcgcacacacacaca	0.421													4	3	---	---	---	---	
SPIRE1	56907	broad.mit.edu	37	18	12478694	12478694	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12478694delA	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0						GGGAGGGAAGAAGAGAATTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15299281	15299282	+	IGR	DEL	CA	-	-	rs113248324		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15299281_15299282delCA								ANKRD30B (446544 upstream) : LOC644669 (14273 downstream)																							gcttgagccccagagtttgagg	0.015													2	4	---	---	---	---	
MIB1	57534	broad.mit.edu	37	18	19320207	19320207	+	5'Flank	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19320207delT	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825	Q86YT6	MIB1_HUMAN	mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)			AGGGACTGAATTTTTTCGTGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22420840	22420841	+	IGR	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22420840_22420841delTG								HRH4 (360920 upstream) : ZNF521 (221047 downstream)																							cgtgtttgtatgtgtgtgtgtg	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35446056	35446058	+	IGR	DEL	GGA	-	-	rs34243270		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35446056_35446058delGGA								CELF4 (300056 upstream) : None (None downstream)																							aagagaaaagggaggaggaggag	0.300													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52322941	52322941	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52322941delT								C18orf26 (56217 upstream) : RAB27B (172899 downstream)																							atcacctgtattttttttttc	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52882454	52882454	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52882454delC								CCDC68 (255715 upstream) : TCF4 (7108 downstream)																							TGtgtcttctcccaagactgt	0.264													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	56034829	56034829	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56034829delA	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						AGCATGTGGTAAGTCAGGTCC	0.388													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57141085	57141086	+	Intron	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57141085_57141086delCT	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				ccactatttcctcccccGACTA	0.030													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	66156844	66156845	+	IGR	INS	-	T	T	rs143597968		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66156844_66156845insT								DSEL (972877 upstream) : TMX3 (184082 downstream)																							aagggtgtgtggggggggcaTC	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71117088	71117088	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71117088delA								NETO1 (582278 upstream) : FBXO15 (623500 downstream)																							catttaacataatgacctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71879574	71879575	+	IGR	INS	-	A	A	rs138920580	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71879574_71879575insA								C18orf55 (53370 upstream) : CYB5A (40953 downstream)																							gtctcaaaaacaaaaaaaaaac	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75978880	75978880	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75978880delG								GALR1 (996786 upstream) : SALL3 (761395 downstream)																							CCTTCAAGGAGGCCAAGTAAG	0.493													4	2	---	---	---	---	
NFIC	4782	broad.mit.edu	37	19	3383138	3383139	+	Intron	INS	-	GAGA	GAGA	rs142707001	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3383138_3383139insGAGA	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_Intron|NFIC_uc010xhj.1_Intron|NFIC_uc002lxq.1_Intron	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)		AGCCCTCCGAGGAGAGCCAAGA	0.599													6	3	---	---	---	---	
C19orf28	126321	broad.mit.edu	37	19	3556883	3556884	+	Intron	INS	-	GACC	GACC	rs146992948	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3556883_3556884insGACC	uc002lxz.2	-						C19orf28_uc002lxw.2_Intron|C19orf28_uc002lxx.2_Intron|C19orf28_uc002lxy.2_Intron	NM_174983	NP_778148	Q6NUT3	CS028_HUMAN	hypothetical protein LOC126321 isoform c						transmembrane transport	integral to membrane				breast(1)|pancreas(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00251)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGACAGACAGAGGGGTGAAA	0.619													4	2	---	---	---	---	
ITGB1BP3	27231	broad.mit.edu	37	19	3938848	3938848	+	Intron	DEL	T	-	-	rs59201914		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3938848delT	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778	Q9NPI5	NRK2_HUMAN	integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		ttttgttttgttttttttttt	0.209													4	2	---	---	---	---	
DPP9	91039	broad.mit.edu	37	19	4704256	4704257	+	Frame_Shift_Ins	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4704256_4704257insC	uc002mba.2	-	6	744_745	c.486_487insG	c.(484-489)CGCCTGfs	p.R162fs	DPP9_uc002mbb.2_Frame_Shift_Ins_p.R162fs|DPP9_uc002mbc.2_Frame_Shift_Ins_p.R162fs	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	133_134					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		AAGACCCCCAGGCGTTTCCGCT	0.644													37	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8946042	8946043	+	IGR	DEL	AG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8946042_8946043delAG								ZNF558 (3067 upstream) : MBD3L1 (7226 downstream)																							aaatgaacaaagagttcgaatc	0.000													2	4	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9013689	9013689	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9013689delA	uc002mkp.2	-						MUC16_uc010xki.1_5'Flank	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						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						ctgtatccctagggtctggta	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	12106737	12106737	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12106737delC	uc002msx.1	+											Homo sapiens cDNA FLJ34878 fis, clone NT2NE2015565, weakly similar to RETROVIRUS-RELATED ENV POLYPROTEIN.																		aggcgcccaacaccacgcctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	12897230	12897230	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12897230delA								HOOK2 (10796 upstream) : JUNB (5056 downstream)																							TGCCAAGACCAAAAGCCCCGA	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13679659	13679660	+	IGR	INS	-	A	A	rs149701238		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13679659_13679660insA								CACNA1A (62385 upstream) : CCDC130 (162914 downstream)																							gactctgcctcaaaaaaaaaaa	0.198													4	2	---	---	---	---	
IL27RA	9466	broad.mit.edu	37	19	14145471	14145471	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14145471delA	uc002mxx.2	+							NM_004843	NP_004834	Q6UWB1	I27RA_HUMAN	class I cytokine receptor precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0						gactctgtctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17108645	17108645	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17108645delA	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						ctgggTTAAGAAAAAAAAAAA	0.274													4	2	---	---	---	---	
SLC27A1	376497	broad.mit.edu	37	19	17595536	17595536	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17595536delA	uc002ngu.1	+						SLC27A1_uc002ngt.1_Intron|SLC27A1_uc010xpp.1_Intron	NM_198580	NP_940982	Q6PCB7	S27A1_HUMAN	solute carrier family 27, member 1						cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0						tgaaagagggaaagaacgaag	0.139													5	3	---	---	---	---	
ZNF254	9534	broad.mit.edu	37	19	24229988	24229989	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24229988_24229989insT	uc010xrk.1	+						uc002nrr.1_Intron|uc002nrs.1_Intron	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				CTATTTTCCTATTtttttctcc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27856247	27856248	+	IGR	INS	-	AA	AA	rs143222131		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27856247_27856248insAA								None (None upstream) : LOC148189 (425154 downstream)																							gcacacatcacaaagtttccca	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27865506	27865507	+	IGR	DEL	TC	-	-	rs71224979		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27865506_27865507delTC								None (None upstream) : LOC148189 (415895 downstream)																							gttgaacgtatcttttTTTTTt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33768714	33768714	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33768714delG								SLC7A10 (51958 upstream) : CEBPA (22128 downstream)																							GCTCCACTGTGGGATAGAAGG	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40288162	40288163	+	IGR	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40288162_40288163delTT								LEUTX (11389 upstream) : DYRK1B (27828 downstream)																							ggatggatgctttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40663085	40663085	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40663085delA								ZNF780A (66240 upstream) : MAP3K10 (34566 downstream)																							gtctcaaaccaaaaaaaaaaa	0.045													4	4	---	---	---	---	
CYP2A7	1549	broad.mit.edu	37	19	41403982	41403983	+	Intron	INS	-	T	T	rs138864799	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41403982_41403983insT	uc002opo.2	-						uc002opp.1_Intron	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			AAAAACACCtgttttattttgt	0.401													3	3	---	---	---	---	
LIPE	3991	broad.mit.edu	37	19	42909030	42909030	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42909030delT	uc002otr.2	-						uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase						cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				tttttttaaattttttttttt	0.224													4	2	---	---	---	---	
ZNF226	7769	broad.mit.edu	37	19	44677476	44677479	+	Intron	DEL	CCTC	-	-	rs72010186		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44677476_44677479delCCTC	uc002oyp.2	+						ZNF226_uc002oyn.2_Intron|ZNF226_uc002oyo.2_Intron|ZNF226_uc002oyq.2_5'UTR|ZNF226_uc002oyr.2_5'UTR|ZNF226_uc010ejg.2_Intron|ZNF226_uc002oys.2_Intron|ZNF226_uc002oyt.2_Intron	NM_001032373	NP_001027545	Q9NYT6	ZN226_HUMAN	zinc finger protein 226 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				gccacattgtcctccctcttgctt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45130218	45130218	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45130218delA	uc002ozk.2	+											SubName: Full=LOC147710 protein; Flags: Fragment;																		actctgtctcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
VASP	7408	broad.mit.edu	37	19	46027681	46027682	+	Intron	INS	-	A	A	rs139129077		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46027681_46027682insA	uc002pcg.2	+						VASP_uc010eki.2_Intron|VASP_uc002pci.2_Intron	NM_003370	NP_003361	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						axon guidance|cell junction assembly|T cell receptor signaling pathway	actin cytoskeleton|cytosol|filopodium membrane|focal adhesion|lamellipodium membrane	actin binding|profilin binding|SH3 domain binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		aaaccaaaaccaaaaaaaaaaa	0.233													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46846757	46846757	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46846757delT								HIF3A (68 upstream) : PPP5C (3537 downstream)																							GCTGAGTGTCTTTTTTTTTtt	0.289													4	2	---	---	---	---	
EHD2	30846	broad.mit.edu	37	19	48216429	48216431	+	5'Flank	DEL	TGC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48216429_48216431delTGC	uc002phj.3	+						EHD2_uc010xyu.1_5'Flank	NM_014601	NP_055416	Q9NZN4	EHD2_HUMAN	EH-domain containing 2						blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TTACTATTATTGCTGCTGCTGTT	0.315													4	2	---	---	---	---	
FLT3LG	2323	broad.mit.edu	37	19	49982452	49982452	+	Intron	DEL	T	-	-	rs33951493		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49982452delT	uc010yau.1	+						FLT3LG_uc002pnv.2_Intron|FLT3LG_uc002pnw.2_Intron|FLT3LG_uc002pnu.2_Intron|FLT3LG_uc002pnx.2_Intron|FLT3LG_uc010yav.1_Intron	NM_001459	NP_001450	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand precursor						positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		AGTTTACCAAttttttttttt	0.249													3	3	---	---	---	---	
PRR12	57479	broad.mit.edu	37	19	50101333	50101334	+	Intron	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50101333_50101334delTT	uc002poo.3	+							NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12								DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TGTTTGAGtctttttttttttt	0.292													4	2	---	---	---	---	
KLKP1	606293	broad.mit.edu	37	19	51394835	51394835	+	5'Flank	DEL	T	-	-	rs68126662		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51394835delT	uc002ptw.2	-						KLKP1_uc002ptx.2_Intron					Homo sapiens kallikrein-related sequence from prostate mRNA, partial cds.												0						CACCTATGTCttttttttttg	0.134													4	2	---	---	---	---	
KLK6	5653	broad.mit.edu	37	19	51463178	51463180	+	Intron	DEL	GAG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51463178_51463180delGAG	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)		aggaggagaagaggaggaaaagg	0.000													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	51774792	51774792	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51774792delC								C19orf75 (2210 upstream) : IGLON5 (40310 downstream)																							TGAGGAAGGACCAGGCTGGAG	0.438													4	2	---	---	---	---	
FPR3	2359	broad.mit.edu	37	19	52320780	52320781	+	Intron	INS	-	A	A	rs145178698	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52320780_52320781insA	uc002pxt.1	+							NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2						cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(4)|breast(1)|skin(1)	6						tttttttttttaaattattgtt	0.000													2	4	---	---	---	---	
MIR522	574495	broad.mit.edu	37	19	54253380	54253380	+	5'Flank	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54253380delT	hsa-mir-522|MI0003177	+						MIR519A1_hsa-mir-519a-1|MI0003178_5'Flank																	0						gcgattctcctgcctcagcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54526458	54526459	+	IGR	INS	-	ATAC	ATAC	rs143337205	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54526458_54526459insATAC								CACNG6 (10540 upstream) : VSTM1 (17626 downstream)																							cgtctcaaaaaatacatacata	0.000													4	5	---	---	---	---	
TARM1	441864	broad.mit.edu	37	19	54585249	54585250	+	5'Flank	DEL	TT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54585249_54585250delTT	uc010yei.1	-							NM_001135686	NP_001129158	B6A8C7	TARM1_HUMAN	OSCAR-like transcript-2							integral to membrane					0						TTCATCACCAtttttttttttt	0.020													4	5	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55648876	55648877	+	Intron	INS	-	C	C			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55648876_55648877insC	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		aggagtccagaccccagcccct	0.000													5	4	---	---	---	---	
BRSK1	84446	broad.mit.edu	37	19	55792498	55792501	+	5'Flank	DEL	TGTG	-	-	rs146164484		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55792498_55792501delTGTG	uc002qkf.2	+						HSPBP1_uc002qjx.2_5'Flank|HSPBP1_uc002qjy.2_5'Flank|HSPBP1_uc002qkb.2_5'Flank|HSPBP1_uc002qka.2_5'Flank|HSPBP1_uc002qkd.2_5'Flank|HSPBP1_uc002qkc.2_5'Flank	NM_032430	NP_115806	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1						establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV	cell junction|cytoplasm|nucleus	magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1)	6		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		tgtgtgtgtatgtgtgtgtgtgtg	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1002683	1002683	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1002683delT								RSPO4 (19779 upstream) : PSMF1 (91223 downstream)																							CTTCTGAGACTTTTTTTTTTT	0.279													4	2	---	---	---	---	
SNPH	9751	broad.mit.edu	37	20	1245708	1245709	+	5'Flank	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1245708_1245709insG	uc002wes.2	+						SNPH_uc002wet.2_5'Flank	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2						aaatacagcaagggaaaaaaac	0.074													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8528981	8528984	+	Intron	DEL	TCTT	-	-	rs10541606		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8528981_8528984delTCTT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						tttttctttctctttgtttctttc	0.078													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12244231	12244233	+	IGR	DEL	TCC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12244231_12244233delTCC								BTBD3 (336989 upstream) : SPTLC3 (745394 downstream)																							cAATGATCAGtcctcctcctcct	0.089													6	3	---	---	---	---	
TASP1	55617	broad.mit.edu	37	20	13534840	13534840	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13534840delA	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron|TASP1_uc010zrj.1_Intron	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0						TGTTAGCCCTAGCATCATCAG	0.423													4	2	---	---	---	---	
BFSP1	631	broad.mit.edu	37	20	17504142	17504144	+	Intron	DEL	AGC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17504142_17504144delAGC	uc002wpo.2	-						BFSP1_uc002wpp.2_Intron|BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						TCAGCAGAATAGCAGAGTGATGT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18063874	18063874	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18063874delT								OVOL2 (25353 upstream) : CSRP2BP (54653 downstream)																							gccttgtgccttccaatccat	0.000													4	2	---	---	---	---	
DTD1	92675	broad.mit.edu	37	20	18723338	18723338	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18723338delA	uc002wrf.3	+							NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						ccctggtgccaaaaatgttgg	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22815244	22815247	+	IGR	DEL	CCTC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22815244_22815247delCCTC								FOXA2 (249143 upstream) : SSTR4 (200810 downstream)																							CCTTCCCTGtcctccctccctccc	0.206													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23248047	23248047	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23248047delC								CD93 (181070 upstream) : NXT1 (83326 downstream)																							GGGTTTCTCTCCAGGCTGATT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23531770	23531770	+	IGR	DEL	G	-	-	rs5840998		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23531770delG								CSTT (9117 upstream) : CST9L (13602 downstream)																							AGGAGTAAAAGTGCTGTGAGT	0.398													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25641427	25641428	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25641427_25641428insT	uc002wuz.2	+											Homo sapiens zinc finger protein 337, mRNA (cDNA clone IMAGE:4826085).																		cttttcattccttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25884965	25884965	+	IGR	DEL	C	-	-	rs112916433		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25884965delC								FAM182B (36179 upstream) : LOC100134868 (105470 downstream)																							attacaggtgcccataaccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074950	26074951	+	IGR	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074950_26074951insA								FAM182A (7398 upstream) : C20orf191 (9102 downstream)																							agtcttgactcaaaaaacaaaa	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26075417	26075418	+	IGR	INS	-	TCC	TCC	rs147363891		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26075417_26075418insTCC								FAM182A (7865 upstream) : C20orf191 (8635 downstream)																							tctcaccatcatcatcctcagc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26078835	26078836	+	IGR	INS	-	AGG	AGG	rs113618308		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26078835_26078836insAGG								FAM182A (11283 upstream) : C20orf191 (5217 downstream)																							TACTGAGAGCCAGAAGACCCAT	0.554													4	2	---	---	---	---	
C20orf191	149934	broad.mit.edu	37	20	26084428	26084428	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084428delC	uc002wvj.3	-							NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						TCTAATGAAACCTTTAGTAGT	0.313													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26251028	26251029	+	IGR	INS	-	A	A	rs151085511	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26251028_26251029insA								MIR663 (62114 upstream) : None (None downstream)																							acctgggaagcagagtttgcag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29431750	29431750	+	IGR	DEL	G	-	-	rs112192023		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29431750delG								None (None upstream) : FRG1B (180129 downstream)																							gtgtagatgtgtttttctctt	0.144													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29607523	29607523	+	IGR	DEL	T	-	-	rs111896705		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29607523delT								None (None upstream) : FRG1B (4356 downstream)																							acatcccccctggctcacttg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29608472	29608472	+	IGR	DEL	G	-	-	rs113600748		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29608472delG								None (None upstream) : FRG1B (3407 downstream)																							ttgctattgtgaatagtgctg	0.000													5	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29636672	29636673	+	Intron	INS	-	A	A	rs67210451		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29636672_29636673insA	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						cctgtctccacaaaaaaTTAtt	0.015													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29918981	29918987	+	IGR	DEL	AGAGAGA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29918981_29918987delAGAGAGA								DEFB116 (22593 upstream) : DEFB118 (37441 downstream)																							gaagaagaagagagagaagaagaagaa	0.000													4	2	---	---	---	---	
C20orf112	140688	broad.mit.edu	37	20	31092360	31092361	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31092360_31092361insA	uc002wxw.1	-									Q96MY1	CT112_HUMAN	Homo sapiens cDNA FLJ31724 fis, clone NT2RI2006703, moderately similar to Homo sapiens nolp mRNA.												0						gagactccatcaaaaaaaaaaa	0.059													4	2	---	---	---	---	
ACSS2	55902	broad.mit.edu	37	20	33489906	33489907	+	Intron	INS	-	C	C	rs142462403	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33489906_33489907insC	uc002xbd.2	+						ACSS2_uc002xbc.2_Intron|ACSS2_uc010zum.1_Intron|ACSS2_uc010gey.2_Intron|ACSS2_uc002xbe.2_Intron|ACSS2_uc002xbf.2_Intron	NM_018677	NP_061147	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2						ethanol oxidation|lipid biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	acetate-CoA ligase activity|ATP binding|protein binding				0					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	agtctacttttccccataatga	0.005													2	4	---	---	---	---	
PHF20	51230	broad.mit.edu	37	20	34440525	34440525	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34440525delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xel.1_Intron	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					TCAAGAAAACttttttttttt	0.234													4	2	---	---	---	---	
LBP	3929	broad.mit.edu	37	20	36992390	36992391	+	Intron	DEL	GC	-	-	rs5741817	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36992390_36992391delGC	uc002xic.1	+							NM_004139	NP_004130	P18428	LBP_HUMAN	lipopolysaccharide-binding protein precursor						acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				gtgtgtgtgtgCGCTTGTCTGG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38658301	38658302	+	IGR	INS	-	GGG	GGG	rs117008347	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38658301_38658302insGGG								LOC339568 (804910 upstream) : MAFB (656217 downstream)																							gaagggaaggaagggagggagg	0.030													5	3	---	---	---	---	
PKIG	11142	broad.mit.edu	37	20	43214010	43214010	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43214010delC	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521	Q9Y2B9	IPKG_HUMAN	cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)			AAAGATGTGTCCAGAGATCTC	0.323													4	2	---	---	---	---	
ZNF335	63925	broad.mit.edu	37	20	44603734	44603735	+	5'Flank	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44603734_44603735insT	uc002xqw.2	-						ZNF335_uc010zxk.1_5'Flank	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				GTCATGTTTTGTTTTTTTTTTT	0.431													4	2	---	---	---	---	
ELMO2	63916	broad.mit.edu	37	20	45053237	45053238	+	Intron	DEL	TG	-	-	rs72406038		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45053237_45053238delTG	uc010zxs.1	-						uc002xry.2_Intron			Q96JJ3	ELMO2_HUMAN	SubName: Full=ELMO2 protein; SubName: Full=Engulfment and cell motility 2;						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				acttaaagtttgtgtgtgtgtg	0.005													4	3	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45270520	45270520	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45270520delT	uc002xsf.1	-						SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc002xsi.3_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ctaccacctctttttgaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46931734	46931737	+	IGR	DEL	CATC	-	-	rs113709833		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46931734_46931737delCATC								SULF2 (516374 upstream) : LOC284749 (56917 downstream)																							atccattcttcatccatccatcca	0.049													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46952465	46952465	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46952465delA								SULF2 (537105 upstream) : LOC284749 (36189 downstream)																							cctggcagccaaaattcctcc	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48236206	48236207	+	IGR	INS	-	GGAT	GGAT	rs141199932	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48236206_48236207insGGAT								PTGIS (51499 upstream) : B4GALT5 (13278 downstream)																							atagatggatgggatggatgga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50627701	50627701	+	IGR	DEL	T	-	-	rs11474942		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50627701delT								SALL4 (208653 upstream) : ZFP64 (72850 downstream)																							CGGTTTCAAATCCTTGTGGGA	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52265128	52265129	+	IGR	INS	-	A	A	rs146478937		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52265128_52265129insA								ZNF217 (54327 upstream) : SUMO1P1 (225913 downstream)																							aactccatgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53906746	53906746	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53906746delT								DOK5 (639037 upstream) : CBLN4 (665751 downstream)																							CTTCTTATCAttttttttttt	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56052501	56052502	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56052501_56052502insT								RBM38 (68117 upstream) : CTCFL (11378 downstream)																							tcttttccttcttttttttttt	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56531135	56531136	+	IGR	INS	-	GG	GG	rs139994223	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56531135_56531136insGG								PMEPA1 (244594 upstream) : C20orf85 (194847 downstream)																							tggaaagaggtggtcgacaggg	0.079													1	6	---	---	---	---	
EEF1A2	1917	broad.mit.edu	37	20	62124168	62124169	+	Intron	INS	-	GGAT	GGAT	rs147190899	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62124168_62124169insGGAT	uc002yfd.1	-						EEF1A2_uc002yfe.1_Intron|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			gatagagagaaggatggatggg	0.000													4	3	---	---	---	---	
EEF1A2	1917	broad.mit.edu	37	20	62127807	62127808	+	Intron	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62127807_62127808delTG	uc002yfd.1	-						EEF1A2_uc002yfe.1_Intron|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			AATAACCCTCTGTGTGTGTGTG	0.545											OREG0026129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9832226	9832227	+	IGR	INS	-	CG	CG			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9832226_9832227insCG								None (None upstream) : None (None downstream)																							catcccctagcagagaaccctg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9850303	9850303	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9850303delG								None (None upstream) : None (None downstream)																							cccaggagtaggtgttggaat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9877101	9877101	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9877101delG								None (None upstream) : None (None downstream)																							tccgcagcgcggttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9878690	9878691	+	IGR	DEL	GT	-	-	rs75951230	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9878690_9878691delGT								None (None upstream) : None (None downstream)																							gggaagacacgttcgttcgtgg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10775910	10775914	+	IGR	DEL	CAGTG	-	-	rs28390091		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10775910_10775914delCAGTG								None (None upstream) : TPTE (130829 downstream)																							gaattgaatacagtggagtggagtg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10837230	10837233	+	IGR	DEL	GAAT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10837230_10837233delGAAT								None (None upstream) : TPTE (69510 downstream)																							gaatagaatggaatgaatggaatg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10879055	10879055	+	IGR	DEL	C	-	-	rs57304473		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10879055delC								None (None upstream) : TPTE (27688 downstream)																							gcaacccctacctttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10888777	10888779	+	IGR	DEL	CTT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10888777_10888779delCTT								None (None upstream) : TPTE (17964 downstream)																							ATAATTTATCCttctagaatatg	0.039													7	4	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10941532	10941533	+	Intron	INS	-	GTC	GTC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10941532_10941533insGTC	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						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)		tggcTCTTTCAGTCGAGGGTAG	0.109													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037608	11037609	+	Intron	INS	-	GA	GA	rs56247503		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037608_11037609insGA	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)		TAACTGTCAAGGAAAATACTTA	0.332													3	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11052683	11052683	+	Intron	DEL	A	-	-	rs111400886		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11052683delA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		accctgtctcaaaaaaaaaaa	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11125889	11125892	+	IGR	DEL	TTAA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11125889_11125892delTTAA								BAGE (26952 upstream) : None (None downstream)																							acttttaTTTTTAATTAATTAAtt	0.098													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11184758	11184759	+	IGR	INS	-	A	A	rs138233859		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11184758_11184759insA								BAGE (85821 upstream) : None (None downstream)																							tctcaaaaaacaaaaaacaaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14900670	14900670	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14900670delG								C21orf99 (410101 upstream) : POTED (81828 downstream)																							AGAGCCTAATGGGAGTCTTCC	0.488													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	27696990	27696990	+	IGR	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27696990delT								APP (153544 upstream) : CYYR1 (141539 downstream)																							cactactagcttttttctttc	0.000													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43226692	43226693	+	Intron	INS	-	A	A			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43226692_43226693insA	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						tcaccaccaccatcactaccac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	48119797	48119797	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:48119797delA								PRMT2 (34935 upstream) : None (None downstream)																							ggttagggttagggttagggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16060516	16060517	+	IGR	DEL	TT	-	-	rs113906074	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16060516_16060517delTT								None (None upstream) : POTEH (195815 downstream)																							tttctttttctttttctttctt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16399272	16399272	+	IGR	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16399272delA								POTEH (111335 upstream) : OR11H1 (49554 downstream)																							TTGAGAGCTGAAGTTTGCAGA	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	18035470	18035470	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18035470delG								CECR2 (1625 upstream) : SLC25A18 (7713 downstream)																							TTCACCCTGTGGGTCACTGTC	0.458													8	4	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19080528	19080528	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19080528delA	uc002zoq.1	-						DGCR2_uc002zor.1_Intron|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					gaggaggaggaagaAAGAGGA	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20292917	20292918	+	RNA	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20292917_20292918insT	uc002zrw.1	+	1		c.1357_1358insT								Homo sapiens mRNA for KIAA1653 protein, partial cds.																		ctggctgtggcttgggcttttt	0.000													5	3	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21147567	21147568	+	Intron	DEL	TG	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21147567_21147568delTG	uc002zsz.3	-							NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			TTAACGAGTATGTGTTTCTTTT	0.257													16	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21490534	21490535	+	IGR	INS	-	G	G			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21490534_21490535insG								LOC400891 (72079 upstream) : POM121L8P (146179 downstream)																							aaaaaaaaaaaGGGGAGTTCCT	0.218													3	3	---	---	---	---	
YPEL1	29799	broad.mit.edu	37	22	22062621	22062621	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22062621delT	uc002zvl.2	-						YPEL1_uc002zvm.2_Intron	NM_013313	NP_037445	O60688	YPEL1_HUMAN	yippee-like 1							nucleus					0	Colorectal(54;0.105)					GGCTTCTGCCttttttttttt	0.239													4	2	---	---	---	---	
CYTSA	23384	broad.mit.edu	37	22	24760630	24760631	+	Intron	DEL	AA	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24760630_24760631delAA	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A						cell cycle|cell division						0						actccctctcaaaaaaaaaaaa	0.178													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25094332	25094333	+	IGR	INS	-	T	T	rs141097386	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25094332_25094333insT								POM121L10P (39218 upstream) : PIWIL3 (20668 downstream)																							ggtcacacagcttctaggtagg	0.129													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25627899	25627900	+	IGR	DEL	GA	-	-	rs33917499	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25627899_25627900delGA								CRYBB2 (63 upstream) : IGLL3 (85988 downstream)																							gtgtgtgtgtgagagagagaga	0.302													6	3	---	---	---	---	
ASPHD2	57168	broad.mit.edu	37	22	26838162	26838163	+	Intron	INS	-	ATTT	ATTT	rs142256476	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26838162_26838163insATTT	uc003acg.2	+							NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2						peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1						atgctgctcccattaggacccc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27233982	27233982	+	IGR	DEL	C	-	-	rs36013255		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27233982delC								MIAT (119033 upstream) : MN1 (910284 downstream)																							ggccagcttacccaagagatc	0.159													3	5	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28601196	28601197	+	Intron	DEL	AC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28601196_28601197delAC	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						TTTTAACGCAACACACACACAC	0.371													4	2	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29516070	29516071	+	Intron	INS	-	AC	AC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29516070_29516071insAC	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						tgatgaaggaaatggaggaggg	0.000													3	3	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33862357	33862358	+	Intron	DEL	CT	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33862357_33862358delCT	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				tttctcttgcctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35136588	35136597	+	IGR	DEL	GTGTGTGTGC	-	-	rs113321477	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35136588_35136597delGTGTGTGTGC								LARGE (818004 upstream) : ISX (325532 downstream)																							gtgtgtgtgtgtgtgtgtgcgcacgcacgt	0.019													6	3	---	---	---	---	
SOX10	6663	broad.mit.edu	37	22	38377950	38377950	+	Intron	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38377950delG	uc003aun.1	-						POLR2F_uc003aum.2_Intron|SOX10_uc003auo.1_Intron	NM_006941	NP_008872	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10							cytoplasm|nucleus	DNA binding|identical protein binding|transcription coactivator activity				0	Melanoma(58;0.045)					GAACAGGCCAGGGGGCGGGAT	0.597													4	2	---	---	---	---	
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45136750	45136751	+	Intron	INS	-	A	A	rs148837254	by1000genomes	TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45136750_45136751insA	uc003bfd.2	+						PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|PRR5-ARHGAP8_uc003bfg.1_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						GGAGGAGTCCCAAGGTGGAGAT	0.604													5	5	---	---	---	---	
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45205158	45205159	+	Intron	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45205158_45205159insT	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|ARHGAP8_uc003bfl.2_Intron|PRR5-ARHGAP8_uc003bfg.1_Frame_Shift_Ins_p.C227fs	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						atattcttctgttttttttttt	0.000													4	2	---	---	---	---	
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45217794	45217795	+	Intron	INS	-	AGAG	AGAG	rs139770690		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45217794_45217795insAGAG	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|ARHGAP8_uc003bfl.2_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						TTCCTCTCCTTAGAAGAGGTGG	0.599											OREG0026635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45670322	45670322	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45670322delG								C22orf9 (33672 upstream) : UPK3A (10567 downstream)																							ccagcactttgggaggccgag	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46413751	46413752	+	IGR	INS	-	T	T	rs61452489		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46413751_46413752insT								LOC730668 (7094 upstream) : LOC100271722 (22037 downstream)																							ttttttctccattttttttttt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49569259	49569259	+	IGR	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49569259delC								FAM19A5 (421517 upstream) : C22orf34 (238917 downstream)																							attcctcaagcccccattact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	698064	698065	+	IGR	INS	-	CGTATC	CGTATC			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:698064_698065insCGTATC								SHOX (77919 upstream) : CRLF2 (616822 downstream)																							TTGTGGGATTGAGTGCATTGTG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	941021	941021	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:941021delG								SHOX (320876 upstream) : CRLF2 (373866 downstream)																							AGAGGTCAGAGTGAAAGAAAC	0.552													5	3	---	---	---	---	
P2RY8	286530	broad.mit.edu	37	X	1613428	1613428	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1613428delA	uc004cpz.2	-							NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		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)				ATTAGGCTTTAAAAAAAAAAA	0.433			T	CRLF2	B-ALL|Downs associated ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	2013159	2013160	+	IGR	DEL	TC	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2013159_2013160delTC								ASMT (251186 upstream) : DHRSX (124397 downstream)																							tgtctctctgtctctctctctc	0.114													4	2	---	---	---	---	
PDHA1	5160	broad.mit.edu	37	X	19363864	19363864	+	Intron	DEL	C	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19363864delC	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	TTTGCAGGGTCCCCCCCCCCC	0.468													5	3	---	---	---	---	
RPS6KA3	6197	broad.mit.edu	37	X	20253005	20253005	+	Intron	DEL	A	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-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													4	2	---	---	---	---	
IL1RAPL1	11141	broad.mit.edu	37	X	29270260	29270260	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29270260delT	uc004dby.2	+							NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						gagggatagctttaggagata	0.000													4	2	---	---	---	---	
MED14	9282	broad.mit.edu	37	X	40588551	40588551	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40588551delT	uc004dex.3	-						MED14_uc010nhe.1_Intron	NM_004229	NP_004220	O60244	MED14_HUMAN	mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4						ACTTTAAGGGTTTTTTTTTTC	0.383													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	89368759	89368759	+	IGR	DEL	G	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89368759delG								TGIF2LX (190879 upstream) : None (None downstream)																							TCGGGACTGAGGGGGAACCGC	0.398													12	18	---	---	---	---	
ENOX2	10495	broad.mit.edu	37	X	129790756	129790756	+	Intron	DEL	T	-	-			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129790756delT	uc004evw.2	-						ENOX2_uc004evx.2_Intron|ENOX2_uc004evy.2_Intron|ENOX2_uc004evv.2_Intron	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b						cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						TAAAGCAGCATTTTTTTTTGA	0.333													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9953181	9953184	+	IGR	DEL	AGGA	-	-	rs144947736		TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9953181_9953184delAGGA								TTTY22 (302327 upstream) : None (None downstream)																							gcaatcagacaggaaggagaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10011935	10011936	+	IGR	INS	-	T	T			TCGA-18-3414-01A-01D-0983-08	TCGA-18-3414-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10011935_10011936insT								TTTY22 (361081 upstream) : None (None downstream)																							GAAAAACTATCACTTGTTACTG	0.257													10	6	---	---	---	---	
