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
CCDC27	148870	broad.mit.edu	37	1	3686367	3686367	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3686367G>A	uc001akv.2	+	11	1845	c.1764G>A	c.(1762-1764)AAG>AAA	p.K588K	LOC388588_uc001akw.3_5'Flank	NM_152492	NP_689705	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	588										skin(1)	1	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		TAAGGAATAAGATCATCCAGG	0.542													8	44	---	---	---	---	PASS
PRAMEF1	65121	broad.mit.edu	37	1	12854302	12854302	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12854302G>A	uc001auj.1	+	3	629	c.526G>A	c.(526-528)GGT>AGT	p.G176S		NM_023013	NP_075389	O95521	PRAM1_HUMAN	PRAME family member 1	176											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCAAAGGAGAGGTTTAGTACA	0.408													33	161	---	---	---	---	PASS
EPHA2	1969	broad.mit.edu	37	1	16458597	16458597	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16458597C>T	uc001aya.1	-	13	2424	c.2287G>A	c.(2287-2289)GTG>ATG	p.V763M		NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	763	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase.|Cytoplasmic (Potential).				activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)	TCCTCCAGCACGCGGGACAGG	0.612													9	39	---	---	---	---	PASS
RAP1GAP	5909	broad.mit.edu	37	1	21991780	21991780	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21991780G>T	uc001bex.2	-						RAP1GAP_uc001bey.2_5'UTR	NM_002885	NP_002876	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein isoform c						regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		GGGTCCGAGGGAGGGTGGCCT	0.159													4	13	---	---	---	---	PASS
CELA3A	10136	broad.mit.edu	37	1	22336260	22336260	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22336260G>T	uc001bfl.2	+	7	724	c.705G>T	c.(703-705)GTG>GTT	p.V235V		NM_005747	NP_005738	P09093	CEL3A_HUMAN	elastase 3A, pancreatic preproprotein	235	Peptidase S1.				cholesterol metabolic process|digestion|proteolysis		serine-type endopeptidase activity			haematopoietic_and_lymphoid_tissue(1)	1						TCCACGGTGTGACCAGCTTTG	0.592													4	25	---	---	---	---	PASS
CLSPN	63967	broad.mit.edu	37	1	36204180	36204180	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36204180T>C	uc001bzi.2	-	21	3514	c.3434A>G	c.(3433-3435)GAT>GGT	p.D1145G	CLSPN_uc009vux.2_Missense_Mutation_p.D1081G	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	1145					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTGGGAAGCATCATCTAAACA	0.433													11	34	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39799732	39799732	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39799732G>T	uc010oiu.1	+	1	2923	c.2792G>T	c.(2791-2793)AGA>ATA	p.R931I	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	2496					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)			CTTTTGGAGAGAGAGGAGGCC	0.403													5	99	---	---	---	---	PASS
DAB1	1600	broad.mit.edu	37	1	57602295	57602295	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57602295C>T	uc001cys.1	-	6	901	c.227G>A	c.(226-228)CGT>CAT	p.R76H	DAB1_uc001cyt.1_Missense_Mutation_p.R76H|DAB1_uc001cyq.1_Missense_Mutation_p.R76H|DAB1_uc001cyr.1_Missense_Mutation_p.R76H|DAB1_uc009vzw.1_Missense_Mutation_p.R76H|DAB1_uc009vzx.1_Missense_Mutation_p.R76H	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	76	PID.				cell differentiation|nervous system development					skin(2)|ovary(1)	3						TCCTTTGGAACGAGCGCCAGC	0.403													5	20	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75037053	75037053	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037053C>G	uc001dgg.2	-	14	4560	c.4341G>C	c.(4339-4341)GAG>GAC	p.E1447D		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1447	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						CTTCCTCTTGCTCCTGTCCTA	0.587													11	46	---	---	---	---	PASS
AK5	26289	broad.mit.edu	37	1	77752691	77752691	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77752691A>C	uc001dhn.2	+	2	383	c.126A>C	c.(124-126)TTA>TTC	p.L42F	AK5_uc001dho.2_Missense_Mutation_p.L16F|AK5_uc001dhm.1_Missense_Mutation_p.L42F	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1	42					ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						AAAGTTGTTTACAAAAAGTAA	0.378													9	57	---	---	---	---	PASS
CHIA	27159	broad.mit.edu	37	1	111860605	111860605	+	Intron	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111860605C>G	uc001eas.2	+						CHIA_uc001ear.2_Intron|CHIA_uc001eaq.2_Intron|CHIA_uc009wgc.2_Intron|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_Intron|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c						apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CACCCCACCTCAGGTACCTGG	0.507													4	52	---	---	---	---	PASS
MAGI3	260425	broad.mit.edu	37	1	114184866	114184866	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114184866C>A	uc001edk.2	+	10	1875	c.1694C>A	c.(1693-1695)TCC>TAC	p.S565Y	MAGI3_uc001edh.3_Missense_Mutation_p.S590Y|MAGI3_uc001edi.3_Missense_Mutation_p.S565Y|MAGI3_uc010owm.1_Missense_Mutation_p.S590Y|MAGI3_uc001edj.2_Missense_Mutation_p.S286Y	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	590					apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGAGAGTATCCATGGCATCG	0.502													19	99	---	---	---	---	PASS
BCL2L15	440603	broad.mit.edu	37	1	114424399	114424399	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114424399C>T	uc001edw.2	-	3	642	c.470G>A	c.(469-471)GGT>GAT	p.G157D	uc001edv.1_Intron|BCL2L15_uc001edx.2_Intron|BCL2L15_uc001edy.2_Intron|BCL2L15_uc001edz.1_RNA	NM_001010922	NP_001010922	Q5TBC7	B2L15_HUMAN	pro-apoptotic Bcl-2 protein	157					apoptosis					ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACTTACCCAACCTCCCTGGCC	0.483													13	19	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115165732	115165732	+	Intron	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115165732A>C	uc001efd.1	-						DENND2C_uc001eez.2_Intron|DENND2C_uc001efc.1_Intron	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ttaaaaaataatttaaaaaaa	0.348													6	74	---	---	---	---	PASS
CD101	9398	broad.mit.edu	37	1	117559924	117559924	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117559924C>A	uc010oxb.1	+	5	1499	c.1441C>A	c.(1441-1443)CAT>AAT	p.H481N	CD101_uc009whd.2_Missense_Mutation_p.H481N|CD101_uc010oxc.1_Missense_Mutation_p.H481N|CD101_uc010oxd.1_Missense_Mutation_p.H419N	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	481	Extracellular (Potential).|Ig-like C2-type 4.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						ACCCAGTTACCATGGCAACAC	0.572													6	149	---	---	---	---	PASS
MAN1A2	10905	broad.mit.edu	37	1	118039520	118039520	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118039520G>T	uc001ehd.1	+	10	2141	c.1420G>T	c.(1420-1422)GGT>TGT	p.G474C	MAN1A2_uc009whg.1_Missense_Mutation_p.G264C	NM_006699	NP_006690	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	474	Lumenal (Potential).				N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity				0	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		AGGAGCAGATGGTTCCAGAGC	0.423													7	133	---	---	---	---	PASS
HMGCS2	3158	broad.mit.edu	37	1	120293471	120293471	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120293471C>G	uc001eid.2	-	9	1532	c.1481G>C	c.(1480-1482)CGA>CCA	p.R494P	HMGCS2_uc010oxj.1_Missense_Mutation_p.R452P|HMGCS2_uc001eie.2_Missense_Mutation_p.R402P	NM_005518	NP_005509	P54868	HMCS2_HUMAN	hydroxymethylglutaryl-CoA synthase 2 isoform 1	494					acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		CTCGTCCACTCGCTCCAGGTA	0.512													3	44	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144912276	144912276	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144912276C>G	uc001elw.3	-	15	2290	c.1999G>C	c.(1999-2001)GTG>CTG	p.V667L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.V733L|PDE4DIP_uc001emc.1_Missense_Mutation_p.V667L|PDE4DIP_uc001emd.1_Missense_Mutation_p.V667L|PDE4DIP_uc001emb.1_Missense_Mutation_p.V830L|PDE4DIP_uc001eme.1_Missense_Mutation_p.V196L|PDE4DIP_uc001emf.1_Missense_Mutation_p.V452L	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	667	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding	p.V667L(1)		ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGGCTTGCACCAACTTCTCT	0.383			T	PDGFRB	MPD								4	59	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152187842	152187842	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152187842G>C	uc001ezt.1	-	3	6339	c.6263C>G	c.(6262-6264)TCC>TGC	p.S2088C		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2088	23.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCGACCGGAGCCAGACCC	0.617													31	90	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152281741	152281741	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152281741G>A	uc001ezu.1	-	3	5657	c.5621C>T	c.(5620-5622)TCA>TTA	p.S1874L		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1874	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCGTCTCCTGATTGTTTCTC	0.572									Ichthyosis				106	240	---	---	---	---	PASS
LCE1E	353135	broad.mit.edu	37	1	152759781	152759781	+	Silent	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152759781C>G	uc001fan.2	+	2	59	c.6C>G	c.(4-6)TCC>TCG	p.S2S		NM_178353	NP_848130	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	2					keratinization						0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGAGATGTCCTGCCAGCAGA	0.488													18	168	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154098875	154098875	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154098875C>A	uc001fdw.2	-	10	1322	c.1250G>T	c.(1249-1251)GGA>GTA	p.G417V	NUP210L_uc009woq.2_5'UTR|NUP210L_uc010peh.1_Missense_Mutation_p.G417V	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	417						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ATGGTAAGATCCATTCACGGT	0.398													17	56	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154098876	154098876	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154098876C>A	uc001fdw.2	-	10	1321	c.1249G>T	c.(1249-1251)GGA>TGA	p.G417*	NUP210L_uc009woq.2_5'UTR|NUP210L_uc010peh.1_Nonsense_Mutation_p.G417*	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	417						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TGGTAAGATCCATTCACGGTA	0.398													17	57	---	---	---	---	PASS
FLAD1	80308	broad.mit.edu	37	1	154962919	154962919	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154962919G>A	uc001fgf.1	+	5	1823	c.1469G>A	c.(1468-1470)CGG>CAG	p.R490Q	FLAD1_uc001fgd.1_3'UTR|FLAD1_uc001fge.1_Missense_Mutation_p.R393Q|FLAD1_uc001fgg.1_Missense_Mutation_p.R393Q|FLAD1_uc001fgh.1_Intron	NM_025207	NP_079483	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase isoform	490	FAD synthase.				FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGCACCCGCCGGACTGACCCC	0.622													4	24	---	---	---	---	PASS
ARHGEF2	9181	broad.mit.edu	37	1	155921325	155921325	+	Splice_Site	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155921325C>A	uc001fmt.2	-	19	2327	c.2209_splice	c.e19-1	p.E737_splice	ARHGEF2_uc001fmq.2_5'Flank|ARHGEF2_uc001fmr.2_Splice_Site_p.E709_splice|ARHGEF2_uc001fms.2_Splice_Site_p.E736_splice|ARHGEF2_uc001fmu.2_Splice_Site_p.E781_splice	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GTAACGCCTCCTGAGGACAGA	0.557													6	100	---	---	---	---	PASS
IQGAP3	128239	broad.mit.edu	37	1	156507028	156507028	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156507028G>A	uc001fpf.2	-	27	3442	c.3367C>T	c.(3367-3369)CTC>TTC	p.L1123F		NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1123	Ras-GAP.				small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTCATGGCGAGGAGGTTGCGT	0.552													43	32	---	---	---	---	PASS
CD1D	912	broad.mit.edu	37	1	158151308	158151308	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158151308C>A	uc001frr.2	+	3	624	c.125C>A	c.(124-126)ACG>AAG	p.T42K	CD1D_uc009wsr.1_Missense_Mutation_p.T42K|CD1D_uc009wss.2_Missense_Mutation_p.T42K|CD1D_uc009wst.1_5'UTR	NM_001766	NP_001757	P15813	CD1D_HUMAN	CD1D antigen precursor	42	Extracellular (Potential).				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)					AGCAGCTGGACGCGCACCGAC	0.632													95	84	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158609467	158609467	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158609467A>G	uc001fst.1	-	35	5084	c.4885T>C	c.(4885-4887)TTG>CTG	p.L1629L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1629	Spectrin 16.				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)					ATGGCCAGCAATGTCTCTGCC	0.468													27	62	---	---	---	---	PASS
RGS5	8490	broad.mit.edu	37	1	163138133	163138133	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163138133C>A	uc001gcn.2	-	2	317	c.70G>T	c.(70-72)GGA>TGA	p.G24*	RGS5_uc009wvb.2_Intron	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5	24					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)			AGGAGAATTCCCAACTTGATC	0.448													6	132	---	---	---	---	PASS
FMO4	2329	broad.mit.edu	37	1	171303694	171303694	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171303694G>C	uc001gho.2	+	8	1189	c.972G>C	c.(970-972)GTG>GTC	p.V324V		NM_002022	NP_002013	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	324					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TTGATGTTGTGATCTTCACTA	0.373													8	98	---	---	---	---	PASS
FMO4	2329	broad.mit.edu	37	1	171303698	171303698	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171303698T>G	uc001gho.2	+	8	1193	c.976T>G	c.(976-978)TTC>GTC	p.F326V		NM_002022	NP_002013	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	326					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TGTTGTGATCTTCACTACAGG	0.363													7	96	---	---	---	---	PASS
RFWD2	64326	broad.mit.edu	37	1	176012899	176012899	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176012899C>A	uc001gku.1	-	13	1733	c.1477G>T	c.(1477-1479)GGC>TGC	p.G493C	RFWD2_uc001gkv.1_Missense_Mutation_p.G469C|RFWD2_uc001gkw.1_Missense_Mutation_p.G253C|RFWD2_uc009wwv.2_Missense_Mutation_p.G292C|RFWD2_uc001gkt.1_Missense_Mutation_p.G332C	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a	493	WD 2.				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						ATAACAGTGCCTTCATAATCA	0.328													7	192	---	---	---	---	PASS
RASAL2	9462	broad.mit.edu	37	1	178425846	178425846	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178425846C>A	uc001glr.2	+	11	1904	c.1779C>A	c.(1777-1779)TCC>TCA	p.S593S	RASAL2_uc001glq.2_Intron|RASAL2_uc009wxc.2_Silent_p.S107S	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	593					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						GTGAAAATTCCTTCCTACAGG	0.468													9	336	---	---	---	---	PASS
IVNS1ABP	10625	broad.mit.edu	37	1	185270621	185270621	+	Silent	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185270621A>C	uc001grl.2	-	9	1463	c.840T>G	c.(838-840)GCT>GCG	p.A280A	IVNS1ABP_uc001gri.2_5'UTR|IVNS1ABP_uc001grj.2_5'UTR|IVNS1ABP_uc009wyj.2_Silent_p.A62A|IVNS1ABP_uc009wyk.2_RNA|IVNS1ABP_uc001grm.2_5'UTR	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	280	Sufficient for AHR interaction and signaling.				interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						TTTGTACTGTAGCATTTGGAG	0.398													37	69	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190195245	190195245	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190195245A>T	uc001gse.1	-	6	1160	c.928T>A	c.(928-930)TGG>AGG	p.W310R	FAM5C_uc010pot.1_Missense_Mutation_p.W208R	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	310						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					TAAGCTTTCCAGGTTTCAGTT	0.368													22	18	---	---	---	---	PASS
CHIT1	1118	broad.mit.edu	37	1	203191413	203191413	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203191413C>A	uc001gzn.2	-	7	742	c.646G>T	c.(646-648)GGC>TGC	p.G216C	FMOD_uc010pqi.1_Intron|CHIT1_uc001gzm.1_RNA|CHIT1_uc009xal.1_Missense_Mutation_p.G7C|CHIT1_uc009xam.1_RNA|CHIT1_uc009xan.1_RNA|CHIT1_uc001gzo.2_Missense_Mutation_p.G207C	NM_003465	NP_003456	Q13231	CHIT1_HUMAN	chitotriosidase precursor	216					chitin catabolic process|immune response|response to bacterium	extracellular space|lysosome	cation binding|chitin binding|endochitinase activity				0						TCCCAAGAGCCATGGAAGTCG	0.562													13	25	---	---	---	---	PASS
LAX1	54900	broad.mit.edu	37	1	203740494	203740494	+	Splice_Site	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203740494G>T	uc001haa.2	+	3	610	c.200_splice	c.e3-1	p.R67_splice	LAX1_uc010pql.1_Splice_Site_p.R51_splice|LAX1_uc001hab.2_Splice_Site	NM_017773	NP_060243	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1 isoform a						B cell activation|immune response|inactivation of MAPK activity|intracellular signal transduction|negative regulation of T cell activation	Golgi apparatus|integral to membrane|plasma membrane	protein kinase binding|SH2 domain binding			central_nervous_system(2)	2	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TTGCCTTGCAGGACAAGTTCC	0.507													7	284	---	---	---	---	PASS
NFASC	23114	broad.mit.edu	37	1	204944555	204944555	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204944555T>C	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AGGTTTCTCTTCCCCCTTCCC	0.547											OREG0014142	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	35	55	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216138829	216138829	+	Intron	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216138829T>G	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CACCTGTGAGTATAAAAAGAT	0.368										HNSCC(13;0.011)			13	71	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216262403	216262403	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216262403T>C	uc001hku.1	-	23	5224	c.4837A>G	c.(4837-4839)ATT>GTT	p.I1613V		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1613	Laminin G-like 1.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGATGCCTAATAGCAATTATT	0.368										HNSCC(13;0.011)			9	104	---	---	---	---	PASS
EPRS	2058	broad.mit.edu	37	1	220179558	220179558	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220179558T>C	uc001hly.1	-	15	2110	c.1840A>G	c.(1840-1842)ACA>GCA	p.T614A	EPRS_uc010puf.1_Missense_Mutation_p.T365A|EPRS_uc001hlz.1_Missense_Mutation_p.T621A|EPRS_uc009xdt.1_Intron	NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase	614	Glutamyl-tRNA synthetase.				glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	AGAGCATGTGTAGTCTCTGCA	0.388													23	69	---	---	---	---	PASS
MIA3	375056	broad.mit.edu	37	1	222835412	222835412	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222835412C>A	uc001hnl.2	+	25	5137	c.5128C>A	c.(5128-5130)CCT>ACT	p.P1710T	MIA3_uc001hnm.2_Missense_Mutation_p.P588T	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1710	Pro-rich.|Cytoplasmic (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		AGTGGACGGGCCTCTACCTCA	0.433													11	59	---	---	---	---	PASS
SUSD4	55061	broad.mit.edu	37	1	223396739	223396739	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223396739G>T	uc001hnx.2	-	7	1930	c.1296C>A	c.(1294-1296)AGC>AGA	p.S432R	SUSD4_uc001hny.3_Missense_Mutation_p.S432R|SUSD4_uc010puw.1_Missense_Mutation_p.S272R	NM_017982	NP_060452	Q5VX71	SUSD4_HUMAN	sushi domain containing 4 isoform a	432	Cytoplasmic (Potential).					integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)		AGCCTGAGACGCTGTCACAGG	0.617													22	15	---	---	---	---	PASS
HIST3H2BB	128312	broad.mit.edu	37	1	228646221	228646221	+	3'UTR	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228646221C>A	uc001hsz.2	+	1					HIST3H2A_uc001hsy.2_5'Flank	NM_175055	NP_778225	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb						nucleosome assembly	nucleosome|nucleus	DNA binding			skin(1)	1		Prostate(94;0.183)				AGGCGTTCCTCGGCGTCCTGA	0.587													5	64	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237991683	237991683	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237991683C>T	uc001hyl.1	+	102	14713	c.14593C>T	c.(14593-14595)CTA>TTA	p.L4865L	RYR2_uc010pyb.1_Silent_p.L298L	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4865	Helical; Name=M10; (Potential).				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AACACCAGGTCTAATTATTGA	0.388													5	14	---	---	---	---	PASS
RGS7	6000	broad.mit.edu	37	1	241031891	241031891	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241031891G>C	uc001hyv.2	-	9	935	c.605C>G	c.(604-606)CCC>CGC	p.P202R	RGS7_uc010pyh.1_Missense_Mutation_p.P176R|RGS7_uc010pyj.1_Missense_Mutation_p.P118R|RGS7_uc001hyu.2_Missense_Mutation_p.P202R|RGS7_uc009xgn.1_Missense_Mutation_p.P149R|RGS7_uc001hyw.2_Missense_Mutation_p.P202R|RGS7_uc001hyt.2_Missense_Mutation_p.P34R	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	202					G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GCTTACCACGGGCCTGTGCAC	0.507													9	135	---	---	---	---	PASS
CNST	163882	broad.mit.edu	37	1	246784903	246784903	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246784903G>T	uc001ibp.2	+	3	930	c.552G>T	c.(550-552)TTG>TTT	p.L184F	CNST_uc001ibo.3_Missense_Mutation_p.L184F	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	184					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						TTGAGCAGTTGGATTCAAGAG	0.453													8	303	---	---	---	---	PASS
NLRP3	114548	broad.mit.edu	37	1	247607428	247607428	+	Nonsense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247607428A>T	uc001icr.2	+	9	2962	c.2824A>T	c.(2824-2826)AAG>TAG	p.K942*	NLRP3_uc001ics.2_Nonsense_Mutation_p.K885*|NLRP3_uc001icu.2_Nonsense_Mutation_p.K942*|NLRP3_uc001icw.2_Nonsense_Mutation_p.K885*|NLRP3_uc001icv.2_Nonsense_Mutation_p.K828*|NLRP3_uc010pyw.1_Nonsense_Mutation_p.K920*	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	942	LRR 8.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding	p.K942N(1)		lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CCCCGACTGCAAGCTTCAGGT	0.507													37	59	---	---	---	---	PASS
OR2T12	127064	broad.mit.edu	37	1	248458889	248458889	+	5'Flank	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248458889C>T	uc010pzj.1	-							NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATAATTTCCCCTGGTGTGATG	0.418													44	75	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525863	248525863	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248525863G>T	uc001ieh.1	+	1	981	c.981G>T	c.(979-981)AAG>AAT	p.K327N		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	327	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTAGGAATAAGGATGTCATGG	0.428													77	92	---	---	---	---	PASS
SNTG2	54221	broad.mit.edu	37	2	1263159	1263159	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1263159G>T	uc002qwq.2	+	13	1151	c.1023G>T	c.(1021-1023)TGG>TGT	p.W341C	SNTG2_uc010ewi.2_Missense_Mutation_p.W214C	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	341	PH.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CATTCGATTGGGTGCGAGCAG	0.393													5	72	---	---	---	---	PASS
TTC15	51112	broad.mit.edu	37	2	3392340	3392340	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3392340A>G	uc002qxm.1	+	2	1152	c.946A>G	c.(946-948)ACG>GCG	p.T316A	TTC15_uc002qxn.1_Missense_Mutation_p.T316A|TTC15_uc010ewm.1_Missense_Mutation_p.T316A|TTC15_uc002qxl.1_Missense_Mutation_p.T316A	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15	316							binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)		CGGCGAGGCTACGCGTGGAGT	0.662													3	4	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15378795	15378795	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15378795G>A	uc002rcc.1	-	45	5766	c.5740C>T	c.(5740-5742)CGT>TGT	p.R1914C	NBAS_uc002rcb.1_5'UTR|NBAS_uc010exl.1_Missense_Mutation_p.R986C|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1914										ovary(2)|liver(1)|skin(1)	4						ATCTCTTTACGGGCTTCCACA	0.368													7	28	---	---	---	---	PASS
SMC6	79677	broad.mit.edu	37	2	17896303	17896303	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17896303G>A	uc002rco.2	-	16	1851	c.1555C>T	c.(1555-1557)CTT>TTT	p.L519F	SMC6_uc010exo.2_Missense_Mutation_p.L519F|SMC6_uc002rcn.2_Missense_Mutation_p.L519F|SMC6_uc002rcp.1_Missense_Mutation_p.L545F|SMC6_uc002rcq.2_Missense_Mutation_p.L545F	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	519	Flexible hinge.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GCCAAAGCAAGTTCTGGGTCC	0.393													67	55	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21227276	21227276	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21227276G>A	uc002red.2	-	28	12080	c.11952C>T	c.(11950-11952)ACC>ACT	p.T3984T		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3984					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	GATGGAGATCGGTGAACGCTG	0.512													10	62	---	---	---	---	PASS
RAB10	10890	broad.mit.edu	37	2	26257592	26257592	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26257592A>T	uc002rgv.2	+	1	864	c.115A>T	c.(115-117)ATT>TTT	p.I39F		NM_016131	NP_057215	P61026	RAB10_HUMAN	ras-related GTP-binding protein RAB10	39	Effector region (By similarity).				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TACTACCTTTATTTCCACCAT	0.493													18	97	---	---	---	---	PASS
SLC30A3	7781	broad.mit.edu	37	2	27481650	27481650	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27481650C>A	uc002rjk.2	-	2	434	c.248G>T	c.(247-249)TGC>TTC	p.C83F	SLC30A3_uc002rjj.2_5'Flank|SLC30A3_uc010ylh.1_Missense_Mutation_p.C78F	NM_003459	NP_003450	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter),	83	Helical; (Potential).				regulation of sequestering of zinc ion	cell junction|integral to plasma membrane|late endosome|membrane fraction|synaptic vesicle membrane	zinc transporting ATPase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGACAAAGCAAACGGCACA	0.612													32	33	---	---	---	---	PASS
FAM179A	165186	broad.mit.edu	37	2	29259412	29259412	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29259412T>C	uc010ezl.2	+	18	2775	c.2424T>C	c.(2422-2424)TTT>TTC	p.F808F	FAM179A_uc010ymm.1_Silent_p.F753F|FAM179A_uc002rmr.3_Silent_p.F335F|FAM179A_uc002rms.1_Silent_p.F106F	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	808							binding			ovary(3)|skin(1)	4						AATAGGTCTTTGATGCTTTCA	0.552													30	21	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29296932	29296932	+	Silent	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29296932T>G	uc002rmt.1	-	1	196	c.196A>C	c.(196-198)AGG>CGG	p.R66R		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	66					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						GTTTGGTTCCTCCTGGGACTT	0.527													18	32	---	---	---	---	PASS
TTC7A	57217	broad.mit.edu	37	2	47273469	47273469	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47273469G>T	uc002rvo.2	+	16	2186	c.1818G>T	c.(1816-1818)AAG>AAT	p.K606N	TTC7A_uc002rvm.2_Missense_Mutation_p.K572N|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Missense_Mutation_p.K606N|TTC7A_uc010fbc.2_Missense_Mutation_p.K252N|TTC7A_uc002rvp.2_Missense_Mutation_p.K487N|TTC7A_uc002rvq.2_Missense_Mutation_p.K346N|TTC7A_uc002rvr.2_Missense_Mutation_p.K55N	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	606							binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TGTTCACCAAGGTGAAGCTGG	0.632													4	27	---	---	---	---	PASS
PSME4	23198	broad.mit.edu	37	2	54175569	54175569	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54175569A>G	uc002rxp.2	-	3	545	c.489T>C	c.(487-489)AAT>AAC	p.N163N	PSME4_uc010yop.1_Silent_p.N49N|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_5'UTR|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	163					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|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|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TAGGAAACCAATTTAATCCTA	0.358													13	84	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54882236	54882236	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54882236A>G	uc002rxu.2	+	28	6101	c.5852A>G	c.(5851-5853)AAT>AGT	p.N1951S	SPTBN1_uc002rxx.2_Missense_Mutation_p.N1938S|SPTBN1_uc002rxy.2_Missense_Mutation_p.N96S|SPTBN1_uc010you.1_5'Flank	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	1951	Spectrin 16.|Interaction with ANK2.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			CTCTTAATGAATAATCATCAA	0.373													16	15	---	---	---	---	PASS
AHSA2	130872	broad.mit.edu	37	2	61413610	61413610	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61413610G>T	uc002sbc.1	+	5	1808	c.222G>T	c.(220-222)TGG>TGT	p.W74C	AHSA2_uc002sbb.1_RNA	NM_152392	NP_689605	Q719I0	AHSA2_HUMAN	AHA1, activator of heat shock 90kDa protein	236					response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)			TCATGAAATGGAGATGTGGGA	0.358													5	66	---	---	---	---	PASS
GMCL1	64395	broad.mit.edu	37	2	70082087	70082087	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70082087C>A	uc002sfu.2	+	9	1274	c.1067C>A	c.(1066-1068)CCT>CAT	p.P356H		NM_178439	NP_848526	Q96IK5	GMCL1_HUMAN	germ cell-less	356					cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3						GCTGTAGTACCTTCAGGTAAG	0.279													6	63	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80136767	80136767	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80136767G>A	uc010ysh.1	+	6	905	c.900G>A	c.(898-900)CGG>CGA	p.R300R	CTNNA2_uc010yse.1_Silent_p.R300R|CTNNA2_uc010ysf.1_Silent_p.R300R|CTNNA2_uc010ysg.1_Silent_p.R300R	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	300					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						CCAGGTTCCGGCCGTCCCTGG	0.597													6	39	---	---	---	---	PASS
KDM3A	55818	broad.mit.edu	37	2	86683959	86683959	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86683959T>A	uc002sri.3	+	7	1040	c.713T>A	c.(712-714)CTG>CAG	p.L238Q	KDM3A_uc010ytj.1_Missense_Mutation_p.L238Q|KDM3A_uc010ytk.1_Missense_Mutation_p.L186Q	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	238					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						GATCCGTCACTGATTCATGTT	0.343													17	16	---	---	---	---	PASS
RPIA	22934	broad.mit.edu	37	2	89028822	89028822	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89028822C>A	uc002ste.2	+	4	470	c.429C>A	c.(427-429)GGC>GGA	p.G143G		NM_144563	NP_653164	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	143					pentose-phosphate shunt, non-oxidative branch	cytosol	ribose-5-phosphate isomerase activity	p.G143D(1)		ovary(1)	1		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				TGCAGTATGGCTTGACCCTCA	0.498													4	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89399590	89399590	+	RNA	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89399590C>A	uc010ytr.1	-	46		c.4855G>T			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		GACTCTGTCTCCTACAGATGC	0.463													84	68	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89399591	89399591	+	RNA	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89399591C>T	uc010ytr.1	-	46		c.4854G>A			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		ACTCTGTCTCCTACAGATGCA	0.463													84	68	---	---	---	---	PASS
ADRA2B	151	broad.mit.edu	37	2	96781011	96781011	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96781011G>A	uc002svi.2	-	1	878	c.878C>T	c.(877-879)CCA>CTA	p.P293L		NM_000682	NP_000673	P18089	ADA2B_HUMAN	alpha-2B-adrenergic receptor	293	Cytoplasmic (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation	integral to plasma membrane	alpha2-adrenergic receptor activity|epinephrine binding|protein binding			ovary(2)|lung(1)	3					Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)	TTCATCCTCTGGAGATGCCCC	0.557													4	8	---	---	---	---	PASS
SNRNP200	23020	broad.mit.edu	37	2	96952549	96952549	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96952549G>T	uc002svu.2	-	28	3792	c.3706C>A	c.(3706-3708)CAT>AAT	p.H1236N	SNRNP200_uc002svt.2_5'Flank|SNRNP200_uc010yuj.1_5'Flank|SNRNP200_uc002svv.1_5'Flank|SNRNP200_uc002svw.1_Missense_Mutation_p.H308N	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1236	SEC63 1.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						AAATACTCATGGTGCAGAATC	0.522													5	81	---	---	---	---	PASS
CNNM3	26505	broad.mit.edu	37	2	97492658	97492658	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97492658T>G	uc002swy.2	+	3	1482	c.1458T>G	c.(1456-1458)GAT>GAG	p.D486E	CNNM3_uc002swz.2_Missense_Mutation_p.D438E	NM_017623	NP_060093	Q8NE01	CNNM3_HUMAN	cyclin M3 isoform 1	486					ion transport	integral to membrane|plasma membrane	protein binding			ovary(1)	1						TGTCTGATGATGAATATAAAG	0.562													9	58	---	---	---	---	PASS
CHST10	9486	broad.mit.edu	37	2	101010038	101010038	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101010038G>A	uc002tam.2	-	7	1099	c.740C>T	c.(739-741)CCG>CTG	p.P247L		NM_004854	NP_004845	O43529	CHSTA_HUMAN	HNK-1 sulfotransferase	247	Lumenal (Potential).				carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1						TCTGTGGTTCGGATCGCCGAG	0.512													19	137	---	---	---	---	PASS
LIMS1	3987	broad.mit.edu	37	2	109300362	109300362	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109300362C>G	uc002teg.2	+	10	1004	c.885C>G	c.(883-885)GAC>GAG	p.D295E	LIMS1_uc002tef.2_Missense_Mutation_p.D307E|LIMS1_uc002teh.2_Missense_Mutation_p.D295E|LIMS1_uc002tei.2_Missense_Mutation_p.D295E|LIMS1_uc002tej.2_Missense_Mutation_p.D332E|LIMS1_uc002tek.3_Missense_Mutation_p.D357E|uc002tel.2_5'Flank	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	295	LIM zinc-binding 5.				cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						TGGAGTTTGACATGAAGCCAG	0.313													7	34	---	---	---	---	PASS
TUBA3E	112714	broad.mit.edu	37	2	130953819	130953819	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130953819A>G	uc002tqv.2	-	2	230	c.129T>C	c.(127-129)GGT>GGC	p.G43G		NM_207312	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	43					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			skin(1)	1	Colorectal(110;0.1)					CGTCCCCGCCACCAATGGTTT	0.562													13	72	---	---	---	---	PASS
POTEE	445582	broad.mit.edu	37	2	131985807	131985807	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131985807G>T	uc002tsn.2	+						PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Intron|POTEE_uc002tsl.2_Intron	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,								ATP binding				0						TCCTATCTCTGTCATTTTAGG	0.338													5	85	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141771263	141771263	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141771263C>A	uc002tvj.1	-	14	3214	c.2242G>T	c.(2242-2244)GGA>TGA	p.G748*	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	748	Extracellular (Potential).|LDL-receptor class B 8.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACATAATTTCCATGATGCGAC	0.383										TSP Lung(27;0.18)			5	61	---	---	---	---	PASS
UPP2	151531	broad.mit.edu	37	2	158974404	158974404	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158974404G>C	uc002tzp.2	+	4	602	c.408G>C	c.(406-408)CGG>CGC	p.R136R	UPP2_uc002tzo.2_Silent_p.R193R	NM_173355	NP_775491	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform a	136					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0						ACCATGCACGGTGCTGCGATG	0.428													15	105	---	---	---	---	PASS
FAP	2191	broad.mit.edu	37	2	163082006	163082006	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163082006C>A	uc002ucd.2	-	4	480	c.272G>T	c.(271-273)AGT>ATT	p.S91I	FAP_uc010zct.1_Missense_Mutation_p.S91I|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Missense_Mutation_p.S58I	NM_004460	NP_004451	Q12884	SEPR_HUMAN	fibroblast activation protein, alpha subunit	91	Extracellular (Potential).				endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3						GGTTCTATTACTCAAAATGGT	0.343													8	37	---	---	---	---	PASS
GCA	25801	broad.mit.edu	37	2	163212953	163212953	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163212953A>T	uc002ucg.2	+	4	444	c.268A>T	c.(268-270)AGT>TGT	p.S90C	GCA_uc010zcu.1_Missense_Mutation_p.S71C	NM_012198	NP_036330	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	90	EF-hand 2.				cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0						TACAGCCTTCAGTTTGGAAAC	0.284													36	14	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166892733	166892733	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166892733C>A	uc010zcz.1	-	16	3239	c.3221G>T	c.(3220-3222)GGT>GTT	p.G1074V	SCN1A_uc002udo.3_Missense_Mutation_p.G954V|SCN1A_uc010fpk.2_Missense_Mutation_p.G926V	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1085						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)	AGTTCCTATACCACTTGTAGT	0.353													36	16	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098945	178098945	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098945G>C	uc002ulh.3	-	2	655	c.100C>G	c.(100-102)CGA>GGA	p.R34G	NFE2L2_uc002ulg.3_Missense_Mutation_p.R18G|NFE2L2_uc010zfa.1_Missense_Mutation_p.R18G|NFE2L2_uc002uli.3_Missense_Mutation_p.R18G|NFE2L2_uc010fra.2_Missense_Mutation_p.R18G|NFE2L2_uc010frb.2_Missense_Mutation_p.R18G	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	34					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AATACTTCTCGACTTACTCCA	0.368			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			23	15	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179582667	179582667	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179582667C>A	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.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)			ACAACACCATCACCTTTGATA	0.398													98	62	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179592919	179592919	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179592919T>G	uc010zfg.1	-	64	16124	c.15900A>C	c.(15898-15900)GAA>GAC	p.E5300D	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.E1961D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6227							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)			TATCTTCTAATTCCAGATTAT	0.378													11	29	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179610662	179610662	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179610662T>G	uc002unb.2	-	46	16689	c.16465A>C	c.(16465-16467)AGT>CGT	p.S5489R	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCATTAAACTGCTTAAAGTC	0.403													30	69	---	---	---	---	PASS
PDE1A	5136	broad.mit.edu	37	2	183387000	183387000	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183387000C>A	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)			AGAGCATACTCACATTCCTTT	0.408													34	20	---	---	---	---	PASS
ZC3H15	55854	broad.mit.edu	37	2	187368929	187368929	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187368929A>G	uc002upo.2	+	6	930	c.705A>G	c.(703-705)CTA>CTG	p.L235L		NM_018471	NP_060941	Q8WU90	ZC3HF_HUMAN	erythropoietin 4 immediate early response	235	Potential.					cytoplasm|nucleolus|plasma membrane	nucleic acid binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TAGAAGATCTAATTGAGAGAG	0.333													35	24	---	---	---	---	PASS
TMEFF2	23671	broad.mit.edu	37	2	192815124	192815124	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192815124G>T	uc002utc.2	-	10	1432	c.1038C>A	c.(1036-1038)CCC>CCA	p.P346P		NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two	346	Cytoplasmic (Potential).					extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TGTTGCTTCTGGGGCATTTCC	0.408													11	48	---	---	---	---	PASS
HSPD1	3329	broad.mit.edu	37	2	198358104	198358104	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198358104C>A	uc002uui.2	-	7	950	c.813G>T	c.(811-813)TTG>TTT	p.L271F	HSPD1_uc002uuj.2_Missense_Mutation_p.L269F|HSPD1_uc010zgx.1_Missense_Mutation_p.L262F|HSPD1_uc010fsm.2_Missense_Mutation_p.L82F|HSPD1_uc002uuk.2_Missense_Mutation_p.L271F	NM_002156	NP_002147	P10809	CH60_HUMAN	chaperonin	271					'de novo' protein folding|activation of caspase activity|B cell cytokine production|B cell proliferation|chaperone-mediated protein complex assembly|interspecies interaction between organisms|isotype switching to IgG isotypes|MyD88-dependent toll-like receptor signaling pathway|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of interferon-alpha production|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of macrophage activation|positive regulation of T cell activation|positive regulation of T cell mediated immune response to tumor cell|protein maturation|protein refolding|protein stabilization|response to unfolded protein|T cell activation	cell surface|coated pit|coated vesicle|cytosol|early endosome|extracellular space|lipopolysaccharide receptor complex|mitochondrial inner membrane|mitochondrial matrix|stored secretory granule	ATP binding|ATPase activity|cell surface binding|chaperone binding|DNA replication origin binding|lipopolysaccharide binding|p53 binding|single-stranded DNA binding				0			Epithelial(96;0.225)			CGATTATGACCAAAGGCTTAC	0.388													5	96	---	---	---	---	PASS
NDUFS1	4719	broad.mit.edu	37	2	207011634	207011634	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207011634C>T	uc002vbe.2	-	8	857	c.730G>A	c.(730-732)GAA>AAA	p.E244K	NDUFS1_uc010ziq.1_Missense_Mutation_p.E258K|NDUFS1_uc010zir.1_Missense_Mutation_p.E208K|NDUFS1_uc010zis.1_Missense_Mutation_p.E187K|NDUFS1_uc010zit.1_Missense_Mutation_p.E133K|NDUFS1_uc010ziu.1_Missense_Mutation_p.E128K	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,	244					apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	TACCTTGTTTCCCAAGGCCGG	0.363													10	59	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219895545	219895545	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219895545G>A	uc002vjl.1	-	9	1111	c.1027C>T	c.(1027-1029)CAG>TAG	p.Q343*	CCDC108_uc010fwa.1_5'Flank|CCDC108_uc010zkp.1_Nonsense_Mutation_p.Q332*|CCDC108_uc010zkq.1_Nonsense_Mutation_p.Q278*	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	343						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCAGCAGCTGGGCGCACTTG	0.637													14	20	---	---	---	---	PASS
PAX3	5077	broad.mit.edu	37	2	223085966	223085966	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223085966A>G	uc010fwo.2	-	6	1299	c.933T>C	c.(931-933)TCT>TCC	p.S311S	PAX3_uc002vmt.1_Silent_p.S311S|PAX3_uc002vmy.1_Silent_p.S310S|PAX3_uc002vmv.1_Silent_p.S311S|PAX3_uc002vmw.1_Silent_p.S311S|PAX3_uc002vmx.1_Silent_p.S311S	NM_181457	NP_852122	P23760	PAX3_HUMAN	paired box 3 isoform PAX3	311					apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGGCTGGTAAGAGGTCTCCG	0.507			T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						59	144	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225638050	225638050	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225638050G>C	uc010fwz.1	-	53	6267	c.6028C>G	c.(6028-6030)CCC>GCC	p.P2010A	DOCK10_uc002vob.2_Missense_Mutation_p.P2004A|DOCK10_uc002voa.2_Missense_Mutation_p.P666A	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2010	DHR-2.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTCACGTAGGGGAACAGGTGA	0.438													28	22	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228846483	228846483	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228846483G>T	uc002vpq.2	-	12	5100	c.5053C>A	c.(5053-5055)CAG>AAG	p.Q1685K	SPHKAP_uc002vpp.2_Missense_Mutation_p.Q1656K|SPHKAP_uc010zlx.1_3'UTR	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1685						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)		CCATCCTTCTGCTCCTCATGC	0.448													15	27	---	---	---	---	PASS
SYN2	6854	broad.mit.edu	37	3	12187261	12187261	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12187261G>T	uc003bwm.2	+	8	774	c.610G>T	c.(610-612)GGT>TGT	p.G204C	SYN2_uc003bwl.1_Missense_Mutation_p.G204C	NM_133625	NP_598328	Q92777	SYN2_HUMAN	synapsin II isoform IIa	204					neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2						CCTGATCATTGGTATGCAGTA	0.557													6	62	---	---	---	---	PASS
AZI2	64343	broad.mit.edu	37	3	28379458	28379458	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28379458G>T	uc003ceb.2	-	4	941	c.409C>A	c.(409-411)CAG>AAG	p.Q137K	AZI2_uc003cec.2_Missense_Mutation_p.Q25K|AZI2_uc003ced.2_Missense_Mutation_p.Q137K|AZI2_uc003cee.3_Missense_Mutation_p.Q137K|AZI2_uc003ceg.2_Missense_Mutation_p.Q137K|AZI2_uc011axd.1_Missense_Mutation_p.Q137K|AZI2_uc003cef.2_Missense_Mutation_p.Q137K	NM_022461	NP_071906	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2 isoform a	137	Potential.					mitochondrion|plasma membrane				ovary(2)	2						GTCCTCAGCTGGAGGAGTTCT	0.333													4	21	---	---	---	---	PASS
OSBPL10	114884	broad.mit.edu	37	3	31725157	31725157	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31725157G>C	uc003cev.2	-	9	2076	c.1695C>G	c.(1693-1695)GGC>GGG	p.G565G	OSBPL10_uc003ceu.1_Silent_p.G322G|OSBPL10_uc011axf.1_Silent_p.G501G	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	565					lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		CCACGGACATGCCCATGAACT	0.488													44	12	---	---	---	---	PASS
TRANK1	9881	broad.mit.edu	37	3	36872547	36872547	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36872547C>A	uc003cgj.2	-	12	7047	c.6745G>T	c.(6745-6747)GAG>TAG	p.E2249*		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	2799					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2						TCCACCTTCTCGTGGAAAAAT	0.532													4	101	---	---	---	---	PASS
OXSR1	9943	broad.mit.edu	37	3	38263138	38263138	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38263138T>C	uc003chy.2	+	6	902	c.560T>C	c.(559-561)GTT>GCT	p.V187A	OXSR1_uc010hhb.2_Missense_Mutation_p.V121A|OXSR1_uc010hha.1_Missense_Mutation_p.V119A	NM_005109	NP_005100	O95747	OXSR1_HUMAN	oxidative-stress responsive 1	187	Protein kinase.				intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAGACCTTTGTTGGCACCCCT	0.383													16	63	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38888793	38888793	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38888793T>C	uc011ays.1	-	26	4967	c.4768A>G	c.(4768-4770)ATC>GTC	p.I1590V		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1590	IV.|Helical; Name=S6 of repeat IV; (By similarity).				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	AGAAAGGAGATGATAATGTAA	0.433													11	36	---	---	---	---	PASS
MIR135A1	406925	broad.mit.edu	37	3	52328291	52328291	+	RNA	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52328291T>A	hsa-mir-135a-1|MI0000452	-			c.34T>A			GLYCTK_uc003ddm.2_RNA|GLYCTK_uc003ddo.2_3'UTR|GLYCTK_uc003ddn.2_RNA|GLYCTK_uc003ddr.2_3'UTR|uc010hmf.2_RNA																	0						TAGAATCACATAGGAATAAAA	0.597													7	44	---	---	---	---	PASS
KBTBD8	84541	broad.mit.edu	37	3	67054263	67054263	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67054263T>G	uc003dmy.2	+	3	925	c.872T>G	c.(871-873)TTT>TGT	p.F291C	KBTBD8_uc011bfv.1_Intron	NM_032505	NP_115894	Q8NFY9	KBTB8_HUMAN	T-cell activation kelch repeat protein	291										ovary(2)|large_intestine(1)|breast(1)	4		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		ATCATATGTTTTGATGCTGCC	0.443													17	54	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	79174687	79174687	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79174687G>T	uc003dqe.2	-	3	299	c.91C>A	c.(91-93)CCT>ACT	p.P31T		NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	31	Extracellular (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ACATCTTCAGGGTCTGTCGGA	0.502													10	7	---	---	---	---	PASS
ZNF654	55279	broad.mit.edu	37	3	88190171	88190171	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88190171C>G	uc003dqv.2	+	1	1910	c.1711C>G	c.(1711-1713)CTC>GTC	p.L571V	CGGBP1_uc003dqu.2_5'UTR	NM_018293	NP_060763	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	571					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		ATGTCAGACACTCTTTGGATT	0.348													8	26	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108300321	108300321	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108300321C>A	uc003dxb.3	-	5	759	c.490G>T	c.(490-492)GGA>TGA	p.G164*	KIAA1524_uc003dxc.1_Nonsense_Mutation_p.G5*|KIAA1524_uc010hpw.1_Nonsense_Mutation_p.G5*	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	164						cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						GCCAATAATCCTAGACAAGGC	0.289													16	23	---	---	---	---	PASS
POPDC2	64091	broad.mit.edu	37	3	119367422	119367422	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119367422G>A	uc003ecx.1	-	3	828	c.694C>T	c.(694-696)CTC>TTC	p.L232F	POPDC2_uc010hqw.1_Missense_Mutation_p.L232F|POPDC2_uc003ecy.1_Missense_Mutation_p.L50F	NM_022135	NP_071418	Q9HBU9	POPD2_HUMAN	popeye protein 2	232						integral to membrane				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.242)		GCCGAGAAGAGGCAGGAGATG	0.507													8	37	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121417220	121417220	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121417220T>C	uc003eei.3	-	13	2261	c.2135A>G	c.(2134-2136)GAT>GGT	p.D712G	GOLGB1_uc010hrc.2_Missense_Mutation_p.D717G|GOLGB1_uc003eej.3_Missense_Mutation_p.D678G|GOLGB1_uc011bjm.1_Missense_Mutation_p.D598G|GOLGB1_uc010hrd.1_Missense_Mutation_p.D676G	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	712	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		AGCTTTCTCATCTAAATTTTT	0.363													18	25	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123382998	123382998	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123382998C>T	uc003ego.2	-	23	4221	c.3939G>A	c.(3937-3939)GAG>GAA	p.E1313E	MYLK_uc010hrr.2_5'UTR|MYLK_uc011bjv.1_Silent_p.E113E|MYLK_uc011bjw.1_Silent_p.E1313E|MYLK_uc003egp.2_Silent_p.E1244E|MYLK_uc003egq.2_Silent_p.E1313E|MYLK_uc003egr.2_Silent_p.E1244E|MYLK_uc003egs.2_Silent_p.E1137E	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1313	Actin-binding (calcium/calmodulin- insensitive) (By similarity).|Ig-like C2-type 8.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CCAGCTTGTTCTCCACCAGCA	0.632													12	60	---	---	---	---	PASS
EEFSEC	60678	broad.mit.edu	37	3	128060451	128060451	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128060451G>A	uc003eki.2	+	5	1200	c.1162G>A	c.(1162-1164)GTG>ATG	p.V388M	EEFSEC_uc003ekj.2_Missense_Mutation_p.V333M	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,	388						cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						GACACCAGCAGTGACAGACAA	0.537													9	18	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140281693	140281693	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140281693C>T	uc003etn.2	+	14	2443	c.2253C>T	c.(2251-2253)CAC>CAT	p.H751H		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	751	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						TGCTACATCACATCCGCTACC	0.552										HNSCC(16;0.037)			5	21	---	---	---	---	PASS
PAQR9	344838	broad.mit.edu	37	3	142681705	142681705	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142681705G>A	uc003evg.2	-	1	474	c.474C>T	c.(472-474)TAC>TAT	p.Y158Y	PAQR9_uc003evf.1_5'Flank	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	158	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						TGATGGACGCGTAGTCCAGGT	0.612													6	14	---	---	---	---	PASS
CPA3	1359	broad.mit.edu	37	3	148614379	148614379	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148614379G>T	uc003ewm.2	+	11	1191	c.1139G>T	c.(1138-1140)CGA>CTA	p.R380L		NM_001870	NP_001861	P15088	CBPA3_HUMAN	carboxypeptidase A3 precursor	380					proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TTTGAGCTCCGAGATAAAGGC	0.418													4	76	---	---	---	---	PASS
GFM1	85476	broad.mit.edu	37	3	158363992	158363992	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158363992C>A	uc003fce.2	+	3	380	c.273C>A	c.(271-273)TCC>TCA	p.S91S	GFM1_uc003fcd.2_Silent_p.S91S|GFM1_uc003fcf.2_RNA|GFM1_uc003fcg.2_Silent_p.S3S	NM_024996	NP_079272	Q96RP9	EFGM_HUMAN	G elongation factor, mitochondrial 1 precursor	91					mitochondrial translational elongation	mitochondrion	GTP binding|GTPase activity|translation elongation factor activity			ovary(3)|central_nervous_system(1)	4			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TCATGGATTCCATGGAACTAG	0.413													5	76	---	---	---	---	PASS
SERPINI2	5276	broad.mit.edu	37	3	167184891	167184891	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167184891T>C	uc003fer.1	-	2	488	c.430A>G	c.(430-432)AAG>GAG	p.K144E	SERPINI2_uc003fes.1_Missense_Mutation_p.K154E|SERPINI2_uc003fet.1_Missense_Mutation_p.K144E	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	144					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						GCACAAGCCTTTGCATCTTGA	0.358													9	46	---	---	---	---	PASS
DCUN1D1	54165	broad.mit.edu	37	3	182679132	182679132	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182679132T>C	uc003fld.1	-	4	451	c.402A>G	c.(400-402)ATA>ATG	p.I134M	DCUN1D1_uc011bqn.1_Translation_Start_Site	NM_020640	NP_065691	Q96GG9	DCNL1_HUMAN	RP42 homolog	134	DCUN1.			I -> T (in Ref. 2; AAL78673).		ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TTAGTTTTTCTATGCTGTCAC	0.308													105	350	---	---	---	---	PASS
EPHB3	2049	broad.mit.edu	37	3	184298901	184298901	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184298901A>G	uc003foz.2	+	14	3117	c.2680A>G	c.(2680-2682)AAG>GAG	p.K894E		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	894	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TACCCTGGACAAGCTCATCCG	0.592													43	117	---	---	---	---	PASS
VPS8	23355	broad.mit.edu	37	3	184612617	184612617	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184612617G>T	uc003fpb.1	+	22	2073	c.1902G>T	c.(1900-1902)ATG>ATT	p.M634I	VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Missense_Mutation_p.M63I	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	636							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)			CCCAAGTAATGAAAGACTTGA	0.358													13	32	---	---	---	---	PASS
ZDHHC19	131540	broad.mit.edu	37	3	195937539	195937539	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195937539G>T	uc003fwc.2	-	2	330	c.216C>A	c.(214-216)ACC>ACA	p.T72T	ZDHHC19_uc010hzz.2_RNA|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_RNA	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19	72	Helical; (Potential).					integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GACTGAAGAAGGTAAGGACAA	0.557													5	47	---	---	---	---	PASS
ZNF595	152687	broad.mit.edu	37	4	59313	59313	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59313G>T	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TGATAAATATGTGTTTTCAGG	0.388													16	230	---	---	---	---	PASS
SLC34A2	10568	broad.mit.edu	37	4	25677955	25677955	+	Missense_Mutation	SNP	C	T	T	rs115500754	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25677955C>T	uc003grr.2	+	13	1738	c.1657C>T	c.(1657-1659)CGG>TGG	p.R553W	SLC34A2_uc003grs.2_Missense_Mutation_p.R552W|SLC34A2_uc010iev.2_Missense_Mutation_p.R552W	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	553	Helical; Name=M8; (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)				GGCCGGCTGGCGGGTGCTGGT	0.597													13	38	---	---	---	---	PASS
ARAP2	116984	broad.mit.edu	37	4	36093640	36093640	+	Missense_Mutation	SNP	G	A	A	rs143499964		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36093640G>A	uc003gsq.1	-	28	4626	c.4288C>T	c.(4288-4290)CGG>TGG	p.R1430W		NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1430					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						AGTGTACTCCGGTCTGTAAAG	0.308													14	37	---	---	---	---	PASS
WDR19	57728	broad.mit.edu	37	4	39241945	39241945	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39241945T>C	uc003gtv.2	+	21	2566	c.2412T>C	c.(2410-2412)GGT>GGC	p.G804G	WDR19_uc011byi.1_Silent_p.G644G|WDR19_uc003gtw.1_Silent_p.G401G	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	804	TPR 2.				cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						GAATAACAGGTGATAATAAGG	0.249													5	2	---	---	---	---	PASS
PDS5A	23244	broad.mit.edu	37	4	39878748	39878748	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39878748G>T	uc003guv.3	-	19	2558	c.2018C>A	c.(2017-2019)TCG>TAG	p.S673*	PDS5A_uc010ifo.2_Nonsense_Mutation_p.S633*	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	673					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						AGAGTGGAACGAGGTAGGATG	0.373													5	191	---	---	---	---	PASS
RHOH	399	broad.mit.edu	37	4	40245213	40245213	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40245213G>A	uc003guz.2	+	3	931	c.207G>A	c.(205-207)CGG>CGA	p.R69R		NM_004310	NP_004301	Q15669	RHOH_HUMAN	ras homolog gene family, member H precursor	69					negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation	cytosol|mitochondrion|plasma membrane	GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding			ovary(1)|lung(1)	2						GAAGCATCCGGCCCCTGTCCT	0.542													8	46	---	---	---	---	PASS
GRXCR1	389207	broad.mit.edu	37	4	42965024	42965024	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42965024G>A	uc003gwt.2	+	2	500	c.500G>A	c.(499-501)CGC>CAC	p.R167H		NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	167	Glutaredoxin.				cell redox homeostasis|inner ear receptor stereocilium organization|sensory perception of sound|vestibular receptor cell development	kinocilium|stereocilium	electron carrier activity|protein disulfide oxidoreductase activity			ovary(1)	1						CAAAACCATCGCGTAAAATTT	0.428													68	233	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46307592	46307592	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46307592G>T	uc003gxc.3	-	6	1369	c.696C>A	c.(694-696)TCC>TCA	p.S232S	GABRA2_uc010igc.2_Silent_p.S232S|GABRA2_uc011bzc.1_Silent_p.S177S|GABRA2_uc003gxe.2_Silent_p.S232S	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	232	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	AACCTGTACTGGATTTAATTG	0.373													5	94	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62542559	62542559	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62542559C>A	uc010ihh.2	+	3	458	c.285C>A	c.(283-285)ACC>ACA	p.T95T	LPHN3_uc003hcq.3_Silent_p.T95T|LPHN3_uc010ihg.1_Silent_p.T163T	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	95	SUEL-type lectin.|Extracellular (Potential).				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						ATAACAGAACCCAGTGTGCAG	0.373													54	105	---	---	---	---	PASS
TMPRSS11B	132724	broad.mit.edu	37	4	69100335	69100335	+	Missense_Mutation	SNP	A	T	T	rs138592272		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69100335A>T	uc003hdw.3	-	5	451	c.315T>A	c.(313-315)AAT>AAA	p.N105K		NM_182502	NP_872308	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	105	SEA.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						AACCATTGGCATTAGGCCTAG	0.333													26	23	---	---	---	---	PASS
SDAD1	55153	broad.mit.edu	37	4	76911921	76911921	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76911921G>C	uc003hje.3	-	1	193	c.74C>G	c.(73-75)CCG>CGG	p.P25R	SDAD1_uc003hjf.3_5'UTR|SDAD1_uc011cbr.1_Missense_Mutation_p.P25R	NM_018115	NP_060585	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	25					protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GATGTAGGCCGGCGGGTCTCG	0.597													32	42	---	---	---	---	PASS
SYNPO2	171024	broad.mit.edu	37	4	119952527	119952527	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119952527C>A	uc003icm.3	+	4	2793	c.2597C>A	c.(2596-2598)CCA>CAA	p.P866Q	SYNPO2_uc010ina.2_Missense_Mutation_p.P866Q|SYNPO2_uc010inb.2_Missense_Mutation_p.P866Q|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Missense_Mutation_p.P794Q	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b	866						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2						AATGAGCTTCCAGGAATGAGT	0.527													9	61	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123260427	123260427	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123260427C>A	uc003ieh.2	+	70	12261	c.12216C>A	c.(12214-12216)TCC>TCA	p.S4072S	KIAA1109_uc003iem.2_Silent_p.S428S|KIAA1109_uc003ien.2_Silent_p.S6S	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	4072					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						AGCTGCCATCCCTGGATTTGG	0.423													5	50	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151749635	151749635	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151749635G>T	uc010ipj.2	-	30	5342	c.4868C>A	c.(4867-4869)CCT>CAT	p.P1623H	LRBA_uc003ilt.3_Missense_Mutation_p.P282H|LRBA_uc003ilu.3_Missense_Mutation_p.P1623H	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1623						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TGCTGTGTGAGGAGTTACTTC	0.483													6	142	---	---	---	---	PASS
NPY1R	4886	broad.mit.edu	37	4	164247530	164247530	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164247530C>A	uc003iqm.1	-	2	443	c.177G>T	c.(175-177)CTG>CTT	p.L59L	NPY1R_uc011cjj.1_Intron	NM_000909	NP_000900	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	59	Helical; Name=1; (Potential).				inhibition of adenylate cyclase activity by G-protein signaling pathway|outflow tract morphogenesis	integral to plasma membrane	protein binding			lung(1)|pancreas(1)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGATCAAGGCCAGGTTTCCAG	0.408													45	34	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897894	175897894	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175897894A>T	uc003iuc.2	+	5	1888	c.1218A>T	c.(1216-1218)GAA>GAT	p.E406D	ADAM29_uc003iud.2_Missense_Mutation_p.E406D|ADAM29_uc010irr.2_Missense_Mutation_p.E406D|ADAM29_uc011cki.1_Missense_Mutation_p.E406D	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	406	Disintegrin.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GTGTTGTTGAAGAAGGAGAAG	0.413													10	75	---	---	---	---	PASS
VEGFC	7424	broad.mit.edu	37	4	177608422	177608422	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177608422G>T	uc003ius.1	-	6	1494	c.1064C>A	c.(1063-1065)CCT>CAT	p.P355H		NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	355	4 X 16 AA repeats of C-X(10)-C-X-C- X(1,3)-C.|4.				angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		ACATTTTCCAGGATTTAGGGG	0.438													5	106	---	---	---	---	PASS
C4orf41	60684	broad.mit.edu	37	4	184585192	184585192	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184585192G>T	uc003ivx.2	+	2	348	c.172G>T	c.(172-174)GGT>TGT	p.G58C	C4orf41_uc003ivw.2_Missense_Mutation_p.G58C|C4orf41_uc010isc.2_Intron	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	58											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;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)		GGTGCTCCCAGGTGACCATGA	0.463													5	41	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13721111	13721111	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13721111T>C	uc003jfd.2	-	71	12319	c.12277A>G	c.(12277-12279)AAC>GAC	p.N4093D	DNAH5_uc003jfc.2_Missense_Mutation_p.N261D	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4093	AAA 6 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					AGCCTTACGTTCGCCATGGTC	0.418									Kartagener_syndrome				8	53	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13913947	13913947	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13913947C>T	uc003jfd.2	-	11	1483	c.1441G>A	c.(1441-1443)GCC>ACC	p.A481T	DNAH5_uc003jfe.1_RNA	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	481	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					ATTATCTTGGCAAGGCGTCGG	0.368									Kartagener_syndrome				8	56	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19747097	19747097	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747097G>C	uc003jgc.2	-	3	854	c.477C>G	c.(475-477)TTC>TTG	p.F159L	CDH18_uc003jgd.2_Missense_Mutation_p.F159L|CDH18_uc011cnm.1_Missense_Mutation_p.F159L	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	159	Extracellular (Potential).|Cadherin 1.				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)					GTCCATCTGTGAATTTTGGAG	0.348													9	84	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24488018	24488018	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24488018G>T	uc003jgr.1	-	12	2453	c.2121C>A	c.(2119-2121)AAC>AAA	p.N707K	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	707	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		GGACGTCCGTGTTATCTGGAG	0.483										HNSCC(23;0.051)			11	49	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24488077	24488077	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24488077G>T	uc003jgr.1	-	12	2394	c.2062C>A	c.(2062-2064)CGA>AGA	p.R688R	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	688	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		ATAATATCTCGCCGGAGCTTT	0.483										HNSCC(23;0.051)			25	17	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24509858	24509858	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24509858C>T	uc003jgr.1	-	7	1405	c.1073G>A	c.(1072-1074)CGT>CAT	p.R358H	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	358	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		GTAATAAAAACGGGGATCTAC	0.363										HNSCC(23;0.051)			25	24	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32074686	32074686	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32074686A>C	uc003jhl.2	+	18	3862	c.3474A>C	c.(3472-3474)AGA>AGC	p.R1158S	PDZD2_uc003jhm.2_Missense_Mutation_p.R1158S|PDZD2_uc011cnx.1_Missense_Mutation_p.R984S	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1158					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						TGGACTCGAGAGTCCAGGCCA	0.547													18	10	---	---	---	---	PASS
IL7R	3575	broad.mit.edu	37	5	35876119	35876119	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35876119T>A	uc003jjs.2	+	8	1000	c.911T>A	c.(910-912)CTG>CAG	p.L304Q	IL7R_uc011cop.1_RNA	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	304	Cytoplasmic (Potential).				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			GAAAGTTTCCTGGACTGCCAG	0.408													6	60	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36035961	36035961	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36035961G>T	uc003jjz.1	-	7	1504	c.1411C>A	c.(1411-1413)CTC>ATC	p.L471I	UGT3A2_uc011cos.1_Missense_Mutation_p.L437I|UGT3A2_uc011cot.1_Missense_Mutation_p.L169I	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	471	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAGGGCTTGAGGTGCGTCGCG	0.617													4	21	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36122985	36122985	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36122985G>T	uc003jkb.1	-	8	1316	c.901C>A	c.(901-903)CCA>ACA	p.P301T		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	301	Cytoplasmic (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTTTCACTTGGATAGATACTA	0.274													4	23	---	---	---	---	PASS
C5orf33	133686	broad.mit.edu	37	5	36226629	36226629	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36226629T>A	uc003jkf.3	-	3	426	c.426A>T	c.(424-426)AGA>AGT	p.R142S	C5orf33_uc010iux.2_5'Flank|C5orf33_uc003jkg.3_5'UTR|C5orf33_uc011cov.1_5'UTR	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1	142							NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATCATATTCTCTCCTCTTTA	0.348													61	44	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37000926	37000926	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37000926G>A	uc003jkl.3	+	13	4009	c.3510G>A	c.(3508-3510)AGG>AGA	p.R1170R	NIPBL_uc003jkk.3_Silent_p.R1170R	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1170					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)			TAGTTGCTAGGAAAATGAAGA	0.294													34	22	---	---	---	---	PASS
FYB	2533	broad.mit.edu	37	5	39202039	39202039	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39202039G>A	uc003jls.2	-	1	1091	c.1024C>T	c.(1024-1026)CCG>TCG	p.P342S	FYB_uc003jlt.2_Missense_Mutation_p.P342S|FYB_uc003jlu.2_Missense_Mutation_p.P342S|FYB_uc011cpl.1_Missense_Mutation_p.P352S	NM_199335	NP_955367	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 2	342					cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)			TTCTGTTTCGGGGTGGCTGAA	0.532													7	73	---	---	---	---	PASS
HTR1A	3350	broad.mit.edu	37	5	63257447	63257447	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257447T>A	uc011cqt.1	-	1	100	c.100A>T	c.(100-102)AGC>TGC	p.S34C		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	34	Extracellular (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	ACTTGGTAGCTGACGGTCACG	0.617													10	29	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70805959	70805959	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70805959G>A	uc003kbp.1	+	17	3303	c.3040G>A	c.(3040-3042)GCA>ACA	p.A1014T	BDP1_uc003kbn.1_Missense_Mutation_p.A1014T|BDP1_uc003kbo.2_Missense_Mutation_p.A1014T	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1014	4.|9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AGATTTGAACGCAACTGGAAG	0.428													14	72	---	---	---	---	PASS
MEF2C	4208	broad.mit.edu	37	5	88119587	88119587	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88119587G>C	uc003kjj.2	-	2	692	c.19C>G	c.(19-21)CAG>GAG	p.Q7E	MEF2C_uc003kji.2_Missense_Mutation_p.Q7E|MEF2C_uc003kjk.2_Missense_Mutation_p.Q7E|MEF2C_uc003kjm.2_Missense_Mutation_p.Q7E|MEF2C_uc003kjl.2_Missense_Mutation_p.Q7E	NM_002397	NP_002388	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C isoform 1	7	Lys-rich (basic).|MADS-box.				apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		CTCGTAATCTGAATCTTTTTT	0.343										HNSCC(66;0.2)			105	44	---	---	---	---	PASS
SLC22A5	6584	broad.mit.edu	37	5	131724606	131724606	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131724606C>A	uc003kww.3	+						SLC22A5_uc003kwx.3_Intron|SLC22A5_uc010jdr.1_Intron	NM_003060	NP_003051	O76082	S22A5_HUMAN	solute carrier family 22 member 5						positive regulation of intestinal epithelial structure maintenance|quorum sensing involved in interaction with host|sodium ion transport|sodium-dependent organic cation transport	apical plasma membrane|brush border membrane|integral to membrane	ATP binding|carnitine transporter activity|PDZ domain binding|symporter activity				0		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	TGATGTTGTTCCTGCAGTTAC	0.463											OREG0003454	type=REGULATORY REGION|Gene=SLC22A5|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	23	---	---	---	---	PASS
HARS	3035	broad.mit.edu	37	5	140058610	140058610	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140058610G>T	uc003lgv.2	-	5	581	c.499C>A	c.(499-501)CGA>AGA	p.R167R	HARS_uc003lgu.2_Silent_p.R98R|HARS_uc011czm.1_Silent_p.R127R|HARS_uc003lgw.2_Intron|HARS_uc011czn.1_Intron|HARS_uc010jfu.2_Silent_p.R167R|HARS_uc011czo.1_Intron|HARS_uc011czp.1_Intron|HARS_uc011czq.1_Intron	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	167					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)	TCCCGGTATCGGCCACGGGTC	0.493													3	16	---	---	---	---	PASS
FAM114A2	10827	broad.mit.edu	37	5	153409093	153409093	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153409093C>A	uc003lvb.2	-	5	1039	c.451G>T	c.(451-453)GCA>TCA	p.A151S	FAM114A2_uc003lvc.2_Missense_Mutation_p.A151S|FAM114A2_uc003lvd.2_Missense_Mutation_p.A151S|FAM114A2_uc003lve.2_5'UTR|FAM114A2_uc011dda.1_Missense_Mutation_p.A81S	NM_018691	NP_061161	Q9NRY5	F1142_HUMAN	hypothetical protein LOC10827	151							purine nucleotide binding				0						ACACCAAATGCCCCAGCCACT	0.448													8	10	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160097667	160097667	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160097667G>T	uc003lym.1	-	7	1325	c.478C>A	c.(478-480)CAG>AAG	p.Q160K	ATP10B_uc003lyp.2_Missense_Mutation_p.Q160K|ATP10B_uc011deg.1_Missense_Mutation_p.Q204K|ATP10B_uc003lyo.2_Missense_Mutation_p.Q132K	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	160	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)			ACATAGGTCTGCTCTTTTCTT	0.458													24	18	---	---	---	---	PASS
HIST1H3I	8354	broad.mit.edu	37	6	27840015	27840015	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27840015G>A	uc003njy.2	-	1	85	c.79C>T	c.(79-81)CGC>TGC	p.R27C		NM_003533	NP_003524	P68431	H31_HUMAN	histone cluster 1, H3i	27					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1						GCGCTCTTGCGAGCCGCCTTG	0.667													4	13	---	---	---	---	PASS
ZKSCAN3	80317	broad.mit.edu	37	6	28327630	28327630	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28327630G>T	uc003nle.3	+	2	483	c.267G>T	c.(265-267)CTG>CTT	p.L89L	ZKSCAN3_uc010jrc.2_Silent_p.L89L|ZKSCAN3_uc003nlf.3_Intron	NM_024493	NP_077819	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	89	SCAN box.				positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	chromatin binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						TGGAGCTGCTGGTGCTGGAGC	0.652													5	22	---	---	---	---	PASS
WDR46	9277	broad.mit.edu	37	6	33255475	33255475	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33255475C>T	uc003ods.2	-	7	688	c.644G>A	c.(643-645)CGC>CAC	p.R215H	WDR46_uc011dra.1_Missense_Mutation_p.R161H|WDR46_uc010juo.1_RNA|PFDN6_uc003odt.1_5'Flank|PFDN6_uc010jup.1_5'Flank	NM_005452	NP_005443	O15213	WDR46_HUMAN	WD repeat domain 46 isoform 1	215	WD 1.										0						ATGACCTCGGCGCCCTCCAAA	0.602													10	9	---	---	---	---	PASS
RGL2	5863	broad.mit.edu	37	6	33262480	33262480	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33262480G>A	uc003odv.2	-	11	1471	c.1338C>T	c.(1336-1338)TCC>TCT	p.S446S	RGL2_uc003odu.2_Silent_p.S6S|RGL2_uc010jur.2_Silent_p.S6S|RGL2_uc003odw.2_Silent_p.S364S|RGL2_uc011drb.1_Silent_p.S364S	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation	446	Ras-GEF.				Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(3)|lung(1)|breast(1)|pancreas(1)	6						ACTCATCCTTGGAGGCTGCAT	0.582													5	12	---	---	---	---	PASS
TAF11	6882	broad.mit.edu	37	6	34850791	34850791	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34850791C>T	uc003ojw.1	-	2	323	c.238G>A	c.(238-240)GCA>ACA	p.A80T	UHRF1BP1_uc010jvm.1_RNA|TAF11_uc011dsr.1_Missense_Mutation_p.A80T	NM_005643	NP_005634	Q15544	TAF11_HUMAN	TBP-associated factor 11	80					positive regulation by host of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIID complex	protein N-terminus binding|thyroid hormone receptor binding|transcription coactivator activity|vitamin D receptor binding				0						TTTTTGGCTGCAGGATTAAGT	0.348													23	33	---	---	---	---	PASS
TCP11	6954	broad.mit.edu	37	6	35089954	35089954	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35089954G>T	uc003okd.2	-	5	738	c.557C>A	c.(556-558)CCA>CAA	p.P186Q	TCP11_uc003ojz.1_Missense_Mutation_p.P111Q|TCP11_uc003oka.2_Missense_Mutation_p.P111Q|TCP11_uc003okb.2_Missense_Mutation_p.P110Q|TCP11_uc003okc.2_Missense_Mutation_p.P110Q|TCP11_uc011dsu.1_Missense_Mutation_p.P168Q|TCP11_uc011dsv.1_Missense_Mutation_p.P135Q|TCP11_uc011dsw.1_Missense_Mutation_p.P140Q	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	173					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						ATCTCGAACTGGTGCACACAG	0.478													5	81	---	---	---	---	PASS
TJAP1	93643	broad.mit.edu	37	6	43471417	43471417	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43471417C>T	uc003ovd.2	+	10	928	c.552C>T	c.(550-552)TCC>TCT	p.S184S	TJAP1_uc003ovf.2_Silent_p.S174S|TJAP1_uc003ove.2_Silent_p.S174S|TJAP1_uc003ovc.2_Silent_p.S174S|TJAP1_uc010jyp.2_Silent_p.S143S|TJAP1_uc011dvh.1_Silent_p.S174S|TJAP1_uc003ovg.2_Silent_p.S50S|TJAP1_uc011dvi.1_Silent_p.S184S|TJAP1_uc011dvj.1_5'UTR|TJAP1_uc003ovi.2_Silent_p.S50S	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a	184						Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GCAACAAGTCCCACTTCCGAA	0.562													11	87	---	---	---	---	PASS
GPR111	222611	broad.mit.edu	37	6	47650109	47650109	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47650109T>A	uc010jzj.1	+	6	1815	c.1814T>A	c.(1813-1815)CTG>CAG	p.L605Q	GPR111_uc010jzk.1_Missense_Mutation_p.L537Q|GPR111_uc003oyy.2_RNA	NM_153839	NP_722581	Q8IZF7	GP111_HUMAN	G-protein coupled receptor 111	605	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						AAAGCCCTCCTGGCCTTCGTG	0.537													27	29	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51640631	51640631	+	Silent	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51640631T>G	uc003pah.1	-	54	8805	c.8529A>C	c.(8527-8529)GGA>GGC	p.G2843G	PKHD1_uc010jzn.1_Silent_p.G826G|PKHD1_uc003pai.2_Silent_p.G2843G	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2843	G8 2.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CAATATGAATTCCATTCATAC	0.333													6	46	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83818789	83818789	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83818789T>C	uc003pjs.1	+	5	741	c.481T>C	c.(481-483)TAC>CAC	p.Y161H	DOPEY1_uc011dyy.1_Missense_Mutation_p.Y161H|DOPEY1_uc010kbl.1_Missense_Mutation_p.Y161H	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	161					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AGGATCAGAGTACTATGAGAG	0.358													9	48	---	---	---	---	PASS
CNR1	1268	broad.mit.edu	37	6	88854625	88854625	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88854625G>T	uc011dzq.1	-	2	3932	c.369C>A	c.(367-369)TCC>TCA	p.S123S	CNR1_uc010kbz.2_Silent_p.S123S|CNR1_uc011dzr.1_Silent_p.S123S|CNR1_uc011dzs.1_Silent_p.S123S|CNR1_uc003pmq.3_Silent_p.S123S|CNR1_uc011dzt.1_Silent_p.S123S|CNR1_uc010kca.2_Silent_p.S90S	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	123	Helical; Name=1; (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)	CCAGCGTGAGGGACAGGACTG	0.587													6	13	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	94120471	94120471	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94120471C>G	uc003poe.2	-	3	821	c.580G>C	c.(580-582)GCT>CCT	p.A194P	EPHA7_uc003pof.2_Missense_Mutation_p.A194P|EPHA7_uc011eac.1_Missense_Mutation_p.A194P|EPHA7_uc003pog.3_Missense_Mutation_p.A194P	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	194	Extracellular (Potential).|Cys-rich.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		GAAACCAAAGCTATGCAAGCC	0.408													12	27	---	---	---	---	PASS
KIAA0776	23376	broad.mit.edu	37	6	96984166	96984166	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96984166G>T	uc003por.2	+	8	750	c.702G>T	c.(700-702)GTG>GTT	p.V234V	KIAA0776_uc010kck.2_RNA	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376	234	Involved in CDK5RAP3-binding.				negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		GAGGCACTGTGGTTGGTGGGA	0.433													5	51	---	---	---	---	PASS
OSTM1	28962	broad.mit.edu	37	6	108375753	108375753	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108375753T>A	uc003psd.2	-	3	642	c.556A>T	c.(556-558)ACA>TCA	p.T186S		NM_014028	NP_054747	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	186	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		AAATATACTGTGCTGTTTGAT	0.264													6	12	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117632279	117632279	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117632279A>T	uc003pxp.1	-	39	6336	c.6137T>A	c.(6136-6138)TTT>TAT	p.F2046Y	ROS1_uc011ebi.1_RNA	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	2046	Protein kinase.|Cytoplasmic (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGGACCATAAAACTGTAAGAA	0.279			T	GOPC|ROS1	glioblastoma|NSCLC								16	18	---	---	---	---	PASS
TAAR8	83551	broad.mit.edu	37	6	132874419	132874419	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132874419C>T	uc011ecj.1	+	1	588	c.588C>T	c.(586-588)GGC>GGT	p.G196G		NM_053278	NP_444508	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	196	Helical; Name=5; (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)		TAAGTCAAGGCTGGGTGTTGA	0.378													14	42	---	---	---	---	PASS
HBS1L	10767	broad.mit.edu	37	6	135290373	135290373	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135290373C>A	uc003qez.2	-						HBS1L_uc003qey.2_Intron|HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TTAAAACACTCACTTAGGCTT	0.338													6	12	---	---	---	---	PASS
AHI1	54806	broad.mit.edu	37	6	135784438	135784438	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135784438C>T	uc003qgi.2	-	8	1140	c.756G>A	c.(754-756)TTG>TTA	p.L252L	AHI1_uc003qgh.2_Silent_p.L252L|AHI1_uc003qgj.2_Silent_p.L252L|AHI1_uc003qgk.3_RNA|AHI1_uc003qgl.3_Silent_p.L252L	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	252						adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CAGAGATGGTCAATGTACTAC	0.323													23	36	---	---	---	---	PASS
STXBP5	134957	broad.mit.edu	37	6	147685233	147685233	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147685233A>G	uc003qlz.2	+	25	3173	c.3012A>G	c.(3010-3012)GCA>GCG	p.A1004A	STXBP5_uc010khz.1_Silent_p.A968A|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_Silent_p.A659A	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	1004	WD 14.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		ATGGACAAGCATTATACCTTG	0.363													16	31	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152605154	152605154	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152605154T>C	uc010kiw.2	-	96	18768	c.18166A>G	c.(18166-18168)ACC>GCC	p.T6056A	SYNE1_uc010kiv.2_Missense_Mutation_p.T580A|SYNE1_uc003qos.3_Missense_Mutation_p.T580A|SYNE1_uc003qot.3_Missense_Mutation_p.T5985A|SYNE1_uc003qou.3_Missense_Mutation_p.T6056A|SYNE1_uc010kiy.1_Missense_Mutation_p.T235A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6056	Spectrin 20.|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)		ATCCTGATGGTGGACATTCGC	0.532										HNSCC(10;0.0054)			7	25	---	---	---	---	PASS
MAD1L1	8379	broad.mit.edu	37	7	2259027	2259027	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2259027C>T	uc003slh.1	-	6	802	c.536G>A	c.(535-537)CGG>CAG	p.R179Q	MAD1L1_uc003slf.1_Missense_Mutation_p.R179Q|MAD1L1_uc003slg.1_Missense_Mutation_p.R179Q|MAD1L1_uc010ksh.1_Missense_Mutation_p.R179Q|MAD1L1_uc003sli.1_Missense_Mutation_p.R87Q|MAD1L1_uc010ksi.1_Missense_Mutation_p.R132Q|MAD1L1_uc010ksj.2_Missense_Mutation_p.R179Q	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	179	Potential.				cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GCGCTTCACCCGCATCTCCTG	0.632													4	12	---	---	---	---	PASS
COL28A1	340267	broad.mit.edu	37	7	7545641	7545641	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7545641T>C	uc003src.1	-						COL28A1_uc011jxe.1_Intron|COL28A1_uc003srd.2_Intron	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		AAGGGTAAGATTACCTTATTG	0.423													3	41	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17915137	17915137	+	Silent	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17915137A>T	uc003stw.1	-	7	843	c.630T>A	c.(628-630)CGT>CGA	p.R210R	SNX13_uc003stv.2_Silent_p.R210R|SNX13_uc010kuc.2_Silent_p.R7R|SNX13_uc003stx.1_Silent_p.R130R			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	210	PXA.				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					ACACTAGATCACGGCAAACCT	0.358													17	32	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17930108	17930108	+	Splice_Site	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17930108C>A	uc003stw.1	-	5	532	c.319_splice	c.e5-1	p.V107_splice	SNX13_uc003stv.2_Splice_Site_p.V107_splice|SNX13_uc010kuc.2_Splice_Site|SNX13_uc003stx.1_Splice_Site_p.V27_splice|SNX13_uc003sty.2_Splice_Site_p.V107_splice			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					ACTGGATAACCTATAACAAAA	0.289													5	50	---	---	---	---	PASS
INMT	11185	broad.mit.edu	37	7	30793552	30793552	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30793552C>G	uc003tbs.1	+	2	376	c.360C>G	c.(358-360)AAC>AAG	p.N120K	FAM188B_uc010kwe.2_5'UTR|INMT_uc010kwc.1_RNA|INMT_uc010kwd.1_Missense_Mutation_p.N119K	NM_006774	NP_006765	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	120						cytoplasm	amine N-methyltransferase activity				0						TGGAAGGAAACAGGTAGGGGT	0.572													9	52	---	---	---	---	PASS
ADCYAP1R1	117	broad.mit.edu	37	7	31142865	31142865	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31142865C>A	uc003tca.1	+	14	1284	c.1061C>A	c.(1060-1062)TCC>TAC	p.S354Y	ADCYAP1R1_uc003tcb.1_Missense_Mutation_p.S333Y|ADCYAP1R1_uc003tcc.1_Missense_Mutation_p.S382Y|ADCYAP1R1_uc003tcd.1_Missense_Mutation_p.S382Y|ADCYAP1R1_uc003tce.1_Missense_Mutation_p.S381Y|ADCYAP1R1_uc003tcf.1_Missense_Mutation_p.S112Y	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1	354	Helical; Name=6; (Potential).				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						CTGGCCCGGTCCACCCTGCTG	0.582													32	59	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57187734	57187734	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57187734C>A	uc010kzo.2	-	5	1659	c.1388G>T	c.(1387-1389)AGA>ATA	p.R463I		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	463					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)			TGTGTAGGGTCTCTCTCCAGT	0.418													34	55	---	---	---	---	PASS
ZNF117	51351	broad.mit.edu	37	7	64439401	64439401	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64439401T>A	uc003ttr.2	-	4	1833	c.548A>T	c.(547-549)CAT>CTT	p.H183L		NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117	183	C2H2-type 3.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AATTCTCTTATGTCTAATAAG	0.348													5	54	---	---	---	---	PASS
ZNF92	168374	broad.mit.edu	37	7	64863284	64863284	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64863284G>A	uc003ttz.2	+	4	400	c.257G>A	c.(256-258)TGG>TAG	p.W86*	ZNF92_uc003tua.2_Nonsense_Mutation_p.W17*|ZNF92_uc010kzu.2_Nonsense_Mutation_p.W54*|ZNF92_uc003tub.2_Nonsense_Mutation_p.W10*	NM_152626	NP_689839	Q03936	ZNF92_HUMAN	zinc finger protein 92 isoform 2	86						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(55;0.159)				CAAGATGTTTGGCCAGAGCAC	0.308													7	53	---	---	---	---	PASS
POM121	9883	broad.mit.edu	37	7	72400567	72400567	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72400567C>G	uc003twk.2	+	5	1193	c.1193C>G	c.(1192-1194)ACA>AGA	p.T398R	POM121_uc003twj.2_Missense_Mutation_p.T133R|POM121_uc010lam.1_Missense_Mutation_p.T133R	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	398	Ser-rich.|Pore side (Potential).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)				AGCTCCTTGACAGGCGCTTAC	0.507													26	161	---	---	---	---	PASS
GTF2IRD1	9569	broad.mit.edu	37	7	73969722	73969722	+	Splice_Site	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73969722G>C	uc003uaq.2	+	19	2360	c.1967_splice	c.e19-1	p.G656_splice	GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						TTGGGTCCCAGGAACTGCCTC	0.632													4	21	---	---	---	---	PASS
STYXL1	51657	broad.mit.edu	37	7	75630284	75630284	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75630284A>T	uc003uej.3	-	8	907	c.734T>A	c.(733-735)TTT>TAT	p.F245Y	STYXL1_uc003uef.2_Intron|STYXL1_uc011kgf.1_Intron|STYXL1_uc011kgg.1_Intron|STYXL1_uc003ueh.2_Missense_Mutation_p.F107Y|STYXL1_uc003uek.3_Missense_Mutation_p.F149Y|STYXL1_uc003uel.2_Missense_Mutation_p.F245Y|STYXL1_uc003uem.2_Missense_Mutation_p.F245Y|STYXL1_uc010ldg.1_Intron|STYXL1_uc010ldh.1_Missense_Mutation_p.F245Y|STYXL1_uc003uen.1_Intron	NM_016086	NP_057170	Q9Y6J8	STYL1_HUMAN	map kinase phosphatase-like protein MK-STYX	245	Tyrosine-protein phosphatase.				intracellular signal transduction|protein dephosphorylation	intracellular	protein binding|protein tyrosine/serine/threonine phosphatase activity				0						TTGGGTGGAAAAGATCAGAAT	0.562													5	73	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79818321	79818321	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79818321T>C	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TAAGTAGATTTAAACACCAAA	0.299													11	29	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81591298	81591298	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81591298G>A	uc003uhr.1	-	36	3134	c.2878C>T	c.(2878-2880)CAG>TAG	p.Q960*	CACNA2D1_uc011kgy.1_Nonsense_Mutation_p.Q172*	NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	972	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	ATGCAGCTCTGCTTGGACAGG	0.448													9	54	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	83037796	83037796	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83037796T>C	uc003uhy.1	-	6	1024	c.558A>G	c.(556-558)GAA>GAG	p.E186E		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	186	Sema.				axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				CAGCAAACAATTCACTACCTA	0.423													14	24	---	---	---	---	PASS
DMTF1	9988	broad.mit.edu	37	7	86823124	86823124	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86823124G>T	uc003uih.2	+	16	2060	c.1734G>T	c.(1732-1734)GAG>GAT	p.E578D	DMTF1_uc003uii.2_Missense_Mutation_p.E312D|DMTF1_uc003uij.2_Missense_Mutation_p.E312D|DMTF1_uc011khb.1_Missense_Mutation_p.E490D|DMTF1_uc003uik.2_RNA|DMTF1_uc003uil.2_Missense_Mutation_p.E578D|DMTF1_uc003uin.2_Missense_Mutation_p.E312D	NM_001142327	NP_001135799	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	578	Interaction with CCND1, CCND2 and CCND3 (By similarity).|Required for transcriptional activation (By similarity).				cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)					TTGCCACAGAGGACATCACTT	0.423													7	103	---	---	---	---	PASS
STEAP2	261729	broad.mit.edu	37	7	89854850	89854850	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89854850T>A	uc003ujz.2	+	2	847	c.454T>A	c.(454-456)TGG>AGG	p.W152R	STEAP2_uc003ujy.2_Missense_Mutation_p.W194R|STEAP2_uc010len.2_Missense_Mutation_p.W152R|STEAP2_uc003uka.2_Missense_Mutation_p.W152R|STEAP2_uc003ukb.2_Missense_Mutation_p.W152R|STEAP2_uc003ukc.2_Missense_Mutation_p.W152R|STEAP2_uc003ukd.2_Missense_Mutation_p.W152R	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the	152					electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					TGTCTCAGCTTGGGCACTTCA	0.363													21	86	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	92098142	92098142	+	IGR	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92098142G>A								GATAD1 (9400 upstream) : PEX1 (18196 downstream)																							cctcaggaggggtgcctttga	0.000													22	67	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94038087	94038087	+	Silent	SNP	C	T	T	rs1800227		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94038087C>T	uc003ung.1	+	16	1215	c.744C>T	c.(742-744)CCC>CCT	p.P248P	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	248					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTCAGGGTCCCATTGGGTCTG	0.443										HNSCC(75;0.22)			10	20	---	---	---	---	PASS
DYNC1I1	1780	broad.mit.edu	37	7	95606829	95606829	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95606829G>T	uc003uoc.3	+	7	824	c.547G>T	c.(547-549)GAG>TAG	p.E183*	DYNC1I1_uc003uod.3_Nonsense_Mutation_p.E166*|DYNC1I1_uc003uob.2_Nonsense_Mutation_p.E146*|DYNC1I1_uc003uoe.3_Nonsense_Mutation_p.E163*|DYNC1I1_uc010lfl.2_Nonsense_Mutation_p.E172*	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	183					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)			TCTAGAGGATGAGGAAGATGA	0.378													4	27	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100390148	100390148	+	Intron	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100390148C>T	uc003uwj.2	+						ZAN_uc003uwk.2_Missense_Mutation_p.R2612W|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_RNA|ZAN_uc011kke.1_Silent_p.G604G	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GGCTGGCTGGCGGGACCGCAC	0.667													5	16	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106545676	106545676	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106545676C>T	uc003vdv.3	+	11	3238	c.3153C>T	c.(3151-3153)ATC>ATT	p.I1051I	PIK3CG_uc003vdu.2_Silent_p.I1051I|PIK3CG_uc003vdw.2_Silent_p.I1051I	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	1051	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding	p.I1051I(1)		lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						TTGAATATATCCGGGATGCCC	0.433													10	113	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117432706	117432706	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117432706A>G	uc003vjf.2	-	4	636	c.544T>C	c.(544-546)TCA>CCA	p.S182P		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	182	Potential.									ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ACTTTGCCTGAGAGCTGCTTG	0.517													6	77	---	---	---	---	PASS
ING3	54556	broad.mit.edu	37	7	120593375	120593375	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120593375G>C	uc003vjn.2	+	3	252	c.118G>C	c.(118-120)GAA>CAA	p.E40Q	ING3_uc011knr.1_Missense_Mutation_p.E40Q|ING3_uc003vjl.2_Missense_Mutation_p.E40Q|ING3_uc003vjm.1_Missense_Mutation_p.E40Q|ING3_uc003vjo.2_5'UTR|ING3_uc003vjp.2_Missense_Mutation_p.E40Q|ING3_uc011kns.1_Missense_Mutation_p.E25Q	NM_019071	NP_061944	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3 isoform 1	40					histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding			ovary(1)	1	all_neural(327;0.117)					GGATCAACTAGAACAAAGAGT	0.308													9	59	---	---	---	---	PASS
TAS2R16	50833	broad.mit.edu	37	7	122635112	122635112	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122635112G>A	uc003vkl.1	-	1	643	c.577C>T	c.(577-579)CTG>TTG	p.L193L		NM_016945	NP_058641	Q9NYV7	T2R16_HUMAN	taste receptor T2R16	193	Helical; Name=5; (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						GTGGAGGCCAGGAACAGGATG	0.448													24	90	---	---	---	---	PASS
CNOT4	4850	broad.mit.edu	37	7	135073610	135073610	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135073610G>T	uc003vsv.1	-	11	1971	c.1664C>A	c.(1663-1665)TCA>TAA	p.S555*	CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron|CNOT4_uc003vsu.1_Nonsense_Mutation_p.S552*|CNOT4_uc011kpy.1_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	555					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						GGAAGAGGTTGACAGTGGCAT	0.463													12	56	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700851	136700851	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700851T>C	uc003vtf.1	+	4	1862	c.1239T>C	c.(1237-1239)TGT>TGC	p.C413C	CHRM2_uc003vtg.1_Silent_p.C413C|CHRM2_uc003vtj.1_Silent_p.C413C|CHRM2_uc003vtk.1_Silent_p.C413C|CHRM2_uc003vtl.1_Silent_p.C413C|CHRM2_uc003vtm.1_Silent_p.C413C|CHRM2_uc003vti.1_Silent_p.C413C|CHRM2_uc003vto.1_Silent_p.C413C|CHRM2_uc003vtn.1_Silent_p.C413C|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	413	Extracellular (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	ACACCTTTTGTGCACCTTGCA	0.473													17	64	---	---	---	---	PASS
TRPV5	56302	broad.mit.edu	37	7	142627186	142627186	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142627186C>T	uc003wby.1	-	3	580	c.316G>A	c.(316-318)GTC>ATC	p.V106I	TRPV5_uc003wbz.2_Missense_Mutation_p.V106I	NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	106	Cytoplasmic (Potential).|ANK 2.				protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)					GGCTCAAAGACCAGCTCTGGG	0.557													7	53	---	---	---	---	PASS
PIP	5304	broad.mit.edu	37	7	142836736	142836736	+	3'UTR	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142836736T>A	uc003wcf.1	+	4						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)		GGTAGAATAATGGAAGCCCTG	0.398													26	123	---	---	---	---	PASS
ABCF2	10061	broad.mit.edu	37	7	150921189	150921189	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150921189G>A	uc003wjp.2	-	4	490	c.379C>T	c.(379-381)CTG>TTG	p.L127L	ABCF2_uc003wjo.1_Silent_p.L127L	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	127	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAGAGAGCAGCATGGACTTT	0.547													29	27	---	---	---	---	PASS
ABCF2	10061	broad.mit.edu	37	7	150921902	150921902	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150921902G>A	uc003wjp.2	-	3	438	c.327C>T	c.(325-327)AAC>AAT	p.N109N	ABCF2_uc003wjo.1_Silent_p.N109N	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	109	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GACGGCCTGAGTTTAATTCCA	0.488													36	45	---	---	---	---	PASS
SH2D4A	63898	broad.mit.edu	37	8	19214747	19214747	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19214747A>G	uc003wzb.2	+	5	883	c.547A>G	c.(547-549)ATG>GTG	p.M183V	SH2D4A_uc011kym.1_Missense_Mutation_p.M138V|SH2D4A_uc003wzc.2_Missense_Mutation_p.M183V	NM_022071	NP_071354	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	183						cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)		TATTCAACAAATGTTGGCAGA	0.403													32	18	---	---	---	---	PASS
PPP3CC	5533	broad.mit.edu	37	8	22368619	22368619	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22368619C>T	uc003xbs.2	+	5	832	c.505C>T	c.(505-507)CAG>TAG	p.Q169*	PPP3CC_uc003xbr.1_Nonsense_Mutation_p.Q169*|PPP3CC_uc011kzi.1_Nonsense_Mutation_p.Q169*|PPP3CC_uc003xbt.2_Nonsense_Mutation_p.Q169*	NM_005605	NP_005596	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma	169					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		ATATTCGGAACAGGTGTATGA	0.398													10	87	---	---	---	---	PASS
NRG1	3084	broad.mit.edu	37	8	32599566	32599566	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32599566G>T	uc003xiv.2	+	7	1190	c.673G>T	c.(673-675)GTG>TTG	p.V225L	NRG1_uc003xip.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Missense_Mutation_p.V225L|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Missense_Mutation_p.V115L|NRG1_uc003xiy.2_Intron|NRG1_uc010lvt.2_Intron|NRG1_uc011lbg.1_Missense_Mutation_p.V71L|NRG1_uc011lbh.1_Intron|NRG1_uc003xiz.1_RNA|NRG1_uc003xja.2_Missense_Mutation_p.V28L	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	225	Extracellular (Potential).				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)		TACTGAGAATGTGCCCATGAA	0.403													33	12	---	---	---	---	PASS
POLB	5423	broad.mit.edu	37	8	42196567	42196567	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42196567C>T	uc003xoz.1	+	2	212	c.99C>T	c.(97-99)ATC>ATT	p.I33I	POLB_uc003xpa.1_Silent_p.I33I|POLB_uc011lcs.1_Intron	NM_002690	NP_002681	P06746	DPOLB_HUMAN	DNA-directed DNA polymerase beta	33					DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	GCCAAGCTATCCACAAGTACA	0.483								DNA_polymerases_(catalytic_subunits)					6	33	---	---	---	---	PASS
RNF170	81790	broad.mit.edu	37	8	42729125	42729125	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42729125T>C	uc003xpo.2	-	3	639	c.162A>G	c.(160-162)CCA>CCG	p.P54P	RNF170_uc011lcx.1_Silent_p.P54P|RNF170_uc010lxp.2_5'UTR|RNF170_uc003xpm.2_Silent_p.P54P|RNF170_uc003xpp.2_5'UTR|RNF170_uc003xpn.2_5'UTR|RNF170_uc003xpq.3_Silent_p.P54P	NM_001160223	NP_001153695	Q96K19	RN170_HUMAN	ring finger protein 170 isoform a	54						integral to membrane	zinc ion binding				0	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CCTGGTTTTCTGGGTGAATGT	0.328													7	39	---	---	---	---	PASS
HGSNAT	138050	broad.mit.edu	37	8	43033220	43033220	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43033220T>C	uc003xpx.3	+	10	903	c.855T>C	c.(853-855)TTT>TTC	p.F285F		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	313	Helical; (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TTTTTAGGTTTGTATTTATTA	0.328													53	51	---	---	---	---	PASS
MCM4	4173	broad.mit.edu	37	8	48874977	48874977	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48874977T>C	uc003xqk.1	+						PRKDC_uc003xqi.2_5'Flank|PRKDC_uc003xqj.2_5'Flank|PRKDC_uc011ldh.1_5'Flank|MCM4_uc003xql.1_Intron|MCM4_uc011ldi.1_Intron|MCM4_uc010lxw.1_Intron	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4						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(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GTGAGCTACATGTATTAAAAT	0.388													6	45	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52320691	52320691	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52320691C>A	uc003xqu.3	-	17	3594	c.3493G>T	c.(3493-3495)GTT>TTT	p.V1165F	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1165					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AAGTTCTTAACTGAAGTCAAA	0.398													8	45	---	---	---	---	PASS
OPRK1	4986	broad.mit.edu	37	8	54142385	54142385	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54142385G>A	uc003xrh.1	-	3	990	c.615C>T	c.(613-615)GTC>GTT	p.V205V	OPRK1_uc003xri.1_Silent_p.V205V|OPRK1_uc010lyc.1_Silent_p.V116V	NM_000912	NP_000903	P41145	OPRK_HUMAN	opioid receptor, kappa 1	205	Extracellular (Potential).				behavior|immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception|synaptic transmission|viral genome replication	integral to plasma membrane	kappa-opioid receptor activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Buprenorphine(DB00921)|Butorphanol(DB00611)|Cocaine(DB00907)|Codeine(DB00318)|Dezocine(DB01209)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Meperidine(DB00454)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Tramadol(DB00193)	CAATGACATCGACGTCTGGAG	0.423													5	42	---	---	---	---	PASS
NKAIN3	286183	broad.mit.edu	37	8	63659590	63659590	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63659590G>T	uc010lyq.1	+	4	505	c.373G>T	c.(373-375)GGC>TGC	p.G125C		NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	125						integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				CTCAGCCCATGGCATGATGGA	0.507													7	37	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72948636	72948636	+	Silent	SNP	C	G	G	rs146434598	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72948636C>G	uc003xza.2	-	21	2617	c.2442G>C	c.(2440-2442)ACG>ACC	p.T814T	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	814	Helical; Name=3; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	AAATGATGCCCGTCGTGTAGA	0.353													5	44	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77775400	77775400	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77775400C>A	uc003yav.2	+	11	9702	c.9315C>A	c.(9313-9315)CTC>CTA	p.L3105L		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3101	Pro-rich.					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)			CCCTGTCTCTCAGCAGTGCCC	0.423										HNSCC(33;0.089)			6	6	---	---	---	---	PASS
FAM92A1	137392	broad.mit.edu	37	8	94717142	94717142	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94717142C>T	uc010maq.2	+	4	439	c.336C>T	c.(334-336)GAC>GAT	p.D112D	FAM92A1_uc003yfu.1_RNA|FAM92A1_uc003yfv.3_RNA	NM_145269	NP_660312	A1XBS5	F92A1_HUMAN	hypothetical protein LOC137392	112	Potential.										0	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TGCAGGATGACCTCAAAGCAA	0.308													22	49	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100050736	100050736	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100050736C>A	uc003yiv.2	+	3	344	c.233C>A	c.(232-234)CCA>CAA	p.P78Q	VPS13B_uc003yiw.2_Missense_Mutation_p.P78Q|VPS13B_uc003yit.2_Missense_Mutation_p.P78Q|VPS13B_uc003yiu.1_Missense_Mutation_p.P78Q|VPS13B_uc003yis.2_Missense_Mutation_p.P78Q|VPS13B_uc011lgy.1_5'UTR	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	78					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGTTCAGAACCAGTGGTAATT	0.318													4	29	---	---	---	---	PASS
PABPC1	26986	broad.mit.edu	37	8	101719181	101719181	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101719181G>C	uc003yjs.1	-	10	1885	c.1381C>G	c.(1381-1383)CCA>GCA	p.P461A	PABPC1_uc011lhc.1_Missense_Mutation_p.P429A|PABPC1_uc011lhd.1_Missense_Mutation_p.P416A|PABPC1_uc003yjt.1_Missense_Mutation_p.P458A|PABPC1_uc003yju.2_Intron	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	461					mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CTAAATGGTGGTCTAGGAGCA	0.418													12	95	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110495260	110495260	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110495260T>C	uc003yne.2	+	57	9606	c.9502T>C	c.(9502-9504)TAT>CAT	p.Y3168H		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3168	Extracellular (Potential).|G8 2.				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)			ACATTCAATATATAAAACTAA	0.408										HNSCC(38;0.096)			18	26	---	---	---	---	PASS
RAD21	5885	broad.mit.edu	37	8	117862949	117862949	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117862949G>T	uc003yod.2	-	12	1816	c.1528C>A	c.(1528-1530)CCA>ACA	p.P510T		NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog	510	Pro-rich.				apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					CAGATATTTGGAGGTTCTTCT	0.328													6	71	---	---	---	---	PASS
TAF2	6873	broad.mit.edu	37	8	120831664	120831664	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120831664C>A	uc003you.2	-	3	491	c.221G>T	c.(220-222)CGA>CTA	p.R74L		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	74					G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GATCCTTACTCGGTATATTCT	0.343													5	100	---	---	---	---	PASS
LRRC6	23639	broad.mit.edu	37	8	133673830	133673830	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133673830A>G	uc003ytk.2	-	2	128	c.54T>C	c.(52-54)TGT>TGC	p.C18C	LRRC6_uc003ytl.2_RNA	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6	18						cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			AAAAAATGACACAGTCGTTGT	0.363													13	39	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	133900281	133900281	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133900281G>T	uc003ytw.2	+	10	2270	c.2229G>T	c.(2227-2229)CAG>CAT	p.Q743H		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	743	Thyroglobulin type-1 7.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGACGGTGCAGGCCCTGCTCT	0.532													9	33	---	---	---	---	PASS
SLC45A4	57210	broad.mit.edu	37	8	142228949	142228949	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142228949G>A	uc003ywd.1	-	4	945	c.637C>T	c.(637-639)CGC>TGC	p.R213C	SLC45A4_uc003ywc.1_Missense_Mutation_p.R213C|SLC45A4_uc010meq.1_Missense_Mutation_p.R211C	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	264					transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			TCAGCGCTGCGCTCCTGCTGC	0.662													26	35	---	---	---	---	PASS
CPSF1	29894	broad.mit.edu	37	8	145634543	145634543	+	5'UTR	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145634543G>T	uc003zcj.2	-	2					CPSF1_uc011lle.1_5'UTR|CPSF1_uc011llf.1_5'UTR|CPSF1_uc003zcl.1_RNA	NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,						mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CGGCGTACATGGCGCCAACCC	0.517													13	34	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78794566	78794566	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794566A>C	uc004ajz.2	+	15	2493	c.1955A>C	c.(1954-1956)CAC>CCC	p.H652P	PCSK5_uc004aka.2_RNA|PCSK5_uc004akb.2_5'Flank	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	652	CRM (Cys-rich motif).				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						GGACCAGACCACTGCAATGAC	0.478													5	25	---	---	---	---	PASS
FLJ46321	389763	broad.mit.edu	37	9	84609023	84609023	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84609023G>T	uc004amn.2	+	4	3685	c.3638G>T	c.(3637-3639)AGG>ATG	p.R1213M		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1213						integral to membrane					0						TTGGTCCAGAGGAAGCATAGC	0.403													6	122	---	---	---	---	PASS
OR13C4	138804	broad.mit.edu	37	9	107289280	107289280	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107289280T>A	uc011lvn.1	-	1	211	c.211A>T	c.(211-213)ATC>TTC	p.I71F		NM_001001919	NP_001001919	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GTATAGCAGATATCCAGGAAA	0.438													11	71	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117130710	117130710	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117130710C>A	uc004biq.3	-						AKNA_uc004bio.3_Intron|AKNA_uc004bip.3_Intron|AKNA_uc004bir.3_Intron|AKNA_uc004bis.3_Intron|AKNA_uc010mve.2_Intron|AKNA_uc004biu.1_Intron|AKNA_uc004biv.1_Intron	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						GCTCTTCTCCCGGACTCACCT	0.667													3	14	---	---	---	---	PASS
SLC25A25	114789	broad.mit.edu	37	9	130854346	130854346	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130854346G>T	uc004btd.2	+	1	219	c.197G>T	c.(196-198)GGA>GTA	p.G66V	SLC25A25_uc004btb.2_Intron|SLC25A25_uc004btc.2_Missense_Mutation_p.G66V	NM_001006642	NP_001006643	Q6KCM7	SCMC2_HUMAN	solute carrier family 25, member 25 isoform c	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0						CTGGTGGTTGGACCTGCAGAG	0.542													35	20	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131374420	131374420	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131374420G>A	uc004bvl.3	+	38	5036	c.4923G>A	c.(4921-4923)CAG>CAA	p.Q1641Q	SPTAN1_uc004bvm.3_Silent_p.Q1646Q|SPTAN1_uc004bvn.3_Silent_p.Q1621Q	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	1641	Spectrin 17.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						ACCAGTGGCAGTTCTTGGTGC	0.493													16	60	---	---	---	---	PASS
GTF3C4	9329	broad.mit.edu	37	9	135554019	135554019	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135554019G>T	uc010mzv.2	+	2	1271	c.1013G>T	c.(1012-1014)GGA>GTA	p.G338V	GTF3C4_uc010mzw.2_RNA	NM_012204	NP_036336	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC 4	338					transcription initiation from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|enzyme activator activity|histone acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		AGTGCTTTTGGACCCATAAAA	0.413													5	67	---	---	---	---	PASS
RXRA	6256	broad.mit.edu	37	9	137328331	137328331	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137328331C>T	uc004cfb.2	+	10	1422	c.1260C>T	c.(1258-1260)CTC>CTT	p.L420L	RXRA_uc004cfc.1_Silent_p.L323L	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha	420	Ligand-binding.				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)	AGCTCTTGCTCCGCCTGCCGG	0.612													38	14	---	---	---	---	PASS
CAMSAP1	157922	broad.mit.edu	37	9	138710429	138710429	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138710429C>A	uc004cgr.3	-	13	3993	c.3993G>T	c.(3991-3993)GAG>GAT	p.E1331D	CAMSAP1_uc004cgq.3_Missense_Mutation_p.E1221D|CAMSAP1_uc010nbg.2_Missense_Mutation_p.E1053D	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1331						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CCTTCTCCTCCTCCTTCCGCA	0.647													4	23	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	373117	373117	+	Splice_Site	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:373117C>A	uc001ifp.2	-	31	3844	c.3754_splice	c.e31-1	p.A1252_splice		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)		GCCCTCGCGCCTGGAGATGAT	0.567													20	8	---	---	---	---	PASS
STAM	8027	broad.mit.edu	37	10	17746497	17746497	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17746497C>A	uc001ipj.1	+	10	1196	c.980C>A	c.(979-981)CCA>CAA	p.P327Q	STAM_uc009xjw.1_Missense_Mutation_p.Q25K	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1	327					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						CCAGACCTACCAGAGCTGCTT	0.373													5	57	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30316392	30316392	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30316392C>T	uc001iux.2	-	2	2744	c.2685G>A	c.(2683-2685)AGG>AGA	p.R895R	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Silent_p.R757R|KIAA1462_uc009xle.1_Silent_p.R895R	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	895										ovary(4)	4						GCACCCACATCCTCGGCTGTG	0.637													10	42	---	---	---	---	PASS
PARD3	56288	broad.mit.edu	37	10	34625161	34625161	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34625161C>T	uc010qej.1	-	18	2580	c.2580G>A	c.(2578-2580)GAG>GAA	p.E860E	PARD3_uc010qek.1_Silent_p.E857E|PARD3_uc010qel.1_Silent_p.E860E|PARD3_uc010qem.1_Silent_p.E844E|PARD3_uc010qen.1_Silent_p.E814E|PARD3_uc010qeo.1_Silent_p.E814E|PARD3_uc010qep.1_Silent_p.E770E|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Silent_p.E573E|PARD3_uc001ixp.1_Silent_p.E691E|PARD3_uc001ixq.1_Silent_p.E814E|PARD3_uc001ixr.1_Silent_p.E857E|PARD3_uc001ixt.1_Silent_p.E678E|PARD3_uc001ixu.1_Silent_p.E802E|PARD3_uc001ixs.1_Silent_p.E483E	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	860	Interacts with PRKCZ (By similarity).				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				TGAGTTTAGTCTCGTCAGCTA	0.408													13	11	---	---	---	---	PASS
ZNF33B	7582	broad.mit.edu	37	10	43089100	43089100	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43089100C>T	uc001jaf.1	-	5	1413	c.1298G>A	c.(1297-1299)AGA>AAA	p.R433K	ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Missense_Mutation_p.R321K|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	433	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TGTGTGTGTTCTCTGATGTTT	0.418													15	54	---	---	---	---	PASS
P4HA1	5033	broad.mit.edu	37	10	74831843	74831843	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74831843C>T	uc010qka.1	-	5	603	c.269G>A	c.(268-270)CGT>CAT	p.R90H	P4HA1_uc001jtg.2_Missense_Mutation_p.R90H|P4HA1_uc001jth.2_Missense_Mutation_p.R90H|P4HA1_uc010qkb.1_Missense_Mutation_p.R90H|P4HA1_uc001jti.2_RNA	NM_001142595	NP_001136067	P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha I subunit isoform 2	90						endoplasmic reticulum lumen|mitochondrion	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			ovary(1)	1	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	AGTATTCAGACGTTTCATTAA	0.408													14	61	---	---	---	---	PASS
NRG3	10718	broad.mit.edu	37	10	84745267	84745267	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84745267C>A	uc001kco.2	+	9	2024	c.1997C>A	c.(1996-1998)GCC>GAC	p.A666D	NRG3_uc010qlz.1_Missense_Mutation_p.A665D|NRG3_uc001kcp.2_Missense_Mutation_p.A469D|NRG3_uc001kcq.2_Missense_Mutation_p.A316D|NRG3_uc001kcr.2_Missense_Mutation_p.A340D	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	690	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GAAAACACAGCCTTTCTCCCC	0.493													5	37	---	---	---	---	PASS
CUTC	51076	broad.mit.edu	37	10	101503802	101503802	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101503802C>G	uc001kqd.3	+	5	560	c.412C>G	c.(412-414)CGC>GGC	p.R138G	CUTC_uc010qpk.1_Missense_Mutation_p.R138G|CUTC_uc001kqe.3_RNA	NM_015960	NP_057044	Q9NTM9	CUTC_HUMAN	cutC copper transporter homolog	138					copper ion homeostasis|copper ion transport|protein tetramerization	cytoplasm|nucleus	copper ion binding			breast(1)	1		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		AGCTATTTGCCGCCCTCTGCC	0.338													5	30	---	---	---	---	PASS
SH3PXD2A	9644	broad.mit.edu	37	10	105372887	105372887	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105372887C>A	uc001kxj.1	-	11	1037	c.897G>T	c.(895-897)CTG>CTT	p.L299L	SH3PXD2A_uc010qqr.1_Silent_p.L189L|SH3PXD2A_uc010qqs.1_Silent_p.L134L|SH3PXD2A_uc010qqt.1_Silent_p.L176L|SH3PXD2A_uc009xxn.1_Silent_p.L134L|SH3PXD2A_uc010qqu.1_Silent_p.L242L	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	327					cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		TCCGGGTTGGCAGGTCATCCT	0.557													36	29	---	---	---	---	PASS
COL17A1	1308	broad.mit.edu	37	10	105807833	105807833	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105807833G>A	uc001kxr.2	-	30	2426	c.2257C>T	c.(2257-2259)CCA>TCA	p.P753S		NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	753	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CAACCTCTTGGGCCTTGGTGT	0.582													29	117	---	---	---	---	PASS
FAM160B1	57700	broad.mit.edu	37	10	116595985	116595985	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116595985C>A	uc001lcb.2	+	5	837	c.502C>A	c.(502-504)CTG>ATG	p.L168M	FAM160B1_uc001lcc.2_Missense_Mutation_p.L168M	NM_020940	NP_065991	Q5W0V3	F16B1_HUMAN	hypothetical protein LOC57700 isoform a	168										lung(1)	1						GGACCCCTACCTGGTTAACTT	0.328													6	124	---	---	---	---	PASS
TNNI2	7136	broad.mit.edu	37	11	1862288	1862288	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1862288G>T	uc010qxe.1	+	5	326	c.304G>T	c.(304-306)GAT>TAT	p.D102Y	TNNI2_uc010qxc.1_Missense_Mutation_p.D100Y|TNNI2_uc010qxd.1_Missense_Mutation_p.D100Y	NM_001145841	NP_001139313	P48788	TNNI2_HUMAN	fast-twitch skeletal muscle troponin I isoform	102	Involved in binding TNC and actin.				muscle filament sliding|positive regulation of transcription, DNA-dependent|skeletal muscle contraction	cytosol|nucleus|troponin complex	actin binding|troponin T binding				0		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|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)		GAAGCTATTTGATCTGCGGGG	0.592													10	4	---	---	---	---	PASS
TNNT3	7140	broad.mit.edu	37	11	1959678	1959678	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1959678G>C	uc001luu.3	+	16	945	c.733G>C	c.(733-735)GCT>CCT	p.A245P	TNNT3_uc001luw.3_Missense_Mutation_p.A237P|TNNT3_uc001luo.3_Missense_Mutation_p.A237P|TNNT3_uc001lup.3_Missense_Mutation_p.A243P|TNNT3_uc001luq.3_Missense_Mutation_p.A237P|TNNT3_uc001lur.2_Missense_Mutation_p.A237P|TNNT3_uc010qxf.1_Missense_Mutation_p.A243P|TNNT3_uc010qxg.1_Missense_Mutation_p.A177P	NM_006757	NP_006748	P45378	TNNT3_HUMAN	troponin T3, skeletal, fast isoform 1	256					muscle filament sliding|regulation of ATPase activity|regulation of striated muscle contraction|skeletal muscle contraction	cytosol|troponin complex	calcium-dependent protein binding|tropomyosin binding|troponin C binding|troponin I binding			ovary(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		CAGCAAGAAGGCTGGGACCCC	0.662													4	26	---	---	---	---	PASS
OR52B4	143496	broad.mit.edu	37	11	4388990	4388990	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4388990G>A	uc010qye.1	-	1	536	c.536C>T	c.(535-537)ACC>ATC	p.T179I		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	179	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCACAAAAGGTGTGTGGAAT	0.348													43	14	---	---	---	---	PASS
OR10A4	283297	broad.mit.edu	37	11	6898522	6898522	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6898522T>A	uc010rat.1	+	1	644	c.644T>A	c.(643-645)ATC>AAC	p.I215N		NM_207186	NP_997069	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A,	215	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTCTTGCTGATCCTGGGATCC	0.522													34	19	---	---	---	---	PASS
PDE3B	5140	broad.mit.edu	37	11	14666331	14666331	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14666331T>C	uc001mln.2	+	1	1063	c.710T>C	c.(709-711)CTC>CCC	p.L237P	PDE3B_uc001mlm.2_Missense_Mutation_p.L237P|PDE3B_uc010rcr.1_Missense_Mutation_p.L237P|PSMA1_uc001mll.2_5'Flank	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	237	Helical; (Potential).				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						TTCACCAGCCTCGGGTCGCTG	0.692													7	2	---	---	---	---	PASS
LDHC	3948	broad.mit.edu	37	11	18456380	18456380	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18456380G>A	uc001mon.3	+	5	624	c.512G>A	c.(511-513)CGT>CAT	p.R171H	LDHC_uc001mom.3_Missense_Mutation_p.R171H|LDHC_uc009yhp.2_Missense_Mutation_p.R171H|LDHC_uc001moo.3_Missense_Mutation_p.R55H|LDHC_uc009yhq.2_RNA|LDHC_uc009yhr.2_Missense_Mutation_p.R55H	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C	171					glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	GCCCGTTTCCGTTACCTAATT	0.373													42	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	30926574	30926574	+	RNA	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30926574T>C	uc001mss.1	-	9		c.1345A>G			uc009yjk.1_Missense_Mutation_p.I862M|uc009yjj.1_RNA					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		TGTATGCAATTATTTTCACTG	0.458													7	45	---	---	---	---	PASS
TSPAN18	90139	broad.mit.edu	37	11	44939553	44939553	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44939553G>T	uc001mye.3	+	4	450	c.289G>T	c.(289-291)GCA>TCA	p.A97S	TP53I11_uc001myf.1_Intron|TSPAN18_uc001myg.2_Missense_Mutation_p.A97S	NM_130783	NP_570139	Q96SJ8	TSN18_HUMAN	tetraspanin 18 isoform 2	97	Helical; (Potential).					integral to membrane					0						CATCTTCCTGGCAGAGCTCTC	0.582													29	18	---	---	---	---	PASS
RAPSN	5913	broad.mit.edu	37	11	47464329	47464329	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47464329G>T	uc001nfi.1	-	3	783	c.569C>A	c.(568-570)GCA>GAA	p.A190E	RAPSN_uc001nfj.1_Missense_Mutation_p.A190E|RAPSN_uc009yls.1_Missense_Mutation_p.A190E	NM_005055	NP_005046	Q13702	RAPSN_HUMAN	43 kD receptor-associated protein of the synapse	190	TPR 4.				synaptic transmission, cholinergic	cell junction|cytoskeleton|postsynaptic membrane	acetylcholine receptor binding|zinc ion binding			ovary(1)	1						GACAAGCTCTGCCGCCTTGCA	0.612													4	70	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136154	55136154	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136154C>A	uc010rif.1	+	1	795	c.795C>A	c.(793-795)TTC>TTA	p.F265L		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	265	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GAAAAGCTTTCTACACCTGTG	0.428													66	30	---	---	---	---	PASS
OR4C15	81309	broad.mit.edu	37	11	55322087	55322087	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55322087T>C	uc010rig.1	+	1	305	c.305T>C	c.(304-306)CTC>CCC	p.L102P		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	48	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GTAACCATTCTCAGCAGCCCT	0.428										HNSCC(20;0.049)			59	32	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944825	55944825	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944825C>A	uc010rjb.1	+	1	732	c.732C>A	c.(730-732)CAC>CAA	p.H244Q		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	244	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					GTGCCTCTCACCTGACTGCTG	0.443													53	19	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043229	56043229	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56043229C>A	uc001nio.1	+	1	115	c.115C>A	c.(115-117)CTA>ATA	p.L39I		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	39	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					GCAAGTCTTCCTATTTTTATT	0.333													5	61	---	---	---	---	PASS
OR8J1	219477	broad.mit.edu	37	11	56128066	56128066	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56128066T>G	uc010rjh.1	+	1	344	c.344T>G	c.(343-345)CTG>CGG	p.L115R		NM_001005205	NP_001005205	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J,	115	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					GTAATCATGCTGGCTTTGATG	0.473													50	31	---	---	---	---	PASS
OR8J1	219477	broad.mit.edu	37	11	56128067	56128067	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56128067G>T	uc010rjh.1	+	1	345	c.345G>T	c.(343-345)CTG>CTT	p.L115L		NM_001005205	NP_001005205	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J,	115	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					TAATCATGCTGGCTTTGATGG	0.468													47	34	---	---	---	---	PASS
FAM111B	374393	broad.mit.edu	37	11	58893299	58893299	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58893299A>G	uc001nnl.2	+	4	1972	c.1729A>G	c.(1729-1731)ATT>GTT	p.I577V	FAM111B_uc001nnm.2_Missense_Mutation_p.I547V|FAM111B_uc010rko.1_Missense_Mutation_p.I547V	NM_198947	NP_945185	Q6SJ93	F111B_HUMAN	hypothetical protein LOC374393 isoform a	577							catalytic activity			ovary(2)	2						GATTTATTTAATTGGTCATCC	0.363													9	42	---	---	---	---	PASS
ZBTB3	79842	broad.mit.edu	37	11	62520528	62520528	+	Silent	SNP	G	A	A	rs148738930		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62520528G>A	uc001nuz.2	-	2	881	c.759C>T	c.(757-759)GAC>GAT	p.D253D		NM_024784	NP_079060	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	253	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3						GATGTGGTGCGTCAACCTCCA	0.552													5	21	---	---	---	---	PASS
MUS81	80198	broad.mit.edu	37	11	65632525	65632525	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65632525G>T	uc001ofv.3	+	13	1663	c.1310G>T	c.(1309-1311)GGG>GTG	p.G437V	MUS81_uc001ofw.3_Intron|MUS81_uc001ofx.3_5'UTR	NM_025128	NP_079404	Q96NY9	MUS81_HUMAN	MUS81 endonuclease homolog	437					DNA recombination|DNA repair	nucleolus	3'-flap endonuclease activity|DNA binding|metal ion binding|protein binding				0				READ - Rectum adenocarcinoma(159;0.166)		GGAACCCCTGGGAACCCTGAA	0.602								Homologous_recombination					6	151	---	---	---	---	PASS
C2CD3	26005	broad.mit.edu	37	11	73768589	73768589	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73768589C>A	uc001ouu.2	-	25	5179	c.4952G>T	c.(4951-4953)GGG>GTG	p.G1651V	C2CD3_uc001out.2_RNA	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1651	C2 2.					centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					CAAGGGGCTCCCTGAAATAGA	0.458													6	60	---	---	---	---	PASS
SFRS2B	10929	broad.mit.edu	37	11	94800939	94800939	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94800939C>A	uc001pff.2	+	2	885	c.550C>A	c.(550-552)CGC>AGC	p.R184S	SFRS2B_uc001pfg.1_5'Flank	NM_032102	NP_115285	Q9BRL6	SRSF8_HUMAN	splicing factor, arginine/serine-rich 2B	184	Arg-rich.				mRNA processing|RNA splicing	nucleus	nucleotide binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAGGGAATCTCGCTACGGCGG	0.567													5	61	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117321399	117321399	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117321399C>T	uc001prh.1	-	20	3756	c.3754G>A	c.(3754-3756)GGT>AGT	p.G1252S		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1192	Extracellular (Potential).|Fibronectin type-III 4.				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)		GCAGGGGGACCTGGAACTGAG	0.567													4	22	---	---	---	---	PASS
HSPA8	3312	broad.mit.edu	37	11	122931821	122931821	+	Intron	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122931821A>T	uc001pyo.2	-						HSPA8_uc009zbc.2_5'Flank|HSPA8_uc001pyp.2_Intron|HSPA8_uc010rzu.1_Intron|HSPA8_uc009zbd.1_Intron|HSPA8_uc010rzv.1_Intron	NM_006597	NP_006588	P11142	HSP7C_HUMAN	heat shock 70kDa protein 8 isoform 1						cellular membrane organization|interspecies interaction between organisms|mRNA metabolic process|negative regulation of transcription, DNA-dependent|neurotransmitter secretion|post-Golgi vesicle-mediated transport|protein folding|response to unfolded protein|transcription, DNA-dependent	cell surface|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|melanosome|plasma membrane|ribonucleoprotein complex	ATP binding|ATPase activity, coupled|protein binding			central_nervous_system(7)|lung(1)	8		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TAAAATTAGGAACTCACCAAA	0.408													19	6	---	---	---	---	PASS
OR10S1	219873	broad.mit.edu	37	11	123848350	123848350	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123848350G>A	uc001pzm.1	-	1	49	c.49C>T	c.(49-51)CCC>TCC	p.P17S		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GTCTGGTTGGGGTTCTCCGTT	0.478													42	18	---	---	---	---	PASS
OR10G9	219870	broad.mit.edu	37	11	123893737	123893737	+	Silent	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123893737C>G	uc010sad.1	+	1	18	c.18C>G	c.(16-18)CTC>CTG	p.L6L		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	6	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AGACCAGCCTCGTGACAGCGT	0.532													61	38	---	---	---	---	PASS
OR8D2	283160	broad.mit.edu	37	11	124189744	124189744	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124189744G>T	uc010sah.1	-	1	350	c.350C>A	c.(349-351)GCC>GAC	p.A117D		NM_001002918	NP_001002918	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D,	117	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)|central_nervous_system(1)|pancreas(1)	3		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		ATATTCCATGGCTGTCAGAAG	0.403													9	45	---	---	---	---	PASS
FLI1	2313	broad.mit.edu	37	11	128628020	128628020	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128628020C>A	uc010sbu.1	+	2	370	c.29C>A	c.(28-30)TCG>TAG	p.S10*	FLI1_uc010sbt.1_5'UTR|FLI1_uc010sbv.1_5'UTR|FLI1_uc009zci.2_5'UTR|FLI1_uc001qen.2_5'UTR	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	10					hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GAGGCTCTGTCGGTGGTGAGC	0.612			T	EWSR1	Ewing sarcoma								8	2	---	---	---	---	PASS
SNX19	399979	broad.mit.edu	37	11	130781571	130781571	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130781571C>A	uc001qgk.3	-	2	2318	c.1770G>T	c.(1768-1770)CAG>CAT	p.Q590H	SNX19_uc010sce.1_5'UTR|SNX19_uc010scf.1_Missense_Mutation_p.Q33H|SNX19_uc010scg.1_5'UTR|SNX19_uc001qgl.3_Missense_Mutation_p.Q590H|SNX19_uc009zcx.1_RNA	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	590	PX.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CCAGACGGGTCTGCAGATTCA	0.552													31	16	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	988914	988914	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:988914A>G	uc001qio.3	+	11	3056	c.2549A>G	c.(2548-2550)CAT>CGT	p.H850R	WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	850					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)			TCAACTCCTCATGTGTCTACG	0.537													53	53	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	1005592	1005592	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1005592C>G	uc001qio.3	+	24	6446	c.5939C>G	c.(5938-5940)CCT>CGT	p.P1980R	WNK1_uc001qip.3_Missense_Mutation_p.P1732R|WNK1_uc001qir.3_Missense_Mutation_p.P1153R	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1980					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)			GCATCTCCTCCTTTTATGGAT	0.448													97	79	---	---	---	---	PASS
PRMT8	56341	broad.mit.edu	37	12	3701428	3701428	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3701428G>T	uc001qmf.2	+	9	1378	c.1011G>T	c.(1009-1011)CAG>CAT	p.Q337H	PRMT8_uc009zed.2_Missense_Mutation_p.Q328H|PRMT8_uc001qmg.2_Missense_Mutation_p.Q151H|PRMT8_uc001qmh.2_RNA	NM_019854	NP_062828	Q9NR22	ANM8_HUMAN	HMT1 hnRNP methyltransferase-like 4	337					regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			ACTGGAAGCAGACCGTCTTCT	0.537													88	81	---	---	---	---	PASS
ANO2	57101	broad.mit.edu	37	12	5744332	5744332	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5744332C>A	uc001qnm.2	-	17	1874	c.1802G>T	c.(1801-1803)TGG>TTG	p.W601L		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	606	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						TTTGGTGAGCCACTTGGCCAC	0.498													4	23	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13717533	13717533	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717533C>T	uc001rbt.2	-	13	2818	c.2639G>A	c.(2638-2640)CGC>CAC	p.R880H		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	880	Cytoplasmic (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)	TACAGACTGGCGCTCCTCGAT	0.537													12	89	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13768055	13768055	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13768055G>T	uc001rbt.2	-	7	1826	c.1647C>A	c.(1645-1647)GCC>GCA	p.A549A		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	549	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)	TACCTAAGAAGGCAGAAGGTG	0.502													6	101	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15669838	15669838	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15669838A>G	uc001rcv.1	+	9	1901	c.1727A>G	c.(1726-1728)GAG>GGG	p.E576G	PTPRO_uc001rcw.1_Missense_Mutation_p.E576G|PTPRO_uc001rcu.1_Missense_Mutation_p.E576G	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	576	Fibronectin type-III 6.|Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				ATGACATCAGAGTGGACCACC	0.448													14	84	---	---	---	---	PASS
PIK3C2G	5288	broad.mit.edu	37	12	18691185	18691185	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18691185G>T	uc001rdt.2	+	24	3412	c.3296G>T	c.(3295-3297)TGC>TTC	p.C1099F	PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Missense_Mutation_p.C1140F|PIK3C2G_uc010sic.1_Missense_Mutation_p.C918F	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma	1099	PI3K/PI4K.				cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				GTGGAACTTTGCTGTCGTGCT	0.383													37	31	---	---	---	---	PASS
PLEKHA5	54477	broad.mit.edu	37	12	19511295	19511295	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19511295A>G	uc001reb.2	+	21	2860	c.2774A>G	c.(2773-2775)AAT>AGT	p.N925S	PLEKHA5_uc010sie.1_Missense_Mutation_p.N1086S|PLEKHA5_uc001rea.2_Missense_Mutation_p.N983S|PLEKHA5_uc009zin.2_Missense_Mutation_p.N683S|PLEKHA5_uc010sif.1_Missense_Mutation_p.N914S|PLEKHA5_uc010sig.1_Missense_Mutation_p.N907S|PLEKHA5_uc010sih.1_Missense_Mutation_p.N880S|PLEKHA5_uc001rec.1_Missense_Mutation_p.N734S|PLEKHA5_uc009zio.2_Missense_Mutation_p.N191S	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	925							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AAAGGGTTAAATGTTATCGGT	0.398													8	48	---	---	---	---	PASS
PDE3A	5139	broad.mit.edu	37	12	20766412	20766412	+	Silent	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20766412C>G	uc001reh.1	+	3	1069	c.1047C>G	c.(1045-1047)GTC>GTG	p.V349V		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	349					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding	p.V349I(1)		ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	ACATCGCCGTCATGGGCGAGG	0.522													9	60	---	---	---	---	PASS
PDE3A	5139	broad.mit.edu	37	12	20766502	20766502	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20766502C>G	uc001reh.1	+	3	1159	c.1137C>G	c.(1135-1137)AAC>AAG	p.N379K		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	379					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	CCGTGAGCAACTTGCTCAGCA	0.552													18	65	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21011372	21011372	+	Splice_Site	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21011372G>T	uc001rek.2	+	4	353	c.227_splice	c.e4-1	p.G76_splice	SLCO1B3_uc001rel.2_Splice_Site_p.G76_splice|SLCO1B3_uc010sil.1_Splice_Site_p.G76_splice|LST-3TM12_uc010sim.1_Splice_Site_p.G76_splice	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						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)					TTTTTTTCTAGGAAATTTGCT	0.274													17	10	---	---	---	---	PASS
LST-3TM12	338821	broad.mit.edu	37	12	21207483	21207483	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21207483G>T	uc010sin.1	+	10	1454	c.1454G>T	c.(1453-1455)AGG>ATG	p.R485M	SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Missense_Mutation_p.R532M	NM_001009562	NP_001009562	Q71QF0	Q71QF0_HUMAN	liver-specific organic anion transporter 3TM12	485						membrane	transporter activity				0						GCTTGTACAAGGAAATCTTAC	0.393													25	15	---	---	---	---	PASS
OVCH1	341350	broad.mit.edu	37	12	29648370	29648370	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29648370G>A	uc001rix.1	-	4	302	c.302C>T	c.(301-303)ACT>ATT	p.T101I		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	101	Peptidase S1 1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGAAGTCACAGTTATATTCTT	0.368													11	37	---	---	---	---	PASS
DDX11	1663	broad.mit.edu	37	12	31254762	31254762	+	Intron	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31254762C>T	uc001rjt.1	+						DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron|DDX11_uc009zjn.1_Intron|DDX11_uc009zjo.1_5'Flank	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CCTTTCCTTCCTTAGATGGAC	0.592										Multiple Myeloma(12;0.14)			34	36	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32137484	32137484	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32137484G>T	uc001rks.2	+	4	4009	c.3595G>T	c.(3595-3597)GAG>TAG	p.E1199*	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1199										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			CTCATCTTCAGAGGAAGAGAA	0.418													15	59	---	---	---	---	PASS
ABCD2	225	broad.mit.edu	37	12	40013232	40013232	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40013232G>T	uc001rmb.2	-	1	612	c.186C>A	c.(184-186)AAC>AAA	p.N62K		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	62	Interaction with PEX19.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						GTATTTCTGTGTTCTCTGCAG	0.448													12	54	---	---	---	---	PASS
COL2A1	1280	broad.mit.edu	37	12	48368455	48368455	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48368455C>A	uc001rqu.2	-						COL2A1_uc001rqt.2_Intron|COL2A1_uc009zkw.2_Intron|COL2A1_uc001rqv.2_Intron	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor						axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CCCAGGTACTCACATGGAAGC	0.478													6	132	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49425673	49425673	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49425673C>T	uc001rta.3	-	39	12815	c.12815G>A	c.(12814-12816)GGC>GAC	p.G4272D		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4272	Pro-rich.|Gln-rich.				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						CTGGAGGGGGCCTGTCTGTGG	0.687			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			6	8	---	---	---	---	PASS
PRPH	5630	broad.mit.edu	37	12	49691473	49691473	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49691473G>A	uc001rtu.2	+	7	1306	c.1231G>A	c.(1231-1233)GTC>ATC	p.V411I		NM_006262	NP_006253	P41219	PERI_HUMAN	peripherin	411	Tail.						structural molecule activity				0						CTCCGTGCCCGTCCATTCTTT	0.428													6	45	---	---	---	---	PASS
KCNH3	23416	broad.mit.edu	37	12	49934881	49934881	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49934881G>T	uc001ruh.1	+	2	536	c.276G>T	c.(274-276)GAG>GAT	p.E92D	KCNH3_uc010smj.1_Missense_Mutation_p.E32D	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	92	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0						AGCACAAGGAGTTCAAGGCTG	0.632													12	13	---	---	---	---	PASS
TMEM5	10329	broad.mit.edu	37	12	64199137	64199137	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64199137G>C	uc001srq.1	+	5	971	c.867G>C	c.(865-867)TTG>TTC	p.L289F	TMEM5_uc001srr.1_Missense_Mutation_p.L186F|TMEM5_uc001srs.1_Missense_Mutation_p.L29F	NM_014254	NP_055069	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	289	Extracellular (Potential).					integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		TGAACATTTTGAAAAAAGATG	0.358													12	59	---	---	---	---	PASS
DYRK2	8445	broad.mit.edu	37	12	68051114	68051114	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68051114A>G	uc001str.3	+	3	829	c.427A>G	c.(427-429)ATG>GTG	p.M143V	DYRK2_uc001sts.3_Missense_Mutation_p.M70V	NM_006482	NP_006473	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	143					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|smoothened signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		TCTAAAGTCCATGGAAGGCAT	0.527													8	10	---	---	---	---	PASS
EEA1	8411	broad.mit.edu	37	12	93221723	93221723	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93221723C>A	uc001tck.2	-	12	1634	c.1369G>T	c.(1369-1371)GAT>TAT	p.D457Y		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	457	Gln/Glu/Lys-rich.|Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3						AGTTGTAAATCAGCCACTTGT	0.403													10	72	---	---	---	---	PASS
ANO4	121601	broad.mit.edu	37	12	101514370	101514370	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101514370A>G	uc010svm.1	+	26	3215	c.2643A>G	c.(2641-2643)CTA>CTG	p.L881L	ANO4_uc001thw.2_Silent_p.L846L|ANO4_uc001thx.2_Silent_p.L881L|ANO4_uc001thy.2_Silent_p.L401L	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	881	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						GGCATGTCCTAGCTGCTCGAT	0.408										HNSCC(74;0.22)			9	13	---	---	---	---	PASS
MYBPC1	4604	broad.mit.edu	37	12	102045125	102045125	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102045125C>A	uc001tii.2	+	14	1507	c.1405C>A	c.(1405-1407)CTA>ATA	p.L469I	MYBPC1_uc001tif.1_Missense_Mutation_p.L482I|MYBPC1_uc001tig.2_Missense_Mutation_p.L494I|MYBPC1_uc010svq.1_Missense_Mutation_p.L456I|MYBPC1_uc001tih.2_Missense_Mutation_p.L494I|MYBPC1_uc001tij.2_Missense_Mutation_p.L469I|MYBPC1_uc010svr.1_Missense_Mutation_p.L469I|MYBPC1_uc010svs.1_Missense_Mutation_p.L469I|MYBPC1_uc010svt.1_Missense_Mutation_p.L457I|MYBPC1_uc010svu.1_Missense_Mutation_p.L450I|MYBPC1_uc001tik.2_Missense_Mutation_p.L443I	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	469	Ig-like C2-type 4.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						TAAAAATGGCCTACCTGTTCA	0.453													6	172	---	---	---	---	PASS
HCFC2	29915	broad.mit.edu	37	12	104487333	104487333	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104487333A>G	uc001tkj.3	+	10	1557	c.1454A>G	c.(1453-1455)AAA>AGA	p.K485R	HCFC2_uc009zul.2_RNA	NM_013320	NP_037452	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	485					regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3						ATGCTAAGGAAAAATGAAGGT	0.318													7	34	---	---	---	---	PASS
IFT81	28981	broad.mit.edu	37	12	110565897	110565897	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110565897G>A	uc001tqi.2	+	3	321	c.191G>A	c.(190-192)CGA>CAA	p.R64Q	IFT81_uc001tqh.2_Missense_Mutation_p.R64Q|IFT81_uc001tqj.2_RNA|IFT81_uc001tqg.2_Missense_Mutation_p.R64Q	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	64					cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1						ACAGCCAAACGAATGTTGAGC	0.343													6	51	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112673472	112673472	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112673472C>T	uc009zwc.2	-	29	4313	c.4295G>A	c.(4294-4296)CGG>CAG	p.R1432Q		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						CAGCGCCGCCCGGCACAGCTG	0.587													16	29	---	---	---	---	PASS
OAS2	4939	broad.mit.edu	37	12	113435444	113435444	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113435444A>G	uc001tuj.2	+	4	887	c.747A>G	c.(745-747)AGA>AGG	p.R249R	OAS2_uc001tui.1_Silent_p.R249R	NM_016817	NP_058197	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2 isoform 1	249	OAS domain 1.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|membrane|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(1)	1						AAGGCGTCAGAACCGTACTGG	0.498													8	28	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	130184572	130184572	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130184572G>A	uc009zyl.1	-	2	1079	c.751C>T	c.(751-753)CGG>TGG	p.R251W		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	251	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGGCCTGTCCGGATCCCATTG	0.617													24	21	---	---	---	---	PASS
GPR133	283383	broad.mit.edu	37	12	131561428	131561428	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131561428T>C	uc001uit.3	+						GPR133_uc010tbm.1_Intron|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		AGGTACCCTCTGCACAGGGGA	0.592													28	24	---	---	---	---	PASS
POLE	5426	broad.mit.edu	37	12	133220500	133220500	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133220500C>T	uc001uks.1	-	33	4257	c.4213G>A	c.(4213-4215)GAC>AAC	p.D1405N	POLE_uc001ukq.1_5'Flank|POLE_uc001ukr.1_Missense_Mutation_p.D209N|POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Missense_Mutation_p.D1378N	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	1405					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		TGGTACATGTCCTCTGGCACT	0.537								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					15	55	---	---	---	---	PASS
ATP8A2	51761	broad.mit.edu	37	13	26436473	26436473	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26436473C>T	uc001uqk.2	+	33	3252	c.3110C>T	c.(3109-3111)ACC>ATC	p.T1037I	ATP8A2_uc010tdi.1_Missense_Mutation_p.T972I|ATP8A2_uc010tdj.1_RNA|ATP8A2_uc010aaj.1_Missense_Mutation_p.T587I	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	997	Helical; (Potential).				ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AGCATGCTGACCTGGCTGGTG	0.532													26	10	---	---	---	---	PASS
SLC7A1	6541	broad.mit.edu	37	13	30091888	30091888	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30091888G>C	uc001uso.2	-	10	1719	c.1332C>G	c.(1330-1332)GCC>GCG	p.A444A		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	444	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CGGAAGTACTGGCCATCTGGT	0.502													6	41	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38143490	38143490	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38143490C>T	uc001uwo.3	-	21	2496	c.2378G>A	c.(2377-2379)GGT>GAT	p.G793D	POSTN_uc010tet.1_Missense_Mutation_p.G294D|POSTN_uc001uwp.3_Missense_Mutation_p.G736D|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Missense_Mutation_p.G766D|POSTN_uc010tev.1_Missense_Mutation_p.G706D|POSTN_uc010tew.1_Intron	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	793					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)		ACCATCACCACCTTCAATGAA	0.363													23	11	---	---	---	---	PASS
NHLRC3	387921	broad.mit.edu	37	13	39612853	39612853	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39612853G>A	uc001uxc.2	+	1	399	c.77G>A	c.(76-78)GGC>GAC	p.G26D	C13orf23_uc001uwy.2_5'Flank|C13orf23_uc001uwz.2_5'Flank|NHLRC3_uc001uxa.1_Missense_Mutation_p.G26D|NHLRC3_uc001uxb.1_Missense_Mutation_p.G26D|NHLRC3_uc001uxd.2_Missense_Mutation_p.G26D|NHLRC3_uc001uxe.2_Intron	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a	26						extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		CGTTTTTGTGGCTCTCCAGTG	0.587													14	43	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109437976	109437976	+	Intron	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109437976T>G	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TTTTTCTTTTTATCTAGGCTG	0.358													6	14	---	---	---	---	PASS
OR4M1	441670	broad.mit.edu	37	14	20249004	20249004	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20249004G>A	uc010tku.1	+	1	523	c.523G>A	c.(523-525)GAC>AAC	p.D175N		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAATGAGTTAGACAGTTACTT	0.488													8	158	---	---	---	---	PASS
OR4K1	79544	broad.mit.edu	37	14	20403995	20403995	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20403995C>T	uc001vwj.1	+	1	170	c.170C>T	c.(169-171)TCT>TTT	p.S57F		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	57	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		CATTTGAACTCTCCTATGTAC	0.363													81	95	---	---	---	---	PASS
SUPT16H	11198	broad.mit.edu	37	14	21831050	21831050	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21831050T>C	uc001wao.2	-	14	1907	c.1568A>G	c.(1567-1569)CAT>CGT	p.H523R		NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation	523					DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TTCCCGAATATGTGGTTCCTT	0.408													54	40	---	---	---	---	PASS
RNF31	55072	broad.mit.edu	37	14	24618034	24618034	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24618034C>G	uc001wmn.1	+	5	829	c.580C>G	c.(580-582)CCC>GCC	p.P194A	PSME2_uc001wmj.2_5'Flank|PSME2_uc001wmk.2_5'Flank|RNF31_uc001wml.1_Missense_Mutation_p.P43A|RNF31_uc001wmm.1_Intron|RNF31_uc010alg.1_Missense_Mutation_p.P9A|RNF31_uc001wmo.1_5'Flank|RNF31_uc001wmp.2_5'Flank	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	194	Polyubiquitin-binding.				CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)		AGAATTTGACCCCCTATTGAG	0.473													23	132	---	---	---	---	PASS
SSTR1	6751	broad.mit.edu	37	14	38679162	38679162	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38679162C>A	uc001wul.1	+	3	1185	c.568C>A	c.(568-570)CTG>ATG	p.L190M	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	190	Helical; Name=4; (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)	GCTCGTCATCCTGCCCATCGT	0.662													18	29	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42356638	42356638	+	Silent	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356638T>C	uc001wvm.2	+	3	2008	c.810T>C	c.(808-810)ACT>ACC	p.T270T	LRFN5_uc010ana.2_Silent_p.T270T	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	270	Extracellular (Potential).|LRRCT.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CACTTTTAACTGGCCGCTACT	0.468										HNSCC(30;0.082)			15	90	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42356639	42356639	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356639G>T	uc001wvm.2	+	3	2009	c.811G>T	c.(811-813)GGC>TGC	p.G271C	LRFN5_uc010ana.2_Missense_Mutation_p.G271C	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	271	Extracellular (Potential).|LRRCT.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		ACTTTTAACTGGCCGCTACTT	0.473										HNSCC(30;0.082)			18	88	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45540921	45540921	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45540921A>T	uc001wvv.2	+	18	5026	c.4817A>T	c.(4816-4818)TAC>TTC	p.Y1606F	FAM179B_uc001wvw.2_Missense_Mutation_p.Y1659F|FAM179B_uc010anc.2_RNA	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1606							binding			skin(2)|upper_aerodigestive_tract(1)	3						TTAGACAATTACTTACTTCTA	0.313													19	27	---	---	---	---	PASS
FERMT2	10979	broad.mit.edu	37	14	53417288	53417288	+	5'UTR	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53417288G>A	uc001xad.2	-	2					FERMT2_uc001xac.2_5'UTR|FERMT2_uc001xae.2_5'UTR|FERMT2_uc001xaf.2_5'UTR	NM_006832	NP_006823	Q96AC1	FERM2_HUMAN	fermitin family homolog 2 isoform 1						actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding				0	Breast(41;0.0342)					CAGAGCCATGGCTCCTTCCTG	0.627													65	65	---	---	---	---	PASS
BMP4	652	broad.mit.edu	37	14	54416746	54416746	+	3'UTR	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54416746G>A	uc001xal.3	-	3					BMP4_uc010aoh.2_3'UTR|BMP4_uc001xao.3_3'UTR|BMP4_uc001xan.3_3'UTR	NM_130851	NP_570912	P12644	BMP4_HUMAN	bone morphogenetic protein 4 preproprotein						activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway	extracellular space|proteinaceous extracellular matrix	BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity				0						AGGACTGCCTGATCTCAGCGG	0.388													26	6	---	---	---	---	PASS
ARID4A	5926	broad.mit.edu	37	14	58817845	58817845	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58817845G>T	uc001xdp.2	+	16	1713	c.1459G>T	c.(1459-1461)GAG>TAG	p.E487*	ARID4A_uc001xdo.2_Nonsense_Mutation_p.E487*|ARID4A_uc001xdq.2_Nonsense_Mutation_p.E487*|ARID4A_uc010apg.1_Nonsense_Mutation_p.E165*	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	487					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6						AATTGAAGAAGAGAAAACAGA	0.328													5	78	---	---	---	---	PASS
DCAF4	26094	broad.mit.edu	37	14	73425438	73425438	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73425438G>T	uc001xng.2	+	14	1633	c.1413G>T	c.(1411-1413)CGG>CGT	p.R471R	DCAF4_uc001xnj.2_Silent_p.R465R|DCAF4_uc010ttr.1_Silent_p.R450R|DCAF4_uc001xnh.2_Silent_p.R371R|DCAF4_uc010tts.1_Silent_p.R411R|DCAF4_uc010ttt.1_Silent_p.R257R|DCAF4_uc001xni.2_Silent_p.R301R	NM_015604	NP_056419	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4 isoform 1	471						CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)|skin(1)	3						TCTCGTCGCGGCTGGGGGGCT	0.647													14	37	---	---	---	---	PASS
C14orf115	55237	broad.mit.edu	37	14	74824319	74824319	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74824319C>A	uc001xpw.3	+	2	1024	c.833C>A	c.(832-834)CCT>CAT	p.P278H		NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	hypothetical protein LOC55237	278					transposition, DNA-mediated		DNA binding|transposase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00147)		AACCGTGAACCTGGCCTCAGC	0.652													25	17	---	---	---	---	PASS
KIAA1737	85457	broad.mit.edu	37	14	77580133	77580133	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77580133G>T	uc001xtd.2	+	4	851	c.672G>T	c.(670-672)GAG>GAT	p.E224D	KIAA1737_uc001xtc.1_Missense_Mutation_p.E126D	NM_033426	NP_219494	Q9C0C6	K1737_HUMAN	KIAA1737 protein	224											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		AACTTGCCGAGGACTCAGCTC	0.602													5	58	---	---	---	---	PASS
FLRT2	23768	broad.mit.edu	37	14	86088550	86088550	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86088550A>T	uc001xvr.2	+	2	1459	c.692A>T	c.(691-693)AAG>ATG	p.K231M	FLRT2_uc010atd.2_Missense_Mutation_p.K231M	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	231	Extracellular (Potential).|LRR 8.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CATCTCACCAAGCTCAAGGAA	0.522													16	90	---	---	---	---	PASS
PPP4R4	57718	broad.mit.edu	37	14	94712742	94712742	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94712742C>A	uc001ycs.1	+	14	1631	c.1477C>A	c.(1477-1479)CGA>AGA	p.R493R		NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1	493						cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4						TGCTGAACAGCGAGCTGCAGC	0.403													15	45	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106067401	106067401	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106067401C>A	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Missense_Mutation_p.G167V|uc001yrx.1_Missense_Mutation_p.G114V|uc001yrv.1_5'Flank|uc001yru.2_5'Flank|uc010axq.1_5'Flank					Parts of antibodies, mostly variable regions.												0						CATGACCTGCCCGTCCTCCAG	0.647													4	23	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107113932	107113932	+	RNA	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107113932G>T	uc010tyt.1	-	84		c.3941C>A								Parts of antibodies, mostly variable regions.												0						CGGACCCAGTGCATAGCATAG	0.547													71	179	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107113933	107113933	+	RNA	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107113933C>T	uc010tyt.1	-	84		c.3940G>A								Parts of antibodies, mostly variable regions.												0						GGACCCAGTGCATAGCATAGC	0.547													69	179	---	---	---	---	PASS
GABRB3	2562	broad.mit.edu	37	15	26812801	26812801	+	Silent	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26812801A>T	uc001zaz.2	-	7	904	c.762T>A	c.(760-762)TCT>TCA	p.S254S	GABRB3_uc010uae.1_Silent_p.S169S|GABRB3_uc001zba.2_Silent_p.S254S|GABRB3_uc001zbb.2_Silent_p.S310S	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	254	Helical; (Probable).				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)	TTATCAGTATAGAGGGCATAT	0.423													19	35	---	---	---	---	PASS
TGM5	9333	broad.mit.edu	37	15	43559035	43559035	+	Intron	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43559035T>C	uc001zrd.1	-						TGM5_uc001zre.1_Intron	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1						epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GGGCTTTCCCTACCTTGGGCC	0.552													17	9	---	---	---	---	PASS
SLC27A2	11001	broad.mit.edu	37	15	50526174	50526174	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50526174G>T	uc001zxw.2	+	9	1897	c.1665G>T	c.(1663-1665)AGG>AGT	p.R555S	SLC27A2_uc010bes.2_Missense_Mutation_p.R502S|SLC27A2_uc001zxx.2_Missense_Mutation_p.R320S	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid	555	Cytoplasmic (Potential).				bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)|skin(1)	2		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		GTTATGCAAGGCCCCGGTTTC	0.433													39	16	---	---	---	---	PASS
CCPG1	9236	broad.mit.edu	37	15	55652654	55652654	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55652654G>T	uc002acv.1	-	8	1482	c.1317C>A	c.(1315-1317)ACC>ACA	p.T439T	CCPG1_uc002acy.2_Silent_p.T439T|CCPG1_uc002acu.1_Silent_p.T295T|CCPG1_uc002acw.1_Silent_p.T164T|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Silent_p.T439T|CCPG1_uc002acz.1_Silent_p.T439T	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	439	Potential.|Lumenal (Potential).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		GCTGTTCGAAGGTTAGCTTCC	0.413													7	142	---	---	---	---	PASS
FAM81A	145773	broad.mit.edu	37	15	59752205	59752205	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59752205C>A	uc002agc.2	+	3	281	c.94C>A	c.(94-96)CAG>AAG	p.Q32K	FAM81A_uc010uha.1_Missense_Mutation_p.Q32K	NM_152450	NP_689663	Q8TBF8	FA81A_HUMAN	hypothetical protein LOC145773	32										ovary(1)	1						CCTCGTGGAGCAGCTGGAAGA	0.532													14	27	---	---	---	---	PASS
SMAD3	4088	broad.mit.edu	37	15	67482744	67482744	+	Intron	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67482744C>G	uc002aqj.2	+						SMAD3_uc010ujr.1_Intron|SMAD3_uc010ujs.1_Intron|SMAD3_uc010ujt.1_Intron	NM_005902	NP_005893	P84022	SMAD3_HUMAN	mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		TTCCCTATTTCTTACAGGAGA	0.517													9	17	---	---	---	---	PASS
HCN4	10021	broad.mit.edu	37	15	73624553	73624553	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73624553G>C	uc002avp.2	-	3	2284	c.1290C>G	c.(1288-1290)CAC>CAG	p.H430Q		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	430	Helical; Name=Segment S5; (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)		AGCCGTCCCAGTGGCAGAGCA	0.612													3	32	---	---	---	---	PASS
C15orf27	123591	broad.mit.edu	37	15	76449078	76449078	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76449078A>G	uc002bbq.2	+	4	516	c.361A>G	c.(361-363)ATA>GTA	p.I121V	C15orf27_uc010bkp.2_Intron|C15orf27_uc002bbr.2_Intron	NM_152335	NP_689548	Q2M3C6	CO027_HUMAN	hypothetical protein LOC123591	121	Helical; (Potential).					integral to membrane					0						GGAACTTCTAATAGATATAAA	0.433													9	34	---	---	---	---	PASS
TM6SF1	53346	broad.mit.edu	37	15	83795599	83795599	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83795599G>C	uc002bjp.2	+	8	910	c.801G>C	c.(799-801)CAG>CAC	p.Q267H	TM6SF1_uc010bmq.2_Intron|TM6SF1_uc002bjq.2_Intron|TM6SF1_uc010bmr.2_Intron|TM6SF1_uc002bjr.2_Missense_Mutation_p.Q119H	NM_023003	NP_075379	Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1 isoform 1	267	Helical; (Potential).					integral to membrane				ovary(1)	1						CTAAAATTCAGGTCAAGTAGT	0.299													33	104	---	---	---	---	PASS
AGBL1	123624	broad.mit.edu	37	15	86800204	86800204	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86800204G>T	uc002blz.1	+	7	798	c.718G>T	c.(718-720)GTC>TTC	p.V240F		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	240					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						TGCCTTCCCGGTCCCCGGGTG	0.507													8	56	---	---	---	---	PASS
OR4F6	390648	broad.mit.edu	37	15	102346508	102346508	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102346508G>C	uc010utr.1	+	1	586	c.586G>C	c.(586-588)GGA>CGA	p.G196R		NM_001005326	NP_001005326	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F,	196	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			CTACACATTGGGATTCATGGT	0.358													38	159	---	---	---	---	PASS
CCNF	899	broad.mit.edu	37	16	2505515	2505515	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2505515G>T	uc002cqd.1	+	16	1923	c.1835G>T	c.(1834-1836)TGC>TTC	p.C612F	CCNF_uc002cqe.1_Missense_Mutation_p.C304F	NM_001761	NP_001752	P41002	CCNF_HUMAN	cyclin F	612	PEST.				cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding			central_nervous_system(1)|kidney(1)	2		Ovarian(90;0.17)				CTGGACTGCTGCTCTGGCTAT	0.642													3	10	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3900926	3900926	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3900926C>A	uc002cvv.2	-	2	374	c.170G>T	c.(169-171)GGG>GTG	p.G57V	CREBBP_uc002cvw.2_Missense_Mutation_p.G57V	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	57					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AACAAGGTTCCCACTGTTTAA	0.428			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				6	56	---	---	---	---	PASS
SRL	6345	broad.mit.edu	37	16	4247818	4247818	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4247818G>C	uc002cvz.3	-	4	371	c.358C>G	c.(358-360)CGC>GGC	p.R120G	SRL_uc002cvy.3_RNA	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin	579						sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5						AGCTGATAGCGAGTATTTTCC	0.383													30	16	---	---	---	---	PASS
CPPED1	55313	broad.mit.edu	37	16	12758807	12758807	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12758807C>A	uc002dca.3	-	4	992	c.881G>T	c.(880-882)AGT>ATT	p.S294I	CPPED1_uc002dcb.3_Missense_Mutation_p.S152I|CPPED1_uc002dbz.3_RNA	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain	294							hydrolase activity|metal ion binding				0						CTCATCTAGACTGTAGTATCG	0.507													12	51	---	---	---	---	PASS
MYH11	4629	broad.mit.edu	37	16	15814079	15814079	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15814079C>T	uc002ddy.2	-	34	4989	c.4882G>A	c.(4882-4884)GAC>AAC	p.D1628N	MYH11_uc002ddv.2_Missense_Mutation_p.D1635N|MYH11_uc002ddw.2_Missense_Mutation_p.D1628N|MYH11_uc002ddx.2_Missense_Mutation_p.D1635N|MYH11_uc010bvg.2_Missense_Mutation_p.D1460N|NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron|MYH11_uc010bvh.2_Missense_Mutation_p.D334N|NDE1_uc002ddz.1_5'Flank	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	1628	Potential.				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						AGCTCCAGGTCTTTCAGGTCC	0.587			T	CBFB	AML								6	48	---	---	---	---	PASS
XPO6	23214	broad.mit.edu	37	16	28109925	28109925	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28109925C>A	uc002dpa.1	-	24	3813	c.3312G>T	c.(3310-3312)CTG>CTT	p.L1104L	XPO6_uc002dpb.1_Silent_p.L1090L|XPO6_uc010vcp.1_Silent_p.L1103L	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6	1104					protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2						GGTCGTTGACCAGCCTGTGCA	0.607													16	8	---	---	---	---	PASS
SULT1A1	6817	broad.mit.edu	37	16	28619685	28619685	+	Missense_Mutation	SNP	G	A	A	rs142537541		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28619685G>A	uc002dqi.2	-	3	772	c.299C>T	c.(298-300)CCG>CTG	p.P100L	uc010vct.1_Intron|SULT1A1_uc002dqj.2_Missense_Mutation_p.P100L|SULT1A1_uc002dqk.2_Missense_Mutation_p.P100L|SULT1A1_uc002dql.2_Missense_Mutation_p.P100L|SULT1A1_uc002dqm.2_Intron|SULT1A1_uc002dqn.2_Missense_Mutation_p.P191L|SULT1A1_uc002dqo.2_Missense_Mutation_p.P100L|SULT1A1_uc002dqp.2_Missense_Mutation_p.P100L	NM_177534	NP_803878	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A,	100					3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						TCGTGGGGCCGGTGTGTCTTT	0.537													21	73	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28841382	28841382	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28841382G>T	uc002drc.2	+						uc010vct.1_Intron|ATXN2L_uc010byl.1_Intron|ATXN2L_uc002drb.2_Intron|ATXN2L_uc002dqy.2_Intron|ATXN2L_uc002dra.2_Intron|ATXN2L_uc002dqz.2_Intron|ATXN2L_uc010vdb.1_Intron|ATXN2L_uc002dre.2_Intron|ATXN2L_uc002drf.2_Intron	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A							membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GCATCCAGGTGACTGTTGCAA	0.587													5	7	---	---	---	---	PASS
SEZ6L2	26470	broad.mit.edu	37	16	29888689	29888689	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29888689G>A	uc002duq.3	-	11	2052	c.1812C>T	c.(1810-1812)CGC>CGT	p.R604R	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Silent_p.R534R|SEZ6L2_uc002dur.3_Silent_p.R534R|SEZ6L2_uc002dus.3_Silent_p.R490R|SEZ6L2_uc010vec.1_Silent_p.R604R|SEZ6L2_uc010ved.1_Silent_p.R560R	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	604	CUB 3.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						AGGAGAGAAGGCGGCGGCGCG	0.662													6	0	---	---	---	---	PASS
SETD1A	9739	broad.mit.edu	37	16	30975589	30975589	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30975589C>T	uc002ead.1	+	6	1500	c.814C>T	c.(814-816)CCC>TCC	p.P272S	SETD1A_uc002eae.1_Missense_Mutation_p.P272S	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	272	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3						CCAAGGAACCCCCTACACGTC	0.632													10	35	---	---	---	---	PASS
CDH16	1014	broad.mit.edu	37	16	66950320	66950320	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66950320G>A	uc002eql.2	-	4	215	c.142C>T	c.(142-144)CGT>TGT	p.R48C	CDH16_uc010cdy.2_Missense_Mutation_p.R48C|CDH16_uc002eqm.2_Missense_Mutation_p.R48C	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	48	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|upper_aerodigestive_tract(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		GCCCCCTCACGGGGCAGCGGC	0.552													7	18	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	71103239	71103239	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71103239C>T	uc002ezr.2	-	14	2033	c.1905G>A	c.(1903-1905)ATG>ATA	p.M635I	HYDIN_uc010cfz.1_Missense_Mutation_p.M380I|HYDIN_uc002ezv.2_Missense_Mutation_p.M635I|HYDIN_uc010vmc.1_Missense_Mutation_p.M652I|HYDIN_uc010vmd.1_Missense_Mutation_p.M662I|HYDIN_uc002ezw.3_Missense_Mutation_p.M652I	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	635										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CTTTTGGTTTCATTGAGGATA	0.483													8	54	---	---	---	---	PASS
PMFBP1	83449	broad.mit.edu	37	16	72159293	72159293	+	Silent	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72159293C>G	uc002fcc.3	-	16	2452	c.2280G>C	c.(2278-2280)GTG>GTC	p.V760V	PMFBP1_uc002fcd.2_Silent_p.V755V|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Silent_p.V610V|PMFBP1_uc010cgo.1_Silent_p.V51V	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	760										ovary(2)	2		Ovarian(137;0.179)				TCTCTGAGGTCACGTGATTGA	0.488											OREG0023927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	93	---	---	---	---	PASS
RFWD3	55159	broad.mit.edu	37	16	74666541	74666541	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74666541T>C	uc002fda.2	-	9	1555	c.1457A>G	c.(1456-1458)AAC>AGC	p.N486S	RFWD3_uc010vmx.1_Missense_Mutation_p.N6S|RFWD3_uc010cgq.2_Missense_Mutation_p.N486S	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	486					DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3						GCTCTTCATGTTGGCAGTACT	0.433													6	28	---	---	---	---	PASS
VAT1L	57687	broad.mit.edu	37	16	77850871	77850871	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77850871C>T	uc002ffg.1	+	2	384	c.287C>T	c.(286-288)CCC>CTC	p.P96L		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	96							oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						GACAACCCTCCCAAGACTCCC	0.438													11	56	---	---	---	---	PASS
LRRC50	123872	broad.mit.edu	37	16	84188191	84188191	+	Missense_Mutation	SNP	G	A	A	rs34897947		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84188191G>A	uc002fhl.3	+	4	543	c.362G>A	c.(361-363)CGC>CAC	p.R121H	LRRC50_uc010chi.1_RNA	NM_178452	NP_848547	Q8NEP3	DAAF1_HUMAN	leucine rich repeat containing 50	121	LRR 1.				axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0						GGTTTTGATCGCATTGAGAAC	0.478									Kartagener_syndrome				5	30	---	---	---	---	PASS
FOXF1	2294	broad.mit.edu	37	16	86544553	86544553	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86544553G>C	uc002fjl.2	+	1	421	c.378G>C	c.(376-378)CCG>CCC	p.P126P	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	126	Fork-head.				branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0						CCATCGACCCGGCCAGCGAGT	0.632													28	21	---	---	---	---	PASS
ZNF778	197320	broad.mit.edu	37	16	89294627	89294627	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89294627C>A	uc002fmv.2	+	6	2186	c.1847C>A	c.(1846-1848)CCC>CAC	p.P616H	ZNF778_uc010vpf.1_Intron|ZNF778_uc002fmw.1_Missense_Mutation_p.P574H|ZNF778_uc010vpg.1_Missense_Mutation_p.P379H	NM_182531	NP_872337	Q96MU6	ZN778_HUMAN	zinc finger protein 778	616					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GGTGAGAAACCCTACATATGT	0.463													19	70	---	---	---	---	PASS
RAP1GAP2	23108	broad.mit.edu	37	17	2866729	2866729	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2866729C>A	uc010ckd.2	+	6	342	c.252C>A	c.(250-252)GAC>GAA	p.D84E	RAP1GAP2_uc010cke.2_Missense_Mutation_p.D69E	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1	84					regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						TGCAGGACGACTATATCCCAT	0.587													25	69	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577046	7577046	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577046C>A	uc002gim.2	-	8	1086	c.892G>T	c.(892-894)GAG>TAG	p.E298*	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Nonsense_Mutation_p.E298*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.E166*|TP53_uc010cng.1_Nonsense_Mutation_p.E166*|TP53_uc002gii.1_Nonsense_Mutation_p.E166*|TP53_uc010cnh.1_Nonsense_Mutation_p.E298*|TP53_uc010cni.1_Nonsense_Mutation_p.E298*|TP53_uc002gij.2_Nonsense_Mutation_p.E298*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	298	Interaction with HIPK1 (By similarity).		E -> V (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> A (in a sporadic cancer; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> D (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.E298*(35)|p.0?(7)|p.E298K(2)|p.?(2)|p.E298V(2)|p.L299fs*2(1)|p.L265_K305del41(1)|p.E298A(1)|p.E298fs*53(1)|p.G293fs*1(1)|p.E298fs*47(1)|p.E298E(1)|p.E298Q(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(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)		GGGGGCAGCTCGTGGTGAGGC	0.567		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)			20	12	---	---	---	---	PASS
CNTROB	116840	broad.mit.edu	37	17	7840130	7840130	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7840130C>A	uc002gjq.2	+	7	1742	c.823C>A	c.(823-825)CAG>AAG	p.Q275K	CNTROB_uc002gjp.2_Missense_Mutation_p.Q275K|CNTROB_uc002gjr.2_Missense_Mutation_p.Q177K|CNTROB_uc010vum.1_5'Flank	NM_053051	NP_444279	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	275	Potential.				centriole replication|centrosome separation|cytokinesis	centriole	protein domain specific binding			breast(1)|central_nervous_system(1)	2		Prostate(122;0.173)				AAGCAAGCAGCAGGAGGTGAG	0.547													21	10	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10426947	10426947	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10426947C>A	uc010coi.2	-	37	5466	c.5338G>T	c.(5338-5340)GAC>TAC	p.D1780Y	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.D1780Y|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1780	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GCGCTGGTGTCCTGCTCCTTC	0.507													34	25	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11547942	11547942	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11547942G>T	uc002gne.2	+							NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TCTTTTGTACGAGTAGTTGCA	0.403											OREG0024185	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	26	---	---	---	---	PASS
FAM83G	644815	broad.mit.edu	37	17	18891670	18891670	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18891670C>G	uc002guw.2	-	3	747	c.580G>C	c.(580-582)GAC>CAC	p.D194H	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	194										ovary(1)|central_nervous_system(1)	2						AAGCCGGCGTCCAGCAGGTCC	0.557													7	84	---	---	---	---	PASS
ATAD5	79915	broad.mit.edu	37	17	29162409	29162409	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29162409T>A	uc002hfs.1	+	2	1656	c.1310T>A	c.(1309-1311)GTA>GAA	p.V437E	ATAD5_uc002hft.1_Missense_Mutation_p.V334E	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	437					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CTATATGAAGTAGGAAGAGAT	0.313													30	44	---	---	---	---	PASS
MYO1D	4642	broad.mit.edu	37	17	31098203	31098203	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31098203A>G	uc002hho.1	-	6	666	c.654T>C	c.(652-654)TCT>TCC	p.S218S	MYO1D_uc002hhp.1_Silent_p.S218S|MYO1D_uc010wcb.1_Silent_p.S218S	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	218	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			GGAGATGTAGAGAGCGTAGCA	0.363													5	37	---	---	---	---	PASS
NLE1	54475	broad.mit.edu	37	17	33463218	33463218	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33463218C>T	uc002hiy.1	-	9	1009	c.981G>A	c.(979-981)GAG>GAA	p.E327E	NLE1_uc010ctn.1_Silent_p.E35E|NLE1_uc002hiz.1_Silent_p.E35E	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a	327	WD 5.					nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)				TCAGAGCCCTCTCCTTCAACT	0.537													10	177	---	---	---	---	PASS
PEX12	5193	broad.mit.edu	37	17	33904432	33904432	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33904432C>A	uc002hjp.2	-	2	921	c.305G>T	c.(304-306)AGA>ATA	p.R102I		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	102	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACTAGCCAATCTCTGAGACTT	0.438													74	106	---	---	---	---	PASS
KRTAP9-2	83899	broad.mit.edu	37	17	39382974	39382974	+	Missense_Mutation	SNP	G	T	T	rs149082553	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39382974G>T	uc002hwf.2	+	1	75	c.68G>T	c.(67-69)TGC>TTC	p.C23F		NM_031961	NP_114167	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9.2	23	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament	protein binding	p.C23*(1)		upper_aerodigestive_tract(1)	1		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			AGGACCACCTGCTGGAAGCCC	0.647													5	79	---	---	---	---	PASS
KRTAP9-4	85280	broad.mit.edu	37	17	39406040	39406040	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39406040G>T	uc002hwi.2	+	1	102	c.68G>T	c.(67-69)TGC>TTC	p.C23F	KRTAP9-9_uc010wfq.1_Intron	NM_033191	NP_149461	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	23	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			AGGACCACCTGCTGGAAGCCC	0.627													27	63	---	---	---	---	PASS
KRT32	3882	broad.mit.edu	37	17	39623327	39623327	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39623327C>T	uc002hwr.2	-	1	312	c.251G>A	c.(250-252)GGC>GAC	p.G84D		NM_002278	NP_002269	Q14532	K1H2_HUMAN	keratin 32	84	Head.				epidermis development	intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000812)				GTACCAGCTGCCGGGGCCCAT	0.622													6	38	---	---	---	---	PASS
FKBP10	60681	broad.mit.edu	37	17	39974690	39974690	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39974690G>A	uc002hxv.2	+	4	963	c.638G>A	c.(637-639)GGC>GAC	p.G213D	FKBP10_uc002hxw.1_5'Flank	NM_021939	NP_068758	Q96AY3	FKB10_HUMAN	FK506 binding protein 10 precursor	213	PPIase FKBP-type 2.				protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		CTGATCAAGGGCATGGACCAG	0.587													18	24	---	---	---	---	PASS
GPATCH8	23131	broad.mit.edu	37	17	42478425	42478425	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42478425G>A	uc002igw.1	-	8	1084	c.1020C>T	c.(1018-1020)GAC>GAT	p.D340D	GPATCH8_uc002igv.1_Silent_p.D262D|GPATCH8_uc010wiz.1_Silent_p.D262D	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	340						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GCAGTCCTTGGTCAGAACTCT	0.483											OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	54	56	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45219266	45219266	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45219266G>A	uc002ild.3	-	12	1631	c.1504C>T	c.(1504-1506)CTG>TTG	p.L502L	CDC27_uc002ile.3_Silent_p.L508L|CDC27_uc002ilf.3_Silent_p.L501L|CDC27_uc010wkp.1_Silent_p.L441L|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	502	TPR 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						ATTTGGCACAGTACCCAACCA	0.348													8	172	---	---	---	---	PASS
PDK2	5164	broad.mit.edu	37	17	48185764	48185764	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48185764G>T	uc002iqc.2	+	8	948	c.844G>T	c.(844-846)GAA>TAA	p.E282*	PDK2_uc002iqb.2_Nonsense_Mutation_p.E218*	NM_002611	NP_002602	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase 2 precursor	282	Histidine kinase.				glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|nucleus	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			central_nervous_system(3)	3						CTTGGGTGAGGAAGATCTGTC	0.577									Autosomal_Dominant_Polycystic_Kidney_Disease				7	19	---	---	---	---	PASS
CUEDC1	404093	broad.mit.edu	37	17	55957105	55957105	+	Intron	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55957105T>A	uc002ivd.1	-						CUEDC1_uc002ive.1_Intron	NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1											skin(2)	2						AAGATCTAAATCAGAGGCaac	0.303													25	27	---	---	---	---	PASS
OR4D2	124538	broad.mit.edu	37	17	56247070	56247070	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56247070G>A	uc010wnp.1	+	1	54	c.54G>A	c.(52-54)TCG>TCA	p.S18S		NM_001004707	NP_001004707	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGGGGCTCTCGCAGACTCGGG	0.468													42	56	---	---	---	---	PASS
EPX	8288	broad.mit.edu	37	17	56270463	56270463	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56270463G>A	uc002ivq.2	+	2	227	c.141G>A	c.(139-141)GTG>GTA	p.V47V		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase preproprotein	47					hydrogen peroxide catabolic process		heme binding|peroxidase activity|protein binding			ovary(2)	2						AGTTGCTGGTGGATGCTGCCT	0.607													24	49	---	---	---	---	PASS
MTMR4	9110	broad.mit.edu	37	17	56573053	56573053	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56573053G>A	uc002iwj.2	-	16	2560	c.2450C>T	c.(2449-2451)CCA>CTA	p.P817L		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	817						cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGCACTCGGTGGGTTGCAAAC	0.562													13	61	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57743957	57743957	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57743957A>G	uc002ixq.1	+	12	2342	c.1899A>G	c.(1897-1899)TTA>TTG	p.L633L	CLTC_uc002ixp.2_Silent_p.L633L|CLTC_uc002ixr.1_Silent_p.L637L	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	633	Heavy chain arm.|Distal segment.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCACTGATTTATATGATATAA	0.398			T	ALK|TFE3	ALCL|renal 								20	26	---	---	---	---	PASS
RNFT1	51136	broad.mit.edu	37	17	58040613	58040613	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58040613G>A	uc002iya.2	-	2	182	c.89C>T	c.(88-90)TCA>TTA	p.S30L	uc002iye.1_5'Flank|RNFT1_uc002iyb.2_RNA|RNFT1_uc002iyc.2_5'UTR|RNFT1_uc010wop.1_Missense_Mutation_p.S30L|RNFT1_uc002iyd.3_Missense_Mutation_p.S30L	NM_016125	NP_057209	Q5M7Z0	RNFT1_HUMAN	PTD016 protein	30						integral to membrane	zinc ion binding				0	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)			CTTTTTCTCTGACCCAGATGT	0.443													17	73	---	---	---	---	PASS
DDX42	11325	broad.mit.edu	37	17	61886176	61886176	+	Intron	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61886176G>A	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron|DDX42_uc002jbx.2_Intron|DDX42_uc002jby.2_5'Flank	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						TCACAACTTTGTAGATCCATG	0.403													17	54	---	---	---	---	PASS
ABCA6	23460	broad.mit.edu	37	17	67077276	67077276	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67077276A>T	uc002jhw.1	-	37	4802	c.4627T>A	c.(4627-4629)TTG>ATG	p.L1543M		NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	1543					transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					TAGGTTAACAAAGAGGAATAC	0.373													13	57	---	---	---	---	PASS
RHBDF2	79651	broad.mit.edu	37	17	74473789	74473789	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74473789C>A	uc002jrq.1	-	7	1131	c.838G>T	c.(838-840)GAG>TAG	p.E280*	RHBDF2_uc002jrp.1_Nonsense_Mutation_p.E251*|RHBDF2_uc002jrr.1_Nonsense_Mutation_p.E132*|RHBDF2_uc010wtf.1_Nonsense_Mutation_p.E251*|RHBDF2_uc002jrs.1_Nonsense_Mutation_p.E275*	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	280	Cytoplasmic (Potential).				negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						ACCACATCCTCCTCCAGGAAG	0.637													6	91	---	---	---	---	PASS
ENGASE	64772	broad.mit.edu	37	17	77082341	77082341	+	Silent	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77082341A>G	uc002jwv.2	+	14	2150	c.2142A>G	c.(2140-2142)GAA>GAG	p.E714E	ENGASE_uc002jww.2_Silent_p.E419E	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	714						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						GTCGCATGGAATTTCTGGTGG	0.617													8	20	---	---	---	---	PASS
ZNF750	79755	broad.mit.edu	37	17	80790192	80790192	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80790192C>A	uc002kga.2	-	2	450	c.139G>T	c.(139-141)GGT>TGT	p.G47C	TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kfz.2_Intron	NM_024702	NP_078978	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	47						intracellular	zinc ion binding			central_nervous_system(1)	1	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TTACAAAGACCATACTTCATG	0.423													5	94	---	---	---	---	PASS
COLEC12	81035	broad.mit.edu	37	18	346412	346412	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:346412C>G	uc002kkm.2	-	5	1425	c.1210G>C	c.(1210-1212)GAT>CAT	p.D404H		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	404	Extracellular (Potential).				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CTCATCAAATCTTGTTGCATC	0.428													14	75	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3189056	3189056	+	Missense_Mutation	SNP	G	A	A	rs140845661	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3189056G>A	uc002klp.2	-	4	795	c.461C>T	c.(460-462)ACG>ATG	p.T154M	MYOM1_uc002klq.2_Missense_Mutation_p.T154M	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	154						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TTCTTCTTCCGTATCAGTAAT	0.383													12	109	---	---	---	---	PASS
APCDD1	147495	broad.mit.edu	37	18	10485545	10485545	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10485545G>C	uc002kom.3	+	4	1215	c.861G>C	c.(859-861)CTG>CTC	p.L287L		NM_153000	NP_694545	Q8J025	APCD1_HUMAN	adenomatosis polyposis coli down-regulated 1	287	Extracellular (Potential).				hair follicle development|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to plasma membrane	Wnt-protein binding				0				READ - Rectum adenocarcinoma(15;0.08)		AGGCAGACCTGACCATCGGCC	0.597													7	46	---	---	---	---	PASS
DSC3	1825	broad.mit.edu	37	18	28612167	28612167	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28612167T>G	uc002kwj.3	-	2	300	c.145A>C	c.(145-147)ATT>CTT	p.I49L	DSC3_uc002kwi.3_Missense_Mutation_p.I49L	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein	49					homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)			CCTCTGCCAATTATTTTGTCT	0.343													8	26	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29487430	29487430	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29487430C>G	uc002kxc.3	-	9	1746	c.1382G>C	c.(1381-1383)GGT>GCT	p.G461A	KIAA1012_uc002kxb.3_Missense_Mutation_p.G407A|KIAA1012_uc002kxd.3_RNA|KIAA1012_uc002kxe.2_Missense_Mutation_p.G461A	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	461					ER to Golgi vesicle-mediated transport	cis-Golgi network					0						AACCAAGGCACCAGCTGCATA	0.338													6	75	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31324142	31324142	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31324142C>A	uc010dmg.1	+	12	4385	c.4330C>A	c.(4330-4332)CGA>AGA	p.R1444R	ASXL3_uc002kxq.2_Silent_p.R1151R	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1444					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TTCAGGGCCTCGAAACAGGGC	0.468											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	190	---	---	---	---	PASS
NOL4	8715	broad.mit.edu	37	18	31432874	31432874	+	Silent	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31432874G>T	uc010dmi.2	-	11	2078	c.1849C>A	c.(1849-1851)CGA>AGA	p.R617R	NOL4_uc010xbs.1_Silent_p.R332R|NOL4_uc002kxr.3_Silent_p.R389R|NOL4_uc010xbt.1_Silent_p.R543R|NOL4_uc010dmh.2_Silent_p.R479R|NOL4_uc010xbu.1_Silent_p.R553R|NOL4_uc002kxt.3_Silent_p.R515R	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4	617						nucleolus	RNA binding			ovary(3)	3						GCTGATTCTCGATATCCTGCA	0.458													18	41	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32455336	32455336	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32455336G>A	uc010dmn.1	+	17	1797	c.1796G>A	c.(1795-1797)GGA>GAA	p.G599E	DTNA_uc002kxw.2_Missense_Mutation_p.G542E|DTNA_uc010dmj.2_Missense_Mutation_p.G539E|DTNA_uc002kxz.2_Missense_Mutation_p.G546E|DTNA_uc002kxy.2_Missense_Mutation_p.G539E|DTNA_uc010xby.1_Missense_Mutation_p.G289E|DTNA_uc010xbz.1_Missense_Mutation_p.G308E|DTNA_uc010xca.1_Missense_Mutation_p.G251E|DTNA_uc002kye.2_Missense_Mutation_p.G247E	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	599					neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						GGAGTAGGGGGAGATGTACAA	0.527													22	10	---	---	---	---	PASS
POLI	11201	broad.mit.edu	37	18	51820157	51820157	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51820157A>G	uc002lfj.3	+	10	1611	c.1543A>G	c.(1543-1545)ATT>GTT	p.I515V	POLI_uc010xds.1_Missense_Mutation_p.I436V|POLI_uc002lfk.3_Missense_Mutation_p.I412V|POLI_uc010dpg.2_Missense_Mutation_p.I111V	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota	515					DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AGAAAAAGACATTAATGAATT	0.378								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					10	18	---	---	---	---	PASS
TCF4	6925	broad.mit.edu	37	18	52924583	52924583	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52924583G>A	uc002lfz.2	-	14	1721	c.1109C>T	c.(1108-1110)TCA>TTA	p.S370L	TCF4_uc002lfw.3_Missense_Mutation_p.S210L|TCF4_uc010xdu.1_Missense_Mutation_p.S240L|TCF4_uc010xdv.1_Missense_Mutation_p.S240L|TCF4_uc002lfx.2_Missense_Mutation_p.S299L|TCF4_uc010xdw.1_Missense_Mutation_p.S240L|TCF4_uc002lfy.2_Missense_Mutation_p.S328L|TCF4_uc010xdx.1_Missense_Mutation_p.S346L|TCF4_uc010dph.1_Missense_Mutation_p.S370L|TCF4_uc010xdy.1_Missense_Mutation_p.S346L|TCF4_uc002lga.2_Missense_Mutation_p.S472L|TCF4_uc002lgb.1_Missense_Mutation_p.S210L|TCF4_uc010dpi.2_Missense_Mutation_p.S376L|TCF4_uc002lfv.2_Missense_Mutation_p.S153L	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b	370					positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA 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 RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		AGGAGACGATGAGGCCTGTCC	0.418													36	51	---	---	---	---	PASS
KIAA1468	57614	broad.mit.edu	37	18	59972682	59972682	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59972682A>C	uc002lil.2	+	29	3781	c.3566A>C	c.(3565-3567)GAT>GCT	p.D1189A	KIAA1468_uc010xel.1_Missense_Mutation_p.D1189A|KIAA1468_uc002lim.2_Missense_Mutation_p.D867A	NM_020854	NP_065905	Q9P260	K1468_HUMAN	hypothetical protein LOC57614	1189							binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)				GTGAGTGAAGATACAAAGACC	0.323													20	98	---	---	---	---	PASS
SERPINB10	5273	broad.mit.edu	37	18	61585188	61585188	+	Intron	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61585188C>G	uc010xev.1	+						SERPINB10_uc010xew.1_Intron	NM_005024	NP_005015	P48595	SPB10_HUMAN	serine (or cysteine) proteinase inhibitor, clade							cytoplasm|nucleus	serine-type endopeptidase inhibitor activity			lung(1)|kidney(1)|skin(1)	3		Esophageal squamous(42;0.131)				CTAGTTCCTTCTCTTTTAAAG	0.328													8	36	---	---	---	---	PASS
ZNF407	55628	broad.mit.edu	37	18	72632562	72632562	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72632562G>T	uc002llw.2	+	7	5399	c.5342G>T	c.(5341-5343)GGG>GTG	p.G1781V	ZNF407_uc010dqu.1_Missense_Mutation_p.G1781V	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	1781	C2H2-type 22.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TGTGACTACGGGACCAACGTC	0.493													4	35	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76756945	76756945	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76756945C>A	uc002lmt.2	+	3	3526	c.3526C>A	c.(3526-3528)CTG>ATG	p.L1176M	SALL3_uc010dra.2_Missense_Mutation_p.L711M	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	1176					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGGCCGCCGCCTGTCTGTGGA	0.617													6	15	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76757113	76757113	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76757113G>A	uc002lmt.2	+	3	3694	c.3694G>A	c.(3694-3696)GTC>ATC	p.V1232I	SALL3_uc010dra.2_Missense_Mutation_p.V767I	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	1232					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGAGATCTCCGTCATCCAGAA	0.622													6	71	---	---	---	---	PASS
EEF2	1938	broad.mit.edu	37	19	3977205	3977205	+	Intron	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3977205G>A	uc002lze.2	-							NM_001961	NP_001952	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2							cytosol|ribonucleoprotein complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCGGGCAGGCACTCACCAA	0.617													5	12	---	---	---	---	PASS
INSR	3643	broad.mit.edu	37	19	7125485	7125485	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7125485T>C	uc002mgd.1	-	17	3176	c.3067A>G	c.(3067-3069)ATC>GTC	p.I1023V	INSR_uc002mge.1_Missense_Mutation_p.I1011V	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	1023	Protein kinase.|Cytoplasmic (Potential).		I -> F.		activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AGGAGGGTGATCTTCTCTCGA	0.577													13	32	---	---	---	---	PASS
KIAA1543	57662	broad.mit.edu	37	19	7675433	7675433	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7675433G>A	uc002mgv.3	+	6	933	c.832G>A	c.(832-834)GCC>ACC	p.A278T	KIAA1543_uc002mgu.3_Missense_Mutation_p.A305T	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	278	CH.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1						GGATTTCTGTGCCTCTCGCCT	0.632													16	54	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9065831	9065831	+	Silent	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9065831T>A	uc002mkp.2	-	3	21819	c.21615A>T	c.(21613-21615)ACA>ACT	p.T7205T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7207	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGGCTTTGGATGTCTCTGAGT	0.488													22	78	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9071159	9071159	+	Silent	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9071159A>T	uc002mkp.2	-	3	16491	c.16287T>A	c.(16285-16287)ACT>ACA	p.T5429T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5431	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						CAGACCCGGAAGTCCCTACAT	0.527													50	173	---	---	---	---	PASS
OR7G3	390883	broad.mit.edu	37	19	9237355	9237355	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9237355G>T	uc010xkl.1	-	1	272	c.272C>A	c.(271-273)TCC>TAC	p.S91Y		NM_001001958	NP_001001958	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GTAATTGATGGATTGAGCCTG	0.483													30	53	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10251824	10251824	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10251824G>T	uc002mng.2	-	30	3483	c.3303C>A	c.(3301-3303)AAC>AAA	p.N1101K	DNMT1_uc002mne.2_5'Flank|DNMT1_uc002mnf.2_Missense_Mutation_p.N25K|DNMT1_uc010xlc.1_Missense_Mutation_p.N1117K|DNMT1_uc002mnh.2_Missense_Mutation_p.N996K|DNMT1_uc010xld.1_Missense_Mutation_p.N1101K	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	1101					chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	TACGGGCATGGTTGGGAGGAT	0.468													11	69	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10477140	10477140	+	Silent	SNP	G	T	T	rs147934502		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10477140G>T	uc002moc.3	-	6	960	c.582C>A	c.(580-582)CTC>CTA	p.L194L	TYK2_uc010dxe.2_Silent_p.L9L|TYK2_uc002mod.2_Silent_p.L194L	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	194	FERM.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GGCGGAGAGCGAGGTGACAGA	0.597													4	70	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14743723	14743723	+	Intron	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14743723C>T	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						TACCATTTGTCACATCCTACC	0.418													70	24	---	---	---	---	PASS
AKAP8	10270	broad.mit.edu	37	19	15484801	15484801	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15484801G>C	uc002nav.2	-	4	228	c.167C>G	c.(166-168)GCC>GGC	p.A56G	AKAP8_uc010dzy.2_5'Flank|AKAP8_uc010dzz.1_RNA|AKAP8_uc010xog.1_Intron	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	56					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						CTCCCACGAGGCTGGGCCGTA	0.622													8	69	---	---	---	---	PASS
IL12RB1	3594	broad.mit.edu	37	19	18186641	18186641	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18186641C>A	uc002nhw.1	-	7	682	c.618G>T	c.(616-618)CAG>CAT	p.Q206H	IL12RB1_uc010xqb.1_Missense_Mutation_p.Q206H|IL12RB1_uc002nhx.1_Missense_Mutation_p.Q246H|IL12RB1_uc002nhy.2_Missense_Mutation_p.Q206H	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1	206	Extracellular (Potential).|Fibronectin type-III 2.				cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1						GCTGGAATTCCTGGGCCACAT	0.572													4	38	---	---	---	---	PASS
GDF1	2657	broad.mit.edu	37	19	18995020	18995020	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18995020C>A	uc002nki.1	-	3	538	c.466G>T	c.(466-468)GGA>TGA	p.G156*	LASS1_uc002nkj.2_Nonsense_Mutation_p.G156*|LASS1_uc010ebx.2_Nonsense_Mutation_p.G58*	NM_021267	NP_067090	P27539	GDF1_HUMAN	LAG1 homolog, ceramide synthase 1 isoform 1	Error:Variant_position_missing_in_P27539_after_alignment					growth	extracellular space	cytokine activity|growth factor activity				0						TAGAAGCTTCCCTGGAGCAGG	0.607													4	17	---	---	---	---	PASS
NCAN	1463	broad.mit.edu	37	19	19338799	19338799	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19338799G>C	uc002nlz.2	+	8	2469	c.2370G>C	c.(2368-2370)CTG>CTC	p.L790L	NCAN_uc010ecc.1_Silent_p.L354L	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	790					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			GCAAAGGGCTGGATGCAAGTT	0.577													46	23	---	---	---	---	PASS
NCAN	1463	broad.mit.edu	37	19	19338800	19338800	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19338800G>T	uc002nlz.2	+	8	2470	c.2371G>T	c.(2371-2373)GAT>TAT	p.D791Y	NCAN_uc010ecc.1_Missense_Mutation_p.D355Y	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	791					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			CAAAGGGCTGGATGCAAGTTC	0.582													44	23	---	---	---	---	PASS
ZNF253	56242	broad.mit.edu	37	19	20003536	20003536	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20003536C>A	uc002noj.2	+	4	1572	c.1480C>A	c.(1480-1482)CTT>ATT	p.L494I	ZNF253_uc002nok.2_Missense_Mutation_p.L418I|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253	494					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGTTCCTCCACTTTTAATTAG	0.343													9	69	---	---	---	---	PASS
ZNF43	7594	broad.mit.edu	37	19	21990988	21990988	+	Silent	SNP	A	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21990988A>T	uc002nqj.2	-	4	1981	c.1851T>A	c.(1849-1851)ACT>ACA	p.T617T	ZNF43_uc010ecv.2_Silent_p.T611T|ZNF43_uc002nql.2_Silent_p.T611T|ZNF43_uc002nqm.2_Silent_p.T611T|ZNF43_uc002nqk.2_Silent_p.T547T	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43	617					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GTTTTCCTCCAGTATGAATTT	0.338													5	78	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22154213	22154213	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22154213C>T	uc002nqp.2	-	6	3388	c.3239G>A	c.(3238-3240)TGG>TAG	p.W1080*	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				GGTTGAGGGCCACTTATAGGC	0.393													82	60	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22362957	22362957	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22362957G>T	uc002nqs.1	-	3	1880	c.1562C>A	c.(1561-1563)ACT>AAT	p.T521N		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	521	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CTTATGTTCAGTAAGGATCGA	0.398													8	184	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23542365	23542365	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23542365C>G	uc002nre.2	-	4	3529	c.3416G>C	c.(3415-3417)TGT>TCT	p.C1139S	ZNF91_uc002nrd.2_5'Flank|ZNF91_uc010xrj.1_Missense_Mutation_p.C1107S	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	1139	C2H2-type 36.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				GGCTTTGCCACATTTTTCACA	0.279													15	29	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30935497	30935497	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30935497A>G	uc002nsu.1	+	2	1166	c.1028A>G	c.(1027-1029)AAC>AGC	p.N343S	ZNF536_uc010edd.1_Missense_Mutation_p.N343S	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	343					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)					CAGTCGGCCAACGAGTTCCGC	0.647													11	101	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30935825	30935825	+	Silent	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30935825C>G	uc002nsu.1	+	2	1494	c.1356C>G	c.(1354-1356)CTC>CTG	p.L452L	ZNF536_uc010edd.1_Silent_p.L452L	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	452					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)					CCAGCCAGCTCTATGGCAAGG	0.657													5	21	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31039661	31039661	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039661C>T	uc002nsu.1	+	4	3273	c.3135C>T	c.(3133-3135)GCC>GCT	p.A1045A	ZNF536_uc010edd.1_Silent_p.A1045A	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1045					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)					AAGACCAAGCCCGGGAGGCGA	0.537													15	44	---	---	---	---	PASS
FXYD1	5348	broad.mit.edu	37	19	35630999	35630999	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35630999C>A	uc002nyc.2	+	2	87	c.16C>A	c.(16-18)CAC>AAC	p.H6N	LGI4_uc002nxy.1_Intron|FXYD1_uc002nyb.1_RNA|FXYD1_uc002nyd.2_Missense_Mutation_p.H6N	NM_021902	NP_068702	O00168	PLM_HUMAN	phospholemman precursor	6					muscle contraction	chloride channel complex|integral to plasma membrane	chloride channel activity				0	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;2.32e-21)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;2.43e-18)|LUSC - Lung squamous cell carcinoma(66;0.0849)			GTCTCTTGGCCACATCTTGGT	0.612													24	26	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36218350	36218350	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36218350G>T	uc010eei.2	+	17	4129	c.4129G>T	c.(4129-4131)GAG>TAG	p.E1377*		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1377	PHD-type 3.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGAAGACTACGAGATCCTTTC	0.622													6	211	---	---	---	---	PASS
TYROBP	7305	broad.mit.edu	37	19	36398473	36398473	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36398473C>A	uc002ocm.2	-	3	160	c.104G>T	c.(103-105)TGC>TTC	p.C35F	TYROBP_uc002ocn.2_Missense_Mutation_p.C35F	NM_003332	NP_003323	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	35	Extracellular (Potential).				axon guidance|cell junction assembly|cellular defense response|intracellular signal transduction|regulation of immune response	integral to plasma membrane|intracellular	identical protein binding|receptor signaling protein activity				0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CACCGTAGAGCAACTGCAATC	0.642													10	23	---	---	---	---	PASS
ZNF461	92283	broad.mit.edu	37	19	37130589	37130589	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37130589C>G	uc002oem.2	-	6	886	c.658G>C	c.(658-660)GAA>CAA	p.E220Q	ZNF461_uc002oen.2_Missense_Mutation_p.E189Q|ZNF461_uc010xtj.1_Missense_Mutation_p.E197Q	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor	220					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TCTTTACATTCAGAAAGTTCT	0.299													29	42	---	---	---	---	PASS
ZNF461	92283	broad.mit.edu	37	19	37149309	37149309	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37149309C>A	uc002oem.2	-	3	256	c.28G>T	c.(28-30)GAT>TAT	p.D10Y	ZNF461_uc002oen.2_5'UTR|ZNF461_uc010xtj.1_Missense_Mutation_p.D10Y	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor	10	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATAGCCACATCTCTGAACATC	0.363													6	35	---	---	---	---	PASS
ZNF585A	199704	broad.mit.edu	37	19	37643905	37643905	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37643905T>A	uc002ofo.1	-	5	1127	c.896A>T	c.(895-897)GAG>GTG	p.E299V	ZNF585A_uc002ofm.1_Missense_Mutation_p.E244V|ZNF585A_uc002ofn.1_Missense_Mutation_p.E244V	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	299	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTTACTGCACTCATATGGTTT	0.438													120	99	---	---	---	---	PASS
RSPH6A	81492	broad.mit.edu	37	19	46313858	46313858	+	Intron	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46313858C>A	uc002pdm.2	-						RSPH6A_uc002pdl.2_Intron	NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1							intracellular				ovary(1)|central_nervous_system(1)	2						CTGGCTCACTCACCACCTCCT	0.607													28	109	---	---	---	---	PASS
ZNF613	79898	broad.mit.edu	37	19	52443504	52443504	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52443504G>T	uc002pxz.1	+	4	481	c.58G>T	c.(58-60)GAG>TAG	p.E20*	ZNF613_uc002pya.1_5'UTR	NM_001031721	NP_001026891	Q6PF04	ZN613_HUMAN	zinc finger protein 613 isoform 1	20	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		GTTCACTTGGGAGGAGTGGCA	0.498													6	116	---	---	---	---	PASS
ZNF813	126017	broad.mit.edu	37	19	53989949	53989949	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53989949C>T	uc002qbu.2	+	3	207	c.79C>T	c.(79-81)CCT>TCT	p.P27S	ZNF813_uc010eqq.1_RNA	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	27	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATGCCTGGACCCTGCTCAGAG	0.483													13	190	---	---	---	---	PASS
MIR519B	574469	broad.mit.edu	37	19	54198504	54198504	+	RNA	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54198504T>C	hsa-mir-519b|MI0003151	+			c.38T>C			MIR525_hsa-mir-525|MI0003152_5'Flank																	0						CTTTCTGTTGTCTGAAAGAAA	0.418													128	124	---	---	---	---	PASS
MIR518A1	574488	broad.mit.edu	37	19	54233183	54233183	+	5'Flank	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54233183G>T	hsa-mir-518a-1|MI0003170	+																							0						TTTGAGAAAAGCAACGTTGAT	0.373													9	80	---	---	---	---	PASS
LILRA6	79168	broad.mit.edu	37	19	54742916	54742916	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54742916C>A	uc002qeu.1	-	8	1483	c.1359G>T	c.(1357-1359)ATG>ATT	p.M453I	LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron|LILRA6_uc002qet.3_RNA|LILRA6_uc002qev.1_Missense_Mutation_p.M297I	NM_024318	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor,	453	Helical; (Potential).					integral to membrane	receptor activity			skin(2)	2	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCAAGCCTGCCATGCCCATGC	0.572													6	97	---	---	---	---	PASS
LILRA4	23547	broad.mit.edu	37	19	54848965	54848965	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54848965C>A	uc002qfj.2	-	5	715	c.658G>T	c.(658-660)GTG>TTG	p.V220L	LILRA4_uc002qfi.2_Missense_Mutation_p.V154L	NM_012276	NP_036408	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor subfamily	220	Extracellular (Potential).					integral to membrane	receptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		TTCCTAGACACGCCTGGAGGG	0.597													9	11	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55086465	55086465	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55086465C>G	uc002qgg.3	+	4	709	c.620C>G	c.(619-621)TCT>TGT	p.S207C	LILRA2_uc010ern.2_Missense_Mutation_p.S207C|LILRA2_uc002qgf.2_Missense_Mutation_p.S207C|LILRA2_uc010yfe.1_Missense_Mutation_p.S207C|LILRA2_uc010yff.1_Missense_Mutation_p.S195C|LILRA2_uc010ero.2_Missense_Mutation_p.S195C|LILRA2_uc010yfg.1_Missense_Mutation_p.S207C	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	207	Extracellular (Potential).|Ig-like C2-type 2.				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		TATGTGTGGTCTCTACCCAGT	0.587													97	73	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56369120	56369120	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369120C>A	uc002qmd.3	+	3	783	c.361C>A	c.(361-363)CTA>ATA	p.L121I	NLRP4_uc002qmf.2_Missense_Mutation_p.L46I|NLRP4_uc010etf.2_5'UTR	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	121							ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TGAGATTCACCTATACTTTGA	0.473													7	163	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57327637	57327637	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327637T>C	uc002qnu.2	-	7	2524	c.2173A>G	c.(2173-2175)AGT>GGT	p.S725G	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.S696G|PEG3_uc002qnv.2_Missense_Mutation_p.S725G|PEG3_uc002qnw.2_Missense_Mutation_p.S601G|PEG3_uc002qnx.2_Missense_Mutation_p.S599G|PEG3_uc010etr.2_Missense_Mutation_p.S725G	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	725					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		AATGGCCCACTATGAATGACA	0.433													31	74	---	---	---	---	PASS
ANGPT4	51378	broad.mit.edu	37	20	855022	855022	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:855022C>A	uc002wei.2	-	8	1359	c.1256G>T	c.(1255-1257)CGC>CTC	p.R419L	ANGPT4_uc010zpn.1_Intron	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	419	Fibrinogen C-terminal.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						GCTGCTCTGGCGCCCTGCTGA	0.612													25	31	---	---	---	---	PASS
PROKR2	128674	broad.mit.edu	37	20	5283148	5283148	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5283148C>A	uc010zqw.1	-	2	693	c.693G>T	c.(691-693)GAG>GAT	p.E231D	PROKR2_uc010zqx.1_Missense_Mutation_p.E231D|PROKR2_uc010zqy.1_Missense_Mutation_p.E231D	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	231	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GGCCCACGAACTCGACACCAA	0.547										HNSCC(71;0.22)			31	34	---	---	---	---	PASS
FERMT1	55612	broad.mit.edu	37	20	6078203	6078203	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6078203C>T	uc002wmr.2	-	7	1714	c.925G>A	c.(925-927)GAG>AAG	p.E309K	FERMT1_uc010gbt.2_Missense_Mutation_p.E52K|FERMT1_uc002wms.2_Missense_Mutation_p.E309K|FERMT1_uc002wmt.2_Missense_Mutation_p.E52K	NM_017671	NP_060141	Q9BQL6	FERM1_HUMAN	kindlin-1	309	FERM.				cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3						ATTTCTTCCTCTGTGCAATCA	0.418													17	63	---	---	---	---	PASS
RRBP1	6238	broad.mit.edu	37	20	17641085	17641085	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17641085A>C	uc010zrq.1	-	3	422	c.68T>G	c.(67-69)ATT>AGT	p.I23S	RRBP1_uc002wpu.2_5'Flank|RRBP1_uc002wpv.1_Missense_Mutation_p.I23S|RRBP1_uc002wpw.1_Missense_Mutation_p.I23S|RRBP1_uc010gcl.1_Intron|RRBP1_uc010zrr.1_Missense_Mutation_p.I23S			Q9P2E9	RRBP1_HUMAN	SubName: Full=RRBP1 protein; Flags: Fragment;	23	Helical; (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						GAAGATGCCAATGGCAGAAAC	0.473													31	47	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20610174	20610174	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20610174C>T	uc002wrz.2	-	10	1209	c.1066G>A	c.(1066-1068)GAG>AAG	p.E356K	RALGAPA2_uc010gcx.2_Missense_Mutation_p.E60K|RALGAPA2_uc010zsg.1_5'UTR	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	356					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						TTGTCCTGCTCCGTGGGCCCA	0.547													32	38	---	---	---	---	PASS
SSTR4	6754	broad.mit.edu	37	20	23016630	23016630	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23016630G>A	uc002wsr.2	+	1	574	c.510G>A	c.(508-510)GTG>GTA	p.V170V		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	170	Helical; Name=4; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity			ovary(1)	1	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					ACCTGGGCGTGTGGCTGGCAT	0.697													11	38	---	---	---	---	PASS
TM9SF4	9777	broad.mit.edu	37	20	30745749	30745749	+	Silent	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30745749G>A	uc002wxj.2	+	14	1717	c.1482G>A	c.(1480-1482)CGG>CGA	p.R494R	TM9SF4_uc010zts.1_Silent_p.R401R|TM9SF4_uc002wxk.2_Silent_p.R477R|TM9SF4_uc010gdz.2_Silent_p.R373R	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	494						integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CCGAGCAGCGGTGGTACATGA	0.617													12	49	---	---	---	---	PASS
KIF3B	9371	broad.mit.edu	37	20	30904548	30904548	+	Intron	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30904548C>T	uc002wxq.2	+						KIF3B_uc010ztw.1_Intron	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B						anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CTGCCTCTCCCCTCATTCCAG	0.522													41	13	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40864878	40864878	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40864878G>C	uc002xkg.2	-	15	2517	c.2333C>G	c.(2332-2334)TCC>TGC	p.S778C	PTPRT_uc010ggj.2_Missense_Mutation_p.S797C	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	778	Cytoplasmic (Potential).				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CAAGTAATAGGAGTAGGAATA	0.388													17	70	---	---	---	---	PASS
CBLN4	140689	broad.mit.edu	37	20	54573767	54573767	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54573767G>T	uc002xxa.2	-	3	1237	c.452C>A	c.(451-453)GCG>GAG	p.A151E		NM_080617	NP_542184	Q9NTU7	CBLN4_HUMAN	cerebellin 4 precursor	151	C1q.					cell junction|extracellular region|synapse				ovary(3)|pancreas(1)	4			Colorectal(105;0.202)			TTTGTCCCCCGCAAAGGCAGA	0.358													25	13	---	---	---	---	PASS
PCK1	5105	broad.mit.edu	37	20	56138076	56138076	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56138076G>T	uc002xyn.3	+						PCK1_uc010zzm.1_Intron	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1						gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGGGGTCCTTGTTCACAGAGC	0.572													19	5	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33044507	33044507	+	Silent	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33044507C>T	uc002ypd.2	-	20	3075	c.2649G>A	c.(2647-2649)CCG>CCA	p.P883P	SFRS15_uc002ype.2_Silent_p.P861P|SFRS15_uc010glu.2_Silent_p.P868P	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	883						nucleus	nucleotide binding|RNA binding				0						GCATCATGTGCGGTGGCATGG	0.642													25	10	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33058012	33058012	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33058012C>A	uc002ypd.2	-	17	2504	c.2078G>T	c.(2077-2079)GGT>GTT	p.G693V	SFRS15_uc002ype.2_Missense_Mutation_p.G693V|SFRS15_uc010glu.2_Missense_Mutation_p.G678V|SFRS15_uc002ypf.1_Missense_Mutation_p.G367V	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	693						nucleus	nucleotide binding|RNA binding				0						CTGGAGAGCACCAACTACAGG	0.547													17	10	---	---	---	---	PASS
SON	6651	broad.mit.edu	37	21	34926741	34926741	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34926741G>A	uc002yse.1	+	3	5253	c.5204G>A	c.(5203-5205)AGA>AAA	p.R1735K	SON_uc002ysb.1_Missense_Mutation_p.R1735K|SON_uc002ysc.2_Missense_Mutation_p.R1735K|SON_uc002ysd.2_Missense_Mutation_p.R726K|SON_uc002ysf.1_Intron|SON_uc002ysg.2_Missense_Mutation_p.R726K	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	1735					anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						GATTTAGTGAGACCGTTACTT	0.448													17	80	---	---	---	---	PASS
FTCD	10841	broad.mit.edu	37	21	47571482	47571482	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47571482C>G	uc002zif.2	-	5	670	c.626G>C	c.(625-627)GGG>GCG	p.G209A	FTCD_uc002zig.2_Missense_Mutation_p.G209A|FTCD_uc002zih.2_Missense_Mutation_p.G209A|FTCD_uc010gqf.2_Missense_Mutation_p.G209A|FTCD_uc010gqg.1_Missense_Mutation_p.G78A	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	209	Formiminotransferase C-subdomain (By similarity).				folic acid-containing compound metabolic process|histidine catabolic process	centriole|cytosol|Golgi apparatus	folic acid binding|formimidoyltetrahydrofolate cyclodeaminase activity|glutamate formimidoyltransferase activity			pancreas(1)|skin(1)	2	Breast(49;0.214)			Colorectal(79;0.235)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	CTGGTCCTTCCCGCGGCCCTG	0.652													11	7	---	---	---	---	PASS
AIFM3	150209	broad.mit.edu	37	22	21330039	21330039	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21330039A>G	uc002ztj.2	+	9	997	c.779A>G	c.(778-780)TAT>TGT	p.Y260C	AIFM3_uc002ztk.2_Missense_Mutation_p.Y260C|AIFM3_uc002ztl.2_Missense_Mutation_p.Y266C|AIFM3_uc011ahx.1_Missense_Mutation_p.Y248C|AIFM3_uc002ztm.1_Missense_Mutation_p.Y72C	NM_144704	NP_653305	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor,	260					activation of caspase activity by cytochrome c|cell redox homeostasis|electron transport chain|induction of apoptosis|mitochondrial depolarization|transport	endoplasmic reticulum|mitochondrial inner membrane	2 iron, 2 sulfur cluster binding|caspase activator activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity|protein binding			ovary(2)|lung(2)	4	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			TTCCGAGCCTATGGCATCGAG	0.592													8	55	---	---	---	---	PASS
C22orf13	83606	broad.mit.edu	37	22	24943946	24943946	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24943946A>C	uc003aah.2	-	3	540	c.224T>G	c.(223-225)ATG>AGG	p.M75R	C22orf13_uc003aal.2_Missense_Mutation_p.M131R|C22orf13_uc003aai.3_Missense_Mutation_p.M75R|C22orf13_uc003aaj.3_Missense_Mutation_p.M75R|C22orf13_uc003aak.3_Missense_Mutation_p.M131R	NM_031444	NP_113632	Q96NT3	CV013_HUMAN	chromosome 22 open reading frame 13	75											0						AAAGTGGTGCATCAGGTAGGC	0.607													32	42	---	---	---	---	PASS
GAS2L1	10634	broad.mit.edu	37	22	29706908	29706908	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29706908G>C	uc003afa.1	+	5	1129	c.930G>C	c.(928-930)GGG>GGC	p.G310G	GAS2L1_uc010gvm.1_Silent_p.G310G|GAS2L1_uc003afb.1_Silent_p.G310G|GAS2L1_uc003afc.1_Silent_p.G310G|GAS2L1_uc003afd.1_Silent_p.G310G|GAS2L1_uc003afe.1_Silent_p.G310G	NM_152236	NP_689422	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1 isoform a	310					cell cycle arrest	cytoplasm|cytoskeleton					0						CAGTCCCTGGGAGTGAGCGCC	0.672													35	37	---	---	---	---	PASS
NEFH	4744	broad.mit.edu	37	22	29885319	29885319	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29885319G>C	uc003afo.2	+	4	1761	c.1690G>C	c.(1690-1692)GCC>CCC	p.A564P	NEFH_uc003afp.2_Intron	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	564	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|5.|Tail.				cell death|nervous system development	neurofilament					0						ACCGCCTGAGGCCAAGTCCCC	0.567													20	145	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	33733695	33733695	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33733695G>T	uc003and.3	-	11	1803	c.1224C>A	c.(1222-1224)GAC>GAA	p.D408E	LARGE_uc011amd.1_Missense_Mutation_p.D207E|LARGE_uc003ane.3_Missense_Mutation_p.D408E|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Missense_Mutation_p.D340E|LARGE_uc011amf.1_Missense_Mutation_p.D408E|LARGE_uc010gwq.1_RNA	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	408	Lumenal (Potential).				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)				GAAGATTGCCGTCATACTCCA	0.562													15	30	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	34000547	34000547	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34000547G>T	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.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)				GGTTCCGTCTGTGGGGAGTGT	0.562													14	69	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41605724	41605724	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41605724G>T	uc003azo.2	+	2	103	c.49G>T	c.(49-51)GAG>TAG	p.E17*	L3MBTL2_uc010gyi.1_5'UTR|L3MBTL2_uc003azn.2_RNA|uc003azp.1_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	17	Poly-Glu.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						AGAACCAATGGAGGAAGAGGA	0.488													6	181	---	---	---	---	PASS
SCUBE1	80274	broad.mit.edu	37	22	43614411	43614411	+	Missense_Mutation	SNP	C	A	A	rs139119420		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43614411C>A	uc003bdt.1	-	15	1829	c.1741G>T	c.(1741-1743)GCC>TCC	p.A581S		NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	581					adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				GTCTTGATGGCGGCCTGCAGG	0.607													45	72	---	---	---	---	PASS
TUBGCP6	85378	broad.mit.edu	37	22	50682676	50682676	+	Silent	SNP	G	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50682676G>C	uc003bkb.1	-	1	725	c.213C>G	c.(211-213)CTC>CTG	p.L71L	TUBGCP6_uc010har.1_Silent_p.L71L|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hau.1_Silent_p.L71L	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	71					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-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)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		AGGACAACATGAGGATCTTGT	0.517													8	77	---	---	---	---	PASS
GPR64	10149	broad.mit.edu	37	X	19025356	19025356	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19025356G>T	uc004cyx.2	-	20	1850	c.1686C>A	c.(1684-1686)AGC>AGA	p.S562R	GPR64_uc004cyy.2_Missense_Mutation_p.S559R|GPR64_uc004cyz.2_Missense_Mutation_p.S548R|GPR64_uc004czb.2_Missense_Mutation_p.S562R|GPR64_uc004czc.2_Missense_Mutation_p.S546R|GPR64_uc004czd.2_Missense_Mutation_p.S538R|GPR64_uc004cze.2_Missense_Mutation_p.S532R|GPR64_uc004czf.2_Missense_Mutation_p.S524R|GPR64_uc004cza.2_Missense_Mutation_p.S540R|GPR64_uc004cyw.2_Missense_Mutation_p.S546R|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	562	Extracellular (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					TCCCCACCTGGCTCGGGTTGA	0.498													16	10	---	---	---	---	PASS
PRDX4	10549	broad.mit.edu	37	X	23689672	23689672	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23689672G>T	uc004dam.2	+	2	311	c.268G>T	c.(268-270)GGA>TGA	p.G90*		NM_006406	NP_006397	Q13162	PRDX4_HUMAN	peroxiredoxin 4	90	Thioredoxin.				cell redox homeostasis|I-kappaB phosphorylation		thioredoxin peroxidase activity			upper_aerodigestive_tract(1)	1						CTACTGGGAAGGAACAGCTGT	0.383													4	33	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26212607	26212607	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26212607C>A	uc004dbr.2	+	2	793	c.644C>A	c.(643-645)TCC>TAC	p.S215Y	MAGEB6_uc010ngc.1_5'UTR	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	215	MAGE.									ovary(3)	3						AAGAAAGAGTCCATTTTGAAG	0.468													26	32	---	---	---	---	PASS
MAGEB4	4115	broad.mit.edu	37	X	30260685	30260685	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30260685G>T	uc004dcb.2	+	1	517	c.433G>T	c.(433-435)GAG>TAG	p.E145*	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	145	MAGE.									ovary(1)	1						AAAGTACAAGGAGCACTTCCC	0.478													6	9	---	---	---	---	PASS
KDM6A	7403	broad.mit.edu	37	X	44922694	44922694	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44922694C>T	uc004dge.3	+	16	1930	c.1555C>T	c.(1555-1557)CGA>TGA	p.R519*	KDM6A_uc010nhk.2_Nonsense_Mutation_p.R485*|KDM6A_uc011mkz.1_Nonsense_Mutation_p.R571*|KDM6A_uc011mla.1_Nonsense_Mutation_p.R474*|KDM6A_uc011mlb.1_Nonsense_Mutation_p.R526*|KDM6A_uc011mlc.1_Nonsense_Mutation_p.R223*|KDM6A_uc011mld.1_Nonsense_Mutation_p.R158*	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	519					histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						TGCACAGGTACGATCTACTGG	0.463			D|N|F|S		renal|oesophageal SCC|MM								26	18	---	---	---	---	PASS
HDAC6	10013	broad.mit.edu	37	X	48674470	48674470	+	Intron	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48674470G>T	uc011mmi.1	+						HDAC6_uc004dks.1_Intron|HDAC6_uc010nig.1_Intron|HDAC6_uc004dkt.1_Intron|HDAC6_uc011mmk.1_Intron|HDAC6_uc004dkv.1_Intron|HDAC6_uc004dkw.1_Intron	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6						aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule 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)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4					Vorinostat(DB02546)	GTAGGCATTTGGAGGGCTGGA	0.567													20	19	---	---	---	---	PASS
ALAS2	212	broad.mit.edu	37	X	55050308	55050308	+	Intron	SNP	G	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55050308G>A	uc004dua.3	-						ALAS2_uc004dub.3_Intron|ALAS2_uc004dud.3_Intron	NM_000032	NP_000023	P22557	HEM0_HUMAN	5-aminolevulinate synthase 2 isoform a						cellular iron ion homeostasis|erythrocyte differentiation|heme biosynthetic process|hemoglobin biosynthetic process|oxygen homeostasis|response to hypoxia	mitochondrial inner membrane|mitochondrial matrix	5-aminolevulinate synthase activity|coenzyme binding|glycine binding|protein binding|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(1)	1					Glycine(DB00145)	GATCTGAGACGGAATGTGAGA	0.478													4	10	---	---	---	---	PASS
SPIN4	139886	broad.mit.edu	37	X	62570653	62570653	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62570653C>T	uc004dvf.2	-	1	566	c.46G>A	c.(46-48)GCA>ACA	p.A16T		NM_001012968	NP_001012986	Q56A73	SPIN4_HUMAN	spindlin family, member 4	16					gamete generation					ovary(1)|lung(1)	2						ATCAGGTATGCGGACACGCCA	0.567													9	13	---	---	---	---	PASS
FAM155B	27112	broad.mit.edu	37	X	68748958	68748958	+	Silent	SNP	C	A	A	rs147997913	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68748958C>A	uc004dxk.2	+	2	1032	c.984C>A	c.(982-984)CCC>CCA	p.P328P		NM_015686	NP_056501	O75949	F155B_HUMAN	transmembrane protein 28	328						integral to membrane				ovary(1)|breast(1)	2						TTATACTCCCCGACAATGAGG	0.612													3	12	---	---	---	---	PASS
RAB41	347517	broad.mit.edu	37	X	69502420	69502420	+	Missense_Mutation	SNP	C	G	G	rs140771923		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69502420C>G	uc004dyc.2	+	2	162	c.162C>G	c.(160-162)AAC>AAG	p.N54K	RAB41_uc010nkv.2_Missense_Mutation_p.N43K	NM_001032726	NP_001027898	Q5JT25	RAB41_HUMAN	RAB41, member RAS oncogene family	54					protein transport|small GTPase mediated signal transduction		GTP binding			ovary(2)|breast(2)	4						TCATGTACAACAGCTTCGGCT	0.527													9	4	---	---	---	---	PASS
ZMYM3	9203	broad.mit.edu	37	X	70464694	70464694	+	Silent	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70464694C>A	uc004dzh.1	-	19	3144	c.3057G>T	c.(3055-3057)CTG>CTT	p.L1019L	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Silent_p.L1019L|ZMYM3_uc004dzj.1_Silent_p.L1007L	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	1019					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					CAGGCCCTACCAGGCCACAAT	0.453													4	18	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	94318131	94318131	+	IGR	SNP	C	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94318131C>T								None (None upstream) : MIR548M (9 downstream)																							GTCTATAATTCCGAGGGGCTA	0.179													9	7	---	---	---	---	PASS
ZCCHC12	170261	broad.mit.edu	37	X	117959988	117959988	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117959988T>A	uc004equ.2	+	4	1254	c.781T>A	c.(781-783)TGC>AGC	p.C261S		NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	261					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1						CAGTGCTGACTGCAATGTGAT	0.557													18	19	---	---	---	---	PASS
FRMD7	90167	broad.mit.edu	37	X	131219751	131219751	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131219751C>A	uc004ewn.2	-	7	681	c.503G>T	c.(502-504)AGG>ATG	p.R168M	FRMD7_uc011muy.1_Missense_Mutation_p.R153M	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	168	FERM.				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)					AGCTGGGCTCCTGCCACTGAA	0.502													4	20	---	---	---	---	PASS
MIR888	100126306	broad.mit.edu	37	X	145076364	145076364	+	RNA	SNP	G	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145076364G>T	hsa-mir-888|MI0005537	-			c.15G>T			MIR890_hsa-mir-890|MI0005533_5'Flank																	0						ACAGCTTTTTGAGTAGAGCAC	0.498													12	4	---	---	---	---	PASS
FAM41C	284593	broad.mit.edu	37	1	812337	812338	+	5'Flank	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:812337_812338insT	uc001abt.3	-							NR_027055				Homo sapiens family with sequence similarity 41, member C, mRNA (cDNA clone IMAGE:5201580), partial cds.												0						TTGTTTACCTCTTGGGTGAGAG	0.569													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	821343	821344	+	IGR	INS	-	CTAGGG	CTAGGG			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:821343_821344insCTAGGG								FAM41C (9161 upstream) : FLJ39609 (31609 downstream)																							accactctttcctagggctgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	1317771	1317771	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1317771delC								AURKAIP1 (6953 upstream) : CCNL2 (3320 downstream)																							ATCCAGAGGTCACCACCCCTT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2371882	2371882	+	IGR	DEL	T	-	-	rs111269301		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2371882delT								PEX10 (27872 upstream) : PLCH2 (35872 downstream)																							GGATCTTGCATTGCTGCGACC	0.662													6	3	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3048417	3048417	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3048417delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CCGCCTGCTTCCCCTCCACTG	0.587			T	EVI1	MDS|AML								4	2	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3098320	3098321	+	Intron	INS	-	GA	GA	rs145463364	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3098320_3098321insGA	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		tcttacacacggtcttacacac	0.000			T	EVI1	MDS|AML								1	5	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10763020	10763021	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10763020_10763021delAG	uc001aro.2	-						CASZ1_uc001arp.1_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)		agggagaggcagagagagagag	0.391													4	2	---	---	---	---	
PRAMEF11	440560	broad.mit.edu	37	1	12889132	12889133	+	Intron	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12889132_12889133delTC	uc001auk.2	-							NM_001146344	NP_001139816	O60813	PRA11_HUMAN	PRAME family member 11												0						Gctttctctttctctctttctt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16889470	16889472	+	RNA	DEL	ACA	-	-	rs35438508		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16889470_16889472delACA	uc001ayw.2	-	1		c.611_613delTGT								Homo sapiens AB5 mRNA, 3' untranslated region.																		accatcaatgacaacaacaaaaa	0.074													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16926278	16926278	+	Intron	DEL	A	-	-	rs67762891		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16926278delA	uc009vos.1	-						NBPF1_uc001aza.3_RNA	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		atctgtgaataaagacagctt	0.000													4	3	---	---	---	---	
MST1P9	11223	broad.mit.edu	37	1	17090902	17090903	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17090902_17090903insT	uc010ock.1	-						CROCC_uc009voy.1_Intron	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						CTTCCTGTTTATTGCACCGGGC	0.599													6	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17229146	17229147	+	Intron	INS	-	AAT	AAT	rs142626284	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229146_17229147insAAT	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ACAACAACAAATTGTCACCTCA	0.248													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21165188	21165189	+	Intron	INS	-	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21165188_21165189insC	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		Cttttttttttccccagacgtg	0.168													4	2	---	---	---	---	
RPA2	6118	broad.mit.edu	37	1	28223824	28223825	+	Intron	INS	-	T	T	rs150650563	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28223824_28223825insT	uc001bpe.1	-						RPA2_uc001bpd.1_Intron|RPA2_uc010ofp.1_Intron	NM_002946	NP_002937	P15927	RFA2_HUMAN	replication protein A2, 32kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|regulation of double-strand break repair via homologous recombination|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor A complex|PML body	protein phosphatase binding|single-stranded DNA binding			skin(1)	1		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		gctaagggacattaataatttt	0.188								Direct_reversal_of_damage|NER					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30543561	30543562	+	IGR	INS	-	TGTA	TGTA	rs150974910	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30543561_30543562insTGTA								PTPRU (890246 upstream) : MATN1 (640564 downstream)																							ACACgtgtgtgtgtatgtgtgt	0.238													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31163607	31163609	+	IGR	DEL	GTG	-	-	rs61239466		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31163607_31163609delGTG								None (None upstream) : MATN1 (20517 downstream)																							GGGtttttttgtgtttttttttt	0.379													3	3	---	---	---	---	
KPNA6	23633	broad.mit.edu	37	1	32571014	32571015	+	5'Flank	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32571014_32571015insA	uc001bug.2	+						KPNA6_uc001buh.2_5'Flank|KPNA6_uc010ogx.1_5'Flank	NM_012316	NP_036448	O60684	IMA7_HUMAN	karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				aactctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41325573	41325580	+	IGR	DEL	CCATTCGA	-	-	rs72341582		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41325573_41325580delCCATTCGA								KCNQ4 (21213 upstream) : CITED4 (1149 downstream)																							tgtcgtaaagCCATTCGACCTTTCTTGT	0.389													1	6	---	---	---	---	
SCMH1	22955	broad.mit.edu	37	1	41566702	41566702	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41566702delA	uc001cgo.2	-						SCMH1_uc010ojr.1_Intron|SCMH1_uc001cgp.2_Intron|SCMH1_uc001cgr.2_Intron|SCMH1_uc001cgs.2_Intron|SCMH1_uc001cgt.2_Intron|SCMH1_uc001cgq.2_Intron|SCMH1_uc010ojs.1_Intron	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1						anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				AGGCGGGGAGAAAAAAAAaaa	0.154													4	2	---	---	---	---	
NSUN4	387338	broad.mit.edu	37	1	46813532	46813532	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46813532delT	uc001cpr.1	+						NSUN4_uc010omc.1_Intron|NSUN4_uc009vyf.1_Intron|NSUN4_uc009vyg.1_Intron|NSUN4_uc001cpt.1_Intron|NSUN4_uc001cps.1_Intron	NM_199044	NP_950245	Q96CB9	NSUN4_HUMAN	NOL1/NOP2/Sun domain family 4 protein								methyltransferase activity				0	Acute lymphoblastic leukemia(166;0.155)					TTTGACtttcttttttttttt	0.209													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49193300	49193300	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49193300delG	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AGGCAACTCAGGCAACCTTAT	0.433													4	2	---	---	---	---	
ZYG11B	79699	broad.mit.edu	37	1	53196514	53196515	+	Intron	INS	-	A	A	rs111735830		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53196514_53196515insA	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						gagacctcattaaaaaaaaaaa	0.064													4	3	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	54022240	54022241	+	Intron	INS	-	GTGT	GTGT	rs138350610	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54022240_54022241insGTGT	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						gtactgcaggggtgtgtgtatg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	54924475	54924475	+	IGR	DEL	G	-	-	rs138187645	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54924475delG								SSBP3 (52383 upstream) : ACOT11 (83455 downstream)																							agggaaggaagggagggaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	64909546	64909547	+	IGR	INS	-	AAT	AAT	rs72501002	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64909546_64909547insAAT								UBE2U (199519 upstream) : CACHD1 (26929 downstream)																							tcttcaccaacgagacacatgg	0.129													2	5	---	---	---	---	
CACHD1	57685	broad.mit.edu	37	1	65016904	65016904	+	Intron	DEL	T	-	-	rs79828346		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65016904delT	uc001dbo.1	+						CACHD1_uc001dbp.1_Intron	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1						calcium ion transport	integral to membrane				ovary(2)	2						ttctttcctcttttttttttt	0.164													3	3	---	---	---	---	
IL12RB2	3595	broad.mit.edu	37	1	67788120	67788124	+	Intron	DEL	AAAAA	-	-	rs67275607		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67788120_67788124delAAAAA	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron|IL12RB2_uc010oqk.1_Intron|IL12RB2_uc010oql.1_Intron|IL12RB2_uc010oqm.1_Intron|IL12RB2_uc010oqn.1_Intron	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3						TGACTCCAGCaaaaaaaaaaaaaaa	0.429													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68715749	68715750	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68715749_68715750insT								WLS (17496 upstream) : RPE65 (178757 downstream)																							cttctccCTGCTCCtttttttt	0.025													4	2	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70150054	70150055	+	Intron	INS	-	AAAAA	AAAAA	rs149355559	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70150054_70150055insAAAAA	uc001deo.1	+									Q96NW7	LRRC7_HUMAN	SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						GTAGGGGAGATGAAGAGAAGGA	0.252													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74084318	74084318	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74084318delA								None (None upstream) : LRRIQ3 (407386 downstream)																							ggcagataggaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	75564298	75564298	+	IGR	DEL	T	-	-	rs34824570		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75564298delT								TYW3 (331940 upstream) : LHX8 (29821 downstream)																							atttttgaaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	76234535	76234535	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76234535delT								ACADM (5182 upstream) : RABGGTB (17351 downstream)																							ttttgaagaATTTATCAGTAG	0.209													4	2	---	---	---	---	
ST6GALNAC5	81849	broad.mit.edu	37	1	77486781	77486781	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77486781delG	uc001dhi.2	+						ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Intron	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						cccatatttagggcaagtgaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	82528191	82528191	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82528191delA								LPHN2 (70085 upstream) : None (None downstream)																							CCATTTACTTAAAAAAAAATT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84042375	84042376	+	RNA	INS	-	T	T	rs112376435		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84042375_84042376insT	uc001diz.3	-	3		c.2260_2261insA								Homo sapiens cDNA clone IMAGE:4815396.																		cttttgtgcacttttttttttt	0.000													4	2	---	---	---	---	
ZNHIT6	54680	broad.mit.edu	37	1	86150150	86150150	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86150150delT	uc001dlh.2	-						ZNHIT6_uc010osc.1_Intron	NM_017953	NP_060423	Q9NWK9	BCD1_HUMAN	zinc finger, HIT type 6						box C/D snoRNP assembly|ribosome biogenesis	pre-snoRNP complex	identical protein binding|metal ion binding			large_intestine(1)	1						cttgtggccctacaaagggct	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89957187	89957187	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89957187delC								LOC400759 (66694 upstream) : LRRC8B (33210 downstream)																							cagtggttctcccagcacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	99533561	99533561	+	Intron	DEL	A	-	-	rs113743115		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99533561delA	uc001dsd.1	+											Homo sapiens cDNA FLJ38225 fis, clone FCBBF2003528.																		TATTATTAAGAAAAAAAAAAA	0.164													3	3	---	---	---	---	
WDR47	22911	broad.mit.edu	37	1	109523350	109523352	+	Intron	DEL	CAA	-	-	rs34767135		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109523350_109523352delCAA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		gattctgtctcaacaacaacaac	0.138													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	113425285	113425286	+	IGR	INS	-	AGA	AGA	rs141871120	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113425285_113425286insAGA								FAM19A3 (155431 upstream) : SLC16A1 (29186 downstream)																							TGTCCCAGAGCAGGAAGAGGAA	0.550													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	113674425	113674432	+	IGR	DEL	TGTGTGTG	-	-	rs150325260		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113674425_113674432delTGTGTGTG								LRIG2 (7083 upstream) : MAGI3 (259043 downstream)																							AGGTAGGTTTtgtgtgtgtgtgtgtgtg	0.308													4	2	---	---	---	---	
TSPAN2	10100	broad.mit.edu	37	1	115598150	115598151	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115598150_115598151insT	uc001eft.2	-							NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TATGATGATTAttttttttttt	0.109													4	3	---	---	---	---	
TSPAN2	10100	broad.mit.edu	37	1	115612995	115612996	+	Intron	INS	-	T	T	rs35027846		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115612995_115612996insT	uc001eft.2	-							NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		CAATAATCTGCTTTTTTTTTTT	0.371													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	117431872	117431873	+	IGR	INS	-	A	A	rs111957071		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117431872_117431873insA								CD2 (120022 upstream) : PTGFRN (20816 downstream)																							ctctgtctcagaaaaaaaaaaa	0.218													1	6	---	---	---	---	
PTGFRN	5738	broad.mit.edu	37	1	117495258	117495259	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117495258_117495259insA	uc001egv.1	+							NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		agagttgagacaaaaaaaaaga	0.000													4	2	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118616767	118616767	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118616767delT	uc001ehk.2	-							NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TGCCTTTGACTTTTTTTTTTA	0.348													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118830625	118830626	+	IGR	DEL	AC	-	-	rs113809230		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118830625_118830626delAC								SPAG17 (102777 upstream) : TBX15 (595040 downstream)																							acacacacagacacacacacac	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118862910	118862911	+	IGR	INS	-	GT	GT	rs142838599	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118862910_118862911insGT								SPAG17 (135062 upstream) : TBX15 (562755 downstream)																							tgcgcgtgcacgtgtgtgtgtg	0.327													5	4	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119452173	119452174	+	Intron	INS	-	TTG	TTG	rs112716321		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119452173_119452174insTTG	uc001ehl.1	-							NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		ATATCTCTGTTttgttgttgtt	0.054													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142602645	142602648	+	IGR	DEL	TAAT	-	-	rs142694571		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142602645_142602648delTAAT								None (None upstream) : None (None downstream)																							tttctatgtctaattaaattcaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142837549	142837550	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142837549_142837550insT	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		cttctgtgagctttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143161518	143161519	+	Intron	INS	-	C	C	rs78859366		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143161518_143161519insC	uc001eiw.1	+						uc001ejf.1_Intron|hsa-mir-3118-2|MI0014132_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		ttaaagtataattaaaaaaaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143506599	143506599	+	IGR	DEL	A	-	-	rs112702416		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143506599delA								None (None upstream) : LOC100286793 (141040 downstream)																							GCAAGGATGGAAAAAAAAATA	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143544423	143544426	+	IGR	DEL	AAAA	-	-	rs113745008		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143544423_143544426delAAAA								None (None upstream) : LOC100286793 (103213 downstream)																							GATTCAAATGAAAAAAAAAAAAAT	0.309													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143964884	143964885	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143964884_143964885insA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		tgctttctggcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143983223	143983224	+	Intron	INS	-	A	A	rs148621543		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143983223_143983224insA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		CTGCTGATTTTAAAAAAACATT	0.307													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144045995	144045996	+	Intron	INS	-	CC	CC	rs147099033	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144045995_144045996insCC	uc010oxm.1	+						uc001eju.1_5'Flank					SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		AAAGGGAAGGTCCCAGGTCTAC	0.455													5	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144533512	144533514	+	Intron	DEL	AAG	-	-	rs66523280		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144533512_144533514delAAG	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						cgtatgtgaaaagaaccgttttt	0.172													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144990950	144990952	+	Intron	DEL	ATA	-	-	rs145512065		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144990950_144990952delATA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_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)		TTTAAATTTTATAATAACTATAA	0.192			T	PDGFRB	MPD								4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145041680	145041681	+	Intron	DEL	AA	-	-	rs10544872		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145041680_145041681delAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'Flank|PDE4DIP_uc001eln.3_5'Flank|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_5'Flank|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AAAAATACAGAAAGTTATATAG	0.272													7	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145071101	145071102	+	Intron	INS	-	ATA	ATA	rs140829774		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145071101_145071102insATA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						gtcaaaaaaccataagatttca	0.000													8	6	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145194931	145194934	+	Intron	DEL	CAAA	-	-	rs139628584		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145194931_145194934delCAAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TATATTTTGTCAAACAAAAAGAAG	0.368													5	4	---	---	---	---	
GJA5	2702	broad.mit.edu	37	1	147231544	147231544	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147231544delC	uc001eps.1	-						GJA5_uc001ept.1_Intron	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40						angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			GCTCTCCTTTCCCAGCAAAAA	0.294													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148847972	148847979	+	IGR	DEL	TCATTTCA	-	-	rs4071443		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148847972_148847979delTCATTTCA								NBPF16 (89661 upstream) : LOC645166 (80307 downstream)																							tttcatcctttcatttcatcatttcatc	0.038													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148850952	148850958	+	IGR	DEL	TTTCATT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148850952_148850958delTTTCATT								NBPF16 (92641 upstream) : LOC645166 (77328 downstream)																							tatgtcatcatttcatttttcatcatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148851645	148851646	+	IGR	INS	-	TA	TA	rs141935458	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148851645_148851646insTA								NBPF16 (93334 upstream) : LOC645166 (76640 downstream)																							AGGTGGCTTTTTTTTTTCCTTA	0.436													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148924072	148924072	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148924072delA								NBPF16 (165761 upstream) : LOC645166 (4214 downstream)																							aaaaaaaaacaaagtatagag	0.000													4	3	---	---	---	---	
MRPS21	54460	broad.mit.edu	37	1	150277471	150277474	+	Intron	DEL	AAAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150277471_150277474delAAAG	uc001euk.2	+						MRPS21_uc001eul.2_Intron	NM_031901	NP_114107	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ctccgtctcaaaagaaagaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150870629	150870630	+	IGR	INS	-	T	T	rs79227017	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150870629_150870630insT								ARNT (21443 upstream) : SETDB1 (28185 downstream)																							TAGATGTGGGGTTTTTTTTTTT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	151951631	151951632	+	IGR	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151951631_151951632delCT								THEM4 (69518 upstream) : S100A10 (3755 downstream)																							ctcactcttgctctctctctct	0.248													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152170253	152170254	+	IGR	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152170253_152170254delCT								RPTN (38549 upstream) : HRNR (14304 downstream)																							ttctttcttcctctctgtctct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152178652	152178652	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152178652delT								RPTN (46948 upstream) : HRNR (5906 downstream)																							AGACAGGCTATTGAAGGAATT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152303016	152303016	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152303016delA	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																		ATGAAACTGGAAAAAAAAAAA	0.408													4	2	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155339238	155339238	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155339238delA	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			actccgtctcaaaaaaaaaaa	0.030													4	2	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155352522	155352522	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155352522delT	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			gtcttagctcttttttttttt	0.000													3	3	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155774575	155774575	+	Intron	DEL	A	-	-	rs77957644		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155774575delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron|GON4L_uc009wrj.1_Intron|GON4L_uc001fme.2_Intron|GON4L_uc001fmf.2_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ctgtctcaggaaaaaaaaaaa	0.104													5	5	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155806041	155806042	+	Intron	DEL	TT	-	-	rs140291845		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155806041_155806042delTT	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					tttgttttcgtttttttttttt	0.173													5	3	---	---	---	---	
CCT3	7203	broad.mit.edu	37	1	156306071	156306072	+	Intron	INS	-	T	T	rs11421979		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156306071_156306072insT	uc001fol.1	-						CCT3_uc001fom.1_Intron|CCT3_uc001fon.1_Intron|CCT3_uc010phj.1_Intron|CCT3_uc010phk.1_Intron|CCT3_uc010phl.1_Intron|C1orf182_uc001foo.2_5'Flank|C1orf182_uc009wry.2_5'Flank|C1orf182_uc001fop.3_5'Flank	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a						'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)					agatactgcaattttttttttt	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158368160	158368161	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158368160_158368161insT								CD1E (40819 upstream) : OR10T2 (153 downstream)																							ATTGACTTGCATTTTTTTTCTT	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158501906	158501907	+	IGR	DEL	TA	-	-	rs151099267		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158501906_158501907delTA								OR10R2 (51232 upstream) : OR6Y1 (15013 downstream)																							ctaggatttttatagtttgagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158962004	158962005	+	IGR	INS	-	CA	CA	rs143500833	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158962004_158962005insCA								PYHIN1 (15163 upstream) : IFI16 (7753 downstream)																							TTAACTTAAACcacacacacac	0.208													4	3	---	---	---	---	
IFI16	3428	broad.mit.edu	37	1	158981173	158981173	+	Intron	DEL	A	-	-	rs149695022		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158981173delA	uc001ftf.1	+						IFI16_uc001ftg.2_Intron|IFI16_uc010pis.1_Intron	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					gctctgtctcaaaaaaaaaaa	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159211496	159211497	+	IGR	DEL	TG	-	-	rs35422025		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159211496_159211497delTG								DARC (35208 upstream) : FCER1A (48009 downstream)																							aatattccactgtgtgtgtgtg	0.000													4	2	---	---	---	---	
ITLN1	55600	broad.mit.edu	37	1	160847031	160847032	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160847031_160847032insA	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)			tgtctcaaaagaaaaaaaaaaa	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161115213	161115214	+	IGR	INS	-	A	A	rs71913909		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161115213_161115214insA								DEDD (12735 upstream) : UFC1 (8320 downstream)																							gactccatctcaaaaaaaaaaa	0.099													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161499355	161499355	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161499355delT								HSPA6 (2670 upstream) : FCGR3A (12198 downstream)																							ttcATGTTACttttttttttt	0.010													4	2	---	---	---	---	
ATF6	22926	broad.mit.edu	37	1	161820945	161820946	+	Intron	INS	-	AA	AA			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161820945_161820946insAA	uc001gbr.2	+						ATF6_uc001gbq.1_Intron	NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			cacacacacacacacacacaca	0.272													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161997799	161997800	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161997799_161997800insT								OLFML2B (4155 upstream) : NOS1AP (41781 downstream)																							acaatttgttctttttttttct	0.000													4	2	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162114359	162114363	+	Intron	DEL	TTTCT	-	-	rs72205911		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162114359_162114363delTTTCT	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)			TGTGTTGGACtttcttttcttttct	0.439													4	2	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162318989	162318989	+	Intron	DEL	A	-	-	rs2003862	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162318989delA	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)			aaaaaaggggaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165148780	165148781	+	IGR	DEL	GC	-	-	rs60015026		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165148780_165148781delGC								PBX1 (294480 upstream) : LMX1A (22324 downstream)																							GGgtgtgtgtgcgtgtgtgtgt	0.366													4	2	---	---	---	---	
RXRG	6258	broad.mit.edu	37	1	165391732	165391733	+	Intron	INS	-	GT	GT	rs144645859	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165391732_165391733insGT	uc001gda.2	-							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)	tgagctgggacgacagccttca	0.178													2	4	---	---	---	---	
UCK2	7371	broad.mit.edu	37	1	165832035	165832036	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165832035_165832036delAG	uc001gdp.2	+						UCK2_uc010plb.1_Intron	NM_012474	NP_036606	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TTCCCGACACAGAGAGAGAGGC	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	167117530	167117530	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167117530delC								DUSP27 (19128 upstream) : POU2F1 (72613 downstream)																							tctctctgtgccaaggatcag	0.000													4	2	---	---	---	---	
CD247	919	broad.mit.edu	37	1	167404048	167404048	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167404048delT	uc001gei.3	-						CD247_uc001gej.3_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			CAGGTGCTGCTGCAGGCCGCA	0.552													5	5	---	---	---	---	
CD247	919	broad.mit.edu	37	1	167431073	167431073	+	Intron	DEL	A	-	-	rs34132569		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167431073delA	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			cgacaggctcaaaaaaaaaag	0.169													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	169001812	169001813	+	IGR	INS	-	T	T	rs150130020	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169001812_169001813insT								MGC4473 (239692 upstream) : ATP1B1 (74134 downstream)																							atccttccagattttttttctg	0.203													3	4	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169515419	169515422	+	Intron	DEL	ACAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169515419_169515422delACAC	uc001ggg.1	-							NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ATGTCTGTGTacacacacacacac	0.363													4	2	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169549627	169549627	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169549627delT	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	gttgttgttgttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171353720	171353720	+	IGR	DEL	T	-	-	rs10567882		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171353720delT								FMO4 (42498 upstream) : BAT2L2 (100946 downstream)																							cTCAACATTCTTTTTTTTTTT	0.055													5	3	---	---	---	---	
BAT2L2	23215	broad.mit.edu	37	1	171475826	171475827	+	Intron	INS	-	TG	TG	rs144658463	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171475826_171475827insTG	uc010pmg.1	+						BAT2L2_uc001ghq.1_Intron|BAT2L2_uc001ghr.1_Intron	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2								protein C-terminus binding				0						ttttttttctTtgtgtgtgtgt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171639404	171639404	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171639404delT								MYOC (17581 upstream) : VAMP4 (29894 downstream)																							gtttgttcccttttttttttt	0.144													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	171810057	171810058	+	5'Flank	INS	-	A	A	rs145553951	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171810057_171810058insA	uc001gie.2	+						DNM3_uc001gid.3_5'Flank|DNM3_uc009wwb.2_5'Flank|DNM3_uc001gif.2_5'Flank	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						TGTATCGGGGCGGTAAACCCTA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172935407	172935408	+	IGR	INS	-	C	C	rs148971818	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172935407_172935408insC								FASLG (299397 upstream) : TNFSF18 (74952 downstream)																							tagtaggcactcctaaaaattt	0.030													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173024284	173024285	+	IGR	DEL	TG	-	-	rs35818102		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173024284_173024285delTG								TNFSF18 (4181 upstream) : TNFSF4 (128586 downstream)																							CATGTTGTTTtgtgtgtgtgtg	0.327													4	2	---	---	---	---	
PRDX6	9588	broad.mit.edu	37	1	173447655	173447656	+	Intron	DEL	TT	-	-	rs35899698	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173447655_173447656delTT	uc001giy.1	+						uc001gix.1_5'Flank	NM_004905	NP_004896	P30041	PRDX6_HUMAN	peroxiredoxin 6						cell redox homeostasis|phospholipid catabolic process	cytoplasmic membrane-bounded vesicle|cytosol|lysosome	peroxiredoxin activity|phospholipase A2 activity|protein binding			central_nervous_system(1)	1						GGTGTTGCCCTTTTTTTTTTTT	0.391													4	2	---	---	---	---	
SLC9A11	284525	broad.mit.edu	37	1	173484970	173484970	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173484970delT	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						ctgttgacccttagatggggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177594061	177594063	+	IGR	DEL	ATC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177594061_177594063delATC								FAM5B (342504 upstream) : SEC16B (303426 downstream)																							taggatgtagatcatcataatac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178027219	178027220	+	IGR	INS	-	G	G	rs10718032		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178027219_178027220insG								SEC16B (20077 upstream) : LOC100302401 (33423 downstream)																							GAAAAAAAAAATAGGGGCCTGC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178676679	178676680	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178676679_178676680insA								C1orf220 (158655 upstream) : RALGPS2 (17620 downstream)																							catctcaaaagaaaaaaaaaaa	0.129													4	2	---	---	---	---	
RALGPS2	55103	broad.mit.edu	37	1	178764315	178764315	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178764315delA	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0						actctgtctcaaaaaaaaaaa	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178969811	178969811	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178969811delT								RALGPS2 (80576 upstream) : FAM20B (25263 downstream)																							tctttcttccttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181812882	181812883	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181812882_181812883insA								CACNA1E (42169 upstream) : ZNF648 (210824 downstream)																							actaagaatacaaaaaattagc	0.000													6	3	---	---	---	---	
LAMC1	3915	broad.mit.edu	37	1	183073109	183073110	+	Intron	INS	-	TG	TG	rs150469978	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183073109_183073110insTG	uc001gpy.3	+						LAMC1_uc001gpx.2_3'UTR	NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AAGAGAACATTTGACCTAATTA	0.307													4	2	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184394402	184394402	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184394402delT	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		TCCTGATATCttttttttttt	0.030													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184622655	184622656	+	IGR	DEL	GT	-	-	rs112791294		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184622655_184622656delGT								C1orf21 (24500 upstream) : EDEM3 (36971 downstream)																							TTAtgtgtgcgtgtgtgtgtgt	0.248													5	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186156127	186156128	+	Intron	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186156127_186156128delCA	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GTCTCTGTCTcacacacacaca	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192746930	192746930	+	IGR	DEL	T	-	-	rs113068486		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192746930delT								RGS13 (117543 upstream) : RGS2 (31239 downstream)																							CCATTTAGCCttttttttttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193458036	193458036	+	IGR	DEL	A	-	-	rs35412403		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193458036delA								CDC73 (234096 upstream) : None (None downstream)																							ccctttaagcAATCTTTCCTG	0.184													3	5	---	---	---	---	
KCNT2	343450	broad.mit.edu	37	1	196465598	196465598	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196465598delA	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	197851637	197851638	+	IGR	INS	-	T	T	rs34154400		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197851637_197851638insT								DENND1B (107014 upstream) : C1orf53 (20044 downstream)																							caacccctgcattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198790978	198790978	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198790978delT								PTPRC (64433 upstream) : MIR181B1 (37024 downstream)																							TTTTGAGGGGTTTTTTTTGGT	0.388													4	4	---	---	---	---	
KIF21B	23046	broad.mit.edu	37	1	200976763	200976764	+	Intron	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200976763_200976764delCA	uc001gvs.1	-						KIF21B_uc001gvr.1_Intron|KIF21B_uc009wzl.1_Intron|KIF21B_uc010ppn.1_Intron|KIF21B_uc001gvt.1_5'Flank	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						cacagacaggcacacacacaca	0.000													3	3	---	---	---	---	
NAV1	89796	broad.mit.edu	37	1	201634991	201634991	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201634991delA	uc001gwu.2	+							NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						TGCTAGTGTTAAAAAAAAAAG	0.443													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202511750	202511750	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202511750delG	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.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)			GAGGAAAGCTGTATTTATAGG	0.463													4	2	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202565423	202565436	+	3'UTR	DEL	ACACACACACACAT	-	-	rs113871158		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202565423_202565436delACACACACACACAT	uc001gye.2	-	9					SYT2_uc010pqb.1_3'UTR|SYT2_uc009xaf.2_3'UTR	NM_001136504	NP_001129976	Q8N9I0	SYT2_HUMAN	synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	acacacacacacacacacacacatacacacacac	0.327													4	5	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202653474	202653475	+	Intron	INS	-	T	T	rs76454500		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202653474_202653475insT	uc010pqb.1	-						SYT2_uc009xaf.2_Intron	NM_177402	NP_796376	Q8N9I0	SYT2_HUMAN	synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	atttattcagcttttttttttt	0.000													4	2	---	---	---	---	
LOC148709	148709	broad.mit.edu	37	1	202838043	202838044	+	Intron	INS	-	T	T	rs140445555	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202838043_202838044insT	uc001gyk.1	+							NR_002929				Homo sapiens cDNA FLJ31247 fis, clone KIDNE2005296, weakly similar to ACTIN, CYTOPLASMIC 1.												0						tcacgcccagcttttttttgtt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203962866	203962867	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203962866_203962867insT								SNRPE (122588 upstream) : C1orf157 (38708 downstream)																							atATGACTCAAttttttttttt	0.020													4	2	---	---	---	---	
NFASC	23114	broad.mit.edu	37	1	204833063	204833066	+	Intron	DEL	AGAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204833063_204833066delAGAG	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ggaggaagaaagagagagagaaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	205270084	205270088	+	IGR	DEL	TTTTT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205270084_205270088delTTTTT								TMCC2 (27614 upstream) : NUAK2 (1105 downstream)																							AAGATCTCTGttttttttttttttt	0.385													4	2	---	---	---	---	
SLC41A1	254428	broad.mit.edu	37	1	205778831	205778831	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205778831delA	uc001hdh.1	-							NM_173854	NP_776253	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 member 1							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			skin(2)	2	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			TGCAGGGGACAAAAGGCATAA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	206931928	206931928	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206931928delT								MAPKAPK2 (24302 upstream) : IL10 (9020 downstream)																							agccaccccattttttcacct	0.000													6	3	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207087783	207087783	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207087783delT	uc001hey.2	-						FAIM3_uc010prz.1_Intron|FAIM3_uc010psa.1_Intron|FAIM3_uc010psb.1_Intron	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					ctttcttttcttttttttttt	0.000													5	3	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097551	207097552	+	5'Flank	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097551_207097552delGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					gtgtccatgagtgtgtgtgtgc	0.000													12	10	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097665	207097666	+	5'Flank	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097665_207097666delGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					gctctgtggagtgtgtgtgtgg	0.000													7	4	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208199997	208199998	+	3'UTR	INS	-	TT	TT	rs112454240		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208199997_208199998insTT	uc001hgz.2	-	32					PLXNA2_uc001hgy.2_3'UTR	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		tcctctttctcttttttttttt	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208731777	208731777	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208731777delG								PLXNA2 (314112 upstream) : LOC642587 (870391 downstream)																							ACCAGAGACTGGTGTATTGAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208844585	208844586	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208844585_208844586delAC								PLXNA2 (426920 upstream) : LOC642587 (757582 downstream)																							TAACATCATTacacacacacac	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208860804	208860805	+	IGR	INS	-	GTC	GTC	rs144993675	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208860804_208860805insGTC								PLXNA2 (443139 upstream) : LOC642587 (741363 downstream)																							ACATTGTGGCTGTCTCTTTTGA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214282141	214282141	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214282141delT								PROX1 (72381 upstream) : SMYD2 (172424 downstream)																							atcttaagtcttttttttttc	0.065													2	4	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214590364	214590364	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214590364delA	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GGGGAAAAGGAAAAAAAAAAA	0.348													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214743134	214743137	+	IGR	DEL	GGAT	-	-	rs112606974		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214743134_214743137delGGAT								PTPN14 (18492 upstream) : CENPF (33395 downstream)																							agaaccagtaggatggatggatgg	0.025													4	2	---	---	---	---	
GPATCH2	55105	broad.mit.edu	37	1	217733216	217733217	+	Intron	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217733216_217733217delGA	uc001hlf.1	-							NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		AATCCagagggagagagagaga	0.307													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218108456	218108457	+	IGR	INS	-	T	T	rs2377713		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218108456_218108457insT								SPATA17 (67954 upstream) : RRP15 (350172 downstream)																							CTTAAAGTTTGTTTTTTTTTTT	0.366													4	4	---	---	---	---	
SLC30A10	55532	broad.mit.edu	37	1	219889972	219889973	+	Intron	INS	-	TG	TG	rs146203961	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219889972_219889973insTG	uc001hlu.1	-									Q6XR72	ZNT10_HUMAN	Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		atatgtgtgtttgtgtgtgtgt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	220486942	220486942	+	IGR	DEL	A	-	-	rs113561692		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220486942delA								RAB3GAP2 (41099 upstream) : MARK1 (214626 downstream)																							caaaaaaaacaaaaaaaaaaa	0.199													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	220537748	220537749	+	IGR	INS	-	CAAAA	CAAAA	rs144424948	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220537748_220537749insCAAAA								RAB3GAP2 (91905 upstream) : MARK1 (163819 downstream)																							TCAAATGGGGTCAAAACAAAAC	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222191152	222191153	+	IGR	INS	-	GT	GT	rs138477560	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222191152_222191153insGT								DUSP10 (275691 upstream) : HHIPL2 (504449 downstream)																							GCCAGTCTTCCgtgtgtgtgtg	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223282293	223282301	+	IGR	DEL	GAAGAAAAC	-	-	rs149044015		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223282293_223282301delGAAGAAAAC								DISP1 (102958 upstream) : TLR5 (1283 downstream)																							GCTGGATTTTGAAGAAAACGAAGAAAACG	0.459													3	4	---	---	---	---	
TLR5	7100	broad.mit.edu	37	1	223288988	223288989	+	Intron	INS	-	AGAC	AGAC	rs141084293	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223288988_223288989insAGAC	uc001hnv.1	-						TLR5_uc001hnw.1_Intron	NM_003268	NP_003259	O60602	TLR5_HUMAN	toll-like receptor 5 precursor						cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)		gaagaggtgataacaaaaggaa	0.000													6	3	---	---	---	---	
NVL	4931	broad.mit.edu	37	1	224417144	224417144	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224417144delT	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)		TAAAAAAAAAttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	225017953	225017953	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225017953delT								CNIH3 (89704 upstream) : DNAH14 (99403 downstream)																							CAGTGGTTCATTTTGGAGGAG	0.418													3	4	---	---	---	---	
DNAH14	127602	broad.mit.edu	37	1	225552306	225552307	+	Intron	INS	-	TT	TT	rs143282372	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225552306_225552307insTT	uc001how.2	+						DNAH14_uc001hox.2_Intron	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						GAAAGCTACTCTTAAAATGTAA	0.267													4	4	---	---	---	---	
ENAH	55740	broad.mit.edu	37	1	225829061	225829062	+	Intron	INS	-	C	C	rs142208599	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225829061_225829062insC	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		TAGAAACTAAgccaagcactgt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	225960958	225960959	+	IGR	INS	-	TT	TT	rs145659967	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225960958_225960959insTT								ENAH (120113 upstream) : SRP9 (4556 downstream)																							AATTTGCCAACAGTAATAATAA	0.337													2	4	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227319817	227319822	+	Intron	DEL	CCCTCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227319817_227319822delCCCTCT	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				AGAAATTCAAccctctccctctccct	0.175													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228178043	228178043	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228178043delA								WNT9A (42367 upstream) : WNT3A (16709 downstream)																							ttcatgatttaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228373942	228373942	+	IGR	DEL	T	-	-	rs79605231		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228373942delT								C1orf69 (3985 upstream) : OBSCN (21919 downstream)																							tttcttcttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229210771	229210772	+	IGR	DEL	TG	-	-	rs34096191		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229210771_229210772delTG								RHOU (328362 upstream) : RAB4A (196107 downstream)																							CATGCCTGTCTGTGTGTAAGTG	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229316163	229316164	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229316163_229316164delAG								RHOU (433754 upstream) : RAB4A (90715 downstream)																							atacacactcagatacactcac	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229977413	229977413	+	IGR	DEL	T	-	-	rs68166351		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229977413delT								URB2 (181467 upstream) : GALNT2 (216123 downstream)																							ACTTTCTTAGTTTAACTTGGC	0.209													4	6	---	---	---	---	
COG2	22796	broad.mit.edu	37	1	230828474	230828475	+	Intron	DEL	TG	-	-	rs77522964		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230828474_230828475delTG	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)				GAtctttctctgtgcgtgtgtg	0.317													5	5	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231979280	231979280	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231979280delC	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				cgagggccatccccctgcagg	0.000													4	2	---	---	---	---	
C1orf57	84284	broad.mit.edu	37	1	233088356	233088356	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233088356delA	uc001hvj.1	+						C1orf57_uc001hvi.2_Intron|C1orf57_uc009xft.1_Intron	NM_032324	NP_115700	Q9BSD7	NTPCR_HUMAN	nucleoside-triphosphatase C1orf57								ATP binding|nucleoside-triphosphatase activity|nucleotide phosphatase activity|transferase activity				0		all_cancers(173;0.0818)|Prostate(94;0.137)				ttccaggctcaaaccatcttc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236084444	236084445	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236084444_236084445delCA								LYST (37504 upstream) : NID1 (54696 downstream)																							cacacacacgcacacacacaca	0.371													6	4	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236171234	236171235	+	Intron	INS	-	T	T	rs144954187	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236171234_236171235insT	uc001hxo.2	-						NID1_uc009xgd.2_Intron|NID1_uc009xgc.2_Intron	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	ggctttctaacttctaaccatg	0.064													3	3	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236210042	236210042	+	Intron	DEL	C	-	-	rs3835671		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236210042delC	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	AGGCATTTATCACCCAAGTGA	0.269													2	6	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236212821	236212821	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236212821delC	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	TAAGGTCCAGCCCCCACCTTT	0.244													6	4	---	---	---	---	
ERO1LB	56605	broad.mit.edu	37	1	236411226	236411227	+	Intron	INS	-	TCACTTAGG	TCACTTAGG	rs140354272	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236411226_236411227insTCACTTAGG	uc001hxt.2	-						ERO1LB_uc010pxt.1_Intron	NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			atgttgtattatcttctctgac	0.000													4	2	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236710980	236710981	+	Intron	INS	-	G	G	rs150744640	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236710980_236710981insG	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ATCGGCGAGGAGGGGCAGCACT	0.589													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238178371	238178380	+	IGR	DEL	TGTGTGTGTG	-	-	rs2487111		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238178371_238178380delTGTGTGTGTG								LOC100130331 (86754 upstream) : LOC339535 (465306 downstream)																							tgcgtgggtatgtgtgtgtgtgtgtgtgtg	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	239333168	239333169	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239333168_239333169delAC								LOC339535 (683851 upstream) : CHRM3 (216696 downstream)																							acatgcacatacacacacacac	0.000													4	2	---	---	---	---	
CHRM3	1131	broad.mit.edu	37	1	239609243	239609243	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239609243delT	uc001hyo.1	+									P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	TGGTGTGCACttttttttttt	0.199													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	240127137	240127142	+	IGR	DEL	GAGAGG	-	-	rs67610528		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240127137_240127142delGAGAGG								CHRM3 (54422 upstream) : FMN2 (128043 downstream)																							gagagagagagagagggagagGCAGG	0.432													3	3	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240604294	240604295	+	Intron	INS	-	T	T	rs34836234		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240604294_240604295insT	uc010pyd.1	+						FMN2_uc010pye.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)			TTGGTGTAAACttttttttttt	0.045													4	5	---	---	---	---	
GREM2	64388	broad.mit.edu	37	1	240713705	240713708	+	Intron	DEL	AAAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240713705_240713708delAAAC	uc001hys.2	-							NM_022469	NP_071914	Q9H772	GREM2_HUMAN	gremlin 2 precursor						BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			TGATTTGTTAaaacaaacaaacaa	0.363													5	3	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241079575	241079579	+	Intron	DEL	AAAAA	-	-	rs33925153		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241079575_241079579delAAAAA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			agacactgtcaaaaaaaaaaaaaaa	0.000													4	4	---	---	---	---	
OPN3	23596	broad.mit.edu	37	1	241764659	241764660	+	Intron	INS	-	T	T	rs34332468		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241764659_241764660insT	uc001hza.2	-						OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_014322	NP_055137	Q9H1Y3	OPN3_HUMAN	opsin 3						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			ggagaactaagttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	243025811	243025814	+	IGR	DEL	AAAA	-	-	rs71996141		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243025811_243025814delAAAA								PLD5 (337813 upstream) : CEP170 (261917 downstream)																							agactccgtcaaaaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244258742	244258742	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244258742delG								ZNF238 (37966 upstream) : C1orf100 (257195 downstream)																							AGTACAGTGTGGGGAGCAGAC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244269267	244269267	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244269267delT								ZNF238 (48491 upstream) : C1orf100 (246670 downstream)																							tctttctgtcttttttttttA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244398902	244398902	+	IGR	DEL	A	-	-	rs72765860	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244398902delA								ZNF238 (178126 upstream) : C1orf100 (117035 downstream)																							ctctctatttaaaaaaaaaaa	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	245901913	245901914	+	IGR	INS	-	TT	TT	rs149216460		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245901913_245901914insTT								KIF26B (35485 upstream) : SMYD3 (10731 downstream)																							ctcattgaagcttttttttttt	0.000													3	3	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	245933143	245933144	+	Intron	INS	-	T	T	rs149509385	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245933143_245933144insT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		atctgtggatgtttaagtctct	0.193													2	4	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246525113	246525114	+	Intron	INS	-	T	T	rs10802396	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246525113_246525114insT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		ttgggaaggggtgagggataaa	0.000													6	3	---	---	---	---	
LOC149134	149134	broad.mit.edu	37	1	246939610	246939611	+	RNA	INS	-	TATT	TATT	rs149331399	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246939610_246939611insTATT	uc001ibs.1	+	1		c.296_297insTATT								Homo sapiens cDNA FLJ12763 fis, clone NT2RP2001450.												0						GGGCATCTCTATATTTATTTTG	0.460													3	4	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247061121	247061121	+	Intron	DEL	A	-	-	rs79322666		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247061121delA	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_Intron	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						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)			tgtctctaccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247460300	247460300	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247460300delG								VN1R5 (39854 upstream) : ZNF496 (3323 downstream)																							CAGATCAGGTGACCAGAACTA	0.358													4	2	---	---	---	---	
C1orf150	148823	broad.mit.edu	37	1	247677292	247677292	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247677292delT	uc009xgw.2	+						C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron			Q5JQS6	CA150_HUMAN	Homo sapiens cDNA FLJ41804 fis, clone NOVAR2000710.												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;0.0241)			CCCCACCGCCtttttttttta	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247820552	247820552	+	IGR	DEL	T	-	-	rs34457351		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247820552delT								OR2G3 (50736 upstream) : OR13G1 (14868 downstream)																							tttaaataagttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248469283	248469288	+	IGR	DEL	GAGTAG	-	-	rs66680533		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248469283_248469288delGAGTAG								OR2T12 (10403 upstream) : OR2M7 (17645 downstream)																							TCCTGCCCTAGAGTAGACAAGGCCTG	0.432													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	913597	913598	+	IGR	INS	-	TCA	TCA	rs77621888		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:913597_913598insTCA								TMEM18 (236158 upstream) : SNTG2 (32957 downstream)																							ACATAAAGAGTTCGATTCTTCA	0.337													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4111876	4111876	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4111876delG								ALLC (361618 upstream) : None (None downstream)																							CATGTTAAAAGGCCAGTCATG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6423502	6423503	+	IGR	INS	-	TG	TG	rs139523940	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6423502_6423503insTG								LOC400940 (295138 upstream) : CMPK2 (557000 downstream)																							GAGTGCGTGCAtgtgtgtgtgt	0.238													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6434742	6434742	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6434742delT								LOC400940 (306378 upstream) : CMPK2 (545761 downstream)																							CATGTAGGCCTTTTCCTGGAG	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6915004	6915004	+	IGR	DEL	A	-	-	rs78544084		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6915004delA								LOC400940 (786640 upstream) : CMPK2 (65499 downstream)																							ACCTTGTTGTAAAAAAAAATG	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7047669	7047670	+	IGR	INS	-	T	T	rs148951869		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7047669_7047670insT								RSAD2 (9306 upstream) : RNF144A (9853 downstream)																							CACCTGCCGTGGGACAGCCTGG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7414601	7414602	+	IGR	DEL	AC	-	-	rs57581690		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7414601_7414602delAC								RNF144A (230294 upstream) : LOC339788 (647956 downstream)																							gatatgtcctacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8311671	8311672	+	Intron	INS	-	TG	TG	rs145564014	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8311671_8311672insTG	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		cattaggggtatgtgtgtgtgt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8380843	8380844	+	Intron	DEL	GG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8380843_8380844delGG	uc010eww.1	-						uc002qyy.1_Intron					Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		cctgaagttaggagttcgagac	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8566425	8566425	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8566425delT								LOC339788 (449448 upstream) : ID2 (252915 downstream)																							TTCGAGGCCATTACCAGGATA	0.547													4	2	---	---	---	---	
HPCAL1	3241	broad.mit.edu	37	2	10522859	10522859	+	Intron	DEL	C	-	-	rs112289870		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10522859delC	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		GCATGCACCACCCCCTCCCTG	0.607													2	4	---	---	---	---	
NOL10	79954	broad.mit.edu	37	2	10759770	10759771	+	Intron	INS	-	A	A	rs148360668	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10759770_10759771insA	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10							nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTAAATAGCATAAAAAAATCCT	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11288245	11288245	+	IGR	DEL	T	-	-	rs35748270		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11288245delT								C2orf50 (1329 upstream) : PQLC3 (7295 downstream)																							TTGCTTCACAttttttttttt	0.279													3	4	---	---	---	---	
LPIN1	23175	broad.mit.edu	37	2	11862169	11862169	+	5'Flank	DEL	A	-	-	rs5829327		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11862169delA	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbs.2_5'Flank	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GAAGGCAGAGAAAAAGAAGGA	0.443													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15952441	15952442	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15952441_15952442insT								DDX1 (181217 upstream) : MYCNOS (127578 downstream)																							CATTTCAGTTCTTTTTTTTTTT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16868008	16868008	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16868008delA								FAM49A (20912 upstream) : RAD51AP2 (823978 downstream)																							ATCTGTCCTTAGAATCTCTCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17383564	17383565	+	IGR	INS	-	TG	TG	rs55902300		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17383564_17383565insTG								FAM49A (536468 upstream) : RAD51AP2 (308421 downstream)																							gtgtgtgtgtatgtgtgtgtgt	0.144													2	6	---	---	---	---	
SMC6	79677	broad.mit.edu	37	2	17866395	17866396	+	Intron	INS	-	AA	AA	rs147124437	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17866395_17866396insAA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					caagcaaaatgaaaaaaaaaga	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19236450	19236452	+	IGR	DEL	TCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19236450_19236452delTCT								NT5C1B (465612 upstream) : OSR1 (314795 downstream)																							CTGTGGCACATCTTCTTCTTCTT	0.429													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19821199	19821200	+	IGR	INS	-	AATT	AATT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19821199_19821200insAATT								OSR1 (262827 upstream) : TTC32 (275318 downstream)																							caatagtggcaaattaattaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22945250	22945251	+	IGR	INS	-	C	C	rs146745283	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22945250_22945251insC								None (None upstream) : KLHL29 (810204 downstream)																							cccagacaaaacatgagctctc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23636185	23636185	+	IGR	DEL	C	-	-	rs112897052		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23636185delC								None (None upstream) : KLHL29 (119270 downstream)																							AACCATGGGGCCAGCCATTTC	0.522													3	3	---	---	---	---	
C2orf39	92749	broad.mit.edu	37	2	26634430	26634439	+	Intron	DEL	AAGTTAATAG	-	-	rs141523185		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26634430_26634439delAAGTTAATAG	uc002rhg.2	+						C2orf39_uc010eym.1_Intron	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGAGATTTAAGTTAATAGTAGTTAATAA	0.110													2	4	---	---	---	---	
RBKS	64080	broad.mit.edu	37	2	28043417	28043418	+	Intron	DEL	TC	-	-	rs113182292		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28043417_28043418delTC	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411	Q9H477	RBSK_HUMAN	ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					gatttactATtctctctctctc	0.000													4	2	---	---	---	---	
PPP1CB	5500	broad.mit.edu	37	2	28982856	28982856	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28982856delA	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010ymk.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)					gcattccaggaaaaaaagctt	0.000													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29955780	29955781	+	Intron	DEL	TA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29955780_29955781delTA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	tttttttttttaagcagcctga	0.149			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
CAPN14	440854	broad.mit.edu	37	2	31446646	31446646	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31446646delG	uc002rnt.1	-									A8MX76	CAN14_HUMAN	RecName: Full=Calpain-14;          EC=3.4.22.-;						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						cacctgccttggccacccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	31649139	31649140	+	IGR	INS	-	CT	CT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31649139_31649140insCT								XDH (11528 upstream) : SRD5A2 (100516 downstream)																							GCCACTGCCAACTCCCCCCGGG	0.579													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	33626067	33626068	+	IGR	INS	-	C	C	rs147847544	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33626067_33626068insC								LTBP1 (1494 upstream) : RASGRP3 (35348 downstream)																							ggaggctgaggcaggagaatcg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34106106	34106107	+	IGR	DEL	AT	-	-	rs58877876		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34106106_34106107delAT								MYADML (152822 upstream) : None (None downstream)																							GAAAGCAGACATGTGCAGGTTC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38099535	38099548	+	IGR	DEL	CAGCTGTCCCTGCT	-	-	rs72207293		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38099535_38099548delCAGCTGTCCCTGCT								CDC42EP3 (200209 upstream) : FAM82A1 (52914 downstream)																							TAGGACATCCCAGCTGTCCCTGCTCCCCAGTCCT	0.533													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42210772	42210773	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42210772_42210773insA								None (None upstream) : PKDCC (64388 downstream)																							gttgggacaagaaaaaaaaatc	0.074													4	2	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42723749	42723749	+	Intron	DEL	A	-	-	rs35316146		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42723749delA	uc002rso.1	+						KCNG3_uc002rsm.2_5'Flank|KCNG3_uc002rsn.2_5'Flank	NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						AGAACCTAGGaaaaaaaaaaa	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43166520	43166521	+	IGR	INS	-	T	T	rs112378364		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43166520_43166521insT								HAAO (146769 upstream) : ZFP36L2 (283021 downstream)																							AAACGAAGGGATtttttttttt	0.213													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47195830	47195830	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47195830delT	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TACTTTGAACTTTTATTTCTC	0.323													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47269815	47269816	+	Intron	DEL	GT	-	-	rs34168527		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47269815_47269816delGT	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			tgagccccaagtgtgtgtgtgt	0.134													4	2	---	---	---	---	
C2orf61	285051	broad.mit.edu	37	2	47359304	47359304	+	Intron	DEL	A	-	-	rs111671524		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47359304delA	uc002rvs.2	-						C2orf61_uc010fbd.2_Intron|C2orf61_uc010yog.1_Intron	NM_173649	NP_775920	Q8N801	CB061_HUMAN	hypothetical protein LOC285051 isoform 2												0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			actcactctgaaaaaaaaaaa	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47997320	47997320	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47997320delT								MSH2 (90812 upstream) : MSH6 (12901 downstream)																							gatgattggattttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49032686	49032689	+	IGR	DEL	AGAC	-	-	rs35192775		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49032686_49032689delAGAC								LHCGR (49806 upstream) : FSHR (156964 downstream)																							agagagacagagacagacagacag	0.000													4	2	---	---	---	---	
ASB3	51130	broad.mit.edu	37	2	53989308	53989309	+	Intron	INS	-	TG	TG	rs145076524	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53989308_53989309insTG	uc002rxg.1	-						ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron|ASB3_uc010yoo.1_Intron	NM_016115	NP_057199	Q9Y575	ASB3_HUMAN	ankyrin repeat and SOCS box-containing protein 3						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			agtgatctaactgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54243863	54243863	+	IGR	DEL	T	-	-	rs72344207		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54243863delT								PSME4 (45886 upstream) : ACYP2 (98547 downstream)																							cttcagtgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54299704	54299704	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54299704delT								PSME4 (101727 upstream) : ACYP2 (42706 downstream)																							ttctttcttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54313811	54313812	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54313811_54313812delTG								PSME4 (115834 upstream) : ACYP2 (28598 downstream)																							aaagacaaattgtgtgtgtgtg	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57997167	57997172	+	IGR	DEL	CACACA	-	-	rs10545482		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57997167_57997172delCACACA								None (None upstream) : VRK2 (137614 downstream)																							TCTCATGCAGcacacacacacacaca	0.218													4	2	---	---	---	---	
REL	5966	broad.mit.edu	37	2	61131720	61131720	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61131720delA	uc002sam.1	+						REL_uc002san.1_Intron	NM_002908	NP_002899	Q04864	REL_HUMAN	v-rel reticuloendotheliosis viral oncogene						positive regulation of I-kappaB kinase/NF-kappaB cascade	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			aaaaataattaaaaaaaaaaa	0.010			A		Hodgkin Lymphoma								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62008849	62008849	+	IGR	DEL	G	-	-	rs36027388		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62008849delG								XPO1 (243431 upstream) : FAM161A (43136 downstream)																							gcaagctgaagaaaggaaata	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67097659	67097660	+	IGR	DEL	CA	-	-	rs146348975		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67097659_67097660delCA								MEIS1 (297769 upstream) : ETAA1 (526782 downstream)																							aggatggtctcacagagaattt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67873523	67873524	+	IGR	INS	-	CT	CT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67873523_67873524insCT								ETAA1 (235990 upstream) : C1D (395809 downstream)																							cactggactcactcttcccact	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70549630	70549631	+	IGR	INS	-	AAC	AAC	rs145630945	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70549630_70549631insAAC								FAM136A (20410 upstream) : TGFA (124788 downstream)																							CATAGTACTTAATGTTTTAgaa	0.178													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71241180	71241180	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71241180delA								TEX261 (19179 upstream) : OR7E91P (10025 downstream)																							ataatatcacagggtgtacat	0.000													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845689	71845690	+	Intron	INS	-	GT	GT	rs151307817		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845689_71845690insGT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						gtagaggtggagtgtgtgtttg	0.178													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72539930	72539930	+	Intron	DEL	A	-	-	rs77181565		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72539930delA	uc010fep.2	-							NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						aacgacaacCAAAAAAAAAAA	0.035													4	2	---	---	---	---	
CCT7	10574	broad.mit.edu	37	2	73479170	73479171	+	Intron	INS	-	GTG	GTG	rs149581390	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73479170_73479171insGTG	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	NM_006429	NP_006420	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0						GGCTTACTGGTGTGGTGAAGCT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75136823	75136823	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75136823delT								HK2 (16349 upstream) : POLE4 (48952 downstream)																							ttcttttttcttttttttttt	0.129													4	3	---	---	---	---	
FAM176A	84141	broad.mit.edu	37	2	75772817	75772818	+	Intron	DEL	AG	-	-	rs144597563		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75772817_75772818delAG	uc002sni.2	-						FAM176A_uc002snj.1_Intron|FAM176A_uc002snk.1_Intron	NM_001135032	NP_001128504	Q9H8M9	F176A_HUMAN	family with sequence similarity 176, member A						apoptosis|autophagy	endoplasmic reticulum membrane|integral to membrane|lysosomal membrane|plasma membrane					0						CACAGGACACAGAAATCattca	0.272													3	3	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89081667	89081669	+	Intron	DEL	AAC	-	-	rs140725239		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89081667_89081669delAAC	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TGGATGAAGAAACTTTCGGAAGG	0.305													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89876259	89876263	+	IGR	DEL	GAGAA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89876259_89876263delGAGAA								FLJ40330 (770134 upstream) : None (None downstream)																							gaagggaatggagaagaatggaatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90403394	90403395	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90403394_90403395insA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		aaatagtcttgaaaaaagaaaa	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90475232	90475233	+	IGR	INS	-	TTCT	TTCT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90475232_90475233insTTCT								None (None upstream) : None (None downstream)																							tctctctctccttctttctttc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90478381	90478382	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90478381_90478382insT								None (None upstream) : None (None downstream)																							ggctggagtgcttttttttcag	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91683264	91683265	+	IGR	INS	-	A	A	rs143557730		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91683264_91683265insA								None (None upstream) : LOC654342 (121927 downstream)																							ccaatatggtgaaaccctgtct	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101230570	101230573	+	IGR	DEL	TTCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101230570_101230573delTTCT								PDCL3 (37369 upstream) : NPAS2 (206040 downstream)																							ctttctttccttctttctttcttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102512054	102512055	+	IGR	INS	-	A	A	rs58467573		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102512054_102512055insA								MAP4K4 (903 upstream) : IL1R2 (96251 downstream)																							GCATCTCCTTCaaaaaaaaaaa	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102591848	102591851	+	IGR	DEL	GCGT	-	-	rs67335329		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102591848_102591851delGCGT								MAP4K4 (80697 upstream) : IL1R2 (16455 downstream)																							atccgtgtgcgcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103918937	103918937	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103918937delG								TMEM182 (484801 upstream) : None (None downstream)																							GAAAATAAATGGGCATAATTG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105030343	105030343	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105030343delT								None (None upstream) : LOC150568 (20462 downstream)																							CAGCCCCAGCTTTTTTTTTTT	0.393													4	2	---	---	---	---	
UXS1	80146	broad.mit.edu	37	2	106734033	106734033	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106734033delA	uc002tdm.2	-						UXS1_uc002tdl.2_Intron|UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						CTATTGATAGAAGGTGGAACA	0.418													4	2	---	---	---	---	
RGPD3	653489	broad.mit.edu	37	2	107037904	107037904	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107037904delA	uc010ywi.1	-							NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3						intracellular transport		binding			ovary(1)	1						TGGTATAATTAAAAAAAAATC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107087414	107087415	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107087414_107087415insA								RGPD3 (2613 upstream) : ST6GAL2 (330643 downstream)																							AAAACATGTGGAAAAAAAAAAT	0.351													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108328515	108328516	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108328515_108328516delGT								ST6GAL2 (824952 upstream) : LOC729121 (111004 downstream)																							atgtgtgcacgtgtgtgtgACA	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108379888	108379889	+	IGR	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108379888_108379889delAA								ST6GAL2 (876325 upstream) : LOC729121 (59631 downstream)																							catatctaccaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	110400771	110400771	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110400771delA								ANKRD57 (24208 upstream) : RGPD5 (149564 downstream)																							ttttcaaaagaaaaaaaaaaa	0.139													3	3	---	---	---	---	
WASH2P	375260	broad.mit.edu	37	2	114344982	114344982	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114344982delG	uc002tka.2	+						WASH2P_uc002tkb.2_Intron|WASH2P_uc010fkx.1_5'Flank|WASH2P_uc002tkd.2_5'Flank	NR_024077				Homo sapiens cDNA FLJ75027 complete cds, highly similar to Homo sapiens CXYorf1-related protein (MGC52000), mRNA.												0						GGCTCCAGCTGGGTGAAGATG	0.483													3	3	---	---	---	---	
WASH2P	375260	broad.mit.edu	37	2	114345023	114345025	+	Intron	DEL	ATT	-	-	rs62160570		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114345023_114345025delATT	uc002tka.2	+						WASH2P_uc002tkb.2_Intron|WASH2P_uc010fkx.1_5'Flank|WASH2P_uc002tkd.2_5'Flank	NR_024077				Homo sapiens cDNA FLJ75027 complete cds, highly similar to Homo sapiens CXYorf1-related protein (MGC52000), mRNA.												0						AAATATACAAATTATTATTGGGA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114588350	114588351	+	IGR	INS	-	AC	AC	rs59403700		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114588350_114588351insAC								SLC35F5 (73950 upstream) : ACTR3 (59186 downstream)																							ACGACAACAAAacacacacaca	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	117709423	117709424	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117709423_117709424delCA								None (None upstream) : DDX18 (862831 downstream)																							cgtgcacatgcacacacacaca	0.228													4	2	---	---	---	---	
TFCP2L1	29842	broad.mit.edu	37	2	122012379	122012379	+	Intron	DEL	A	-	-	rs35562172		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122012379delA	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)					actccgtttcaaaaaaaaaaa	0.234													2	4	---	---	---	---	
CLASP1	23332	broad.mit.edu	37	2	122236598	122236599	+	Intron	INS	-	CACACAC	CACACAC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122236598_122236599insCACACAC	uc002tnc.2	-						CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					cacaccacacacacacacaccc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124344852	124344852	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124344852delT								None (None upstream) : CNTNAP5 (438012 downstream)																							agaaaagacatttatttctca	0.085													4	2	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125232683	125232684	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125232683_125232684insT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CAGAGAATTCATTTTTTTTTTT	0.356													6	3	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125300888	125300888	+	Intron	DEL	A	-	-	rs35714087		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125300888delA	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CTTGTGCCTTAAAAAAAAAAA	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129164260	129164261	+	IGR	INS	-	AGG	AGG	rs140753792	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129164260_129164261insAGG								HS6ST1 (88089 upstream) : None (None downstream)																							CTGCCTTTCCCAGGAGCAAGTG	0.485													4	2	---	---	---	---	
FAM168B	130074	broad.mit.edu	37	2	131827433	131827434	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131827433_131827434insT	uc002tsd.2	-							NM_001009993	NP_001009993	A1KXE4	F168B_HUMAN	hypothetical protein LOC130074												0						cctcatcaaacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133028785	133028786	+	IGR	INS	-	AGA	AGA	rs138015528		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028785_133028786insAGA								NCRNA00164 (13243 upstream) : GPR39 (145361 downstream)																							tggacaggcagaggagagtaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134780694	134780694	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134780694delT								NCKAP5 (454663 upstream) : MGAT5 (231136 downstream)																							TCCTTAATGAttttttttttc	0.070													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	138486605	138486606	+	IGR	DEL	TG	-	-	rs72109814		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138486605_138486606delTG								THSD7B (51318 upstream) : HNMT (234984 downstream)																							gttttggttttgtgtgtgtgtg	0.054													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	143493659	143493660	+	IGR	INS	-	T	T	rs12478146		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143493659_143493660insT								LRP1B (604389 upstream) : KYNU (141535 downstream)																							ttttttttttgttttttttttt	0.000													1	5	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	144379570	144379571	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144379570_144379571delTG	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		TAGAGATAGTtgtgtgtgtgtg	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	145800156	145800156	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145800156delC	uc002twc.2	+						uc002twd.2_Intron|uc002twe.2_Intron					Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																		acacaacctgcccaggaaaat	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151190732	151190733	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151190732_151190733insT								MMADHC (746402 upstream) : RND3 (133979 downstream)																							ttttttgattcttttttttctg	0.178													9	5	---	---	---	---	
RBM43	375287	broad.mit.edu	37	2	152112779	152112779	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152112779delT	uc002txh.2	-							NM_198557	NP_940959	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43								nucleotide binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)		ccagccACCCTTTTTTTCATA	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	153035989	153035989	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153035989delT								STAM2 (3483 upstream) : FMNL2 (155762 downstream)																							accttgcaaattttttttttc	0.000													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	154954603	154954604	+	Intron	INS	-	T	T	rs10673538		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154954603_154954604insT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						GCTTGTCTTTCTTTTTTTTTTT	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	158564496	158564496	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158564496delA								ACVR1C (79097 upstream) : ACVR1 (28462 downstream)																							ggcaataattaagagcctacc	0.000													4	2	---	---	---	---	
MARCH7	64844	broad.mit.edu	37	2	160610062	160610062	+	Intron	DEL	A	-	-	rs112033189		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160610062delA	uc002uax.2	+						MARCH7_uc010foq.2_Intron|MARCH7_uc010zcn.1_Intron|MARCH7_uc010for.2_Intron|MARCH7_uc002uay.2_Intron	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin								ligase activity|zinc ion binding				0						actccatgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161621057	161621058	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161621057_161621058insT								RBMS1 (270739 upstream) : TANK (372408 downstream)																							ctctctctctcttttttttttt	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168647840	168647840	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168647840delA								XIRP2 (531581 upstream) : B3GALT1 (27342 downstream)																							TATCACACTGAAAAAAAAATC	0.289													4	2	---	---	---	---	
KBTBD10	10324	broad.mit.edu	37	2	170336534	170336534	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170336534delA	uc010zdh.1	+						BBS5_uc002uet.2_Intron|BBS5_uc010fpw.2_Intron	NM_152384	NP_689597	O60662	KBTBA_HUMAN	Bardet-Biedl syndrome 5						striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0						gtagatgtgtaatatcgaccc	0.159													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171494125	171494126	+	Intron	INS	-	TTAT	TTAT	rs151129612	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171494125_171494126insTTAT	uc002ufy.2	+						MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						CATTTTATGCATTATTTCCGTA	0.366													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174214542	174214542	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174214542delT								ZAK (81806 upstream) : CDCA7 (5019 downstream)																							agacccagcctttttttaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177121149	177121149	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177121149delT								HOXD1 (65514 upstream) : MTX2 (12974 downstream)																							GATATCACTCttttttttttt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177655219	177655220	+	IGR	INS	-	C	C	rs140253548	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177655219_177655220insC								MIR1246 (189439 upstream) : HNRNPA3 (422202 downstream)																							TTGAAGAGAGACCCCCACCCCC	0.475													4	4	---	---	---	---	
NFE2L2	4780	broad.mit.edu	37	2	178252874	178252875	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178252874_178252875insT	uc002uli.3	-						LOC100130691_uc002ulk.1_Intron	NM_001145412	NP_001138884	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CCTATTTAGACTTTTTTTTGTG	0.351			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	178445568	178445569	+	IGR	INS	-	AC	AC	rs71410747		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178445568_178445569insAC								TTC30B (28044 upstream) : TTC30A (33458 downstream)																							AGTGGTGGGAAacacacacaca	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181727901	181727902	+	IGR	INS	-	T	T	rs71405431		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181727901_181727902insT								CWC22 (856061 upstream) : UBE2E3 (117210 downstream)																							gtattttatggttttttttttt	0.054													4	3	---	---	---	---	
ITGA4	3676	broad.mit.edu	37	2	182325294	182325295	+	Intron	DEL	GT	-	-	rs28600304		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182325294_182325295delGT	uc002unu.2	+						ITGA4_uc010zfl.1_Intron	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	CTGTAGAAGAgtgtgtgtgtgt	0.252													4	2	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182910843	182910843	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182910843delC	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			ttccttccttccttccttcct	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184950848	184950849	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184950848_184950849delTG								NUP35 (924441 upstream) : ZNF804A (512244 downstream)																							tggcagttattgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187548244	187548244	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187548244delA								ITGAV (2617 upstream) : FAM171B (10545 downstream)																							ctatagaagtaaaaaaaaaaa	0.000													6	4	---	---	---	---	
GULP1	51454	broad.mit.edu	37	2	189181303	189181303	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189181303delT	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399	Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			tgactgctcctccccagctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190423673	190423676	+	IGR	DEL	AACA	-	-	rs112240286		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190423673_190423676delAACA								WDR75 (83409 upstream) : SLC40A1 (1642 downstream)																							tctcaaaaacaacaaacaaacaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	196426079	196426079	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196426079delA								None (None upstream) : SLC39A10 (95453 downstream)																							agttgaagctaaaaaaaaaaa	0.000													2	4	---	---	---	---	
SATB2	23314	broad.mit.edu	37	2	200231625	200231626	+	Intron	INS	-	CACA	CACA	rs140638022	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200231625_200231626insCACA	uc002uuy.1	-						SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Intron|SATB2_uc002uva.1_Intron	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						ATGTGCGAATGcacacacacac	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201967197	201967197	+	IGR	DEL	A	-	-	rs77338628		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201967197delA								NDUFB3 (16726 upstream) : CFLAR (13619 downstream)																							actctgtctcaaaaaaaaaaa	0.174													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206167807	206167807	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206167807delA	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		acttttgggtaaaaaaaaAAG	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206485404	206485404	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206485404delT								PARD3B (4867 upstream) : NRP2 (61820 downstream)																							agcttaggcctcagccacccc	0.000													4	2	---	---	---	---	
CREB1	1385	broad.mit.edu	37	2	208405944	208405944	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208405944delA	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron	NM_134442	NP_604391	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|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		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)	actccatctcaaaaaaaaaaa	0.000			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212820982	212820983	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212820982_212820983insA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		CGCATAAATGCAAAAATAGTAA	0.287										TSP Lung(8;0.080)			4	2	---	---	---	---	
FN1	2335	broad.mit.edu	37	2	216235278	216235278	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216235278delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Intron|FN1_uc010fvb.1_Intron|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	aacaaaaaacaaaaaaaaaaa	0.413													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218703967	218703967	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218703967delG	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGAGAAGGCTGGGGTACCCTT	0.572													4	2	---	---	---	---	
VIL1	7429	broad.mit.edu	37	2	219299818	219299819	+	Intron	DEL	CT	-	-	rs67794207		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219299818_219299819delCT	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGAAAAGACTCTCTAGTTTC	0.490													2	10	---	---	---	---	
CCDC108	255101	broad.mit.edu	37	2	219901167	219901167	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219901167delT	uc002vjl.1	-						CCDC108_uc010zkp.1_Intron|CCDC108_uc010zkq.1_Intron|CCDC108_uc002vjn.2_Intron	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1							integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAttttatcttttttttttt	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221496746	221496747	+	IGR	INS	-	T	T	rs138897046	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221496746_221496747insT								SLC4A3 (990045 upstream) : EPHA4 (786002 downstream)																							TAATTATGTGGTTTTTTTCTCT	0.272													3	3	---	---	---	---	
KIAA1486	57624	broad.mit.edu	37	2	226431632	226431633	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226431632_226431633delTG	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		TACAGTAATAtgtgtgtgtgtg	0.223													4	2	---	---	---	---	
SP110	3431	broad.mit.edu	37	2	231068684	231068684	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231068684delA	uc002vqh.3	-						SP110_uc002vqg.3_Intron|SP110_uc002vqi.3_Intron|SP110_uc010fxk.2_Intron|SP110_uc010fxj.2_Intron	NM_004509	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein isoform a						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		tgagctatgcacctaaaaatg	0.055													4	2	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234074497	234074498	+	Intron	DEL	TG	-	-	rs72375698		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234074497_234074498delTG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		TCtgtgtgtttgtgtgtgtgtg	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234207940	234207940	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234207940delT								ATG16L1 (3621 upstream) : SAG (8369 downstream)																							CTTGGGTCACttttttttttt	0.134													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235756784	235756789	+	IGR	DEL	ACACAC	-	-	rs111602192		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235756784_235756789delACACAC								ARL4C (351091 upstream) : SH3BP4 (103839 downstream)																							CTCTCAAAATacacacacacacacac	0.330													4	2	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237300417	237300417	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237300417delG	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						actctcagatggttgggttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240812231	240812234	+	IGR	DEL	TTTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240812231_240812234delTTTG								HDAC4 (488885 upstream) : NDUFA10 (87924 downstream)																							CCAGCCTGtttttgtttgtttgtt	0.044													3	4	---	---	---	---	
BOK	666	broad.mit.edu	37	2	242510737	242510737	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242510737delG	uc002wbq.2	+						BOK_uc002wbr.2_5'Flank	NM_032515	NP_115904	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer						activation of caspase activity|cell proliferation|signal transduction by p53 class mediator resulting in induction of apoptosis	mitochondrial membrane|nucleus				ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		CGCAGTTGCCGCTGGGCCCTG	0.652													4	2	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4689837	4689837	+	Intron	DEL	A	-	-	rs35484832		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4689837delA	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		actctgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
ATG7	10533	broad.mit.edu	37	3	11447350	11447350	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11447350delC	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						gccttggcctcccaaagtgct	0.104													4	2	---	---	---	---	
SYN2	6854	broad.mit.edu	37	3	12202512	12202512	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12202512delT	uc003bwm.2	+						SYN2_uc003bwl.1_Intron|SYN2_uc003bwn.2_Intron|TIMP4_uc003bwo.2_5'Flank	NM_133625	NP_598328	Q92777	SYN2_HUMAN	synapsin II isoform IIa						neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2						TGTTTGGTGGTGAGATTGGGG	0.458													4	2	---	---	---	---	
SH3BP5	9467	broad.mit.edu	37	3	15336595	15336596	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15336595_15336596delAC	uc003bzp.1	-						SH3BP5_uc010hem.1_Intron|SH3BP5_uc003bzq.1_Intron|SH3BP5_uc003bzr.1_Intron	NM_004844	NP_004835	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)						intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0						TCTCCCGCCAACACACACACAC	0.545													4	2	---	---	---	---	
METTL6	131965	broad.mit.edu	37	3	15424170	15424171	+	3'UTR	INS	-	A	A	rs35840597		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15424170_15424171insA	uc010hen.1	-	3						NM_152396	NP_689609	Q8TCB7	METL6_HUMAN	methyltransferase like 6								methyltransferase activity				0						agacttgcttcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
TBC1D5	9779	broad.mit.edu	37	3	17496425	17496427	+	Intron	DEL	ACA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17496425_17496427delACA	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						actgaagaggacaacaacaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	24055773	24055773	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24055773delT								NR1D2 (33664 upstream) : LOC152024 (82007 downstream)																							aattcttttctttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	32549855	32549855	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32549855delA								CMTM6 (5452 upstream) : DYNC1LI1 (17614 downstream)																							ATAAAATTGCAAAAAAAAAAC	0.189													4	2	---	---	---	---	
GLB1	2720	broad.mit.edu	37	3	33112187	33112187	+	Intron	DEL	A	-	-	rs113590310		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33112187delA	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)				aaagcaaaacaaaaaaattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35989228	35989235	+	IGR	DEL	TGTGTGTG	-	-	rs71967921		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35989228_35989235delTGTGTGTG								ARPP21 (153241 upstream) : STAC (432862 downstream)																							GTATTTCCACtgtgtgtgtgtgtgtgtg	0.183													3	3	---	---	---	---	
CLEC3B	7123	broad.mit.edu	37	3	45067805	45067809	+	5'UTR	DEL	TCGGA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45067805_45067809delTCGGA	uc003cok.3	+	1						NM_003278	NP_003269	P05452	TETN_HUMAN	C-type lectin domain family 3, member B						skeletal system development	extracellular space	protein binding|sugar binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTCACTGCGTTCGGACCCAGACCCG	0.663													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46547585	46547585	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46547585delG								RTP3 (5146 upstream) : LRRC2 (9295 downstream)																							TCACCACTGTGGTAATTAGCA	0.517													4	2	---	---	---	---	
ARIH2	10425	broad.mit.edu	37	3	49012722	49012722	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49012722delA	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_Intron|ARIH2_uc010hkl.2_Intron	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		CAAGGCAGGTAAGTAGCTTGG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	49860721	49860722	+	IGR	INS	-	AA	AA			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49860721_49860722insAA								UBA7 (9330 upstream) : TRAIP (5306 downstream)																							gacttcatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	53416136	53416136	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53416136delA								DCP1A (34499 upstream) : CACNA1D (112895 downstream)																							ggctatgatgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	58310824	58310824	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58310824delT								RPP14 (4905 upstream) : PXK (7793 downstream)																							ttttctattcttttttttttt	0.204													4	2	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65354658	65354658	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65354658delC	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TGGGGCATCTCCATACAATGC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	74047999	74047999	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74047999delT								PDZRN3 (373927 upstream) : CNTN3 (263723 downstream)																							cttataaaggttttttttttt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	74215293	74215294	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74215293_74215294delAG								PDZRN3 (541221 upstream) : CNTN3 (96428 downstream)																							agccttAAAAAGAGAGAGAGAG	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75995110	75995111	+	IGR	INS	-	G	G	rs140929806		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75995110_75995111insG								ZNF717 (160440 upstream) : None (None downstream)																							TCTACAGTCAAGATACTTGAAA	0.371													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90366880	90366880	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90366880delA								EPHA3 (835598 upstream) : None (None downstream)																							gcttctgtgtagtttttatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	96485916	96485916	+	IGR	DEL	A	-	-	rs113528002		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96485916delA								None (None upstream) : EPHA6 (47509 downstream)																							TAAGAAAaggaaaaaaaaaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97572251	97572254	+	Intron	DEL	ACAC	-	-	rs141359748		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97572251_97572254delACAC	uc011bgq.1	+											SubName: Full=cDNA FLJ60082, weakly similar to Uro-adherence factor A; Flags: Fragment;																		cacatacaatacacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104120636	104120637	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104120636_104120637insT								None (None upstream) : ALCAM (965076 downstream)																							tagttcaaccattgtgaaaagc	0.000													4	3	---	---	---	---	
CBLB	868	broad.mit.edu	37	3	105556928	105556928	+	Intron	DEL	T	-	-	rs11294272		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105556928delT	uc003dwc.2	-						CBLB_uc011bhi.1_Intron|CBLB_uc003dwd.1_Intron|CBLB_uc003dwe.1_Intron|CBLB_uc011bhj.1_Intron	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						cctttttttcttttttttttt	0.154			Mis S		AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109041737	109041737	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109041737delA								DPPA2 (6373 upstream) : DPPA4 (3252 downstream)																							actccgtttcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109331535	109331536	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109331535_109331536insT								FLJ25363 (117521 upstream) : None (None downstream)																							TGCGCTACCCATTTTTTTTTTT	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110782266	110782266	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110782266delC								None (None upstream) : PVRL3 (8599 downstream)																							cttcactgttcccttcctcta	0.000													4	2	---	---	---	---	
TAGLN3	29114	broad.mit.edu	37	3	111719102	111719103	+	Intron	DEL	TA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111719102_111719103delTA	uc003dym.2	+						TAGLN3_uc003dyl.2_Intron|TAGLN3_uc003dyn.2_Intron|TAGLN3_uc003dyo.2_Intron	NM_001008272	NP_001008273	Q9UI15	TAGL3_HUMAN	transgelin 3						central nervous system development|muscle organ development						0						GAGCTTGGGTTATATATATATA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117802348	117802348	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117802348delA								None (None upstream) : IGSF11 (817133 downstream)																							AACCACCCATAAAGTTGGTGT	0.398													4	2	---	---	---	---	
ARHGAP31	57514	broad.mit.edu	37	3	119104079	119104080	+	Intron	INS	-	T	T	rs145852804	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119104079_119104080insT	uc003ecj.3	+							NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						ctagctgactgttttttttttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	119873026	119873027	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119873026_119873027delAG								GSK3B (59762 upstream) : GPR156 (12853 downstream)																							agagagagacagagagagagag	0.000													4	2	---	---	---	---	
KPNA1	3836	broad.mit.edu	37	3	122171392	122171395	+	Intron	DEL	GGAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122171392_122171395delGGAG	uc003efd.1	-						KPNA1_uc003efb.1_Intron|KPNA1_uc003efc.1_Intron|KPNA1_uc011bjr.1_Intron|KPNA1_uc010hrh.2_Intron|KPNA1_uc003efe.2_Intron	NM_002264	NP_002255	P52294	IMA1_HUMAN	karyopherin alpha 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|regulation of DNA recombination|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein binding|protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.0898)		aaggagggaaggagggagggaggg	0.000													4	3	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	123772600	123772600	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123772600delG	uc003ehd.2	+									O60229	KALRN_HUMAN	Homo sapiens cDNA FLJ41073 fis, clone 3NB692008178.						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						CTCATGCTTTGGATATGAATG	0.408													4	2	---	---	---	---	
MUC13	56667	broad.mit.edu	37	3	124628333	124628338	+	Intron	DEL	GTGTGT	-	-	rs113008807		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124628333_124628338delGTGTGT	uc003ehq.1	-							NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0						gtgtgcttgcgtgtgtgtgtgtgtgt	0.180													5	4	---	---	---	---	
TXNRD3IT1	645840	broad.mit.edu	37	3	126374636	126374636	+	5'Flank	DEL	A	-	-	rs72300055		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126374636delA	uc003ejd.1	-						TXNRD3IT1_uc011bkl.1_5'Flank			Q6F5E7	TR3N_HUMAN	RecName: Full=Thioredoxin reductase 3;          EC=1.8.1.9; AltName: Full=Thioredoxin reductase TR2; AltName: Full=Thioredoxin and glutathione reductase;												0						actccgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
KIAA1257	57501	broad.mit.edu	37	3	128670080	128670080	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128670080delA	uc003elh.1	-						KIAA1257_uc003elg.1_Intron			Q9ULG3	K1257_HUMAN	RecName: Full=Uncharacterized protein FLJ43738;												0						tccatctcagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
KIAA1257	57501	broad.mit.edu	37	3	128691091	128691091	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128691091delT	uc003elj.3	-						KIAA1257_uc003elg.1_Intron|KIAA1257_uc003elh.1_5'Flank|KIAA1257_uc003eli.3_Intron	NM_020741	NP_065792	Q9ULG3	K1257_HUMAN	hypothetical protein LOC57501												0						GAtttctttcttttttttttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135167836	135167836	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135167836delC								EPHB1 (188531 upstream) : PPP2R3A (516731 downstream)																							CATGTGTCATCAAAATGGGCG	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135964113	135964113	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135964113delA								MSL2 (49425 upstream) : PCCB (5054 downstream)																							actctgtcttaaaaaaaaaaa	0.000													6	3	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136110139	136110140	+	Intron	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136110139_136110140delGA	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						CTCCTCCCAGGAGAGAAAAAAA	0.376													4	2	---	---	---	---	
IL20RB	53833	broad.mit.edu	37	3	136720068	136720068	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136720068delC	uc003eri.1	+						IL20RB_uc003erj.1_Intron|IL20RB_uc010hud.1_Intron	NM_144717	NP_653318	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta precursor							integral to membrane	receptor activity			ovary(1)	1						CCTTTTGCTTCCCTGTTCTCT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140923204	140923204	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140923204delG								SPSB4 (55752 upstream) : ACPL2 (27478 downstream)																							TGTGACATGTGGATGTGAGAT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142797722	142797722	+	IGR	DEL	T	-	-	rs5853090		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142797722delT								SR140 (18155 upstream) : CHST2 (40946 downstream)																							TTTTTACAGGTTTTTTTTTTC	0.353													4	2	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143203485	143203485	+	Intron	DEL	G	-	-	rs35515723		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143203485delG	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						AGGTTTGCATGAGGGACATGT	0.483													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147175033	147175033	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147175033delT								ZIC1 (40529 upstream) : None (None downstream)																							AGAGAAAGCCttttttttttt	0.214													3	5	---	---	---	---	
CP	1356	broad.mit.edu	37	3	148931416	148931419	+	Intron	DEL	TGGG	-	-	rs143884391	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148931416_148931419delTGGG	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003ewz.2_Intron	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CTCATCATCATGGgtgtgtgtgtg	0.333													4	3	---	---	---	---	
SELT	51714	broad.mit.edu	37	3	150332195	150332196	+	Intron	INS	-	G	G	rs62284030		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150332195_150332196insG	uc011bnx.1	+							NM_016275	NP_057359	P62341	SELT_HUMAN	selenoprotein T precursor						cell redox homeostasis|selenocysteine incorporation		selenium binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GAAATGGAGGTGGGTTTTTTTT	0.322													4	2	---	---	---	---	
FAM194A	131831	broad.mit.edu	37	3	150393495	150393495	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150393495delT	uc003eyg.2	-						FAM194A_uc003eyh.2_Intron	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831											skin(2)|ovary(1)	3						ttggccattgttttttttttt	0.000													4	3	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155250074	155250075	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155250074_155250075insA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ccaggaaaaccaaaagaattca	0.000													4	2	---	---	---	---	
LEKR1	389170	broad.mit.edu	37	3	156722665	156722665	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156722665delT	uc003fba.1	+							NM_001004316	NP_001004316	Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			cagcttccactttaggcaatt	0.000													4	2	---	---	---	---	
VEPH1	79674	broad.mit.edu	37	3	157036413	157036414	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157036413_157036414insA	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			caaaacaaaacaaaaaaaaaaa	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157472943	157472944	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157472943_157472944delAG								C3orf55 (153924 upstream) : SHOX2 (340857 downstream)																							TAGCTTTAAAAGAGAGAGAGAG	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165972610	165972610	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165972610delA								BCHE (417357 upstream) : ZBBX (985471 downstream)																							tagaagaaataaaaaaaaaaT	0.065													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167838692	167838692	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167838692delC								GOLIM4 (25275 upstream) : MIR551B (430950 downstream)																							ATATCCTGTTCCCTCTTATGA	0.378													4	3	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169194458	169194458	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169194458delT	uc011bpj.1	-						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						GCAAGTAATCTTTTTTTTCTC	0.438													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169352030	169352033	+	Intron	DEL	ACAC	-	-	rs113206940		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169352030_169352033delACAC	uc011bpj.1	-						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						GTGTGcacaaacacacacacacac	0.319													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169600780	169600781	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169600780_169600781insA								LRRC31 (13120 upstream) : SAMD7 (28701 downstream)																							gattctgtctcaaaaaaaaaaa	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169720594	169720594	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169720594delA								SEC62 (4435 upstream) : GPR160 (35141 downstream)																							actctgtctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170145595	170145595	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170145595delA	uc003fgx.2	+						CLDN11_uc011bpt.1_Intron|CLDN11_uc003fgy.2_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			agactgtctcaaaaaaaaaaa	0.100													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171894970	171894971	+	Intron	INS	-	A	A	rs146847040	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171894970_171894971insA	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron|FNDC3B_uc003fhx.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		catatgggcctagcggaagata	0.005													3	3	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173240931	173240932	+	Intron	INS	-	ATC	ATC	rs74826835		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173240931_173240932insATC	uc003fio.1	+							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)			ttgttgttgttattgagatgtt	0.000													3	3	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174766299	174766299	+	Intron	DEL	T	-	-	rs112154800		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174766299delT	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCTAAAACCATTTTTTTTTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177306758	177306758	+	IGR	DEL	C	-	-	rs11350527		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177306758delC								TBL1XR1 (391710 upstream) : KCNMB2 (947466 downstream)																							TCCCTCTTGTCCCCACCTCCG	0.438													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177417108	177417109	+	IGR	INS	-	T	T	rs35175514		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177417108_177417109insT								TBL1XR1 (502060 upstream) : KCNMB2 (837115 downstream)																							caaaacaatgattttttttttt	0.000													4	2	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178257529	178257530	+	Intron	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178257529_178257530delGT	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_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)			gtgtgtgtgcgtgtgtgtgtgt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179784854	179784854	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179784854delA								PEX5L (30337 upstream) : TTC14 (535064 downstream)																							TTTAGGATCCAAAATGTTCAT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181075013	181075014	+	IGR	INS	-	T	T	rs147543939	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181075013_181075014insT								DNAJC19 (367483 upstream) : SOX2OT (206495 downstream)																							ctaagttcttcttatttctttc	0.000													1	5	---	---	---	---	
SOX2OT	347689	broad.mit.edu	37	3	181326447	181326448	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181326447_181326448insA	uc003fkv.2	+						SOX2OT_uc003fkw.3_5'Flank					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0						aaatccatctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
SOX2OT	347689	broad.mit.edu	37	3	181436274	181436274	+	Intron	DEL	T	-	-	rs74448297		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181436274delT	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0						TCATTCTCTGTTTTTTTTTTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181523540	181523541	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181523540_181523541insA								SOX2OT (64537 upstream) : ATP11B (987750 downstream)																							GCAGCATCGACAAAAAAAAAAA	0.109													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181741199	181741200	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181741199_181741200insT								SOX2OT (282196 upstream) : ATP11B (770091 downstream)																							TGTAGACTACATTTTTTTTCCC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182413172	182413173	+	IGR	INS	-	T	T	rs67076402		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182413172_182413173insT								SOX2OT (954169 upstream) : ATP11B (98118 downstream)																							tgtcttcactcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183339369	183339370	+	IGR	INS	-	C	C	rs143629962	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183339369_183339370insC								KLHL6 (65870 upstream) : KLHL24 (14041 downstream)																							ttgattgctattcttaagaatt	0.074													3	4	---	---	---	---	
KLHL24	54800	broad.mit.edu	37	3	183376928	183376929	+	Intron	INS	-	G	G	rs144858643	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183376928_183376929insG	uc003flv.2	+						KLHL24_uc003flw.2_Intron|KLHL24_uc003flx.2_Intron	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein							axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			tgtaGGTTGTTGATTTTTTTCT	0.173													3	4	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183470118	183470118	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183470118delT	uc003fly.2	+							NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			AGACCTATAGTATATGGAAAA	0.388													32	20	---	---	---	---	
HTR3E	285242	broad.mit.edu	37	3	183821108	183821108	+	Intron	DEL	A	-	-	rs147495791		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183821108delA	uc010hxq.2	+						HTR3E_uc003fml.3_Intron|HTR3E_uc003fmm.2_Intron|HTR3E_uc010hxr.2_Intron|HTR3E_uc003fmn.2_Intron	NM_182589	NP_872395	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine receptor 3 subunit E							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			catctctaccaaaaatataaa	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184170417	184170420	+	IGR	DEL	CACA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184170417_184170420delCACA								CHRD (62798 upstream) : EPHB3 (109167 downstream)																							cccccatctccacacacacacaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184342795	184342796	+	IGR	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184342795_184342796delTT								EPHB3 (42600 upstream) : MAGEF1 (85360 downstream)																							ttatgaacacttttatggccct	0.079													4	3	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184651316	184651317	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184651316_184651317delTG	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)			tttcgatctttgtgtgtgtgtg	0.000													3	3	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184767912	184767912	+	Intron	DEL	T	-	-	rs13321192	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184767912delT	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)			TGGGaaataattttttttttt	0.383													9	4	---	---	---	---	
MAP3K13	9175	broad.mit.edu	37	3	185094038	185094039	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185094038_185094039delAG	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc003fph.3_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			gactcaacaaagagtgagtaca	0.000													3	7	---	---	---	---	
MAP3K13	9175	broad.mit.edu	37	3	185114827	185114828	+	Intron	INS	-	T	T	rs149723176	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185114827_185114828insT	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc003fph.3_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ATTCTTGTTTGTTTTTTTTTCA	0.218													4	2	---	---	---	---	
ETV5	2119	broad.mit.edu	37	3	185788988	185788989	+	Intron	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185788988_185788989delAA	uc003fpz.2	-						ETV5_uc003fpy.2_Intron	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)						cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TGCTCACAGGAAAAAAAAAAAG	0.411			T	TMPRSS2|SCL45A3	Prostate 								5	3	---	---	---	---	
ETV5	2119	broad.mit.edu	37	3	185800218	185800218	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185800218delT	uc003fpz.2	-						ETV5_uc003fpy.2_Intron	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)						cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			CACttttctcttttttttttt	0.139			T	TMPRSS2|SCL45A3	Prostate 								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186580875	186580878	+	IGR	DEL	AGAC	-	-	rs67175993		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186580875_186580878delAGAC								ADIPOQ (4625 upstream) : ST6GAL1 (67638 downstream)																							gcataagaatagacagacaggtta	0.103													5	6	---	---	---	---	
MASP1	5648	broad.mit.edu	37	3	187002945	187002945	+	Intron	DEL	T	-	-	rs11311151		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187002945delT	uc003frh.1	-						MASP1_uc003fri.2_Intron|MASP1_uc003frj.2_Intron|MASP1_uc003frk.1_Intron|MASP1_uc011bse.1_Intron	NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		ACCCATGGAATTTTTTTTTTT	0.358													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187227387	187227388	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187227387_187227388delAG								RTP4 (138020 upstream) : SST (159308 downstream)																							acagagagaaagagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187607947	187607947	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187607947delA								BCL6 (144472 upstream) : LPP (263772 downstream)																							AGGCAAACAGAAAAAAAAAAA	0.174													3	3	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188367508	188367509	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188367508_188367509delAG	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		GGTCTGAGACAGAGAGAGAGAG	0.218			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188447611	188447611	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188447611delA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		acaaaaagtgaaaaaaaaaaa	0.000			T	HMGA2|MLL|C12orf9	lipoma|leukemia								5	3	---	---	---	---	
TPRG1	285386	broad.mit.edu	37	3	188903347	188903347	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188903347delT	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		ATTTACGACATTTTTTTTTCC	0.204													4	2	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189497956	189497959	+	Intron	DEL	AAAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189497956_189497959delAAAG	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TGTGGGTGTTAAAGAATGTGTTTG	0.392									Hay-Wells_syndrome	HNSCC(45;0.13)			4	4	---	---	---	---	
LEPREL1	55214	broad.mit.edu	37	3	189752383	189752386	+	Intron	DEL	GAAC	-	-	rs63061560		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189752383_189752386delGAAC	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	gaggaagaaagaacaaacaaatgg	0.034													6	5	---	---	---	---	
IL1RAP	3556	broad.mit.edu	37	3	190280539	190280540	+	Intron	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190280539_190280540delCA	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		gctacataaccacacacacaca	0.139													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190393572	190393573	+	IGR	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190393572_190393573delTC								IL1RAP (17729 upstream) : LOC647309 (176953 downstream)																							ttcttttctttctctctctctc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193599509	193599510	+	IGR	INS	-	C	C	rs143951072	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193599509_193599510insC								OPA1 (183910 upstream) : LOC100128023 (111374 downstream)																							GCCCTGGGCCACCTTCTGTGTA	0.619													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193994156	193994156	+	IGR	DEL	A	-	-	rs11291880		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193994156delA								HES1 (137760 upstream) : LOC100131551 (23268 downstream)																							ctaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
C3orf21	152002	broad.mit.edu	37	3	194833606	194833607	+	Intron	DEL	AT	-	-	rs145315677		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194833606_194833607delAT	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.2_Intron	NM_152531	NP_689744	Q8NBI6	CC021_HUMAN	hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)		gcatgcacacatgtgcgcacat	0.277													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195438500	195438502	+	RNA	DEL	AAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195438500_195438502delAAG	uc003fux.1	+	3		c.2487_2489delAAG								Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		GAGGAGAATAAAGAAGAGAGCCT	0.567													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195442466	195442467	+	IGR	INS	-	AAAA	AAAA	rs10663077		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195442466_195442467insAAAA								MIR570 (16098 upstream) : MUC20 (5286 downstream)																							accctgtctctaaaaaaaaaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195585971	195585971	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195585971delT								MUC4 (46823 upstream) : TNK2 (4265 downstream)																							CATAAAAACATTTTTTTTTAA	0.428											OREG0016000	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
UBXN7	26043	broad.mit.edu	37	3	196153719	196153719	+	Intron	DEL	A	-	-	rs76975599		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196153719delA	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron|UBXN7_uc010iaf.2_Intron	NM_015562	NP_056377	O94888	UBXN7_HUMAN	UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3						actctgtctcaaaaaaaaaaa	0.134													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196265125	196265125	+	IGR	DEL	T	-	-	rs11323612		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196265125delT								C3orf43 (22888 upstream) : WDR53 (15936 downstream)																							ctcctccttcttcctcctcct	0.169													5	6	---	---	---	---	
WDR53	348793	broad.mit.edu	37	3	196287118	196287119	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196287118_196287119insT	uc003fwt.2	-							NM_182627	NP_872433	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53											breast(1)|skin(1)	2	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		tttcttttttcttttttttttt	0.188													5	5	---	---	---	---	
SENP5	205564	broad.mit.edu	37	3	196601741	196601741	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196601741delA	uc003fwz.3	+						SENP5_uc011bty.1_Intron	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5						cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		caagagtgggaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197115305	197115305	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197115305delG								DLG1 (89162 upstream) : BDH1 (121350 downstream)																							TAGTGTATTTGCGATAGTTTA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197133510	197133510	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197133510delT								DLG1 (107367 upstream) : BDH1 (103145 downstream)																							ggaaatggaCttttttttttt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197391777	197391778	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197391777_197391778delGT								LOC220729 (37025 upstream) : KIAA0226 (6481 downstream)																							cacgtgtggagtgtgtgcgtgc	0.248													8	4	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2414389	2414389	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2414389delC	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						CACCTTTGCACCCGGCACACC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3600936	3600937	+	IGR	DEL	AT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3600936_3600937delAT								LRPAP1 (66712 upstream) : ADRA2C (167138 downstream)																							aggtgtgcacatgtgtatgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4336869	4336869	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4336869delC								ZBTB49 (13357 upstream) : D4S234E (13000 downstream)																							gccaggtgtacagggtggaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9677588	9677588	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9677588delT								MIR548I2 (119651 upstream) : DRD5 (105670 downstream)																							tcccagctacttgggagactg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14783953	14783956	+	Intron	DEL	AGAT	-	-	rs66921199		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14783953_14783956delAGAT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																		ATCATGATAAagatagatagatag	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19527092	19527092	+	IGR	DEL	G	-	-	rs76616756		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19527092delG								None (None upstream) : SLIT2 (728143 downstream)																							aaaagaagaagaaaaaaaaaa	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27521286	27521287	+	IGR	INS	-	T	T	rs75355312	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27521286_27521287insT								STIM2 (495478 upstream) : None (None downstream)																							GTTTTGTAGCATTTTTTTTTTT	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	30059863	30059864	+	IGR	INS	-	T	T	rs139852781		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30059863_30059864insT								None (None upstream) : PCDH7 (662173 downstream)																							ctctgtctTTGTTTTTTTTTTT	0.193													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33842579	33842579	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33842579delA								None (None upstream) : None (None downstream)																							TAAAAGACATAAATAGAAGTA	0.343													4	4	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38011962	38011962	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38011962delC	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						CCCCCCAGGTCCCCATCTTCT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	39791078	39791079	+	IGR	INS	-	CAAAA	CAAAA	rs142929403		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39791078_39791079insCAAAA								UBE2K (6670 upstream) : PDS5A (33405 downstream)																							aacatctctgccaaaacaaaac	0.000													4	2	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39862086	39862086	+	Intron	DEL	A	-	-	rs35765967		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39862086delA	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						cacttgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39882634	39882634	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39882634delT	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						agagatctacttttttttttt	0.000													9	4	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	40861305	40861305	+	Intron	DEL	T	-	-	rs71648930		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40861305delT	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc003gvk.2_5'Flank	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						gctgctgtcattttttttttt	0.000													5	4	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	41194561	41194561	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41194561delA	uc003gvl.2	-						APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						acacggaaagaaaaacaccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42359224	42359225	+	IGR	INS	-	AGAA	AGAA	rs143116976	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42359224_42359225insAGAA								BEND4 (204329 upstream) : SHISA3 (40631 downstream)																							gaaagaaagagagaaagaaaga	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43105829	43105832	+	IGR	DEL	TGTA	-	-	rs10615851		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43105829_43105832delTGTA								GRXCR1 (73156 upstream) : None (None downstream)																							TATTCACAtgtgtatgtatgtatg	0.245													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	46159713	46159713	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46159713delT								GABRG1 (33631 upstream) : GABRA2 (91868 downstream)																							ctgatgaatcttttttttttt	0.000													4	2	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47102979	47102979	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47102979delT	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_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			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	GGACAGTATGTTGTCTATAAA	0.378													4	2	---	---	---	---	
CORIN	10699	broad.mit.edu	37	4	47738718	47738718	+	Intron	DEL	T	-	-	rs34027409		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47738718delT	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						attcttatcatttagctaagt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49213584	49213585	+	IGR	INS	-	A	A	rs141768505		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49213584_49213585insA								CWH43 (149491 upstream) : None (None downstream)																							gggacttgcttaaaaaaaagtc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49561206	49561225	+	5'Flank	DEL	GGTCTTGTCAGTGGGAACCC	-	-	rs145376476		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49561206_49561225delGGTCTTGTCAGTGGGAACCC	uc011bzm.1	+						uc003gza.1_5'Flank					DQ582260																		GGTAAATTGTGGTCTTGTCAGTGGGAACCCggtcttgtca	0.355													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49649280	49649283	+	IGR	DEL	ATGC	-	-	rs138495585		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49649280_49649283delATGC								CWH43 (585187 upstream) : None (None downstream)																							atggaatggaatgcatggaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55626756	55626757	+	IGR	DEL	TT	-	-	rs141748649		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55626756_55626757delTT								KIT (19877 upstream) : KDR (317670 downstream)																							tttttttttgtttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57026351	57026352	+	IGR	INS	-	TT	TT	rs114084144		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57026351_57026352insTT								CEP135 (126825 upstream) : KIAA1211 (10009 downstream)																							CCATATTTTGAttttttttttt	0.139													4	2	---	---	---	---	
PPAT	5471	broad.mit.edu	37	4	57274601	57274601	+	Intron	DEL	A	-	-	rs35013647		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57274601delA	uc003hbr.2	-							NM_002703	NP_002694	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)	actccgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63845914	63845915	+	IGR	INS	-	A	A	rs113770843		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63845914_63845915insA								LPHN3 (907747 upstream) : None (None downstream)																							aaagaaaaaagaaaaaaaaaaa	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	64318192	64318195	+	IGR	DEL	TTTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64318192_64318195delTTTG								None (None upstream) : TECRL (825990 downstream)																							GGTAGTATTTtttgtttgtttgtt	0.275													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	65499025	65499026	+	IGR	INS	-	GTGT	GTGT	rs143937302	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65499025_65499026insGTGT								TECRL (223847 upstream) : EPHA5 (686256 downstream)																							tatgtgtgtgcgtgtgtgtgtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	66792326	66792326	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66792326delG								EPHA5 (256673 upstream) : MIR1269 (350216 downstream)																							ctgtatgtgtggtaaacttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72841776	72841776	+	IGR	DEL	C	-	-	rs5859295		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72841776delC								GC (172018 upstream) : NPFFR2 (55745 downstream)																							CCATGAAGCTCTGTCCACTAA	0.224													1	7	---	---	---	---	
ANKRD17	26057	broad.mit.edu	37	4	74010556	74010556	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74010556delA	uc003hgp.2	-						ANKRD17_uc003hgo.2_Intron|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron|ANKRD17_uc011cbd.1_Intron	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTTCCTGTTTAAAAAAAAAAA	0.313													14	10	---	---	---	---	
MTHFD2L	441024	broad.mit.edu	37	4	74985702	74985702	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74985702delA	uc003hhn.1	+							NM_001144978	NP_001138450	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase 2-like						folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)			ttttcaaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77669967	77669968	+	Intron	INS	-	TT	TT	rs34047499		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77669967_77669968insTT	uc011cbx.1	+						SHROOM3_uc003hkg.2_Intron	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			tctgactctgcttttttttttt	0.327													5	3	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79161208	79161208	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79161208delT	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						cactcaataattttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82574232	82574233	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82574232_82574233delTG								RASGEF1B (181171 upstream) : HNRNPD (700234 downstream)																							tatgtgtgtttgtgtgtgtgtg	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82683610	82683610	+	IGR	DEL	C	-	-	rs34257779		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82683610delC								RASGEF1B (290549 upstream) : HNRNPD (590857 downstream)																							caaactaccacattctctcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	95654725	95654725	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95654725delT								PDLIM5 (65349 upstream) : BMPR1B (24403 downstream)																							cctttaactattTTTTTGCAG	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	107384136	107384137	+	IGR	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107384136_107384137delGA								AIMP1 (113757 upstream) : DKK2 (458823 downstream)																							gagtgggggtgagagagagaga	0.124													4	2	---	---	---	---	
CFI	3426	broad.mit.edu	37	4	110693074	110693075	+	Intron	INS	-	GA	GA			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110693074_110693075insGA	uc003hzr.3	-						CFI_uc011cft.1_Intron|CFI_uc003hzs.3_Intron	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		ttttcaagaaggagagagaggg	0.030													4	2	---	---	---	---	
NDST3	9348	broad.mit.edu	37	4	119006277	119006278	+	Intron	INS	-	AAC	AAC	rs139423039	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119006277_119006278insAAC	uc003ibx.2	+						NDST3_uc011cgf.1_Intron	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						gactccgtAAAaacaacaacaa	0.114													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134496161	134496161	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134496161delG								PCDH10 (383430 upstream) : PABPC4L (621330 downstream)																							ATTTAGTACTGGGGGGACCCT	0.498													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	146337899	146337900	+	IGR	DEL	CT	-	-	rs112551531		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146337899_146337900delCT								OTUD4 (237067 upstream) : SMAD1 (65051 downstream)																							AGGCTTTAGACTCTGGAACCTA	0.460													2	4	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152364493	152364493	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152364493delT	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						tttttgaggattgatcttgct	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152791362	152791363	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152791362_152791363delGT								PET112L (109216 upstream) : FBXW7 (451048 downstream)																							gtgtgtgtgagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
FBXW7	55294	broad.mit.edu	37	4	153295955	153295955	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153295955delT	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc003imr.2_Intron	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AAGAGAGAGGTAAGCTGGACC	0.463			Mis|N|D|F		colorectal|endometrial|T-ALL								4	2	---	---	---	---	
FHDC1	85462	broad.mit.edu	37	4	153889445	153889446	+	Intron	INS	-	T	T	rs75046217		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153889445_153889446insT	uc003inf.2	+							NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1						actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)					AGCCTGATATATTTTTTTTTTT	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157575104	157575104	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157575104delG								CTSO (700056 upstream) : PDGFC (107660 downstream)																							agggagtggtggggaggactc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158605986	158605987	+	IGR	INS	-	A	A	rs144346959	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158605986_158605987insA								LOC340017 (108691 upstream) : FAM198B (439746 downstream)																							CCACTCAGAATAAAAAAAAATA	0.327													4	2	---	---	---	---	
PALLD	23022	broad.mit.edu	37	4	169698254	169698255	+	Intron	INS	-	AC	AC	rs146373300	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169698254_169698255insAC	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		cacacacatatacacacacaca	0.322									Pancreatic_Cancer_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171418457	171418457	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171418457delC								AADAT (407085 upstream) : None (None downstream)																							GCTCCAGCTTCCCTACCCTCG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182576649	182576650	+	IGR	INS	-	G	G	rs144113615	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182576649_182576650insG								None (None upstream) : MGC45800 (483509 downstream)																							tgagcaagagagagcatgcctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183022448	183022463	+	IGR	DEL	GAAGGAGGGAGGGAAA	-	-	rs111832319		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183022448_183022463delGAAGGAGGGAGGGAAA								None (None upstream) : MGC45800 (37696 downstream)																							agggaggaaggaaggagggagggaaagaaggaaaga	0.032													7	4	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183080601	183080604	+	Intron	DEL	GTGT	-	-	rs112827364		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183080601_183080604delGTGT	uc010irv.1	+									Q9P273	TEN3_HUMAN	Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		gtgtgtatgagtgtgtgtgtgtgt	0.176													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190626821	190626822	+	IGR	DEL	TT	-	-	rs150059094		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190626821_190626822delTT								None (None upstream) : FRG1 (235152 downstream)																							TTAATGCCTCTTATCAATAAAT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190643932	190643932	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190643932delA								None (None upstream) : FRG1 (218042 downstream)																							agcGTGCttcaacgcccttcg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190797948	190797949	+	Intron	INS	-	G	G	rs141913305		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190797948_190797949insG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		TTGATATGTTTGAGAGTGAGGT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190808293	190808296	+	Intron	DEL	AAGA	-	-	rs34942986		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190808293_190808296delAAGA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		AGCCAAGTTGAAGAAAGAGGCTGA	0.382													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190917343	190917343	+	IGR	DEL	G	-	-	rs151260771		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190917343delG								TUBB4Q (11319 upstream) : LOC653545 (91223 downstream)																							ttctgtgcctgacttatttca	0.000													1	5	---	---	---	---	
EXOC3	11336	broad.mit.edu	37	5	447386	447386	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:447386delG	uc003jba.2	+							NM_007277	NP_009208	O60645	EXOC3_HUMAN	Sec6 protein						exocytosis|protein transport						0		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CCAGGTGTGAGGCTAGATGAG	0.517											OREG0016472	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	5	2779574	2779574	+	IGR	DEL	A	-	-	rs67037951		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2779574delA								C5orf38 (24062 upstream) : IRX1 (816594 downstream)																							ttttgggggtaaaggagacca	0.194													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3052635	3052635	+	IGR	DEL	T	-	-	rs72363577		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3052635delT								C5orf38 (297123 upstream) : IRX1 (543533 downstream)																							GCTACTCTAAttttttttttt	0.274													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4977980	4977981	+	IGR	DEL	TG	-	-	rs35730416		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4977980_4977981delTG								None (None upstream) : LOC340094 (56491 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.347													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6286043	6286043	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6286043delG								KIAA0947 (795706 upstream) : FLJ33360 (24511 downstream)																							tccagcctttggaataagcag	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8050588	8050589	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8050588_8050589insA								MTRR (149355 upstream) : SEMA5A (984549 downstream)																							ggaaggaaaggaaggaaagaag	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12148005	12148006	+	IGR	INS	-	CTCCTT	CTCCTT	rs149630409	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12148005_12148006insCTCCTT								CTNND2 (243895 upstream) : None (None downstream)																							tcctcctcctcctccttctcct	0.035													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13977606	13977607	+	IGR	INS	-	CA	CA	rs140900191	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13977606_13977607insCA								DNAH5 (33017 upstream) : TRIO (166222 downstream)																							TCCCTCATTCTCACATCCCAAG	0.307													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14896296	14896297	+	IGR	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14896296_14896297delTT								ANKH (24409 upstream) : FBXL7 (604008 downstream)																							gctcccagccTttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17985273	17985273	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17985273delT								BASP1 (708338 upstream) : None (None downstream)																							gattcattccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18673727	18673727	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18673727delC								None (None upstream) : CDH18 (799430 downstream)																							ttgcccctctcccagaaaagt	0.000													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22841693	22841694	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22841693_22841694insT	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						gagatctctaagggcgtgggtg	0.000										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24277456	24277456	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24277456delT								PRDM9 (748752 upstream) : CDH10 (209754 downstream)																							caaatccttgttttatatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25753557	25753557	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25753557delG								None (None upstream) : None (None downstream)																							atggatgccaggggggcgtgc	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31347203	31347203	+	IGR	DEL	G	-	-	rs67653085		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31347203delG								CDH6 (21966 upstream) : RNASEN (53399 downstream)																							TTTTAAACAAGGGAAGCTCCA	0.249													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33105432	33105432	+	IGR	DEL	G	-	-	rs111852274		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33105432delG								C5orf23 (313613 upstream) : TARS (335370 downstream)																							gatctttctaggggtggagca	0.000													1	5	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33791876	33791876	+	Intron	DEL	T	-	-	rs34517781		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33791876delT	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TTTCCTTTTCTTTTTTTTTTT	0.373										HNSCC(64;0.19)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34629076	34629076	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34629076delC								C1QTNF3 (585759 upstream) : RAI14 (27357 downstream)																							CCCCTTTGCTCCATAAGTAGA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34631104	34631107	+	IGR	DEL	AGGC	-	-	rs150047945		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34631104_34631107delAGGC								C1QTNF3 (587787 upstream) : RAI14 (25326 downstream)																							tgaggctgttaggcagagattagg	0.000													0	6	---	---	---	---	
SPEF2	79925	broad.mit.edu	37	5	35797420	35797425	+	Intron	DEL	GTGTGT	-	-	rs71981361		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35797420_35797425delGTGTGT	uc003jjo.2	+						SPEF2_uc003jjp.1_Intron|SPEF2_uc003jjr.2_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGGCTGACGGgtgtgtgtgtgtgtgt	0.379													4	2	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37497616	37497620	+	Intron	DEL	CTTCC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37497616_37497620delCTTCC	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			tctcttccctcttcccttcccttcc	0.137													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38103034	38103034	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38103034delG								GDNF (263252 upstream) : EGFLAM (155499 downstream)																							GAGCAAGAGTGGCGGAAACTC	0.438													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39274028	39274028	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39274028delT								FYB (3269 upstream) : C9 (10351 downstream)																							TCTATTATGCttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	54839464	54839464	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54839464delA								PPAP2A (8591 upstream) : SLC38A9 (82212 downstream)																							ACATGCAGTTAAAAAAAAAAA	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56361637	56361652	+	IGR	DEL	CTTCCTTCCTTCCTTC	-	-	rs11950232	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56361637_56361652delCTTCCTTCCTTCCTTC								MIER3 (94136 upstream) : GPBP1 (108123 downstream)																							ttctttctttcttccttccttccttccttccttcct	0.046													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	60526419	60526420	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60526419_60526420delGT								C5orf43 (68117 upstream) : ZSWIM6 (101680 downstream)																							CTCTCTCCTCgtgtgtgtgtgt	0.054													4	2	---	---	---	---	
ZSWIM6	57688	broad.mit.edu	37	5	60831400	60831400	+	Frame_Shift_Del	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60831400delC	uc003jsr.2	+	10	2335	c.2335delC	c.(2335-2337)CCTfs	p.P779fs		NM_020928	NP_065979	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	779							zinc ion binding				0						CTCTCTCCTACCTCACGATGC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62682375	62682375	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62682375delT								ISCA1P1 (609205 upstream) : HTR1A (573904 downstream)																							CATATCCATCttttttttttt	0.209													2	4	---	---	---	---	
C5orf44	80006	broad.mit.edu	37	5	64931971	64931972	+	Intron	INS	-	T	T	rs71760261		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64931971_64931972insT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2											ovary(1)	1						atacaTTTACCttttttttttt	0.020													3	4	---	---	---	---	
ZNF366	167465	broad.mit.edu	37	5	71772762	71772762	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71772762delT	uc003kce.1	-							NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		GGCTGTGGGATTTTTTTTTTT	0.423													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71909940	71909940	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71909940delT								ZNF366 (106691 upstream) : TNPO1 (202478 downstream)																							tccttgatgattagtgatgtt	0.000													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75406355	75406355	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75406355delG	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		cggggtttctggagttaacat	0.164													4	2	---	---	---	---	
F2R	2149	broad.mit.edu	37	5	76009835	76009836	+	5'Flank	INS	-	AG	AG	rs145897341	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76009835_76009836insAG	uc003ken.3	+							NM_001992	NP_001983	P25116	PAR1_HUMAN	coagulation factor II receptor precursor						activation of caspase activity|anatomical structure morphogenesis|connective tissue replacement involved in inflammatory response wound healing|negative regulation of cell proliferation|platelet activation|positive regulation of blood coagulation|positive regulation of cell migration|positive regulation of collagen biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JAK-STAT cascade|positive regulation of MAPKKK cascade|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of transcription, DNA-dependent|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	caveola|extracellular region|Golgi apparatus|integral to plasma membrane|platelet dense tubular network	receptor binding|thrombin receptor activity			ovary(3)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	ataagaaAGACAGAGAGAGAGA	0.045													3	3	---	---	---	---	
LHFPL2	10184	broad.mit.edu	37	5	77904755	77904755	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77904755delA	uc003kfo.2	-							NM_005779	NP_005770	Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2							integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		actccatctcaaaaaaaaaaa	0.085													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77971922	77971922	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77971922delC								LHFPL2 (27274 upstream) : ARSB (101117 downstream)																							TAGGTTCTTTCAGGGCAAAGA	0.403													4	2	---	---	---	---	
ARSB	411	broad.mit.edu	37	5	78266795	78266798	+	Intron	DEL	AGAA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78266795_78266798delAGAA	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		tctcaaaaagagaaagaaagaaag	0.000													4	2	---	---	---	---	
ZFYVE16	9765	broad.mit.edu	37	5	79737009	79737009	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79737009delC	uc003kgr.3	+						ZFYVE16_uc003kgp.2_Intron|ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_5'Flank	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		ATAATTATCTCCCCCACTTAA	0.363													4	2	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	79998841	79998841	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79998841delA	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GCAACAAAACaaaaataaaaa	0.035								MMR					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	83838656	83838657	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83838656_83838657delTG								EDIL3 (158045 upstream) : None (None downstream)																							ACATCCTCAATGTGTGTGTGTG	0.416													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90584863	90584863	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90584863delG								GPR98 (124831 upstream) : ARRDC3 (79678 downstream)																							tactggagctgggcctaccaa	0.000													4	2	---	---	---	---	
GLRX	2745	broad.mit.edu	37	5	95150257	95150257	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95150257delT	uc003klo.3	-						GLRX_uc003kln.3_3'UTR	NM_001118890	NP_001112362	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)						cell redox homeostasis|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|transport	cytosol	electron carrier activity|glutathione disulfide oxidoreductase activity|protein disulfide oxidoreductase activity|protein N-terminus binding				0		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	AGCAAAATGATTTTAGCTAAT	0.388													4	2	---	---	---	---	
TSLP	85480	broad.mit.edu	37	5	110407274	110407274	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110407274delT	uc003kpb.2	+						TSLP_uc003kpa.2_Intron|TSLP_uc010jbt.1_5'Flank	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1							extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		TAGCTACTCCTTTTTTTTTTT	0.368													6	3	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110703573	110703573	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110703573delC	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		gtaccatgtgcccattggatg	0.000													4	2	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118455229	118455230	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118455229_118455230insT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GATTCTTCCAAttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124171948	124171949	+	IGR	INS	-	AC	AC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124171948_124171949insAC								ZNF608 (87448 upstream) : None (None downstream)																							tgtctcaaaaTacacacaaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135922256	135922256	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135922256delA								TRPC7 (229183 upstream) : SPOCK1 (388732 downstream)																							TTTCATAGTGAAAAAAAATTA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141484865	141484865	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141484865delT								GNPDA1 (92245 upstream) : NDFIP1 (3459 downstream)																							AACAAAGCCCTTTTCTCGTTC	0.219													4	2	---	---	---	---	
SPINK14	408187	broad.mit.edu	37	5	147553573	147553573	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147553573delA	uc003loz.1	+							NM_001001325	NP_001001325	Q6IE38	ISK14_HUMAN	Kazal type serine protease inhibitor 5-like 2							extracellular region	serine-type endopeptidase inhibitor activity				0						caggctaattaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172128144	172128145	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172128144_172128145delAC								NEURL1B (9613 upstream) : DUSP1 (66957 downstream)																							CACCCCAAGAacacacacacac	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8231724	8231725	+	IGR	INS	-	A	A	rs68127790		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8231724_8231725insA								EEF1E1 (128896 upstream) : SLC35B3 (180008 downstream)																							ccctgtctcacaaaaaaaaaaa	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9866797	9866797	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9866797delA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_Intron|uc003myj.1_Intron|uc003myk.1_Intron|uc010joh.1_Intron|uc003myl.1_5'Flank|uc003mym.1_5'Flank					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																		GGAAAGAGGTAAGGGGCACCT	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19302988	19302990	+	IGR	DEL	TGT	-	-	rs146522343		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19302988_19302990delTGT								MIR548A1 (730877 upstream) : ID4 (534627 downstream)																							ATAAGGTTTCtgttgttgttgtt	0.350													4	2	---	---	---	---	
KIAA1949	170954	broad.mit.edu	37	6	30649169	30649169	+	Intron	DEL	T	-	-	rs66845631		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30649169delT	uc003nra.2	-						KIAA1949_uc003nrb.3_Intron	NM_001134870	NP_001128342	Q6NYC8	PHTNS_HUMAN	phostensin							cytoplasm|cytoskeleton	actin binding				0						cactgttctatttttttttcc	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31410118	31410118	+	IGR	DEL	G	-	-	rs112344639		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31410118delG								MICA (27028 upstream) : HCP5 (20839 downstream)																							ttctttataaGggggggggag	0.204													1	6	---	---	---	---	
HLA-DQB1	3119	broad.mit.edu	37	6	32634204	32634204	+	Intron	DEL	C	-	-	rs66662713		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32634204delC	uc003obw.2	-						HLA-DQB1_uc010juc.1_5'Flank|HLA-DQB1_uc003obv.2_Intron|HLA-DQB1_uc011dqd.1_Intron|HLA-DQB1_uc011dqe.1_Intron	NM_002123	NP_002114	P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ						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	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AGATCACCATCCCCCATACCC	0.512									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				3	4	---	---	---	---	
TCP11	6954	broad.mit.edu	37	6	35087761	35087761	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35087761delT	uc003okd.2	-						TCP11_uc003ojz.1_Intron|TCP11_uc003oka.2_Intron|TCP11_uc003okb.2_Intron|TCP11_uc003okc.2_Intron|TCP11_uc011dsu.1_Intron|TCP11_uc011dsv.1_Intron|TCP11_uc011dsw.1_Intron	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						GGAAGAAAGGTTTTTTTTTGT	0.423													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	35528603	35528603	+	IGR	DEL	A	-	-	rs35200111		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35528603delA								TULP1 (47956 upstream) : FKBP5 (12759 downstream)																							CTCAATGACCAAAAAAAAAGG	0.209													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38175458	38175458	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38175458delA	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						ACCTTGAAGGAAAAAAAAAAG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	39138417	39138417	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39138417delG								C6orf64 (55552 upstream) : KCNK5 (18331 downstream)																							GGAGCTTCCTGGACCCTGGAT	0.299													4	2	---	---	---	---	
PGC	5225	broad.mit.edu	37	6	41716808	41716808	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41716808delT	uc003ora.1	-							NM_002630	NP_002621	P20142	PEPC_HUMAN	progastricsin (pepsinogen C) precursor						digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CATTGGAAtcttttttttttt	0.214													4	4	---	---	---	---	
USP49	25862	broad.mit.edu	37	6	41850364	41850365	+	Intron	INS	-	AAC	AAC	rs144379920	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41850364_41850365insAAC	uc003ori.2	-							NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin thioesterase 49						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			attcggtaaagaacaaggcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42087985	42087985	+	IGR	DEL	T	-	-	rs72239330		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42087985delT								C6orf132 (15496 upstream) : GUCA1A (35159 downstream)																							TGCGAGGttcttttttttttt	0.194													4	3	---	---	---	---	
UBR2	23304	broad.mit.edu	37	6	42553941	42553941	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42553941delA	uc011dur.1	+						UBR2_uc003osf.2_Intron	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			catctctaccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43132899	43132900	+	IGR	INS	-	T	T	rs35507235		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43132899_43132900insT								PTK7 (3442 upstream) : SRF (6020 downstream)																							CCGTCCCCACCttttttttttt	0.243													4	3	---	---	---	---	
ZNF318	24149	broad.mit.edu	37	6	43319884	43319886	+	Intron	DEL	ATC	-	-	rs71774410		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43319884_43319886delATC	uc003oux.2	-						ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			ttcgtctcaaatcatcatcatca	0.000													4	4	---	---	---	---	
SUPT3H	8464	broad.mit.edu	37	6	44968934	44968934	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44968934delG	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						GGATGGAGGTGGGTGGGGTTG	0.294													4	2	---	---	---	---	
CLIC5	53405	broad.mit.edu	37	6	45898594	45898594	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45898594delC	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron|CLIC5_uc003oxw.2_Intron|CLIC5_uc003oxx.2_Intron	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2						attacaatctccatattaccg	0.060													4	2	---	---	---	---	
ENPP5	59084	broad.mit.edu	37	6	46134184	46134185	+	Intron	INS	-	TT	TT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46134184_46134185insTT	uc003oxz.1	-						ENPP5_uc003oya.1_Intron|ENPP5_uc011dvz.1_Intron|ENPP5_uc010jzc.1_Intron	NM_021572	NP_067547	Q9UJA9	ENPP5_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase							extracellular region|integral to membrane	hydrolase activity				0						acaccaggctattttttttttt	0.000													4	4	---	---	---	---	
RCAN2	10231	broad.mit.edu	37	6	46195157	46195157	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46195157delT	uc003oyb.1	-						RCAN2_uc003oyc.1_Intron|RCAN2_uc003oyd.1_Intron	NM_005822	NP_005813	Q14206	RCAN2_HUMAN	Down syndrome critical region gene 1-like 1						calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0						ggttctggactttttttggtt	0.000													4	2	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46822637	46822638	+	Intron	INS	-	A	A	rs140681028	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46822637_46822638insA	uc003oyo.3	-						GPR116_uc011dwj.1_Intron|GPR116_uc011dwk.1_Intron|GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			AATTGAAGCAGAAAAAACCCAA	0.381													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48388379	48388380	+	IGR	DEL	CA	-	-	rs34877155		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48388379_48388380delCA								C6orf138 (309436 upstream) : None (None downstream)																							ggtgcatgcgcacacacacaca	0.158													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48563751	48563752	+	IGR	DEL	TG	-	-	rs10545650		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48563751_48563752delTG								C6orf138 (484808 upstream) : MUT (835242 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48636223	48636223	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48636223delT								C6orf138 (557280 upstream) : MUT (762771 downstream)																							CCAAACATAATTTGACATAAG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52812230	52812231	+	IGR	INS	-	CA	CA	rs10643650		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52812230_52812231insCA								GSTA3 (37734 upstream) : GSTA4 (30516 downstream)																							ccccatctatgcacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	53598113	53598130	+	IGR	DEL	ATGATGTTGCTGCTTATA	-	-	rs143646486		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53598113_53598130delATGATGTTGCTGCTTATA								KLHL31 (67607 upstream) : LRRC1 (61648 downstream)																							aatcactatcatgatgttgctgcttataatcaagatct	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57197600	57197602	+	Intron	DEL	TCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57197600_57197602delTCT	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)		agttggatcatcttcttttcttt	0.000													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57376681	57376681	+	Intron	DEL	T	-	-	rs10716374		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57376681delT	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)		atgaatatgattgcttagatg	0.045													8	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57381739	57381740	+	Intron	DEL	CG	-	-	rs144084337		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57381739_57381740delCG	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)		GGTTGCCTCACGTGATGTTAGG	0.312													3	7	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57413029	57413030	+	Intron	INS	-	TT	TT	rs145147559		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57413029_57413030insTT	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)		TGGTTGAGACATTTTTTAAGCT	0.361													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57500198	57500198	+	Intron	DEL	A	-	-	rs11329134		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57500198delA	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)		aagatccatgaccctcccaaa	0.114													7	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57507455	57507458	+	Intron	DEL	AGAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57507455_57507458delAGAC	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)		caccactaatagacagagacccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57540277	57540278	+	IGR	INS	-	G	G	rs141654716		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57540277_57540278insG								PRIM2 (26902 upstream) : GUSBL2 (705881 downstream)																							CATGCAAGGCAGGCTACGTTAA	0.381													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57544113	57544116	+	IGR	DEL	AAAG	-	-	rs78073104		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57544113_57544116delAAAG								PRIM2 (30738 upstream) : GUSBL2 (702043 downstream)																							ttaagaaaaaaaagaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57549953	57549954	+	IGR	DEL	AG	-	-	rs141685078		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57549953_57549954delAG								PRIM2 (36578 upstream) : GUSBL2 (696205 downstream)																							aggtaccatcagagaatacata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57558058	57558058	+	IGR	DEL	T	-	-	rs74318708		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57558058delT								PRIM2 (44683 upstream) : GUSBL2 (688101 downstream)																							tatgacaaagttctaatatcc	0.000													5	4	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65007129	65007129	+	Intron	DEL	C	-	-	rs112948039		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65007129delC	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						tgtcacacttcccccccattg	0.000													3	4	---	---	---	---	
RIMS1	22999	broad.mit.edu	37	6	72667884	72667884	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72667884delT	uc003pga.2	+							NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1						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)				TTTTGGTTGGTGATCATAACA	0.249													4	2	---	---	---	---	
LYRM2	57226	broad.mit.edu	37	6	90351024	90351028	+	5'Flank	DEL	CTGGC	-	-	rs11278724		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90351024_90351028delCTGGC	uc003pnm.2	-						LYRM2_uc010kce.1_5'Flank|LYRM2_uc003png.2_5'Flank|LYRM2_uc010kcf.1_5'Flank|LYRM2_uc010kcg.2_5'Flank|LYRM2_uc003pnl.3_5'Flank	NM_020466	NP_065199	Q9NU23	LYRM2_HUMAN	LYR motif containing 2												0		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		AGAGAAGTTACTGGCCTGGCCAGGA	0.463													3	3	---	---	---	---	
KIAA0776	23376	broad.mit.edu	37	6	96972044	96972044	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96972044delA	uc003por.2	+						KIAA0776_uc010kck.2_Intron	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376						negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		GATGttatttaaaaaaaaaaa	0.333													4	4	---	---	---	---	
AIM1	202	broad.mit.edu	37	6	106993002	106993002	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106993002delT	uc003prh.2	+						AIM1_uc003pri.2_Intron	NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ATACCATCTCTTCTTTTTACG	0.323													4	2	---	---	---	---	
RTN4IP1	84816	broad.mit.edu	37	6	107020208	107020210	+	Intron	DEL	CTC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107020208_107020210delCTC	uc003prj.2	-						RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Intron	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor							mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		AGTCTTACTTCTCCTCCATGCTG	0.557													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	122669507	122669507	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122669507delG								GJA1 (898635 upstream) : HSF2 (51189 downstream)																							CAATTAAAGTGGGAAGAAAGA	0.403													4	2	---	---	---	---	
EPB41L2	2037	broad.mit.edu	37	6	131322453	131322454	+	Intron	INS	-	AGGGCA	AGGGCA	rs150801062	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131322453_131322454insAGGGCA	uc003qch.2	-						EPB41L2_uc003qcg.1_5'Flank|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		gagcaagagagagggcaaggga	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	133928910	133928911	+	Intron	INS	-	A	A	rs113102278		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133928910_133928911insA	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																		gactccatctcaaaaaaaaaaa	0.158													4	2	---	---	---	---	
UTRN	7402	broad.mit.edu	37	6	144991093	144991096	+	Intron	DEL	GTGT	-	-	rs149421263		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144991093_144991096delGTGT	uc003qkt.2	+							NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		gtattccatggtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145917181	145917181	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145917181delC								UTRN (743013 upstream) : EPM2A (29265 downstream)																							ATTTAAAAGTCCTAAACAACT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148372769	148372770	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148372769_148372770delAG								SAMD5 (481612 upstream) : SASH1 (290959 downstream)																							tcatgaggaaagagagagagag	0.000													4	2	---	---	---	---	
LATS1	9113	broad.mit.edu	37	6	150010555	150010555	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150010555delA	uc003qmu.1	-						LATS1_uc010kif.1_Intron|LATS1_uc003qmv.1_Intron|LATS1_uc003qmw.2_Intron|LATS1_uc010kig.1_Intron	NM_004690	NP_004681	O95835	LATS1_HUMAN	LATS homolog 1						cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TGCCTGTCTCAAAAAAAAAAA	0.363													4	2	---	---	---	---	
PPP1R14C	81706	broad.mit.edu	37	6	150489101	150489101	+	Intron	DEL	T	-	-	rs74508153		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150489101delT	uc003qnt.2	+							NM_030949	NP_112211	Q8TAE6	PP14C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of phosphorylation	cytoplasm|membrane					0		Ovarian(120;0.0284)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;9.14e-12)		tctcctcccctctttctctcc	0.194													4	2	---	---	---	---	
IPCEF1	26034	broad.mit.edu	37	6	154618181	154618182	+	Intron	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154618181_154618182delTC	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0						tcttttcttttctctctctctc	0.188													4	2	---	---	---	---	
TMEM181	57583	broad.mit.edu	37	6	158991266	158991266	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158991266delT	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron|TMEM181_uc003qri.1_5'UTR|TMEM181_uc003qrj.1_5'UTR|TMEM181_uc003qrk.1_5'Flank	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		TTCCGTACACttttttttttt	0.219													4	4	---	---	---	---	
EZR	7430	broad.mit.edu	37	6	159189423	159189423	+	Intron	DEL	T	-	-	rs67259053		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159189423delT	uc003qrt.3	-						EZR_uc011efr.1_Intron|EZR_uc011efs.1_Intron|EZR_uc003qru.3_Intron	NM_003379	NP_003370	P15311	EZRI_HUMAN	ezrin						actin filament bundle assembly|axon guidance|cytoskeletal anchoring at plasma membrane|leukocyte cell-cell adhesion|membrane to membrane docking|regulation of cell shape	actin filament|apical plasma membrane|basolateral plasma membrane|cortical cytoskeleton|cytosol|extrinsic to membrane|filopodium|microvillus membrane|nucleolus|ruffle membrane	actin filament binding|cell adhesion molecule binding			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		tttatagccgttgtgagaaca	0.259													3	3	---	---	---	---	
IGF2R	3482	broad.mit.edu	37	6	160526938	160526939	+	3'UTR	DEL	TG	-	-	rs71748848		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160526938_160526939delTG	uc003qta.2	+	48						NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor						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)		TTtgtgtgtttgtgtgtgtgtg	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164392080	164392080	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164392080delC								QKI (397188 upstream) : None (None downstream)																							CAGACACCCTCCCCCTGGCCC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165161587	165161588	+	IGR	INS	-	A	A	rs66502865		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165161587_165161588insA								None (None upstream) : C6orf118 (531567 downstream)																							gaggctgatttaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166664204	166664205	+	IGR	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166664204_166664205insG								T (82073 upstream) : PRR18 (54963 downstream)																							TGGAGAATGCTGGGGTTTTTTT	0.302													4	2	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	167060651	167060651	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167060651delT	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|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|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TGTTCTCCTATTTTTTTTTTA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169359236	169359237	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169359236_169359237delTG								SMOC2 (290565 upstream) : THBS2 (256639 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.124													4	2	---	---	---	---	
THBS2	7058	broad.mit.edu	37	6	169642802	169642802	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169642802delC	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)		caccttcccaccactcccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170529464	170529464	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170529464delG								C6orf208 (326495 upstream) : LOC154449 (33958 downstream)																							GACTCCATACGGGGAGTCAGT	0.587													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	374463	374464	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:374463_374464delAC								FAM20C (73752 upstream) : PDGFA (162435 downstream)																							gcatgcagagacacacacacaa	0.025													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	414108	414111	+	IGR	DEL	GGAG	-	-	rs139925018	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:414108_414111delGGAG								FAM20C (113397 upstream) : PDGFA (122788 downstream)																							gagggaggaaggagggagggaggg	0.181													7	4	---	---	---	---	
MICALL2	79778	broad.mit.edu	37	7	1485933	1485934	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1485933_1485934delAG	uc003skj.3	-							NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		agggggaaaaagggggaggagg	0.000													4	2	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2273614	2273615	+	5'Flank	INS	-	A	A	rs71550334		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2273614_2273615insA	uc003slh.1	-						MAD1L1_uc003slf.1_5'Flank|MAD1L1_uc003slg.1_5'Flank|MAD1L1_uc010ksh.1_5'Flank|MAD1L1_uc003sli.1_5'Flank|MAD1L1_uc010ksi.1_5'Flank|MAD1L1_uc010ksj.2_5'Flank	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		gtttctcaaagaaaaaaaaaaa	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4348198	4348198	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4348198delC								SDK1 (39569 upstream) : FOXK1 (335190 downstream)																							ttctggtggtcccccccccct	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6682474	6682482	+	IGR	DEL	GGGCTCTTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6682474_6682482delGGGCTCTTG								ZNF853 (18555 upstream) : ZNF12 (45582 downstream)																							CAAGCCAGGAGGGCTCTTGGGCCGACAGG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7080912	7080912	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7080912delA								C7orf28B (215051 upstream) : C1GALT1 (141334 downstream)																							gaaagcaattaacataaagga	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10450353	10450354	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10450353_10450354delAC								PER4 (774906 upstream) : NDUFA4 (522461 downstream)																							CATATGGAAGacacacacacac	0.312													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15556604	15556604	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15556604delT	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						CACAAGAGTCTTTTTTTTTTG	0.323													4	2	---	---	---	---	
SNX13	23161	broad.mit.edu	37	7	17952038	17952039	+	Intron	INS	-	T	T	rs34849896		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17952038_17952039insT	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc003stx.1_Intron|SNX13_uc003sty.2_Intron			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					gaggaaaatgcttttttttttt	0.000													6	4	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18205422	18205422	+	Intron	DEL	A	-	-	rs72036451		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18205422delA	uc011jya.1	+							NM_014707	NP_055522	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|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)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	accctgtctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19546213	19546213	+	IGR	DEL	T	-	-	rs67506004		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19546213delT								FERD3L (361169 upstream) : TWISTNB (188872 downstream)																							gccaataggattttttTTTTT	0.179													3	3	---	---	---	---	
C7orf46	340277	broad.mit.edu	37	7	23738918	23738919	+	Intron	INS	-	G	G	rs142028325	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23738918_23738919insG	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587	A4D161	CG046_HUMAN	hypothetical protein LOC340277 isoform 1												0						aaactttttttttgcagcagca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24409486	24409487	+	IGR	DEL	TT	-	-	rs113932355		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24409486_24409487delTT								NPY (78009 upstream) : MPP6 (203598 downstream)																							GTTTGCTTGAtttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25333429	25333429	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25333429delT								NPVF (65324 upstream) : MIR148A (656110 downstream)																							tcttattccatctgtaataca	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	27706553	27706554	+	IGR	INS	-	A	A	rs142518715		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27706553_27706554insA								HIBADH (3951 upstream) : TAX1BP1 (72438 downstream)																							gactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28683806	28683810	+	Intron	DEL	GGAAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28683806_28683810delGGAAG	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						aaaagggaaaggaagggaagggaag	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	28916252	28916253	+	IGR	INS	-	A	A	rs79476428		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28916252_28916253insA								CREB5 (50743 upstream) : TRIL (76723 downstream)																							gactctgtctcaaaaaaaaaaa	0.099													3	3	---	---	---	---	
PLEKHA8	84725	broad.mit.edu	37	7	30140797	30140798	+	Intron	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30140797_30140798delAA	uc003tap.1	+						PLEKHA8_uc003tao.2_Intron	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						gacttgggggaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30925322	30925322	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30925322delC	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_Intron|FAM188B_uc003tbu.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						GCAGTGCCCACCCCCCCCCCA	0.363													3	6	---	---	---	---	
ADCYAP1R1	117	broad.mit.edu	37	7	31132571	31132572	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31132571_31132572delAG	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron|ADCYAP1R1_uc003tcf.1_Intron	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						ATGGGCAGGAagagagagagag	0.376													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34189450	34189450	+	Intron	DEL	C	-	-	rs34421431		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34189450delC	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						GGAAGATGAGCCTGTCAACAT	0.423													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36093525	36093525	+	IGR	DEL	G	-	-	rs113901436		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36093525delG								SEPT7 (148610 upstream) : EEPD1 (99311 downstream)																							tctcctcctcgtcctcttcct	0.189													5	3	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39331546	39331546	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39331546delT	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						TCCCTTTACCTTTTTTTTTTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46365107	46365108	+	IGR	INS	-	A	A	rs145290565	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46365107_46365108insA								IGFBP3 (404236 upstream) : TNS3 (949645 downstream)																							ggcaaaaggtcaaaactaaaga	0.000													0	8	---	---	---	---	
UPP1	7378	broad.mit.edu	37	7	48135246	48135246	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48135246delT	uc003toj.2	+						UPP1_uc003tok.2_Intron|UPP1_uc003tol.2_Intron|UPP1_uc011kcg.1_Intron|UPP1_uc011kch.1_Intron|UPP1_uc003ton.2_Intron|UPP1_uc003too.2_Intron	NM_181597	NP_853628	Q16831	UPP1_HUMAN	uridine phosphorylase 1						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage	cytosol	uridine phosphorylase activity				0						CCTGCAGTGAttttttttttt	0.244													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48889407	48889407	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48889407delC								ABCA13 (202316 upstream) : CDC14C (74750 downstream)																							CTGTTATCTACCCTTTCAGCC	0.438													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51950436	51950437	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51950436_51950437delAC								COBL (565921 upstream) : None (None downstream)																							CACCACAGAAacacacacacac	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52118073	52118074	+	IGR	INS	-	AC	AC	rs143541912	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52118073_52118074insAC								COBL (733558 upstream) : POM121L12 (985275 downstream)																							AGCAAAACTATACCTCTCGGTA	0.361													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52896150	52896151	+	IGR	INS	-	T	T	rs138097265	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52896150_52896151insT								None (None upstream) : POM121L12 (207198 downstream)																							gtcaattttacttttttgcaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54754130	54754130	+	IGR	DEL	T	-	-	rs35038644		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54754130delT								VSTM2A (115943 upstream) : SEC61G (65811 downstream)																							cttttcattctttttttttgt	0.025													2	4	---	---	---	---	
EGFR	1956	broad.mit.edu	37	7	55164697	55164698	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55164697_55164698insT	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	CCCTGGCTCCCTTTCCCTAGTA	0.525		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			4	2	---	---	---	---	
LANCL2	55915	broad.mit.edu	37	7	55458471	55458472	+	Intron	INS	-	AA	AA			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55458471_55458472insAA	uc003tqp.2	+							NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2						negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			aaaactgtctcaaaaaaaaaaa	0.153													4	2	---	---	---	---	
CCT6A	908	broad.mit.edu	37	7	56125055	56125056	+	Intron	DEL	GT	-	-	rs72000687		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56125055_56125056delGT	uc003trl.1	+						PSPH_uc003trj.2_Intron|CCT6A_uc003trm.1_Intron|CCT6A_uc011kcu.1_Intron	NM_001762	NP_001753	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A isoform						'de novo' posttranslational protein folding	cytosol	ATP binding|unfolded protein binding			upper_aerodigestive_tract(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCCCTTTGGGgtgtgtgtgtgt	0.153													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57609203	57609203	+	IGR	DEL	A	-	-	rs113052160		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57609203delA								ZNF716 (75938 upstream) : None (None downstream)																							GTAGTGGCATAATTTTGTCTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57636038	57636040	+	IGR	DEL	CTT	-	-	rs76032099		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57636038_57636040delCTT								ZNF716 (102773 upstream) : None (None downstream)																							TGGTCATATACTTCTTAAGCCAA	0.350													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57712895	57712896	+	IGR	DEL	CA	-	-	rs67169169		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57712895_57712896delCA								ZNF716 (179630 upstream) : None (None downstream)																							cacacacactcacacacacaca	0.084													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57717584	57717593	+	IGR	DEL	AATGTATCTG	-	-	rs115222846	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57717584_57717593delAATGTATCTG								ZNF716 (184319 upstream) : None (None downstream)																							CCTCTATGCAAATGTATCTGAATGTATTTG	0.214													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57734142	57734143	+	IGR	INS	-	T	T	rs144782587	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57734142_57734143insT								ZNF716 (200877 upstream) : None (None downstream)																							GTACTAAATGATTTTTTAAGAT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57914096	57914097	+	IGR	INS	-	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57914096_57914097insC								ZNF716 (380831 upstream) : None (None downstream)																							atgattctgttttttctgatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57914929	57914929	+	IGR	DEL	A	-	-	rs142189571	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57914929delA								ZNF716 (381664 upstream) : None (None downstream)																							catttacactaaaagccacaa	0.025													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57915810	57915811	+	IGR	DEL	TA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57915810_57915811delTA								ZNF716 (382545 upstream) : None (None downstream)																							atgacaattctatgtttaatat	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57921285	57921285	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57921285delA								ZNF716 (388020 upstream) : None (None downstream)																							TTTGGTCAATAAAACACCCCT	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	58027905	58027905	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:58027905delC								ZNF716 (494640 upstream) : None (None downstream)																							caaatgtccacttgcagattc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61750494	61750495	+	IGR	INS	-	A	A	rs139756826		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61750494_61750495insA								None (None upstream) : None (None downstream)																							gacgcgaatggatcatcattga	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61866881	61866882	+	IGR	INS	-	T	T	rs149926706	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61866881_61866882insT								None (None upstream) : LOC643955 (884790 downstream)																							ctgggatattatttttttgcca	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64895997	64895998	+	IGR	INS	-	TAAG	TAAG	rs139654707	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64895997_64895998insTAAG								ZNF92 (30000 upstream) : INTS4L2 (216779 downstream)																							TGACACATGACTGTGTGACACT	0.416													5	4	---	---	---	---	
VKORC1L1	154807	broad.mit.edu	37	7	65410252	65410252	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65410252delA	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)	tctcaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RABGEF1	27342	broad.mit.edu	37	7	66193938	66193939	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66193938_66193939insT	uc003tvf.2	+						RABGEF1_uc003tvg.2_Intron	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						ttcacctccacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68665481	68665482	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68665481_68665482delGT								None (None upstream) : AUTS2 (398423 downstream)																							TGGTGGACACgtgtgtgtgtgt	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68905997	68905998	+	IGR	DEL	TA	-	-	rs142038557	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68905997_68905998delTA								None (None upstream) : AUTS2 (157907 downstream)																							tttttttttttaaattgttttt	0.203													0	7	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69559256	69559256	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69559256delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GCTTGTTGCATTTTGCTGTAT	0.358													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69957321	69957322	+	Intron	INS	-	TA	TA	rs34391284		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69957321_69957322insTA	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)		GCTGTTCATGTTGACACTGATG	0.505													5	4	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70751768	70751769	+	Intron	INS	-	TTTG	TTTG	rs139670524	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70751768_70751769insTTTG	uc003tvy.2	+							NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				tttgttatgtttttgtttgttt	0.050													2	4	---	---	---	---	
TYW1B	441250	broad.mit.edu	37	7	72261916	72261916	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72261916delG	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kek.1_Intron	NM_001145440	NP_001138912	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						tccacctcctggggtcaagtg	0.080													4	4	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73274315	73274318	+	Intron	DEL	ACAC	-	-	rs148206108		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73274315_73274318delACAC	uc011kfa.1	-						WBSCR28_uc003tzk.2_5'Flank|WBSCR28_uc003tzl.2_5'Flank	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						gaggaattaaacacacacacacac	0.000													5	3	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	73886594	73886595	+	Intron	INS	-	C	C	rs144613433	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73886594_73886595insC	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CCCCCCTCTTTCCCTTCCTTGG	0.450													4	5	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76921952	76921953	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76921952_76921953delAG	uc003uga.2	+						CCDC146_uc010ldp.2_Intron|CCDC146_uc003ugc.2_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				aaaaaaaaaaagaaCATCCCTT	0.183													3	3	---	---	---	---	
PHTF2	57157	broad.mit.edu	37	7	77514769	77514770	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77514769_77514770insT	uc003ugs.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugr.3_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						TATTGTTATACttttttttttg	0.089													6	4	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78031695	78031696	+	Intron	DEL	GT	-	-	rs78031324	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78031695_78031696delGT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				tccacctggggtgtgtgtgtgt	0.238													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78326299	78326302	+	Intron	DEL	TCAT	-	-	rs146691604		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78326299_78326302delTCAT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TTTGCTTTCATCATTCAAAGCTTT	0.343													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81092166	81092169	+	IGR	DEL	ACAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81092166_81092169delACAC								SEMA3C (540491 upstream) : HGF (239276 downstream)																							acacacacatacacacacacacac	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84894535	84894535	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84894535delC								SEMA3D (78364 upstream) : None (None downstream)																							AATATTTTTACCAAAAAAAAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	92576238	92576238	+	IGR	DEL	A	-	-	rs71739605		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92576238delA								CDK6 (110297 upstream) : SAMD9 (152594 downstream)																							GGATTTAGTTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
CALCR	799	broad.mit.edu	37	7	93117275	93117275	+	Intron	DEL	C	-	-	rs10719420		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93117275delC	uc003umv.1	-						CALCR_uc003ums.1_5'Flank|CALCR_uc003umt.1_5'Flank|CALCR_uc003umu.1_Intron|CALCR_uc003umw.2_Intron	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor						activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)	tcatcagattctccaaggttg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93927868	93927869	+	IGR	INS	-	CT	CT	rs150650461	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93927868_93927869insCT								BET1 (294178 upstream) : COL1A2 (96004 downstream)																							TTCTCTTACTCctctctctctc	0.218													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	94508433	94508434	+	IGR	INS	-	AGAG	AGAG	rs145936827	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94508433_94508434insAGAG								PEG10 (209429 upstream) : PPP1R9A (28515 downstream)																							gagaaagagacagtcagagaga	0.000													4	2	---	---	---	---	
PPP1R9A	55607	broad.mit.edu	37	7	94673683	94673683	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94673683delA	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			AGTTTAAAAGAAAAAAAATAT	0.343										HNSCC(28;0.073)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98107786	98107786	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98107786delT								BAIAP2L1 (77359 upstream) : NPTX2 (138811 downstream)																							tgaattctCCTTTTTTTTAAA	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98409104	98409109	+	IGR	DEL	TGGTGG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98409104_98409109delTGGTGG								NPTX2 (149923 upstream) : TMEM130 (35003 downstream)																							atagtggtaatggtggtggtggtggt	0.000													4	2	---	---	---	---	
ARPC1A	10552	broad.mit.edu	37	7	98963741	98963742	+	3'UTR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98963741_98963742insT	uc003upx.1	+	10					ARPC1A_uc010lfu.1_RNA|ARPC1A_uc003upy.1_3'UTR|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			TTTTTTGTTTGTTTTTTTGCGA	0.327													4	2	---	---	---	---	
PDAP1	11333	broad.mit.edu	37	7	98999324	98999324	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98999324delT	uc003uqe.2	-							NM_014891	NP_055706	Q13442	HAP28_HUMAN	PDGFA associated protein 1						cell proliferation|signal transduction						0	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)		Becaplermin(DB00102)	TAAAATAAtcttttttttttt	0.139													5	3	---	---	---	---	
AGFG2	3268	broad.mit.edu	37	7	100156841	100156842	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100156841_100156842insA	uc003uvf.2	+						AGFG2_uc010lgy.2_Intron	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						CTTCATGCATTATGTCCATGAG	0.431													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100554239	100554240	+	Intron	INS	-	CAA	CAA	rs112039084		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100554239_100554240insCAA	uc003uxk.1	+						uc003uxl.1_Intron					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		agaccctatctcaacaataaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100608467	100608468	+	Intron	INS	-	T	T	rs139602002	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100608467_100608468insT	uc003uxl.1	+						uc003uxm.1_RNA|uc003uxn.1_RNA|uc010lhn.1_5'Flank					SubName: Full=Intestinal mucin; Flags: Fragment;																		AGGGAGAGACCTTTGCGGGAGG	0.624													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101963169	101963172	+	IGR	DEL	TCTT	-	-	rs142666100		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101963169_101963172delTCTT								SH2B2 (992 upstream) : SPDYE6 (23021 downstream)																							tctctttctctctttctttccttt	0.078													7	5	---	---	---	---	
FBXL13	222235	broad.mit.edu	37	7	102543522	102543522	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102543522delT	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron	NM_145032	NP_659469	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13 isoform												0						gtttttccaatttttggtgtc	0.000													4	2	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104179285	104179286	+	Intron	DEL	TA	-	-	rs66471430		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104179285_104179286delTA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						gcgaggaccttaagatgaggaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108323776	108323776	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108323776delT								DNAJB9 (108484 upstream) : C7orf66 (200264 downstream)																							CTTGTATCAGTTAGAGcagtg	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109880886	109880889	+	IGR	DEL	GTGT	-	-	rs3900331		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109880886_109880889delGTGT								EIF3IP1 (280616 upstream) : IMMP2L (422221 downstream)																							tatgcctgtggtgtgtgtgtgtgt	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112625730	112625731	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112625730_112625731insT								C7orf60 (45798 upstream) : GPR85 (94737 downstream)																							CTCAGGACATCTTTTTTTGTAG	0.376													4	5	---	---	---	---	
CAV1	857	broad.mit.edu	37	7	116057901	116057902	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116057901_116057902delAC	uc010lkd.1	+						CAV2_uc003vhv.2_Intron|CAV2_uc003vhw.2_Intron|CAV2_uc003vhx.2_Intron|CAV2_uc010lkb.1_Intron|CAV2_uc010lkc.2_Intron|CAV2_uc003vib.2_Intron|CAV2_uc003vhz.2_Intron|CAV2_uc003via.2_Intron|CAV1_uc010lke.1_Intron	NM_001753	NP_001744	Q03135	CAV1_HUMAN	caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			atgcacacagacacacacacac	0.337													6	3	---	---	---	---	
CAPZA2	830	broad.mit.edu	37	7	116543288	116543289	+	Intron	DEL	GT	-	-	rs12706114	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116543288_116543289delGT	uc003vil.2	+						CAPZA2_uc011knk.1_Intron	NM_006136	NP_006127	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line,						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			gcagagaagAgtgtgtgtgtgt	0.074													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117689039	117689039	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117689039delC								CTTNBP2 (175478 upstream) : NAA38 (135047 downstream)																							cctcctgtatccctgagttac	0.000													3	3	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120762193	120762194	+	Intron	INS	-	TT	TT	rs34817474		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120762193_120762194insTT	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.3_Intron|C7orf58_uc010lkk.1_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					ACTCATCTGGAttttttttttt	0.173													3	3	---	---	---	---	
IQUB	154865	broad.mit.edu	37	7	123092987	123092988	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123092987_123092988insA	uc003vkn.2	-						IQUB_uc011kny.1_Intron|IQUB_uc003vko.2_Intron|IQUB_uc010lkt.2_Intron	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing											ovary(3)|large_intestine(1)	4						TCCCTGCAAAGAAAAAAATCAA	0.243													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129611778	129611778	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129611778delT								UBE2H (18989 upstream) : ZC3HC1 (46349 downstream)																							atcccagcactttgggaggcc	0.020													4	2	---	---	---	---	
TSGA13	114960	broad.mit.edu	37	7	130357305	130357306	+	Intron	INS	-	T	T	rs71960059		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130357305_130357306insT	uc003vqi.2	-						TSGA13_uc003vqj.2_Intron	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13											ovary(2)	2	Melanoma(18;0.0435)					ATTGAGGGTACTTTTTTTTTTT	0.381													3	6	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132325546	132325547	+	Intron	DEL	AG	-	-	rs33964886		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132325546_132325547delAG	uc003vrb.2	-							NM_181775	NP_861440	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 2							integral to membrane|intracellular|plasma membrane				ovary(1)	1						aaaaaaaaaaaggggggggccc	0.000													3	3	---	---	---	---	
CALD1	800	broad.mit.edu	37	7	134521785	134521785	+	Intron	DEL	T	-	-	rs141345132		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134521785delT	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1						cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0						ATAAGATCTGTTTTTTTTTTT	0.333													4	2	---	---	---	---	
PARP12	64761	broad.mit.edu	37	7	139759201	139759202	+	Intron	INS	-	CT	CT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139759201_139759202insCT	uc003vvl.1	-						PARP12_uc003vvk.1_5'Flank|PARP12_uc010lnf.1_Intron	NM_022750	NP_073587	Q9H0J9	PAR12_HUMAN	poly ADP-ribose polymerase 12							nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)					CCTGAACCTAGCTTTTTTTTTT	0.406													4	2	---	---	---	---	
DENND2A	27147	broad.mit.edu	37	7	140324505	140324506	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140324505_140324506insT	uc010lnk.2	-						DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)					ATTTCTTTTCCTTTTTTTTTTC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145150402	145150402	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145150402delT								TPK1 (617256 upstream) : CNTNAP2 (663051 downstream)																							tgcctggttattttttttttc	0.000													4	2	---	---	---	---	
ZNF398	57541	broad.mit.edu	37	7	148847784	148847800	+	Intron	DEL	CCCCGCCTCCCGCGCCC	-	-	rs72215493		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148847784_148847800delCCCCGCCTCCCGCGCCC	uc003wfl.2	+						ZNF398_uc011kul.1_Intron|ZNF398_uc011kum.1_Intron	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			ggtgattcTTCCCCGCCTCCCGCGCCCCCCCGCCTCC	0.152													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149596848	149596849	+	IGR	INS	-	A	A	rs140226956	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149596848_149596849insA								ATP6V0E2 (19062 upstream) : ACTR3C (347453 downstream)																							aatttggcaagaaaaaaaaaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150248415	150248426	+	IGR	DEL	TGTGCACAGGAG	-	-	rs111495872		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150248415_150248426delTGTGCACAGGAG								GIMAP7 (30255 upstream) : GIMAP4 (16032 downstream)																							ccagtgccactgtgcacaggaggaccttgcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	151115242	151115244	+	IGR	DEL	AAA	-	-	rs80002334		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151115242_151115244delAAA								WDR86 (7502 upstream) : CRYGN (11813 downstream)																							acaccatctcaaaaaaaaaaaaa	0.020													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151282545	151282546	+	Intron	INS	-	AGTT	AGTT	rs139248943	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151282545_151282546insAGTT	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc003wkl.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		GAAAAACTCTCAGCCACTAGTC	0.460													4	4	---	---	---	---	
GALNTL5	168391	broad.mit.edu	37	7	151697996	151697997	+	Intron	INS	-	T	T	rs66497039		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151697996_151697997insT	uc003wkp.2	+						GALNTL5_uc003wkq.2_Intron|GALNTL5_uc003wkr.2_Intron|GALNTL5_uc003wks.2_Intron|GALNTL5_uc010lqf.2_Intron	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							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)		ttttttctttcttttttttttt	0.000													4	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152103075	152103075	+	Intron	DEL	G	-	-	rs66994474		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152103075delG	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ctctgtctcagaaaaaaaaaa	0.114			N		medulloblastoma								6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153049187	153049188	+	IGR	INS	-	A	A	rs144210851	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153049187_153049188insA								ACTR3B (496724 upstream) : DPP6 (535231 downstream)																							gcatgaatgataaaaaaaagtg	0.000													4	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154207780	154207780	+	Intron	DEL	A	-	-	rs67365097		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154207780delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			caggtgtctcaaaaaaaaaaa	0.129													4	3	---	---	---	---	
SHH	6469	broad.mit.edu	37	7	155605315	155605315	+	5'Flank	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155605315delA	uc003wmk.1	-							NM_000193	NP_000184	Q15465	SHH_HUMAN	sonic hedgehog preproprotein						androgen metabolic process|axon guidance|branching involved in ureteric bud morphogenesis|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment|embryonic digit morphogenesis|hindbrain development|intein-mediated protein splicing|lymphoid progenitor cell differentiation|metanephric mesenchymal cell proliferation involved in metanephros development|midbrain development|negative regulation of cell migration|negative regulation of kidney smooth muscle cell differentiation|negative regulation of ureter smooth muscle cell differentiation|negative thymic T cell selection|neural crest cell migration|neuroblast proliferation|patterning of blood vessels|positive regulation of alpha-beta T cell differentiation|positive regulation of immature T cell proliferation in thymus|positive regulation of kidney smooth muscle cell differentiation|positive regulation of mesenchymal cell proliferation involved in ureter development|positive regulation of T cell differentiation in thymus|positive regulation of ureter smooth muscle cell differentiation|positive thymic T cell selection|proteolysis|sclerotome development|stem cell development|thymus development|vasculogenesis|ventral midline development	cell surface|extracellular space|membrane raft|plasma membrane	calcium ion binding|laminin-1 binding|peptidase activity|signal transducer activity|zinc ion binding			central_nervous_system(3)|lung(1)	4	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GATTCGAGTTAAAAAAAAAAA	0.428													4	2	---	---	---	---	
UBE3C	9690	broad.mit.edu	37	7	156967169	156967170	+	Intron	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156967169_156967170delTC	uc010lqs.2	+						UBE3C_uc003wnf.2_Intron|UBE3C_uc003wng.2_Intron	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		ggagacagggtctctctctctc	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157092390	157092398	+	IGR	DEL	TGTGTGGTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157092390_157092398delTGTGTGGTG								UBE3C (30325 upstream) : DNAJB6 (37312 downstream)																							tgcggtgtgttgtgtggtgtgtgtggtgt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157226044	157226045	+	IGR	DEL	AT	-	-	rs60991448		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157226044_157226045delAT								DNAJB6 (15912 upstream) : PTPRN2 (105706 downstream)																							atgcacacacatgcatgcacac	0.000													6	4	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157892937	157892940	+	Intron	DEL	GTGT	-	-	rs3065708		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157892937_157892940delGTGT	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)		attccatggggtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158999828	158999829	+	IGR	INS	-	AG	AG			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158999828_158999829insAG								VIPR2 (62179 upstream) : None (None downstream)																							caaaggagagaagagaggggac	0.163													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1197216	1197217	+	IGR	INS	-	G	G	rs143735419	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1197216_1197217insG								ERICH1 (515990 upstream) : DLGAP2 (252352 downstream)																							GAGATCAGTGTGGAGTGATGGT	0.584													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10353615	10353615	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10353615delG	uc010lru.2	-											Homo sapiens cDNA, FLJ97155.																		gtgggagaatggaAAGGAAGA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10408825	10408828	+	IGR	DEL	CTCA	-	-	rs112578028		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10408825_10408828delCTCA								PRSS55 (6118 upstream) : RP1L1 (55034 downstream)																							TTAAAATGCCCTCACTCACTCatt	0.240													4	3	---	---	---	---	
NEIL2	252969	broad.mit.edu	37	8	11624560	11624575	+	5'Flank	DEL	GAAAGAAAGAAAGAAA	-	-	rs12547004	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11624560_11624575delGAAAGAAAGAAAGAAA	uc003wug.2	+						NEIL2_uc003wue.2_5'Flank|NEIL2_uc003wuf.2_5'Flank|NEIL2_uc011kxd.1_5'Flank	NM_145043	NP_659480	Q969S2	NEIL2_HUMAN	nei like 2 isoform a						base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding				0	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		aggaaggaaggaaagaaagaaagaaagaaagaaaga	0.000								BER_DNA_glycosylases					4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12439870	12439870	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12439870delA	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		GAAAACACTTAAAAAAAAAAG	0.204													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13271009	13271012	+	Intron	DEL	ATAT	-	-	rs112147102		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13271009_13271012delATAT	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.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						gtgtgcacacatatatatatatat	0.098													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14513995	14513996	+	Intron	INS	-	TT	TT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14513995_14513996insTT	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		CTCTTTCTCCCTCTCTTTCCtc	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	19101121	19101122	+	IGR	INS	-	T	T	rs149222457		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19101121_19101122insT								PSD3 (229925 upstream) : SH2D4A (70085 downstream)																							tgcccagccaattttttttttt	0.000													1	5	---	---	---	---	
LZTS1	11178	broad.mit.edu	37	8	20104857	20104857	+	3'UTR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20104857delT	uc003wzr.2	-	3						NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1						cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		TTTCCTGGAGTTGGGGGGGGG	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23791938	23791938	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23791938delA								STC1 (79618 upstream) : ADAM28 (359642 downstream)																							GGCAACTGTGAAGAGTTTTAG	0.388													4	2	---	---	---	---	
ADAM7	8756	broad.mit.edu	37	8	24327987	24327987	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24327987delA	uc003xeb.2	+							NM_003817	NP_003808	Q9H2U9	ADAM7_HUMAN	a disintegrin and metalloproteinase domain 7						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		atttgaaaataaaaaaaaaaa	0.050													4	2	---	---	---	---	
DOCK5	80005	broad.mit.edu	37	8	25152793	25152794	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25152793_25152794insT	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_5'Flank|DOCK5_uc003xef.2_Intron	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		catctctacaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29517575	29517576	+	IGR	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29517575_29517576delAA								DUSP4 (309390 upstream) : C8orf75 (61202 downstream)																							cgtctcaggcaaaaaaaaaaaa	0.188													5	3	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32255724	32255724	+	Intron	DEL	A	-	-	rs34669986		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32255724delA	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)		CAGCAAAAATAAAAAAAGAAA	0.408													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	35800812	35800812	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35800812delT								UNC5D (148632 upstream) : KCNU1 (841030 downstream)																							GTAGCTTTGGTTttttttttt	0.169													5	3	---	---	---	---	
GPR124	25960	broad.mit.edu	37	8	37682008	37682009	+	Intron	DEL	TT	-	-	rs146295798		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37682008_37682009delTT	uc003xkj.2	+						GPR124_uc003xki.2_Intron|GPR124_uc010lvy.2_Intron	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor						central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			taaggtgcaatttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38078090	38078090	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38078090delT								BAG4 (9553 upstream) : DDHD2 (10919 downstream)																							tcctggcTAAttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42529877	42529880	+	IGR	DEL	ATGG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42529877_42529880delATGG								C8orf40 (121738 upstream) : CHRNB3 (22682 downstream)																							agatggataaatggatggatggat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42548322	42548322	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42548322delC								C8orf40 (140183 upstream) : CHRNB3 (4240 downstream)																							TACTTTGGATCCTGAATCCAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49746793	49746793	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49746793delG								EFCAB1 (98923 upstream) : SNAI2 (83446 downstream)																							TCGCCTTCCCGGCACAGCCTT	0.572													3	3	---	---	---	---	
CHCHD7	79145	broad.mit.edu	37	8	57129756	57129756	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57129756delT	uc003xsx.2	+						CHCHD7_uc003xss.2_Intron|CHCHD7_uc003xst.2_Intron|CHCHD7_uc003xsu.2_Intron|CHCHD7_uc003xsv.2_Intron|CHCHD7_uc003xsw.2_Intron	NM_001011671	NP_001011671	Q9BUK0	CHCH7_HUMAN	coiled-coil-helix-coiled-coil-helix domain										CHCHD7/PLAG1(12)	salivary_gland(12)	12		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00159)|all cancers(17;0.0112)			GGTTTTGGGATTTTTTTTTTA	0.289			T	PLAG1	salivary adenoma								5	3	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	59817219	59817219	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59817219delT	uc003xtw.1	-							NM_014729	NP_055544	O94900	TOX_HUMAN	thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				AGCAGGGGCCTGACCATGGTA	0.363													4	2	---	---	---	---	
CA8	767	broad.mit.edu	37	8	61183888	61183889	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61183888_61183889insA	uc003xtz.1	-						CA8_uc003xua.1_Intron|CA8_uc003xub.2_Intron	NM_004056	NP_004047	P35219	CAH8_HUMAN	carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)				atgagagcctgaaaaaaaaaag	0.149													4	2	---	---	---	---	
ARMC1	55156	broad.mit.edu	37	8	66516481	66516481	+	3'UTR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66516481delC	uc003xvl.2	-	7					ARMC1_uc011leo.1_3'UTR	NM_018120	NP_060590	Q9NVT9	ARMC1_HUMAN	armadillo repeat-containing protein						metal ion transport		metal ion binding			skin(1)	1			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			GGTAAAATGTCCAATAAAACG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70121896	70121896	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70121896delA								C8orf34 (390640 upstream) : SULF1 (256963 downstream)																							attaaatttgaaagaactaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70804367	70804367	+	IGR	DEL	A	-	-	rs142250291		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70804367delA								SLCO5A1 (57068 upstream) : PRDM14 (159658 downstream)																							CAAGCCAATTAAAAAAAAAAA	0.264													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	74669287	74669287	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74669287delC								STAU2 (9344 upstream) : UBE2W (23045 downstream)																							ATTACAAACACCAGATTGAAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	74961015	74961016	+	IGR	INS	-	GAAG	GAAG	rs145966856	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74961015_74961016insGAAG								LY96 (19710 upstream) : JPH1 (185925 downstream)																							gtggtccatatgaaggaaggaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	77848815	77848837	+	IGR	DEL	CTTTCTTTCTTTCTTCTTTCTTT	-	-	rs67087632		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77848815_77848837delCTTTCTTTCTTTCTTCTTTCTTT								ZFHX4 (69295 upstream) : PEX2 (43659 downstream)																							tccttccttcctttctttctttcttctttctttctttctttct	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81203038	81203038	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81203038delG								TPD52 (119202 upstream) : ZBTB10 (194816 downstream)																							TGAAAACTCAGAAGTTTTTGA	0.542													4	2	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81650808	81650808	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81650808delT	uc003yby.1	-							NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			ctccagagtcttttttttttt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82554964	82554965	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82554964_82554965insA								FABP12 (111414 upstream) : IMPA1 (14186 downstream)																							tctgtctcaggaaaaaaaaaaa	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84526647	84526648	+	IGR	DEL	TC	-	-	rs144135500	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84526647_84526648delTC								None (None upstream) : RALYL (568805 downstream)																							tttctttctttctctctctttc	0.000													3	3	---	---	---	---	
CA13	377677	broad.mit.edu	37	8	86348807	86348807	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86348807delT	uc003ydf.1	+						CA3_uc003ydj.2_5'Flank|CA3_uc011lfv.1_5'Flank			Q8N1Q1	CAH13_HUMAN	Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0						TTGCTCACTCTTTTTTTTTTC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89639491	89639492	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89639491_89639492delGT								MMP16 (299774 upstream) : None (None downstream)																							taatggaaacgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96621564	96621565	+	IGR	DEL	TC	-	-	rs72239058		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96621564_96621565delTC								C8orf37 (340127 upstream) : GDF6 (532995 downstream)																							TTCCTTCCTTtctctctctctc	0.064													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96919509	96919510	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96919509_96919510delTG								C8orf37 (638072 upstream) : GDF6 (235050 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.183													4	2	---	---	---	---	
SDC2	6383	broad.mit.edu	37	8	97548763	97548764	+	Intron	INS	-	AAT	AAT	rs142607683	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97548763_97548764insAAT	uc003yhv.1	+							NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	ttgcctaggccaatctccaact	0.045													4	2	---	---	---	---	
MTDH	92140	broad.mit.edu	37	8	98704606	98704607	+	Intron	INS	-	T	T	rs144055473	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98704606_98704607insT	uc003yhz.2	+						MTDH_uc010mbf.2_Intron	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			agtaattttccttttttttttg	0.000													4	2	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101057500	101057501	+	Intron	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101057500_101057501delAA	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc011lgz.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			aacaaaaaagaaaaaaaaaaGA	0.040													4	2	---	---	---	---	
RGS22	26166	broad.mit.edu	37	8	101096059	101096060	+	Intron	DEL	TT	-	-	rs113743299		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101096059_101096060delTT	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			ATTTCTTTTCTTTTtttttttt	0.203													4	2	---	---	---	---	
SPAG1	6674	broad.mit.edu	37	8	101179501	101179501	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101179501delT	uc003yjh.1	+						SPAG1_uc003yjg.1_Intron|SPAG1_uc003yji.1_Intron	NM_172218	NP_757367	Q07617	SPAG1_HUMAN	sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		tagtcccttcttatctttggg	0.129													4	2	---	---	---	---	
SPAG1	6674	broad.mit.edu	37	8	101188225	101188225	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101188225delT	uc003yjh.1	+						SPAG1_uc003yjg.1_Intron|SPAG1_uc003yji.1_Intron	NM_172218	NP_757367	Q07617	SPAG1_HUMAN	sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		ccttcctgccttaaatcctgg	0.000													4	2	---	---	---	---	
SNX31	169166	broad.mit.edu	37	8	101614126	101614127	+	Intron	INS	-	T	T	rs142408820	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101614126_101614127insT	uc003yjr.2	-						SNX31_uc011lha.1_Intron|SNX31_uc011lhb.1_Intron	NM_152628	NP_689841	Q8N9S9	SNX31_HUMAN	sorting nexin 31						cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			CCTCCCTGAGCAGGCACCTTTT	0.569													5	3	---	---	---	---	
LRP12	29967	broad.mit.edu	37	8	105556475	105556475	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105556475delA	uc003yma.2	-						LRP12_uc003ymb.2_Intron|LRP12_uc003ymc.3_Intron	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12						endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			aggcggcttcaaaagaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	107850000	107850000	+	IGR	DEL	C	-	-	rs112688120		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107850000delC								ABRA (67528 upstream) : ANGPT1 (411711 downstream)																							agttccagaactttttcacca	0.000													3	7	---	---	---	---	
TMEM74	157753	broad.mit.edu	37	8	109651231	109651231	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109651231delC	uc003ymx.2	-									Q96NL1	TMM74_HUMAN	Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			agtgaacaggccatcagtctc	0.000													4	2	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110461578	110461578	+	Frame_Shift_Del	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110461578delG	uc003yne.2	+	40	6141	c.6037delG	c.(6037-6039)GGGfs	p.G2013fs		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2013	Extracellular (Potential).|IPT/TIG 13.				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)			GAGCTTTGGTGGGGGTCAAAC	0.333										HNSCC(38;0.096)			20	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112913696	112913697	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112913696_112913697delCA								None (None upstream) : CSMD3 (321464 downstream)																							CTGAAGCACGCACACACACACA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	113166049	113166049	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113166049delA								None (None upstream) : CSMD3 (69112 downstream)																							tatcatccccaaaagtttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	115314399	115314399	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115314399delA								CSMD3 (865157 upstream) : None (None downstream)																							ccttgccctgaaaaaaaaAAT	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116303421	116303421	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116303421delT								None (None upstream) : TRPS1 (117304 downstream)																							GTGCTAAACCTTAGACTTGGC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119160151	119160152	+	IGR	INS	-	TG	TG	rs138853978	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119160151_119160152insTG								EXT1 (36093 upstream) : SAMD12 (41543 downstream)																							TTTTTTTTTTCTGTGTGTGTGT	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123423295	123423295	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123423295delA								HAS2AS (766362 upstream) : ZHX2 (370606 downstream)																							TTTGTTATGGAAAAAAAAAGT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123596192	123596192	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123596192delC								HAS2AS (939259 upstream) : ZHX2 (197709 downstream)																							tgagggggcacccagcctagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124071909	124071910	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124071909_124071910insT								DERL1 (17261 upstream) : WDR67 (13010 downstream)																							ttttctttttcttttttttttt	0.059													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127198505	127198505	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127198505delC								TRIB1 (747863 upstream) : FAM84B (366182 downstream)																							TCAAGCTTTGCCACATGCTAA	0.318													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127368020	127368020	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127368020delT								TRIB1 (917378 upstream) : FAM84B (196667 downstream)																							ttgatggatattaaggcagtt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129297791	129297793	+	IGR	DEL	AGG	-	-	rs74872571	byFrequency	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129297791_129297793delAGG								MIR1208 (135357 upstream) : None (None downstream)																							aagaagaagaaggagaagaggag	0.153													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130132504	130132505	+	IGR	DEL	CA	-	-	rs113096516		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130132504_130132505delCA								MIR1208 (970070 upstream) : GSDMC (627938 downstream)																							AAAacacacgcacacacacaca	0.366													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130499851	130499851	+	IGR	DEL	A	-	-	rs77275264		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130499851delA								None (None upstream) : GSDMC (260592 downstream)																							CTCATTTGCCAAAAAAAAAAA	0.318													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130739245	130739246	+	IGR	INS	-	AC	AC	rs7016792		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130739245_130739246insAC								None (None upstream) : GSDMC (21197 downstream)																							CCAATacacatacacacacaca	0.317													5	4	---	---	---	---	
ASAP1	50807	broad.mit.edu	37	8	131067782	131067782	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131067782delA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						tctagccagtAAAAAAAAAAA	0.189													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131421152	131421152	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131421152delG								ASAP1 (6936 upstream) : ADCY8 (371396 downstream)																							AAGGCACTATGGATCATGACC	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131514393	131514393	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131514393delA								ASAP1 (100177 upstream) : ADCY8 (278155 downstream)																							gatattggccacccccagtga	0.000													4	2	---	---	---	---	
ST3GAL1	6482	broad.mit.edu	37	8	134580787	134580787	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134580787delT	uc003yuk.2	-						ST3GAL1_uc003yum.2_Intron	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			ACTGGAAAGCTTTTACAAGAT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137490653	137490653	+	IGR	DEL	G	-	-	rs34672468		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137490653delG								KHDRBS3 (830807 upstream) : None (None downstream)																							GAATACTTTCGGGGAAGAGGA	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137897579	137897580	+	IGR	INS	-	T	T	rs138490132	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137897579_137897580insT								None (None upstream) : None (None downstream)																							gtgacatgatattatttgtggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137915548	137915551	+	IGR	DEL	AGAC	-	-	rs71671062		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137915548_137915551delAGAC								None (None upstream) : None (None downstream)																							acagagacagagacagacagagaa	0.230													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138268690	138268691	+	IGR	INS	-	T	T	rs150441147	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138268690_138268691insT								None (None upstream) : FAM135B (873577 downstream)																							AGAACCCTACATTTTTTTTTTA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138630776	138630777	+	IGR	DEL	AT	-	-	rs76486389		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138630776_138630777delAT								None (None upstream) : FAM135B (511491 downstream)																							ATAATCTACCATATGTGTTAAT	0.178													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140504340	140504341	+	IGR	INS	-	T	T	rs140692646	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140504340_140504341insT								COL22A1 (578104 upstream) : KCNK9 (108741 downstream)																							actgcgagtgatttttcccaga	0.010													3	3	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140656958	140656959	+	Intron	INS	-	C	C	rs72230243		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140656958_140656959insC	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)			TCCTGCCCTGTCCCCCCCCCCC	0.569													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141001799	141001799	+	Intron	DEL	T	-	-	rs113883389		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141001799delT	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						TTTGGGTTTGTTTTTTTTTTT	0.418													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141167060	141167060	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141167060delT	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						AAAGCCTCCCTTTTCCATTCA	0.438													5	3	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141407068	141407069	+	Intron	INS	-	CTCA	CTCA	rs145410164	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141407068_141407069insCTCA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_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						ACAACGCCCTCCTAAGTATCTG	0.356													6	4	---	---	---	---	
DENND3	22898	broad.mit.edu	37	8	142164654	142164654	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142164654delT	uc003yvy.2	+						DENND3_uc010mep.2_Intron|DENND3_uc003yvz.1_5'Flank	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3											ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TATTGGAAtcttttttttttc	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143661939	143661939	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143661939delA								BAI1 (35572 upstream) : ARC (30471 downstream)																							CATGGCATGTAGGGTTTGGCT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144147199	144147200	+	IGR	DEL	TT	-	-	rs28578939		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144147199_144147200delTT								C8orf31 (11479 upstream) : LY6H (92132 downstream)																							tctttctttctttttctttctt	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	13438115	13438116	+	IGR	DEL	CC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13438115_13438116delCC								MPDZ (158552 upstream) : NFIB (643732 downstream)																							TAGGGACACACCCACACACTAT	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16996641	16996641	+	IGR	DEL	G	-	-	rs77882549		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16996641delG								BNC2 (125855 upstream) : CNTLN (138397 downstream)																							aaaaaaaaaagagagaaagaa	0.000													2	4	---	---	---	---	
ADAMTSL1	92949	broad.mit.edu	37	9	18853614	18853614	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18853614delT	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		gcaaaggcagtttagattcag	0.000													4	2	---	---	---	---	
CDKN2A	1029	broad.mit.edu	37	9	21971019	21971019	+	Frame_Shift_Del	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21971019delC	uc003zpk.2	-	2	551	c.339delG	c.(337-339)CTGfs	p.L113fs	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Frame_Shift_Del_p.A169fs	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	113	ANK 4.				cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(13)|p.H83fs*2(2)|p.L113L(1)|p.L113M(1)|p.A68fs*3(1)|p.L113P(1)|p.R112fs*32(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GGTCCACGGGCAGACGGCCCC	0.726		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25565419	25565420	+	IGR	INS	-	CTT	CTT	rs148384604	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25565419_25565420insCTT								None (None upstream) : TUSC1 (110974 downstream)																							CCTCTACTCTCCTTCTTCCTTT	0.366													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32102164	32102165	+	IGR	INS	-	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32102164_32102165insC								None (None upstream) : ACO1 (282436 downstream)																							gcagagacacaacaaaaaaaga	0.000													4	2	---	---	---	---	
ACO1	48	broad.mit.edu	37	9	32428841	32428842	+	Intron	INS	-	A	A	rs112618859		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32428841_32428842insA	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		gactccgtctcaaaaaaaaaaa	0.020													5	3	---	---	---	---	
UBE2R2	54926	broad.mit.edu	37	9	33918831	33918831	+	3'UTR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33918831delC	uc003ztm.2	+	5						NM_017811	NP_060281	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme UBC3B						protein K48-linked ubiquitination|protein monoubiquitination		ATP binding|ubiquitin-protein ligase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		CAGGAGGGATCCTAGGATGGC	0.502													4	2	---	---	---	---	
RGP1	9827	broad.mit.edu	37	9	35752278	35752278	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35752278delC	uc011lpf.1	+						GBA2_uc011lpd.1_5'Flank|RGP1_uc011lpe.1_Intron	NM_001080496	NP_001073965	Q92546	RGP1_HUMAN	RGP1 retrograde golgi transport homolog											ovary(1)	1	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GGAACAGTTTCTCAGACCTTC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36730023	36730024	+	IGR	DEL	GA	-	-	rs10532562		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36730023_36730024delGA								MELK (52345 upstream) : PAX5 (108507 downstream)																							CCAAgtgagtgagtgtgtgtgt	0.139													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44128423	44128423	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44128423delG								FAM75A6 (497693 upstream) : FAM27C (861813 downstream)																							GCCCTCTAAAGAATGATAGCT	0.303													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44878998	44878998	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44878998delG								None (None upstream) : FAM27C (111238 downstream)																							AAGAGAGAATGGGAGacacac	0.199													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68409028	68409029	+	5'Flank	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68409028_68409029insG	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																		ctggtaatagcggtaccgtagg	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68473268	68473269	+	IGR	INS	-	T	T	rs145086865		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68473268_68473269insT								FAM27B (679079 upstream) : MIR1299 (528970 downstream)																							TGGATCCTGTGTTTTTTTTACA	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68693088	68693089	+	IGR	INS	-	C	C	rs146537073		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68693088_68693089insC								FAM27B (898899 upstream) : MIR1299 (309150 downstream)																							ACCATGTTCCACATTCCATCTC	0.411													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69000319	69000320	+	IGR	INS	-	TGTT	TGTT	rs149203682		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69000319_69000320insTGTT								None (None upstream) : MIR1299 (1919 downstream)																							gagtgtctgaatgttcctcaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70149380	70149381	+	IGR	INS	-	TTCC	TTCC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70149380_70149381insTTCC								LOC100133920 (484431 upstream) : FOXD4L5 (26328 downstream)																							tctctctctctctctctctctc	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70933247	70933247	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70933247delA								FOXD4L3 (13247 upstream) : LOC572558 (36864 downstream)																							tatttgaagtaatatcatgct	0.000													4	2	---	---	---	---	
APBA1	320	broad.mit.edu	37	9	72090892	72090892	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72090892delT	uc004ahh.2	-							NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						GGATGCTGTATTAGGAAGCAC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	75469926	75469927	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75469926_75469927insA								TMC1 (18659 upstream) : ALDH1A1 (45661 downstream)																							ctaaaactaccaaaaaaaagta	0.000													4	2	---	---	---	---	
GOLM1	51280	broad.mit.edu	37	9	88741374	88741375	+	Intron	INS	-	AAAC	AAAC	rs150439613	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88741374_88741375insAAAC	uc010mqd.1	-									Q8NBJ4	GOLM1_HUMAN	Homo sapiens golgi membrane protein GP73 mRNA, complete cds.							Golgi apparatus|integral to plasma membrane					0						gtctcaaaacaaaacaaacaaa	0.183													2	4	---	---	---	---	
SPIN1	10927	broad.mit.edu	37	9	91090645	91090646	+	3'UTR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91090645_91090646delAC	uc010mqj.2	+	6					SPIN1_uc004apy.2_3'UTR|SPIN1_uc004apz.2_3'UTR|SPIN1_uc010mqk.2_3'UTR	NM_006717	NP_006708	Q9Y657	SPIN1_HUMAN	spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0						atacaagtgtacacacacacac	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93444450	93444450	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93444450delG								DIRAS2 (39342 upstream) : SYK (119562 downstream)																							ccagcactttgggaggccaag	0.080													4	2	---	---	---	---	
NOL8	55035	broad.mit.edu	37	9	95071926	95071926	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95071926delA	uc004arv.2	-						NOL8_uc010mqw.2_Intron|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1						TACTGCTGTGAAAAATGCTAT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95692901	95692901	+	IGR	DEL	A	-	-	rs34786112		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95692901delA								ANKRD19 (41928 upstream) : FGD3 (16700 downstream)																							actccgtctcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
PTPDC1	138639	broad.mit.edu	37	9	96816702	96816705	+	Intron	DEL	ATTA	-	-	rs5899205		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96816702_96816705delATTA	uc004auf.1	+						PTPDC1_uc004aug.1_Intron	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						tctcagagatattaataaatgtgc	0.240													0	6	---	---	---	---	
C9orf3	84909	broad.mit.edu	37	9	97684916	97684916	+	Intron	DEL	T	-	-	rs113040711		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97684916delT	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron|uc004avb.1_Intron	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		TCCTTCCTTGTTTTTTTTTTT	0.453													4	2	---	---	---	---	
HSD17B3	3293	broad.mit.edu	37	9	99051410	99051410	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99051410delA	uc004awa.1	-						HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3						androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)	acaaaaacagaaaaaaaaaaG	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	99199566	99199566	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99199566delT								ZNF367 (18897 upstream) : HABP4 (12848 downstream)																							acagaatatcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101668659	101668659	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101668659delG								GALNT12 (56301 upstream) : COL15A1 (37479 downstream)																							CCGCTGGGGTGGAGTGGATTA	0.408													4	2	---	---	---	---	
LPAR1	1902	broad.mit.edu	37	9	113731994	113731994	+	Intron	DEL	A	-	-	rs75890644		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113731994delA	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						tctgtctcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PTGR1	22949	broad.mit.edu	37	9	114319657	114319658	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114319657_114319658insA	uc011lwr.1	-						ZNF483_uc004bfg.2_Intron	NM_001146109	NP_001139581	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 2						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						ccatctccagtaaaaaaaaaaa	0.114													2	4	---	---	---	---	
ROD1	9991	broad.mit.edu	37	9	114994246	114994247	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114994246_114994247delAG	uc004bfw.2	-						ROD1_uc004bfv.2_Intron|ROD1_uc004bfx.2_Intron|ROD1_uc011lwu.1_Intron|ROD1_uc004bfy.2_Intron|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1						agagaagagaagagagaagaga	0.045													4	2	---	---	---	---	
SLC46A2	57864	broad.mit.edu	37	9	115655874	115655875	+	5'Flank	DEL	AA	-	-	rs147564161		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115655874_115655875delAA	uc004bgk.2	-							NM_033051	NP_149040	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2							integral to membrane|plasma membrane	symporter activity			central_nervous_system(1)	1						AAGGAGGGAGAAGAGAGGGGAA	0.525													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116628490	116628492	+	IGR	DEL	TAT	-	-	rs35215360		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116628490_116628492delTAT								RGS3 (268473 upstream) : ZNF618 (10070 downstream)																							tacaatgaaatattattcagcct	0.000													1	5	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116812723	116812724	+	3'UTR	DEL	CA	-	-	rs113819665		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116812723_116812724delCA	uc004bid.2	+	15					ZNF618_uc004bic.2_3'UTR|ZNF618_uc011lxi.1_3'UTR|ZNF618_uc011lxj.1_3'UTR|ZNF618_uc010mvb.2_3'UTR	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGcacacacgcacacacacaca	0.465													5	3	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	120096764	120096764	+	Intron	DEL	T	-	-	rs113282368		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120096764delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						atatcagggctttttTTTTTT	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122796085	122796085	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122796085delT								DBC1 (664346 upstream) : MIR147 (211172 downstream)																							CCCTGGAGGATTTTTtttttc	0.159													4	2	---	---	---	---	
TTLL11	158135	broad.mit.edu	37	9	124765910	124765910	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124765910delC	uc004blt.1	-						TTLL11_uc011lyl.1_Intron|TTLL11_uc004blr.2_Intron|TTLL11_uc011lym.1_Intron|TTLL11_uc004blu.1_Intron	NM_194252	NP_919228	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0						attacaggcacctgccaccac	0.000													4	2	---	---	---	---	
OR1J2	26740	broad.mit.edu	37	9	125260340	125260340	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125260340delT	uc004bmj.1	+							NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5						atgatttgggttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126852076	126852079	+	IGR	DEL	TTTT	-	-	rs71896698		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126852076_126852079delTTTT								LHX2 (56634 upstream) : NEK6 (167807 downstream)																							Atttcttttctttttttttttttt	0.132													2	4	---	---	---	---	
NUP188	23511	broad.mit.edu	37	9	131707778	131707778	+	5'Flank	DEL	A	-	-	rs112403860		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131707778delA	uc004bws.1	+						NUP188_uc004bwq.1_Intron	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7						aaaaaaaaataaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133436822	133436822	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133436822delT								ASS1 (60162 upstream) : LOC100272217 (15917 downstream)																							AAATTTGGGCttttttttttc	0.189													4	2	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136780791	136780792	+	Intron	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136780791_136780792delCA	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		cgcacacatgcacacacacaca	0.035													4	2	---	---	---	---	
EXD3	54932	broad.mit.edu	37	9	140225055	140225056	+	Intron	INS	-	G	G	rs139044502	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140225055_140225056insG	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0						actacacaggactacacaggac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	141075588	141075588	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141075588delA								TUBBP5 (3704 upstream) : FAM157B (31049 downstream)																							GTCACTGTGTAAAGGTCAGAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103592	103592	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103592delG								TUBB8 (8088 upstream) : ZMYND11 (76832 downstream)																							ccaggatgcagggagccatgt	0.000													4	2	---	---	---	---	
C10orf110	55853	broad.mit.edu	37	10	1089534	1089534	+	Frame_Shift_Del	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1089534delA	uc001ifw.3	+	4	481	c.479delA	c.(478-480)GAAfs	p.E160fs	C10orf110_uc010qaf.1_RNA|C10orf110_uc001ifx.3_RNA|C10orf110_uc001ify.3_RNA|IDI1_uc001ifz.2_Intron|IDI1_uc001iga.2_Intron|IDI1_uc001igb.2_Intron|IDI1_uc001igc.2_Intron	NR_024628				Homo sapiens uncharacterized hypothalamus protein HT009 mRNA, complete cds.												0						CGAGTGAAGGAAATGGTGATG	0.517													4	2	---	---	---	---	
PFKP	5214	broad.mit.edu	37	10	3142248	3142249	+	Intron	INS	-	GT	GT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3142248_3142249insGT	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet						glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		gtaggtgtgtggtgtgtgtgtg	0.183													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12500458	12500459	+	Intron	INS	-	A	A	rs140250784	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12500458_12500459insA	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		cactgtcacccaggctggagtg	0.099													1	6	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12517764	12517765	+	Intron	INS	-	TAGA	TAGA	rs142517304	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12517764_12517765insTAGA	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		GCATATGATGTTAGAGATGGAC	0.436													4	3	---	---	---	---	
LOC283070	283070	broad.mit.edu	37	10	12872926	12872927	+	5'Flank	DEL	AC	-	-	rs71862980		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12872926_12872927delAC	uc001ilp.3	+							NR_027322				Homo sapiens cDNA FLJ40058 fis, clone TCOLN1000180.												0						CTCTCAATAAacacacacacac	0.396													4	4	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14600193	14600196	+	Intron	DEL	CACT	-	-	rs80227155		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14600193_14600196delCACT	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						TGTGTGcacacactcacgtgcacg	0.255													4	2	---	---	---	---	
ARL5B	221079	broad.mit.edu	37	10	18958845	18958845	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18958845delC	uc001iqd.1	+							NM_178815	NP_848930	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 8						small GTPase mediated signal transduction	intracellular	GTP binding			ovary(1)	1						atcgcttgaacccaggaggca	0.000													3	3	---	---	---	---	
WAC	51322	broad.mit.edu	37	10	28850426	28850427	+	Intron	INS	-	T	T	rs150546717	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28850426_28850427insT	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712	Q9BTA9	WAC_HUMAN	WW domain-containing adapter with a coiled-coil						cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2						ACTTTTAAATGTTTTTTTTTTA	0.282													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30036294	30036305	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs72192564		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30036294_30036305delTGTGTGTGTGTG								SVIL (10430 upstream) : KIAA1462 (265424 downstream)																							TTAGAGCTTTtgtgtgtgtgtgtgtgtgtgtg	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37244411	37244411	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37244411delA								None (None upstream) : ANKRD30A (170374 downstream)																							ATTAATTACTAAGAAAGGTAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37922637	37922638	+	IGR	INS	-	T	T	rs113236347		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37922637_37922638insT								ANKRD30A (401142 upstream) : ZNF248 (167809 downstream)																							GTGAGATGCAAttttttttttt	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38779690	38779694	+	IGR	DEL	GGAAC	-	-	rs145176661	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38779690_38779694delGGAAC								LOC399744 (38610 upstream) : None (None downstream)																							ggacaagaatggaacggaatggaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42657263	42657264	+	IGR	INS	-	A	A	rs143591854	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42657263_42657264insA								None (None upstream) : LOC441666 (170051 downstream)																							ctaccatgtctggttatatggt	0.000													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47036053	47036054	+	Intron	INS	-	CA	CA	rs138001329		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47036053_47036054insCA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						acatatatattcacacacacac	0.129													4	4	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55888295	55888295	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55888295delA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				GTTTTGTGTGAATTTCTTTGG	0.338										HNSCC(58;0.16)			4	2	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65173746	65173746	+	Intron	DEL	T	-	-	rs71891266		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65173746delT	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTATCAATACttttttttttt	0.144													4	2	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65202608	65202608	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65202608delT	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					AAGTATTGAGTTTTTTTTCct	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67149135	67149135	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67149135delC								ANXA2P3 (562501 upstream) : CTNNA3 (530590 downstream)																							GAGGGAGAGTCCCAAAGACCT	0.323													4	2	---	---	---	---	
CCDC109A	90550	broad.mit.edu	37	10	74485325	74485325	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74485325delG	uc001jtc.2	+						CCDC109A_uc009xqp.1_Intron|CCDC109A_uc009xqq.1_Intron|CCDC109A_uc010qjy.1_Intron|CCDC109A_uc009xqr.2_Intron|CCDC109A_uc001jtd.2_Intron	NM_138357	NP_612366	Q8NE86	MCU_HUMAN	coiled-coil domain containing 109A						elevation of mitochondrial calcium ion concentration|mitochondrial calcium ion transport|protein complex oligomerization	integral to membrane|mitochondrial inner membrane	protein binding				0	Prostate(51;0.0198)					gagccattgtgcctggcTCAT	0.020													4	2	---	---	---	---	
ANXA11	311	broad.mit.edu	37	10	81928846	81928847	+	Frame_Shift_Ins	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81928846_81928847insG	uc001kbq.1	-	6	1264_1265	c.439_440insC	c.(439-441)CAGfs	p.Q147fs	ANXA11_uc010qlx.1_Frame_Shift_Ins_p.Q247fs|ANXA11_uc001kbr.1_Frame_Shift_Ins_p.Q147fs|ANXA11_uc001kbs.1_Frame_Shift_Ins_p.Q147fs|ANXA11_uc001kbt.1_Frame_Shift_Ins_p.Q147fs|ANXA11_uc010qly.1_Frame_Shift_Ins_p.Q114fs|ANXA11_uc009xsq.1_Frame_Shift_Ins_p.Q147fs|ANXA11_uc001kbu.1_Frame_Shift_Ins_p.Q147fs	NM_145869	NP_665876	P50995	ANX11_HUMAN	annexin A11	147					cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			CACTGGTGGCTGCCCAGGGTAG	0.698													4	2	---	---	---	---	
GRID1	2894	broad.mit.edu	37	10	88041903	88041903	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88041903delG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	catggctactggaagaatgaa	0.109										Multiple Myeloma(13;0.14)			4	3	---	---	---	---	
IFIT1	3434	broad.mit.edu	37	10	91159622	91159623	+	Intron	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91159622_91159623delCT	uc001kgi.2	+						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|IFIT1_uc009xtt.2_Intron|IFIT1_uc001kgj.2_5'UTR	NM_001548	NP_001539	P09914	IFIT1_HUMAN	interferon-induced protein with						cellular response to exogenous dsRNA|intracellular transport of viral proteins in host cell|negative regulation of defense response to virus by host|negative regulation of helicase activity|negative regulation of protein binding|negative regulation of viral genome replication|positive regulation of viral genome replication|response to virus|type I interferon-mediated signaling pathway	cytoplasm	protein binding				0						ccaaagctcactctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	114021491	114021492	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114021491_114021492delCA								GPAM (77966 upstream) : TECTB (22001 downstream)																							GACCAACAGGCACACACAGAAG	0.243													4	2	---	---	---	---	
ABLIM1	3983	broad.mit.edu	37	10	116275728	116275728	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116275728delT	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc010qsf.1_Intron|ABLIM1_uc009xyn.2_Intron|ABLIM1_uc010qsj.1_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		taaatttgtcttttttaaaac	0.025													4	2	---	---	---	---	
ATE1	11101	broad.mit.edu	37	10	123674025	123674025	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123674025delA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				ccaacagtggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
LHPP	64077	broad.mit.edu	37	10	126210438	126210439	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126210438_126210439delAC	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron	NM_022126	NP_071409	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		acttacacgtacacacacacac	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126979745	126979745	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126979745delA								CTBP2 (130121 upstream) : LOC100169752 (283195 downstream)																							ctcatcccttaaaaaaaaaaa	0.199													4	3	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127596210	127596212	+	Intron	DEL	GAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127596210_127596212delGAG	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				gggaagaggagaggaggaggagg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129642816	129642817	+	IGR	INS	-	CA	CA	rs144680297	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129642816_129642817insCA								FOXI2 (103366 upstream) : CLRN3 (33297 downstream)																							CATGGTacacgcacacacacac	0.480													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130174408	130174408	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130174408delG								MKI67 (249940 upstream) : None (None downstream)																							CTGCAAATTTGGGTCAGAGAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	131108985	131108985	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131108985delT								None (None upstream) : MGMT (156469 downstream)																							GTTGCCTCCATTTTTTTTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133551413	133551413	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133551413delT								TCERG1L (441429 upstream) : PPP2R2D (196547 downstream)																							attgagatgattttatggctt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133652239	133652242	+	IGR	DEL	AGTT	-	-	rs71217072		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133652239_133652242delAGTT								TCERG1L (542255 upstream) : PPP2R2D (95718 downstream)																							actgtactggagttagttaggcaa	0.132													4	2	---	---	---	---	
INPP5A	3632	broad.mit.edu	37	10	134434994	134434994	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134434994delA	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		tttgttctggaaaggtggtac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134791779	134791779	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134791779delT								C10orf93 (35715 upstream) : GPR123 (92654 downstream)																							GGGCAGGATatcaaaagaggc	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134825215	134825216	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134825215_134825216delAG								C10orf93 (69151 upstream) : GPR123 (59217 downstream)																							gatgtgtgttagtgtgtgatgt	0.035													5	3	---	---	---	---	
MIR202	574448	broad.mit.edu	37	10	135063800	135063801	+	5'Flank	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135063800_135063801delAG	hsa-mir-202|MI0003130	-						uc009ybh.1_5'Flank																	0						agacagagtcagagagagagag	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135446925	135446926	+	IGR	INS	-	C	C	rs140691302	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135446925_135446926insC								FRG2B (6626 upstream) : LOC653544 (43353 downstream)																							TCTTTATCCCTTCATCTGTCGA	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	2044733	2044733	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2044733delC								H19 (25668 upstream) : IGF2 (105615 downstream)																							AAGTGGCTCTCCCTGCACTGT	0.632													1	5	---	---	---	---	
AMPD3	272	broad.mit.edu	37	11	10472493	10472493	+	5'UTR	DEL	C	-	-	rs76111890		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10472493delC	uc001min.1	+	1					AMPD3_uc010rbz.1_Intron|AMPD3_uc009yfw.1_RNA|AMPD3_uc009yfx.1_Intron	NM_000480	NP_000471	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3 isoform 1A						AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GGCCTCAGTGCCCAGCAGCCC	0.537													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15614654	15614655	+	IGR	DEL	CT	-	-	rs147863986		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15614654_15614655delCT								INSC (345902 upstream) : SOX6 (373341 downstream)																							ggaaaacagactctgctcactc	0.084													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25256614	25256615	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25256614_25256615delGT								LUZP2 (152432 upstream) : ANO3 (954214 downstream)																							TAAGTTAGAAgtgtgtgtgtgt	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	27222684	27222685	+	IGR	INS	-	AG	AG	rs143037665	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27222684_27222685insAG								BBOX1 (73330 upstream) : CCDC34 (137376 downstream)																							actccccaaacaattcattttc	0.000													2	4	---	---	---	---	
ELP4	26610	broad.mit.edu	37	11	31792385	31792385	+	Intron	DEL	A	-	-	rs112436797		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31792385delA	uc001mtb.2	+						ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)					GTCaaaaaagaaaaaaaaaaa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44517926	44517926	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44517926delC								ALX4 (186210 upstream) : CD82 (69215 downstream)																							cttccattgtcacatttcctc	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45581940	45581940	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45581940delC								SYT13 (274056 upstream) : CHST1 (88487 downstream)																							GTCTCTCCTGCCCAAACCCCT	0.612													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47216442	47216442	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47216442delA								PACSIN3 (8484 upstream) : DDB2 (20051 downstream)																							TGTTTGAAGGAAAAAAAAAAG	0.383													3	3	---	---	---	---	
KBTBD4	55709	broad.mit.edu	37	11	47597411	47597412	+	Intron	INS	-	T	T	rs35653820		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47597411_47597412insT	uc001nfx.2	-						NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Intron|KBTBD4_uc001nfz.2_Intron|KBTBD4_uc001nfy.2_Intron	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4											ovary(1)|central_nervous_system(1)	2						CCTAAAATTGCttttttttttt	0.173													3	3	---	---	---	---	
FAM180B	399888	broad.mit.edu	37	11	47606231	47606232	+	5'Flank	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47606231_47606232insT	uc001ngb.1	+									Q6P0A1	F180B_HUMAN	RecName: Full=Protein FAM180B;							integral to membrane					0						TCTTTGATGGGttttttttttt	0.267													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48356195	48356196	+	IGR	INS	-	A	A	rs66848134		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48356195_48356196insA								OR4C3 (8715 upstream) : OR4C45 (10706 downstream)																							tttagctacttaccttgaacac	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48359344	48359345	+	IGR	INS	-	C	C	rs151275604	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48359344_48359345insC								OR4C3 (11864 upstream) : OR4C45 (7557 downstream)																							atggtctcttttctttctgggc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48391950	48391950	+	IGR	DEL	T	-	-	rs72314732		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48391950delT								OR4C45 (17951 upstream) : OR4A47 (118395 downstream)																							AATTACTGACttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48850450	48850451	+	IGR	INS	-	A	A	rs140754283		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48850450_48850451insA								OR4A47 (339178 upstream) : FOLH1 (317737 downstream)																							gaatctgcaatggatatttgga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56638341	56638342	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56638341_56638342insA	uc001nji.1	+						uc001njj.1_Intron					Homo sapiens cDNA FLJ34816 fis, clone NT2NE2007877.																		ctttgtctcacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
ASRGL1	80150	broad.mit.edu	37	11	62136056	62136056	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62136056delG	uc001nte.3	+						ASRGL1_uc001ntf.3_Intron|ASRGL1_uc001ntg.3_Intron|ASRGL1_uc001nth.1_Intron	NM_025080	NP_079356	Q7L266	ASGL1_HUMAN	asparaginase-like 1						asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	acaaagtatagaagaaaagtg	0.005													4	2	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63907435	63907436	+	Intron	INS	-	A	A	rs146344788	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63907435_63907436insA	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						ctcaaaaaaagaaaaaaaaaag	0.262													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64752658	64752658	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64752658delT								C11orf85 (13101 upstream) : BATF2 (2759 downstream)																							gtgctttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67629556	67629557	+	IGR	INS	-	A	A	rs149124986	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67629556_67629557insA								LOC645332 (56749 upstream) : UNC93B1 (129018 downstream)																							aactccgtctcaaaaaaaagaa	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69406007	69406008	+	IGR	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69406007_69406008insG								MYEOV (249558 upstream) : CCND1 (49865 downstream)																							ACACTTAGGAAGGGGAAAAGAA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69860652	69860654	+	IGR	DEL	GCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69860652_69860654delGCT								FGF3 (226460 upstream) : ANO1 (63754 downstream)																							gcctgcccaggctgctgctgctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70286249	70286249	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70286249delT								CTTN (3560 upstream) : SHANK2 (27713 downstream)																							gcctggctaattttttttttt	0.000													4	2	---	---	---	---	
KRTAP5-7	440050	broad.mit.edu	37	11	71237233	71237235	+	5'Flank	DEL	TGG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71237233_71237235delTGG	uc001oqq.1	+							NM_001012503	NP_001012521	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7							keratin filament					0						cagacatgcatggggtctgtagc	0.000													4	2	---	---	---	---	
C11orf30	56946	broad.mit.edu	37	11	76246874	76246875	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76246874_76246875insT	uc001oxl.2	+						C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron|C11orf30_uc001oxo.1_Intron|C11orf30_uc010rse.1_Intron	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6						AAAATTGTTTGTTTTTTTTTTT	0.312													4	3	---	---	---	---	
PAK1	5058	broad.mit.edu	37	11	77116720	77116721	+	Intron	DEL	AC	-	-	rs72497267		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77116720_77116721delAC	uc001oyh.3	-						PAK1_uc010rso.1_Intron|PAK1_uc001oyg.3_Intron|PAK1_uc001oyi.1_Intron	NM_002576	NP_002567	Q13153	PAK1_HUMAN	p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)					agacagacagacacacacacac	0.099													4	4	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83322337	83322338	+	Intron	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83322337_83322338delGA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ggggaagggggagagagagaga	0.252													4	2	---	---	---	---	
CCDC83	220047	broad.mit.edu	37	11	85612685	85612685	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85612685delA	uc001pbh.1	+						CCDC83_uc001pbg.1_Intron|CCDC83_uc001pbi.1_Intron|CCDC83_uc001pbj.1_Intron	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83											skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				accacaatacaaaaaaaaaaa	0.035													4	2	---	---	---	---	
NOX4	50507	broad.mit.edu	37	11	89177693	89177694	+	Intron	DEL	AC	-	-	rs146012925		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89177693_89177694delAC	uc001pct.2	-						NOX4_uc009yvr.2_Intron|NOX4_uc001pcu.2_Intron|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_Intron|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Intron|NOX4_uc009yvs.1_Intron	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				taacacacatacacacacacac	0.198													4	2	---	---	---	---	
CCDC67	159989	broad.mit.edu	37	11	93126173	93126173	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93126173delC	uc001pdq.2	+						CCDC67_uc001pdo.1_Intron|CCDC67_uc001pdp.2_Intron	NM_181645	NP_857596	Q05D60	CCD67_HUMAN	coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				ccttctttctcctcctcctcc	0.010													4	2	---	---	---	---	
MTMR2	8898	broad.mit.edu	37	11	95639058	95639059	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95639058_95639059insA	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240	Q13614	MTMR2_HUMAN	myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				aaatggaaaacaaaaaaaaaaa	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	98551636	98551636	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98551636delG								None (None upstream) : CNTN5 (340235 downstream)																							tttgttttttgtttgagatgg	0.000													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99024547	99024547	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99024547delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		tttgaatggcttttttttttt	0.000													6	3	---	---	---	---	
YAP1	10413	broad.mit.edu	37	11	102073616	102073616	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102073616delA	uc001pgt.2	+						YAP1_uc001pgs.2_Intron|YAP1_uc001pgu.2_Intron|YAP1_uc001pgv.2_Intron|YAP1_uc010ruo.1_Intron|YAP1_uc001pgw.2_Intron|YAP1_uc010rup.1_Intron	NM_001130145	NP_001123617	P46937	YAP1_HUMAN	Yes-associated protein 1, 65kDa isoform 1						cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		tattcttgccaaaaattgtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107646341	107646341	+	IGR	DEL	A	-	-	rs75714997		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107646341delA								SLN (63554 upstream) : SLC35F2 (15379 downstream)																							tctgtctcagaaaaaaaaaaa	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109427512	109427512	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109427512delG								C11orf87 (127674 upstream) : ZC3H12C (536414 downstream)																							accaaacaccgcatgttctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111317350	111317351	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111317350_111317351delAC								POU2AF1 (67193 upstream) : BTG4 (20907 downstream)																							ACACCAATAAacacacacacac	0.302											OREG0021327	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FAM55A	120400	broad.mit.edu	37	11	114422372	114422373	+	Intron	INS	-	TGTT	TGTT	rs141660305		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114422372_114422373insTGTT	uc001ppa.2	-						FAM55A_uc001ppb.1_Intron	NM_152315	NP_689528	Q8N323	FA55A_HUMAN	hypothetical protein LOC120400							extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)		AAAGCCAGTCCTGTTAACTGGG	0.416													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114982831	114982831	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114982831delT								FAM55B (405179 upstream) : CADM1 (57122 downstream)																							GACATTGAGATTTTTTTTTTA	0.204													3	3	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116942642	116942643	+	Intron	INS	-	TGTT	TGTT	rs146385703	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116942642_116942643insTGTT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|uc001pqc.2_5'Flank	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						gccAAGAGTTGTGTTTGTTTGT	0.168											OREG0003482	type=REGULATORY REGION|Gene=BC042385|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119693903	119693930	+	IGR	DEL	GCACGTGTGTGCGTGCACATGTGTGTGC	-	-	rs490489	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119693903_119693930delGCACGTGTGTGCGTGCACATGTGTGTGC								PVRL1 (94468 upstream) : TRIM29 (288065 downstream)																							gtgtgtgcgtgcacgtgtgtgcgtgcacatgtgtgtgcgcacgtgtgt	0.184													4	2	---	---	---	---	
ROBO3	64221	broad.mit.edu	37	11	124734461	124734461	+	5'Flank	DEL	C	-	-	rs5795434		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124734461delC	uc001qbc.2	+							NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3						axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TTTCTTTTCGCCCCCCCCAGG	0.468													1	5	---	---	---	---	
ROBO4	54538	broad.mit.edu	37	11	124767607	124767607	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124767607delG	uc001qbg.2	-						ROBO4_uc010sas.1_Intron|ROBO4_uc001qbh.2_Intron|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout						angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGCCAGGAGAGGGAGAGCAAC	0.632													6	15	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126422767	126422767	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126422767delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		caagaaaagctttttttttta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127748821	127748821	+	IGR	DEL	C	-	-	rs79423023		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127748821delC								KIRREL3 (875466 upstream) : ETS1 (579835 downstream)																							ACCAAGtattcctttatctca	0.055													2	4	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131371773	131371774	+	Intron	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131371773_131371774delGT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						gtgtgtgtgagtgtgtgtgtgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	2877580	2877580	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2877580delC								CACNA1C (70465 upstream) : FKBP4 (26528 downstream)																							gtgaacccctcgaagccaggT	0.040													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4041207	4041208	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4041207_4041208insT								PARP11 (58599 upstream) : CCND2 (341694 downstream)																							TCCCCCCAAGATTTTTTTTTTA	0.455													4	2	---	---	---	---	
FAM66C	440078	broad.mit.edu	37	12	8357154	8357155	+	Intron	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8357154_8357155delCT	uc001qug.3	+											Homo sapiens cDNA FLJ38982 fis, clone NT2RI2005239.												0						CCCCCCTTCACTCTCTTTTCTC	0.505													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	9212825	9212825	+	5'Flank	DEL	A	-	-	rs35963762		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9212825delA	uc009zgh.1	-						uc009zgi.1_Intron					Homo sapiens cDNA FLJ41814 fis, clone NT2RI2011683.																		tcattgtgttagccaggatgg	0.030													1	5	---	---	---	---	
A2M	2	broad.mit.edu	37	12	9260471	9260471	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9260471delT	uc001qvk.1	-						A2M_uc009zgk.1_Intron	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor						blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	TTTTTCCTCGTTTTTTTTTAG	0.239													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11171384	11171384	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11171384delG	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						tgaggtctaaggggaacccct	0.000										HNSCC(22;0.051)			4	4	---	---	---	---	
LOH12CR1	118426	broad.mit.edu	37	12	12611512	12611513	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12611512_12611513insT	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron	NM_058169	NP_477517	Q969J3	L12R1_HUMAN	LOH1CR12											ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		Cttttctttccttttttttttt	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14413856	14413856	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14413856delG								GRIN2B (280834 upstream) : ATF7IP (104755 downstream)																							GCGCATTGAAGGTTGTCCCTT	0.532													4	2	---	---	---	---	
RERG	85004	broad.mit.edu	37	12	15264621	15264621	+	Intron	DEL	T	-	-	rs66885563		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15264621delT	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1						TATACtttccttttttttttt	0.209													4	2	---	---	---	---	
PTPRO	5800	broad.mit.edu	37	12	15511578	15511578	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15511578delA	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcu.1_Intron	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				tgaagtgtccaagatctcaca	0.119													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24377478	24377479	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24377478_24377479delTG	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TGAGGAtgtatgtgtgtgtgtg	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25968246	25968246	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25968246delG								IFLTD1 (166758 upstream) : RASSF8 (143723 downstream)																							tctccagcctgaggacttttc	0.020													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29537949	29537950	+	IGR	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29537949_29537950delCT								ERGIC2 (3806 upstream) : OVCH1 (42539 downstream)																							catggctttcctctctgtcgac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30058624	30058625	+	IGR	INS	-	C	C	rs142083794	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30058624_30058625insC								TMTC1 (120932 upstream) : IPO8 (723298 downstream)																							cccattgccttccccttcTTTT	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32165482	32165482	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32165482delG								C12orf35 (19451 upstream) : BICD1 (94703 downstream)																							ttgttgtcccggttttccttc	0.000													4	2	---	---	---	---	
FGD4	121512	broad.mit.edu	37	12	32786157	32786157	+	Intron	DEL	G	-	-	rs150951121		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32786157delG	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rlb.1_Intron	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					gttgggaggAGGGGGTGGGAT	0.239													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38033626	38033626	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38033626delT								None (None upstream) : ALG10B (676931 downstream)																							tgtgaagatattcccgtatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38039250	38039250	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38039250delT								None (None upstream) : ALG10B (671307 downstream)																							acataaaagctagagagaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38738288	38738288	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38738288delT								ALG10B (14761 upstream) : CPNE8 (307714 downstream)																							ccctatgtacttataacttgt	0.000													4	2	---	---	---	---	
CPNE8	144402	broad.mit.edu	37	12	39279675	39279676	+	Intron	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39279675_39279676delTC	uc001rls.1	-							NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				acttcccccttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	41537114	41537115	+	IGR	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41537114_41537115delGA								CNTN1 (73020 upstream) : PDZRN4 (45672 downstream)																							gtattggaatgagaaggatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45542029	45542030	+	IGR	INS	-	GAAT	GAAT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45542029_45542030insGAAT								RACGAP1P (82835 upstream) : PLEKHA9 (24817 downstream)																							TCACTGTGAAGGAATACACTAT	0.401													3	5	---	---	---	---	
DDX23	9416	broad.mit.edu	37	12	49238093	49238094	+	Intron	INS	-	CT	CT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49238093_49238094insCT	uc001rsm.2	-							NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6						atggagtctcactctcacgccc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	49267841	49267841	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49267841delA								RND1 (8188 upstream) : CCDC65 (30052 downstream)																							TTCTCAAACTAAAAAAAAATT	0.234													4	2	---	---	---	---	
ANKRD33	341405	broad.mit.edu	37	12	52279202	52279202	+	5'Flank	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52279202delC	uc001rzf.3	+						ANKRD33_uc001rzh.3_5'Flank|ANKRD33_uc001rzd.2_5'Flank|ANKRD33_uc001rze.2_5'Flank|ANKRD33_uc001rzg.3_5'Flank|ANKRD33_uc001rzi.3_5'Flank	NM_001130015	NP_001123487	Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33 isoform 1												0				BRCA - Breast invasive adenocarcinoma(357;0.0969)		tcccattttgcTGTGATGGCT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52501561	52501562	+	RNA	INS	-	T	T	rs145272216	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52501561_52501562insT	uc009zme.1	+	3		c.960_961insT								Homo sapiens olfactory receptor, family 7, subfamily E, member 47 pseudogene, mRNA (cDNA clone IMAGE:5590288).																		GTTTTGCTGTCTTTTTTTTTTC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53049516	53049516	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53049516delT								KRT2 (3557 upstream) : KRT1 (19004 downstream)																							TCCTTTTCAGTTTTTTTTTTT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53392098	53392099	+	IGR	INS	-	T	T	rs142512409		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53392098_53392099insT								KRT18 (45414 upstream) : EIF4B (7963 downstream)																							ctaaccagatcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53742559	53742574	+	IGR	DEL	ACACACACACACACAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53742559_53742574delACACACACACACACAC								SP7 (12393 upstream) : SP1 (31405 downstream)																							tccgtctcaaacacacacacacacacacacacacac	0.074													2	4	---	---	---	---	
NCKAP1L	3071	broad.mit.edu	37	12	54909417	54909417	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54909417delA	uc001sgc.3	+						NCKAP1L_uc010sox.1_Intron|NCKAP1L_uc010soy.1_Intron	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like						actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4						GTGGTGTGGGAAAATAAGCAG	0.448													4	2	---	---	---	---	
PDE1B	5153	broad.mit.edu	37	12	54967640	54967641	+	Intron	INS	-	GAGAGAGAGA	GAGAGAGAGA	rs142403478	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54967640_54967641insGAGAGAGAGA	uc001sgd.1	+						PDE1B_uc010soz.1_Intron|PDE1B_uc010spa.1_Intron|PDE1B_uc001sgf.2_Intron|PDE1B_uc001sge.2_Intron|PDE1B_uc009znq.2_Intron	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1						activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						CATCTCTATGTGAGAGAGAGAG	0.342													5	3	---	---	---	---	
PRIM1	5557	broad.mit.edu	37	12	57126642	57126643	+	Intron	INS	-	T	T	rs62773961		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57126642_57126643insT	uc001smd.2	-							NM_000946	NP_000937	P49642	PRI1_HUMAN	DNA primase polypeptide 1						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	DNA primase activity|metal ion binding				0						GGGATTAGAAAttttttttttt	0.183													4	2	---	---	---	---	
LRP1	4035	broad.mit.edu	37	12	57547694	57547695	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57547694_57547695insA	uc001snd.2	+						LRP1_uc001snc.1_Intron	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1						aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	aaAGCAAAGTTAAAAAAAAAAA	0.233													3	3	---	---	---	---	
GNS	2799	broad.mit.edu	37	12	65130628	65130629	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65130628_65130629insA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		GGAAGTTAAGGAAAAAAAAAAG	0.381													5	3	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	67121245	67121246	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67121245_67121246delAG	uc010sta.1	-							NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		ggttgcagaaagagagacccat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68143730	68143730	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68143730delC								DYRK2 (87287 upstream) : IFNG (404820 downstream)																							tggcttccttcattctccagc	0.000													4	2	---	---	---	---	
YEATS4	8089	broad.mit.edu	37	12	69766666	69766666	+	Intron	DEL	T	-	-	rs141462665		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69766666delT	uc001sux.2	+							NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41						histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			atatataatgttttatctttc	0.000													3	4	---	---	---	---	
PTPRR	5801	broad.mit.edu	37	12	71238005	71238005	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71238005delT	uc001swi.1	-							NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		tctcactccattttaaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76419127	76419128	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76419127_76419128insT								KRR1 (513709 upstream) : PHLDA1 (100 downstream)																							CAAAAATGGTCTTTTTTTTTCC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77607226	77607227	+	IGR	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77607226_77607227delCT								E2F7 (147866 upstream) : NAV3 (617842 downstream)																							TTTTTCTTGACTCTAATATAAT	0.426													2	5	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86230254	86230254	+	5'UTR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86230254delA	uc001taf.1	-	1						NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						GCAGGAAAAGAAAAAAAAAAA	0.468													4	2	---	---	---	---	
PLEKHG7	440107	broad.mit.edu	37	12	93155336	93155339	+	Intron	DEL	GAAG	-	-	rs117312592	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93155336_93155339delGAAG	uc001tcj.2	+							NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						aagaaagaaagaaggaaggaagga	0.162													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93737318	93737319	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93737318_93737319delCA								EEA1 (414211 upstream) : NUDT4 (34382 downstream)																							cttctatgAGcacacacacaca	0.134													3	4	---	---	---	---	
NEDD1	121441	broad.mit.edu	37	12	97317128	97317129	+	Intron	DEL	AT	-	-	rs142167666		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97317128_97317129delAT	uc001teu.3	+						NEDD1_uc001tev.3_Intron|NEDD1_uc010svc.1_Intron|NEDD1_uc001tew.2_Intron|NEDD1_uc001tex.2_Intron	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally						cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						tttaagatacatgtttttattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97409795	97409796	+	IGR	INS	-	AACC	AACC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97409795_97409796insAACC								NEDD1 (62334 upstream) : RMST (449003 downstream)																							ctgtctcaaaaaaccaaccaac	0.000													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100008953	100008956	+	Intron	DEL	ACAG	-	-	rs35569353		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100008953_100008956delACAG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		gatagATTACacagacagacagac	0.181													4	2	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103695744	103695744	+	3'UTR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103695744delT	uc001tjt.2	-	6					C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_3'UTR|C12orf42_uc001tju.2_3'UTR	NM_198521	NP_940923	Q96LP6	CL042_HUMAN	hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2						ACTTTTGACATTATTTATTAG	0.398													4	2	---	---	---	---	
C12orf76	400073	broad.mit.edu	37	12	110482784	110482784	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110482784delA	uc001tqd.1	-						C12orf76_uc001tqe.1_Intron|C12orf76_uc010sxx.1_Intron|C12orf76_uc001tqb.1_Intron|C12orf76_uc001tqc.1_Intron	NM_207435	NP_997318	Q8N812	CL076_HUMAN	hypothetical protein LOC400073											large_intestine(1)	1						gtctcaaaataaaaaaaaaga	0.174													4	2	---	---	---	---	
ARPC3	10094	broad.mit.edu	37	12	110883965	110883965	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110883965delT	uc001tqq.2	-							NM_005719	NP_005710	O15145	ARPC3_HUMAN	actin related protein 2/3 complex subunit 3						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton			ovary(1)	1						tcatcacttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112054761	112054761	+	IGR	DEL	A	-	-	rs72159975		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112054761delA								ATXN2 (17281 upstream) : BRAP (25190 downstream)																							agactccgttaaaaaaaaaaa	0.000													2	4	---	---	---	---	
NAA25	80018	broad.mit.edu	37	12	112534292	112534293	+	Intron	INS	-	ACTT	ACTT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112534292_112534293insACTT	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GAGTTCAATGCACTTAATGCAC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114235313	114235313	+	IGR	DEL	T	-	-	rs61120592		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114235313delT								LHX5 (325436 upstream) : RBM19 (19230 downstream)																							TCTCCCTCCCTGCTCCGGCCC	0.398													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114532445	114532446	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114532445_114532446insA								RBM19 (128269 upstream) : TBX5 (259290 downstream)																							tactcaaatccaaaaaaacctg	0.050													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	118335727	118335728	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118335727_118335728delTG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACACACCGTCTGTGTGTGTGTC	0.450													4	2	---	---	---	---	
SUDS3	64426	broad.mit.edu	37	12	118819850	118819850	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118819850delT	uc001twz.2	+							NM_022491	NP_071936	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3						chromatin modification|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	Sin3 complex	histone deacetylase binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GATGGATTACttttttttttt	0.204													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119462924	119462925	+	Intron	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119462924_119462925delGT	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						gtgcattagggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119471761	119471761	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119471761delT	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						CCTTCTGGTGTTTTTGCTTAA	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	121116643	121116643	+	IGR	DEL	G	-	-	rs11320521		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121116643delG								CABP1 (11518 upstream) : MLEC (8306 downstream)																							gggatgctgaggggggggcag	0.100													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	121503400	121503400	+	IGR	DEL	T	-	-	rs35252699		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121503400delT								OASL (26620 upstream) : P2RX7 (67278 downstream)																							aacgtaattcttttttttttt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	122040183	122040190	+	IGR	DEL	TTGTTTGT	-	-	rs34976454		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122040183_122040190delTTGTTTGT								KDM2B (21263 upstream) : ORAI1 (24265 downstream)																							tttgtgatggttgtttgtttgtttgttt	0.067													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125525874	125525874	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125525874delT								BRI3BP (15525 upstream) : AACS (24051 downstream)																							agtgctgggattacaggtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125783861	125783861	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125783861delT								AACS (155989 upstream) : TMEM132B (27301 downstream)																							ccctgggccctgggactcatc	0.000													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129686558	129686558	+	Intron	DEL	A	-	-	rs62931261		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129686558delA	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGCCTTCTTGAAAAAAAAAAT	0.398													4	2	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	131088483	131088484	+	Intron	INS	-	AAT	AAT	rs140537809	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131088483_131088484insAAT	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)		cctacttataaaataactgtag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132339886	132339887	+	IGR	DEL	CA	-	-	rs67954174		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132339886_132339887delCA								MMP17 (3570 upstream) : ULK1 (39392 downstream)																							cacacacacgcacacacacaca	0.238													6	3	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133374766	133374766	+	Intron	DEL	G	-	-	rs33920278		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133374766delG	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GATGAGGGGTGGGGGGGGGGT	0.567													4	2	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24589887	24589888	+	Intron	DEL	CA	-	-	rs140755270	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24589887_24589888delCA	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron|uc001upc.2_Intron	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GGCCCCCCCCCAATTCCTAGGT	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29313751	29313751	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29313751delT								SLC46A3 (20601 upstream) : MTUS2 (284997 downstream)																							atctctacaattttttttttt	0.000													3	3	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48954160	48954160	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48954160delT	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AAACAACTTCTTTTTTTTTTT	0.129		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	49501592	49501592	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49501592delT								CYSLTR2 (218094 upstream) : FNDC3A (48456 downstream)																							ttctttggccttttggctctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	50392224	50392224	+	IGR	DEL	T	-	-	rs142198737		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50392224delT								KPNA3 (25167 upstream) : LOC220429 (72321 downstream)																							tttgcagttcttttttttttt	0.000													3	3	---	---	---	---	
DHRS12	79758	broad.mit.edu	37	13	52343500	52343501	+	Intron	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52343500_52343501delAA	uc001vfq.2	-						DHRS12_uc001vfr.1_Intron			A0PJE2	DHR12_HUMAN	RecName: Full=Dehydrogenase/reductase SDR family member 12;          EC=1.1.-.-;								binding|oxidoreductase activity				0		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		CCCttaatttaaaaaaaaaaaa	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59273558	59273558	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59273558delG								PCDH17 (970493 upstream) : DIAPH3 (966167 downstream)																							acaggaccaagggaatggtgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60198245	60198246	+	IGR	INS	-	T	T	rs142596136	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60198245_60198246insT								None (None upstream) : DIAPH3 (41479 downstream)																							AAAGAAACTGATTTTTTTTttc	0.163													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74245500	74245501	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74245500_74245501insT								KLF5 (593825 upstream) : KLF12 (14649 downstream)																							TAGGATTACAGTTTTTTTTTTC	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75732844	75732845	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75732844_75732845insA								None (None upstream) : LOC647288 (79045 downstream)																							acaagtatatgaaaaaaaattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77312482	77312483	+	IGR	INS	-	T	T	rs141155743		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77312482_77312483insT								LMO7 (878478 upstream) : KCTD12 (141821 downstream)																							cttcattttcattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77392314	77392314	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77392314delT								LMO7 (958310 upstream) : KCTD12 (61990 downstream)																							AACAATGGCCTTTTTTTTTTA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82145445	82145445	+	IGR	DEL	T	-	-	rs67952926		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82145445delT								None (None upstream) : None (None downstream)																							ATGGTATGGAttttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	84422399	84422399	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84422399delA								None (None upstream) : SLITRK1 (28945 downstream)																							actccgtctcaaaaaaaaaaa	0.104													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92839737	92839737	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92839737delA	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				GTCAATGCTTAAAAATACCCT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95332365	95332366	+	IGR	DEL	AC	-	-	rs71703845		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95332365_95332366delAC								GPR180 (50421 upstream) : SOX21 (29516 downstream)																							ATAAGGAGGAacacacacacac	0.342													3	4	---	---	---	---	
DOCK9	23348	broad.mit.edu	37	13	99488999	99488999	+	Intron	DEL	T	-	-	rs34971128		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99488999delT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc001vnq.2_Intron|DOCK9_uc001vnr.2_Intron|DOCK9_uc010tin.1_Intron|DOCK9_uc001vns.2_Intron|DOCK9_uc010tio.1_Intron|DOCK9_uc010tip.1_Intron|DOCK9_uc001vnu.1_Intron|DOCK9_uc010tiq.1_Intron	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTCATTATTCTTCCTAATAAA	0.398													2	5	---	---	---	---	
TM9SF2	9375	broad.mit.edu	37	13	100210977	100210978	+	Intron	DEL	TG	-	-	rs67145592		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100210977_100210978delTG	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TGTTGCATTTtgtgtgtgtgtg	0.134													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107532415	107532415	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107532415delT								ARGLU1 (311901 upstream) : FAM155A (288465 downstream)																							AGGAAAGACCttttttttttt	0.224													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107680456	107680457	+	IGR	INS	-	TG	TG	rs146386957	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107680456_107680457insTG								ARGLU1 (459942 upstream) : FAM155A (140423 downstream)																							AGAATATGAGatgtgtgtgtgt	0.129													4	3	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107915114	107915115	+	Intron	INS	-	GC	GC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107915114_107915115insGC	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						ATAACCCACAGGCGctctctct	0.347													2	4	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108143063	108143063	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108143063delT	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						aacttaaaaGTTTTTTTTTTA	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109140253	109140253	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109140253delC								TNFSF13B (180889 upstream) : MYO16 (108247 downstream)																							atggtgaagtcccatctctac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110169722	110169723	+	IGR	DEL	AT	-	-	rs139516571	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110169722_110169723delAT								MYO16 (309367 upstream) : IRS2 (236463 downstream)																							Ggtgtgtgtgattgtgtgtgtg	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110280087	110280087	+	IGR	DEL	T	-	-	rs34285240		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110280087delT								MYO16 (419732 upstream) : IRS2 (126099 downstream)																							TGGTACTGTATTTTTTTTTTT	0.124													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110865616	110865616	+	Intron	DEL	A	-	-	rs3837555		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110865616delA	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)			aaattgaaataaaaaaaAACA	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111696810	111696811	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111696810_111696811delCA								ANKRD10 (129394 upstream) : ARHGEF7 (70813 downstream)																							acatacgcagcacacacacaca	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111962552	111962553	+	IGR	INS	-	CTC	CTC	rs151242583	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111962552_111962553insCTC								ARHGEF7 (4472 upstream) : C13orf16 (10462 downstream)																							AGGTGTCAGTTCTCCGTGTTGA	0.470													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19000528	19000528	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19000528delT								None (None upstream) : OR11H12 (377066 downstream)																							ttctgtctactttttatgtga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19035224	19035225	+	IGR	INS	-	T	T	rs142975778		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19035224_19035225insT								None (None upstream) : OR11H12 (342369 downstream)																							agcgttccaaatattcacttgc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19038307	19038308	+	IGR	INS	-	A	A	rs151060759		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19038307_19038308insA								None (None upstream) : OR11H12 (339286 downstream)																							gcagattttactaaagagtgtt	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19795722	19795723	+	IGR	DEL	AA	-	-	rs66743629		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19795722_19795723delAA								POTEG (210780 upstream) : P704P (188231 downstream)																							ctcaaatattaaaaagacattt	0.000													3	3	---	---	---	---	
EDDM3A	10876	broad.mit.edu	37	14	21210924	21210924	+	Intron	DEL	T	-	-	rs113097213		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21210924delT	uc001vyb.2	+							NM_006683	NP_006674	Q14507	EP3A_HUMAN	human epididymis-specific 3 alpha precursor						sperm displacement	extracellular space					0						AAAAtttttcttttttttttt	0.005													4	2	---	---	---	---	
HNRNPC	3183	broad.mit.edu	37	14	21701196	21701196	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21701196delA	uc001vzy.2	-						HNRNPC_uc001vzw.2_Intron|HNRNPC_uc001wad.2_Intron|HNRNPC_uc001vzx.2_Intron|HNRNPC_uc001vzz.2_Intron|HNRNPC_uc001waa.2_Intron|HNRNPC_uc010ail.2_Intron|HNRNPC_uc010tlq.1_Intron|HNRNPC_uc001wab.2_Intron|HNRNPC_uc001wac.2_Intron|HNRNPC_uc010tlr.1_5'Flank|HNRNPC_uc001waf.2_Intron|HNRNPC_uc001wae.2_Intron	NM_031314	NP_112604	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C							catalytic step 2 spliceosome|nucleoplasm	identical protein binding|nucleotide binding|RNA binding				0	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		actctgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22049398	22049398	+	IGR	DEL	T	-	-	rs112563063		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22049398delT								OR10G3 (10523 upstream) : OR10G2 (52669 downstream)																							tgggcatgggttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22124567	22124568	+	IGR	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22124567_22124568delCT								OR10G2 (21569 upstream) : OR4E2 (8729 downstream)																							cagagtgagactctctctcTCT	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22872189	22872199	+	Intron	DEL	GACACAGAGTA	-	-	rs145051627		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22872189_22872199delGACACAGAGTA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		CGGGCATTAGGACACAGAGTAGACATAACGT	0.389													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	24758607	24758607	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24758607delC								RABGGTA (17804 upstream) : DHRS1 (1199 downstream)																							actgagattacaggtgtaaac	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29274266	29274266	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29274266delT								C14orf23 (10267 upstream) : PRKD1 (771423 downstream)																							cttctcactattttttttttc	0.000													4	2	---	---	---	---	
SCFD1	23256	broad.mit.edu	37	14	31146163	31146163	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31146163delT	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010amd.1_Intron|SCFD1_uc010ame.1_Intron	NM_016106	NP_057190	Q8WVM8	SCFD1_HUMAN	vesicle transport-related protein isoform a						post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		TTCAGATCAGTTTTTGCTAAC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31307904	31307904	+	IGR	DEL	T	-	-	rs75398554		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31307904delT								SCFD1 (102886 upstream) : COCH (35837 downstream)																							aatccttgagtttagttgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31955983	31955983	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31955983delA								HEATR5A (29303 upstream) : NUBPL (74608 downstream)																							taataattataatctatttgc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31998558	31998562	+	IGR	DEL	TACTT	-	-	rs10584965		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31998558_31998562delTACTT								HEATR5A (71878 upstream) : NUBPL (32029 downstream)																							ttgggattcatactttacttgtttg	0.034													4	2	---	---	---	---	
NUBPL	80224	broad.mit.edu	37	14	32114276	32114276	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32114276delT	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		ttttcttttcttttttttttt	0.000													3	4	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34172530	34172530	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34172530delA	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)		ccatttctacaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34684032	34684032	+	IGR	DEL	A	-	-	rs67204205		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34684032delA								EGLN3 (263745 upstream) : C14orf147 (218113 downstream)																							ccatctctacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FAM177A1	283635	broad.mit.edu	37	14	35551771	35551772	+	3'UTR	DEL	AT	-	-	rs72664805		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35551771_35551772delAT	uc001wsp.2	+	7					FAM177A1_uc001wsq.2_3'UTR	NM_001079519	NP_001072987	Q8N128	F177A_HUMAN	hypothetical protein LOC283635 isoform 2												0						acacacacacaTATATCTCTAA	0.178													3	9	---	---	---	---	
RALGAPA1	253959	broad.mit.edu	37	14	36270450	36270451	+	Intron	INS	-	AC	AC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36270450_36270451insAC	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						tatatacacagacacacacaca	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	37122528	37122528	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37122528delT								NKX2-8 (70742 upstream) : PAX9 (4254 downstream)																							ATCCTTCCTCTCCCCCCTGCA	0.443													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37479882	37479890	+	Intron	DEL	TTTTAAATG	-	-	rs36204314		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37479882_37479890delTTTTAAATG	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)		TTTAAAGTACTTTTAAATGTTTAAATGTA	0.086													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38155668	38155668	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38155668delG	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		ACTAGTACATggaagtctcgt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	41515859	41515860	+	IGR	DEL	GG	-	-	rs71982856		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41515859_41515860delGG								None (None upstream) : LRFN5 (560904 downstream)																							gtgtgggtgtgggtgtgtgtgt	0.272													0	6	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47585495	47585495	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47585495delT	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						agacatcacattttatggatt	0.000													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	48082662	48082663	+	Intron	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48082662_48082663delTC	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						ACTTCATTTAtctctctctctc	0.272													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	48088320	48088321	+	Intron	DEL	AC	-	-	rs58765072	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48088320_48088321delAC	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						CAGTTTAATTacacacacacac	0.272													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50076965	50076966	+	Intron	INS	-	TT	TT	rs72348180		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50076965_50076966insTT	uc010anj.1	-						PPIL5_uc001wwn.2_Intron|PPIL5_uc001wwo.2_Intron|PPIL5_uc010ank.2_Intron|PPIL5_uc001wwp.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TTTGTTGAGGGttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51427983	51427984	+	IGR	INS	-	A	A	rs146708481	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51427983_51427984insA								PYGL (16735 upstream) : TRIM9 (13998 downstream)																							gactctgtctcaaaaaaaaaag	0.099													4	5	---	---	---	---	
PTGER2	5732	broad.mit.edu	37	14	52790010	52790011	+	Intron	INS	-	A	A	rs138817349	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52790010_52790011insA	uc001wzr.2	+							NM_000956	NP_000947	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa							integral to plasma membrane	prostaglandin E receptor activity			lung(1)|breast(1)	2	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Iloprost(DB01088)	ctcactctgtcacccaggctga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53471359	53471360	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53471359_53471360insT								FERMT2 (53544 upstream) : DDHD1 (32099 downstream)																							ttattttttaattttttttttt	0.168													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54352151	54352152	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54352151_54352152insA								DDHD1 (732105 upstream) : BMP4 (64305 downstream)																							TTCATTGGAAGAAAAAAAAAAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54742621	54742623	+	IGR	DEL	TTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54742621_54742623delTTG								BMP4 (319067 upstream) : CDKN3 (121050 downstream)																							CTTTGGGGCTttgttgttgttgt	0.281													3	5	---	---	---	---	
CNIH	10175	broad.mit.edu	37	14	54903237	54903237	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54903237delA	uc001xat.1	-						CNIH_uc001xav.1_Intron	NM_005776	NP_005767	O95406	CNIH_HUMAN	cornichon-like						immune response|intracellular signal transduction|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0				GBM - Glioblastoma multiforme(112;0.00341)		AATAATTATTAAAGTTAATAA	0.294													2	10	---	---	---	---	
DLGAP5	9787	broad.mit.edu	37	14	55660347	55660348	+	5'Flank	INS	-	A	A	rs76704928		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55660347_55660348insA	uc001xbs.2	-						DLGAP5_uc001xbt.2_5'Flank	NM_014750	NP_055565	Q15398	DLGP5_HUMAN	discs large homolog 7 isoform a						cell proliferation|cell-cell signaling|mitotic chromosome movement towards spindle pole|positive regulation of mitotic metaphase/anaphase transition	nucleus|spindle pole centrosome	phosphoprotein phosphatase activity|protein binding			ovary(1)|skin(1)	2						gaacctgtctcaaaaaaaaaaa	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57368981	57368982	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57368981_57368982delAC	uc001xcr.1	+											Homo sapiens cDNA clone IMAGE:5492202, partial cds.																		TTTAAAGATTacacacacacac	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59420790	59420790	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59420790delC								DACT1 (305754 upstream) : DAAM1 (234609 downstream)																							tatcacaccacccaaatcacc	0.000													4	2	---	---	---	---	
SLC38A6	145389	broad.mit.edu	37	14	61508677	61508678	+	Intron	INS	-	T	T	rs144531121	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61508677_61508678insT	uc001xfg.1	+						SLC38A6_uc001xfh.1_Intron|SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfj.1_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		CATCCTCATCGTTTTTTTTTGT	0.233													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62073832	62073833	+	Intron	INS	-	GTGT	GTGT			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62073832_62073833insGTGT	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																		tgtccatCATGgtgcgtgtgtg	0.084													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62913923	62913924	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62913923_62913924insT								FLJ43390 (316691 upstream) : KCNH5 (260023 downstream)																							tcttctaggacttttttttttt	0.000													4	2	---	---	---	---	
KCNH5	27133	broad.mit.edu	37	14	63462621	63462621	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63462621delA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron|KCNH5_uc001xga.2_Intron	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TTTGGTTGGGAAAAAAAAAAT	0.224													4	2	---	---	---	---	
FNTB	2342	broad.mit.edu	37	14	65518516	65518516	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65518516delT	uc001xia.2	+						FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|MAX_uc001xic.1_Intron|FNTB_uc001xid.2_Intron|FNTB_uc010tso.1_Intron	NM_002028	NP_002019	P49356	FNTB_HUMAN	farnesyltransferase, CAAX box, beta						protein farnesylation	microtubule associated complex	protein binding|protein farnesyltransferase activity			ovary(1)	1				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)		ACCATAGGAAttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	65640924	65640925	+	IGR	INS	-	TG	TG	rs147608091	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65640924_65640925insTG								MAX (71697 upstream) : LOC645431 (236388 downstream)																							gttgtgtgtgatgtgtgagttg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	65690976	65690977	+	5'Flank	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65690976_65690977insA	uc001xil.2	-											human full-length cDNA clone CS0DI006YN07 of Placenta of Homo sapiens (human).																		gactctgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	65771297	65771297	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65771297delA								MAX (202070 upstream) : LOC645431 (106016 downstream)																							TGCCAGTGAGAATAACACTTG	0.373													4	2	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67515928	67515929	+	Intron	INS	-	TTGTTG	TTGTTG	rs139585227	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67515928_67515929insTTGTTG	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GCTGATTAAGTttgttgttgtt	0.153			T	MLL	AL								4	3	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68523807	68523807	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68523807delA	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		actccgtctcaaaaaaaaaaa	0.144			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					5	3	---	---	---	---	
SLC10A1	6554	broad.mit.edu	37	14	70261514	70261515	+	Intron	INS	-	A	A	rs145260192	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70261514_70261515insA	uc001xlr.2	-							NM_003049	NP_003040	Q14973	NTCP_HUMAN	solute carrier family 10, member 1						bile acid metabolic process|organic anion transport	integral to plasma membrane	bile acid:sodium symporter activity			ovary(1)	1				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)		GTAAAAATGACAGTCATCAGGG	0.535													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70773302	70773303	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70773302_70773303insT								ADAM21P1 (58784 upstream) : COX16 (18496 downstream)																							aatgcttgtgattttttcacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	72307531	72307531	+	IGR	DEL	C	-	-	rs111375853		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72307531delC								SIPA1L1 (101413 upstream) : RGS6 (91625 downstream)																							ctttttatgtcccccttctcc	0.000													4	2	---	---	---	---	
KIAA1737	85457	broad.mit.edu	37	14	77575035	77575035	+	Intron	DEL	A	-	-	rs77502668		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77575035delA	uc001xtd.2	+						KIAA1737_uc001xtc.1_Intron	NM_033426	NP_219494	Q9C0C6	K1737_HUMAN	KIAA1737 protein												0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79706991	79706991	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79706991delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TTGTGGCATCTTTGGCTGCCC	0.418													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	80246504	80246504	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80246504delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		GCCTTTGGGGAAAAAAAAAAA	0.333													4	2	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	81262803	81262803	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81262803delA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		gattcagtccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85025301	85025301	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85025301delA								None (None upstream) : FLRT2 (971187 downstream)																							gaatgaaggtaagaacagcaa	0.000													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89763472	89763473	+	Intron	INS	-	A	A	rs148015229	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89763472_89763473insA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						GTAAAACTAACAAGAGGAAAGG	0.376													3	4	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89764528	89764529	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89764528_89764529insA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						aagccagtcacaaaaaagacaa	0.000													6	5	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89985943	89985943	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89985943delA	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						GTGAAGGGACAAAAGCCTGTC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90225808	90225809	+	IGR	INS	-	TC	TC	rs142862415	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90225808_90225809insTC								FOXN3 (140314 upstream) : C14orf143 (37662 downstream)																							TTCCTTTTCTATCTCTTAACTT	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90918519	90918519	+	IGR	DEL	G	-	-	rs3832954		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90918519delG								CALM1 (43909 upstream) : TTC7B (88414 downstream)																							gagaggtggtgggcagctgga	0.159													3	3	---	---	---	---	
SMEK1	55671	broad.mit.edu	37	14	91928846	91928846	+	Intron	DEL	T	-	-	rs66705519		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91928846delT	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		CTGTTTGGTCTTTTTTTTTTT	0.328													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92724879	92724879	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92724879delA								CPSF2 (94336 upstream) : SLC24A4 (64046 downstream)																							aaaagaaaagaaAAAAAAAAA	0.204													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93162844	93162844	+	IGR	DEL	A	-	-	rs35584657		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93162844delA								RIN3 (7512 upstream) : LGMN (7313 downstream)																							actctgtctcaaaaaaaaaaa	0.025													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93240372	93240372	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93240372delA								LGMN (25360 upstream) : GOLGA5 (20278 downstream)																							gaccccatttaaaaaaaaaag	0.000													4	2	---	---	---	---	
KIAA1409	57578	broad.mit.edu	37	14	93850258	93850259	+	Intron	INS	-	CT	CT	rs138806289	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93850258_93850259insCT	uc001ybs.1	+							NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		ccctgcacaaactctgtctgcc	0.000													2	4	---	---	---	---	
SERPINA3	12	broad.mit.edu	37	14	95077293	95077293	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95077293delT	uc001ydp.2	+						SERPINA3_uc001ydo.3_Intron|SERPINA3_uc010avf.1_5'Flank|SERPINA3_uc001ydr.2_5'Flank|SERPINA3_uc001ydq.2_5'Flank|SERPINA3_uc001yds.2_5'Flank|SERPINA3_uc010avg.2_5'Flank	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3						acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1)	6		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		AGAGGAAGGAttttttttttt	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95121476	95121478	+	IGR	DEL	AGA	-	-	rs146867224		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95121476_95121478delAGA								SERPINA13 (8146 upstream) : GSC (113083 downstream)																							aaggagaaggagaagaagaaaaa	0.123													3	4	---	---	---	---	
AK7	122481	broad.mit.edu	37	14	96912668	96912669	+	Intron	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96912668_96912669delTT	uc001yfn.2	+							NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		caccgaaccctttagcatcttc	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97073759	97073760	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97073759_97073760insT								PAPOLA (40313 upstream) : VRK1 (189924 downstream)																							CATCCAGGGACTTGATGACTGC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97524878	97524879	+	IGR	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97524878_97524879delTC								VRK1 (176928 upstream) : C14orf64 (867068 downstream)																							atacaatgCAtctctctctctc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97698494	97698495	+	IGR	INS	-	C	C	rs147543558	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97698494_97698495insC								VRK1 (350544 upstream) : C14orf64 (693452 downstream)																							cataggaaagacccccccccat	0.079													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97808425	97808426	+	IGR	INS	-	A	A	rs146499167	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97808425_97808426insA								VRK1 (460475 upstream) : C14orf64 (583521 downstream)																							attcccacatcccattgcataa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98269421	98269422	+	IGR	INS	-	CA	CA	rs147580245	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98269421_98269422insCA								VRK1 (921471 upstream) : C14orf64 (122525 downstream)																							AATAGAGCATGcacacacacac	0.465													4	2	---	---	---	---	
BCL11B	64919	broad.mit.edu	37	14	99685383	99685383	+	Intron	DEL	T	-	-	rs5810929		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99685383delT	uc001yga.2	-						BCL11B_uc001ygb.2_Intron	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1							nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		ttatttcttcttttttttttt	0.000			T	TLX3	T-ALL								1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99847642	99847642	+	IGR	DEL	T	-	-	rs78111563	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99847642delT								BCL11B (109820 upstream) : SETD3 (16442 downstream)																							CTGAACCCTCTTCTCCATTCA	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100655823	100655823	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100655823delC								DEGS2 (29811 upstream) : YY1 (49279 downstream)																							ctgcagagagcccccaccaac	0.005													4	2	---	---	---	---	
WDR25	79446	broad.mit.edu	37	14	100982331	100982331	+	Intron	DEL	T	-	-	rs143630748		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100982331delT	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25												0		Melanoma(154;0.212)				tattgacagattttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101189452	101189452	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101189452delA								C14orf70 (50371 upstream) : DLK1 (3801 downstream)																							CCACCCCGGCaaaaaaaaaaa	0.512													4	2	---	---	---	---	
CDC42BPB	9578	broad.mit.edu	37	14	103459589	103459591	+	Intron	DEL	ATA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103459589_103459591delATA	uc001ymi.1	-							NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TTCATACGTTATATATACTACGT	0.404													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	105020514	105020514	+	IGR	DEL	A	-	-	rs150447739	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105020514delA								KIF26A (373280 upstream) : C14orf180 (25542 downstream)																							TCAGCCTGGGACCCCCCCCCC	0.672													3	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107157560	107157561	+	Intron	INS	-	T	T	rs72527153	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107157560_107157561insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						atttgtgccaaggggggatggc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20083052	20083052	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20083052delA								None (None upstream) : GOLGA6L6 (654042 downstream)																							attccatcttaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20101495	20101495	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20101495delT								None (None upstream) : GOLGA6L6 (635599 downstream)																							tggtgcactgtttagaataaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20107766	20107766	+	IGR	DEL	T	-	-	rs149228256		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20107766delT								None (None upstream) : GOLGA6L6 (629328 downstream)																							tgaaatgaaattgaaataatg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20435563	20435563	+	IGR	DEL	C	-	-	rs4931876		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20435563delC								None (None upstream) : GOLGA6L6 (301531 downstream)																							ttttctttttctttttttttt	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20455645	20455646	+	IGR	INS	-	C	C	rs149683037	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20455645_20455646insC								None (None upstream) : GOLGA6L6 (281448 downstream)																							CTggccaggcaccgtggctcat	0.094													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20515151	20515153	+	IGR	DEL	ATG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20515151_20515153delATG								None (None upstream) : GOLGA6L6 (221941 downstream)																							aaatgatgaaatgatgagatgtg	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20553517	20553523	+	IGR	DEL	TTTTTTT	-	-	rs137898354		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20553517_20553523delTTTTTTT								None (None upstream) : GOLGA6L6 (183571 downstream)																							cacacaaagcttttttttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20573861	20573862	+	IGR	DEL	TG	-	-	rs144738379		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20573861_20573862delTG								None (None upstream) : GOLGA6L6 (163232 downstream)																							AAAGAAAAACTGAAAGAAAAGT	0.292													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21902347	21902348	+	IGR	INS	-	TAA	TAA	rs111550006		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21902347_21902348insTAA								NF1P1 (767722 upstream) : LOC646214 (30166 downstream)																							acctcatctcttattattctgc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22470594	22470595	+	IGR	INS	-	AA	AA	rs77118326		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22470594_22470595insAA								OR4N3P (56209 upstream) : MIR1268 (42634 downstream)																							tcaagttgctgaaaaaaaaagc	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22539625	22539626	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22539625_22539626delCA								MIR1268 (26345 upstream) : GOLGA8DP (162659 downstream)																							acacacataccacacagataca	0.069													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22559840	22559843	+	IGR	DEL	ACTC	-	-	rs113173249		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22559840_22559843delACTC								MIR1268 (46560 upstream) : GOLGA8DP (142442 downstream)																							ACAAATAGATACTCACAGAACTTG	0.431													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23043258	23043258	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23043258delA								NIPA2 (8848 upstream) : NIPA1 (23 downstream)																							AAGTAAAGGGAAAAAAAAAAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26483881	26483881	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26483881delC								ATP10A (373564 upstream) : GABRB3 (304814 downstream)																							TTATTCCCTACCCCCCCACCT	0.463													4	2	---	---	---	---	
HERC2	8924	broad.mit.edu	37	15	28539038	28539038	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28539038delT	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ATAAAACTCCTTACACAGTAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30465302	30465303	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30465302_30465303delGT								FAM7A3 (41356 upstream) : DKFZP434L187 (22936 downstream)																							gatgtgtgtggtgtgtgtgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31078360	31078363	+	IGR	DEL	CATT	-	-	rs34812218		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31078360_31078363delCATT								ARHGAP11B (100551 upstream) : MTMR15 (117692 downstream)																							GCCATTATTCcattcattcattca	0.196													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31095906	31095906	+	5'Flank	DEL	A	-	-	rs35412923		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31095906delA	uc001zfb.2	-						uc010ubj.1_5'Flank					DQ572979																		aaaaaaatacaaaaaaaaaaa	0.005													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38668148	38668148	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38668148delC								SPRED1 (18699 upstream) : FAM98B (78180 downstream)																							tctaggaattccacttactgg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41177870	41177870	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41177870delT								RHOV (11383 upstream) : VPS18 (8758 downstream)																							catttttgtattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	42910988	42910988	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42910988delT	uc001zqg.2	+											Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																		agagatggggtttcaccatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46154563	46154564	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46154563_46154564delCA								SQRDL (171085 upstream) : None (None downstream)																							CTTTTCACTCCACACTACCCGT	0.446													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48059138	48059138	+	Intron	DEL	T	-	-	rs35781153		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48059138delT	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		atttatagtcttttttttttt	0.229													6	3	---	---	---	---	
C2CD4A	145741	broad.mit.edu	37	15	62357290	62357290	+	5'Flank	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62357290delA	uc002ahf.3	+							NM_207322	NP_997205	Q8NCU7	C2C4A_HUMAN	nuclear localized factor 1							nucleus					0						ccatctctccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63366358	63366358	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63366358delT								TPM1 (2247 upstream) : LACTB (47674 downstream)																							CAGTCCCAGATTTCAGAATGA	0.398													4	2	---	---	---	---	
HERC1	8925	broad.mit.edu	37	15	64026056	64026057	+	Intron	INS	-	A	A	rs59274228	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64026056_64026057insA	uc002amp.2	-						HERC1_uc010uil.1_Intron	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						gtctcaaaaagaaaaataaaaa	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	64361076	64361077	+	IGR	INS	-	A	A	rs113841815		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64361076_64361077insA								DAPK2 (22555 upstream) : FAM96A (3684 downstream)																							ccatgtcccagaaaaaaaaaaa	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	65100899	65100900	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65100899_65100900insA								RBPMS2 (33129 upstream) : PIF1 (6933 downstream)																							aattccgtctcaaaaaaaaaaa	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70490624	70490625	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70490624_70490625delCA								TLE3 (100368 upstream) : UACA (456270 downstream)																							Tacacacacgcacacacacaca	0.416													3	3	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73454307	73454308	+	Intron	INS	-	T	T	rs1479336	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73454307_73454308insT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_Intron	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						AAGTTTGTTTGTTTTTTTTTCT	0.351													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77803938	77803938	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77803938delA								HMG20A (25995 upstream) : LINGO1 (101431 downstream)																							caacccaattaaaaaggactt	0.000													4	2	---	---	---	---	
ACSBG1	23205	broad.mit.edu	37	15	78526038	78526039	+	Intron	DEL	GC	-	-	rs1519817	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78526038_78526039delGC	uc002bdh.2	-						ACSBG1_uc010umw.1_Intron|ACSBG1_uc010umx.1_Intron|ACSBG1_uc010umy.1_Intron	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin						long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						CCGTGTGTGTGCGTGTGCGCGT	0.614													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	80972463	80972463	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80972463delT								ARNT2 (82191 upstream) : FAM108C1 (15189 downstream)																							CATTTCTGGATTCCTGGCCCT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81885717	81885717	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81885717delA								TMC3 (219299 upstream) : MEX3B (448411 downstream)																							gcaagtggggaagaaataact	0.000													4	2	---	---	---	---	
WHAMM	123720	broad.mit.edu	37	15	83502439	83502439	+	3'UTR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83502439delT	uc002bje.2	+	10						NM_001080435	NP_001073904	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi							cytoplasmic vesicle membrane|ER-Golgi intermediate compartment|Golgi apparatus	actin binding				0						TGCTGCAGCAttttttttttt	0.259													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84023844	84023845	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84023844_84023845insT								BNC1 (70376 upstream) : SH3GL3 (92246 downstream)																							AATAAttcttcttttttttttg	0.168													4	2	---	---	---	---	
SH3GL3	6457	broad.mit.edu	37	15	84278607	84278608	+	Intron	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84278607_84278608delGA	uc002bjw.2	+						SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3						TGGCATGTGGGAGAGAGAGAGA	0.559													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85167602	85167603	+	IGR	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85167602_85167603delAA								ZSCAN2 (654 upstream) : SCAND2 (7088 downstream)																							agaaaaagagaaaaaaaaaaaA	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85903397	85903398	+	IGR	INS	-	AAG	AAG	rs143977499	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85903397_85903398insAAG								PDE8A (221027 upstream) : AKAP13 (20473 downstream)																							gtagaccggtaaaggagggtga	0.188													3	5	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87079099	87079099	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87079099delC	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						TGTTTTATTTCCACTTTATTC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87606959	87606960	+	IGR	INS	-	A	A	rs143169228	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87606959_87606960insA								AGBL1 (34676 upstream) : NCRNA00052 (513200 downstream)																							AAATTCAGATGAAAAAATAAGA	0.322													3	3	---	---	---	---	
ISG20	3669	broad.mit.edu	37	15	89183802	89183802	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89183802delG	uc002bmv.1	+						ISG20_uc002bmu.1_Intron|ISG20_uc002bmw.1_Intron|ISG20_uc010upn.1_Intron	NM_002201	NP_002192	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease						cell proliferation|DNA catabolic process, exonucleolytic|response to virus|RNA catabolic process|type I interferon-mediated signaling pathway	PML body	3'-5'-exoribonuclease activity|exoribonuclease II activity|metal ion binding|RNA binding|single-stranded DNA specific 3'-5' exodeoxyribonuclease activity				0	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			tttgtacccagtaaaagaaaa	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90867050	90867051	+	IGR	INS	-	T	T	rs10624880		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90867050_90867051insT								TTLL13 (51607 upstream) : GABARAPL3 (22714 downstream)																							AATGCAAATCCttttttttttt	0.153													3	3	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91011280	91011281	+	Intron	INS	-	TTTG	TTTG	rs140381026	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91011280_91011281insTTTG	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						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)			ATTCAACAGtttttgtttgttt	0.158													2	4	---	---	---	---	
SV2B	9899	broad.mit.edu	37	15	91704260	91704261	+	Intron	DEL	AT	-	-	rs146481354		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91704260_91704261delAT	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			acctcaaaacatacgctaaatg	0.000													0	9	---	---	---	---	
SV2B	9899	broad.mit.edu	37	15	91729115	91729115	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91729115delC	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CATCACTACACCACTCCATGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92001290	92001290	+	IGR	DEL	T	-	-	rs72208096		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92001290delT								SV2B (162642 upstream) : SLCO3A1 (395648 downstream)																							gacagaatgcttttttttttt	0.000													4	2	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92512635	92512635	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92512635delA	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			tcctaggttcaagtgattctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94071128	94071129	+	Intron	DEL	CT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94071128_94071129delCT	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		agagagctagctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94204479	94204479	+	IGR	DEL	T	-	-	rs139698367	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94204479delT								RGMA (572046 upstream) : MCTP2 (570322 downstream)																							ggtgaaaccctgggcgtggtg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94573441	94573441	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94573441delT								RGMA (941008 upstream) : MCTP2 (201360 downstream)																							GAAACTTGCATTTTTTTTCAC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94617930	94617930	+	IGR	DEL	A	-	-	rs35057773		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94617930delA								RGMA (985497 upstream) : MCTP2 (156871 downstream)																							CTAGCATACGAAAAAAAAAAT	0.358													0	6	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94841158	94841158	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94841158delT	uc002btj.2	+						MCTP2_uc010urg.1_Intron|MCTP2_uc002bti.2_Intron|MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_5'Flank|MCTP2_uc002btg.3_Intron|MCTP2_uc002bth.3_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TCATGAAGCATTTTTTTTTTT	0.343													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96067939	96067939	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96067939delA								LOC145820 (16865 upstream) : NR2F2 (801218 downstream)																							AACAGAAAGGAAAAAAAAAAT	0.119													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96105027	96105028	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96105027_96105028delAC								LOC145820 (53953 upstream) : NR2F2 (764129 downstream)																							acatacacagacacacacacac	0.168													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96556416	96556417	+	IGR	INS	-	GT	GT	rs144576647	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96556416_96556417insGT								LOC145820 (505342 upstream) : NR2F2 (312740 downstream)																							AATATGATTGAGTGTGTGTGGG	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98104621	98104622	+	IGR	DEL	TG	-	-	rs72516647		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98104621_98104622delTG								SPATA8 (775777 upstream) : LOC91948 (181224 downstream)																							GGGgtgtgtatgtgtgtgtgtg	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98158474	98158475	+	IGR	INS	-	TTC	TTC	rs35229447		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98158474_98158475insTTC								SPATA8 (829630 upstream) : LOC91948 (127371 downstream)																							tcttccttcctttttttctttc	0.015													2	4	---	---	---	---	
LOC91948	91948	broad.mit.edu	37	15	98335735	98335736	+	Intron	INS	-	A	A	rs35707611		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98335735_98335736insA	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0						GGGCTGTCAGGAAAAAAAAAAA	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98948943	98948958	+	IGR	DEL	ACACACACACACACAC	-	-	rs10535521		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98948943_98948958delACACACACACACACAC								ARRDC4 (431876 upstream) : FAM169B (31433 downstream)																							CCTCTCTcatacacacacacacacacacacacacac	0.329													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	99076717	99076720	+	IGR	DEL	AAAG	-	-	rs71844015		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99076717_99076720delAAAG								FAM169B (19106 upstream) : IGF1R (116041 downstream)																							gtgagggaaaaaagaaagaaagaa	0.098													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	100328703	100328704	+	IGR	INS	-	CTTC	CTTC	rs56252855		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100328703_100328704insCTTC								LYSMD4 (55077 upstream) : C15orf51 (1657 downstream)																							tccctccctttcttccttcctt	0.139													6	3	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100601942	100601942	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100601942delA	uc002bvv.1	-							NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GTCGGAAGCCAAGGGACTTAC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102293062	102293064	+	Intron	DEL	CTC	-	-	rs62026972		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102293062_102293064delCTC	uc010usj.1	+						uc002bxo.2_5'Flank|uc002bxp.3_RNA|uc002bxq.2_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank|uc002bys.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AGTTCATCTTCTCAGAGCTGCTG	0.576													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	896601	896602	+	IGR	INS	-	A	A	rs146575915	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:896601_896602insA								PRR25 (32741 upstream) : LMF1 (7033 downstream)																							CGGTTTCCTGTAACCCGTGTGT	0.455													3	4	---	---	---	---	
DNAJA3	9093	broad.mit.edu	37	16	4487632	4487633	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4487632_4487633insA	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4						TTAAGAAAAATAAAAAAAAAGA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10596629	10596630	+	IGR	INS	-	A	A	rs118081663		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10596629_10596630insA								ATF7IP2 (19135 upstream) : EMP2 (25650 downstream)																							tccaaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11318744	11318745	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11318744_11318745delGT								CLEC16A (42700 upstream) : C16orf75 (24761 downstream)																							gactttccccgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12421593	12421594	+	Intron	DEL	AG	-	-	rs3975335		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12421593_12421594delAG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GGAGAGAGACAGAGAGAGGAAA	0.391													3	5	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12815167	12815167	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12815167delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						GTAAAAGAAGAAGGAAACTGC	0.418													4	2	---	---	---	---	
BFAR	51283	broad.mit.edu	37	16	14738020	14738020	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14738020delA	uc002dco.2	+						BFAR_uc002dcm.2_Intron|BFAR_uc002dcn.2_Intron|BFAR_uc002dcp.2_Intron|BFAR_uc010uzh.1_5'Flank	NM_016561	NP_057645	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2						actgtgtctcaaaaaaaaaaa	0.119													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16697890	16697894	+	IGR	DEL	TCAAG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16697890_16697894delTCAAG								LOC339047 (253453 upstream) : XYLT1 (498289 downstream)																							actcctggcctcaagtgatccttct	0.068													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17867760	17867761	+	IGR	INS	-	A	A	rs74483297		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17867760_17867761insA								XYLT1 (303022 upstream) : NOMO2 (643422 downstream)																							ACGAAAAATGCAAAAAAAAAAA	0.416													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24647293	24647293	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24647293delT								RBBP6 (63112 upstream) : TNRC6A (93756 downstream)																							CATCCATTCCTTAATTCATTA	0.119													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	26060792	26060793	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26060792_26060793delTG	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		TGCGTGCCTCtgtgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27184247	27184248	+	IGR	DEL	AA	-	-	rs34363295		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27184247_27184248delAA								C16orf82 (103761 upstream) : JMJD5 (30559 downstream)																							gctctgtctcaaaaaaaaaaaa	0.208													4	2	---	---	---	---	
KIAA0556	23247	broad.mit.edu	37	16	27595558	27595559	+	Intron	INS	-	AG	AG			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27595558_27595559insAG	uc002dow.2	+							NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						AACTTCAGCAAAGAGTGAGCGC	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29294632	29294632	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29294632delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		atttaagatctttggcccact	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32399155	32399155	+	IGR	DEL	C	-	-	rs149453033		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32399155delC								HERC2P4 (235281 upstream) : TP53TG3B (285686 downstream)																							tgtgatccagcccacctcagc	0.040													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32407001	32407002	+	IGR	INS	-	T	T	rs140894241		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32407001_32407002insT								HERC2P4 (243127 upstream) : TP53TG3B (277839 downstream)																							ctctttctgtattttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32489886	32489887	+	IGR	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32489886_32489887insG								HERC2P4 (326012 upstream) : TP53TG3B (194954 downstream)																							AAAGCCGCGGCGGCAAAAAGCC	0.658													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32536718	32536719	+	IGR	INS	-	GT	GT	rs146380532		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32536718_32536719insGT								HERC2P4 (372844 upstream) : TP53TG3B (148122 downstream)																							ggacaaaaagagtttccaaact	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32546850	32546850	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32546850delA								HERC2P4 (382976 upstream) : TP53TG3B (137991 downstream)																							ggaacagtttaagtctgtgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32846111	32846111	+	IGR	DEL	A	-	-	rs77630803		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32846111delA								TP53TG3B (157233 upstream) : SLC6A10P (42686 downstream)																							GATTTTTTTTAAAAAAGGAAA	0.204													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33052524	33052524	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33052524delC								SLC6A10P (156061 upstream) : MIR1826 (912984 downstream)																							aacctgtgtactacattacta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33343169	33343170	+	IGR	DEL	TA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33343169_33343170delTA								SLC6A10P (446706 upstream) : MIR1826 (622338 downstream)																							ttcatttcattatgtcatttca	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33950129	33950132	+	IGR	DEL	GGAT	-	-	rs75785649		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33950129_33950132delGGAT								None (None upstream) : MIR1826 (15376 downstream)																							CGGGTGGGCCGGATGGATGGGACG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33952873	33952874	+	IGR	INS	-	A	A	rs150976456		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33952873_33952874insA								None (None upstream) : MIR1826 (12634 downstream)																							tctgcacactgaacccccgtca	0.015													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34179236	34179236	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34179236delC								MIR1826 (213644 upstream) : UBE2MP1 (224566 downstream)																							GATTCTAAGGCAATCCTTAAG	0.443													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46474617	46474617	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46474617delA								None (None upstream) : ANKRD26P1 (28632 downstream)																							GGAGGGGAATACATCATTACT	0.323													4	3	---	---	---	---	
CHD9	80205	broad.mit.edu	37	16	53097113	53097113	+	Intron	DEL	T	-	-	rs35279032		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53097113delT	uc002egy.2	+							NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				gtagggactctttgccccatg	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55477059	55477062	+	IGR	DEL	CACA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55477059_55477062delCACA								IRX6 (112388 upstream) : MMP2 (36019 downstream)																							ATCCACTCACcacacacacacaca	0.402													3	3	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55854986	55854987	+	Intron	INS	-	AGAG	AGAG	rs146078635	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55854986_55854987insAGAG	uc002eim.2	-						CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	gagagagagaaagagagagaga	0.396													5	4	---	---	---	---	
CKLF	51192	broad.mit.edu	37	16	66585687	66585687	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66585687delT	uc002eow.2	+						CKLF_uc002eox.1_5'Flank|CKLF_uc002eot.2_5'Flank|CKLF_uc002eou.2_5'Flank|CKLF_uc002eov.2_5'Flank	NM_016951	NP_058647	Q9UBR5	CKLF_HUMAN	chemokine-like factor isoform a						cell proliferation|lymphocyte chemotaxis|macrophage chemotaxis|neutrophil chemotaxis|secretion by cell	extracellular space|integral to membrane	chemokine activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0689)|Epithelial(162;0.217)		atgggcaggatccaaacagat	0.015											OREG0023858	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
NRN1L	123904	broad.mit.edu	37	16	67920066	67920068	+	In_Frame_Del	DEL	GCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67920066_67920068delGCT	uc002euu.2	+	3	428_430	c.402_404delGCT	c.(400-405)ACGCTG>ACG	p.L135del	EDC4_uc002eut.1_3'UTR	NM_198443	NP_940845	Q496H8	NRN1L_HUMAN	neuritin 1-like precursor	135						anchored to membrane|plasma membrane				central_nervous_system(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		ACCAGGAGACGCTGCGGGCTACA	0.675													7	9	---	---	---	---	
WWP2	11060	broad.mit.edu	37	16	69891200	69891200	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69891200delG	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron|WWP2_uc010vlm.1_Intron	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6						ggtttcacctgttggccaggc	0.010													4	2	---	---	---	---	
VAC14	55697	broad.mit.edu	37	16	70779386	70779387	+	Intron	DEL	GT	-	-	rs55846638		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70779386_70779387delGT	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				AGGGGCTTCAgtgtgtgtgtgt	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74326560	74326560	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74326560delT								None (None upstream) : PSMD7 (4121 downstream)																							TCCATTTGCAttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77648935	77648937	+	IGR	DEL	AGG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77648935_77648937delAGG								ADAMTS18 (179924 upstream) : NUDT7 (107474 downstream)																							tgagagagaaaggaggaggagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	81431297	81431297	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81431297delC								GAN (17496 upstream) : CMIP (47478 downstream)																							CTCAGGACATCTTGGAAATGA	0.493													4	3	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984532	83984537	+	Intron	DEL	ACACAT	-	-	rs59635067		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984532_83984537delACACAT	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						acacgtacacacacatgcacacgtga	0.000													4	3	---	---	---	---	
KIAA1609	57707	broad.mit.edu	37	16	84535750	84535751	+	Intron	INS	-	A	A	rs77402126		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84535750_84535751insA	uc002fib.2	-						KIAA1609_uc010vod.1_Intron|KIAA1609_uc002fic.2_Intron	NM_020947	NP_065998	Q6P9B6	K1609_HUMAN	hypothetical protein LOC57707								protein binding			ovary(2)	2						aactcggtctcaaaaaaaaaaa	0.134													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84960175	84960175	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84960175delA								CRISPLD2 (17059 upstream) : ZDHHC7 (47892 downstream)																							cacagtagccaaaaaaagtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85178473	85178474	+	IGR	DEL	CT	-	-	rs150540350		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85178473_85178474delCT								FAM92B (32359 upstream) : KIAA0182 (466555 downstream)																							tggccccttcctctttctccaa	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88226387	88226388	+	IGR	INS	-	TGA	TGA			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88226387_88226388insTGA								BANP (115464 upstream) : ZNF469 (267491 downstream)																							gatgatggtggtgatagtggtg	0.000													4	2	---	---	---	---	
ZFPM1	161882	broad.mit.edu	37	16	88585146	88585149	+	Intron	DEL	TGGA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88585146_88585149delTGGA	uc002fkv.2	+							NM_153813	NP_722520	Q8IX07	FOG1_HUMAN	zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)		gctgagagggtggatggatggatg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4518364	4518365	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4518364_4518365delTG	uc002fyg.1	+											Homo sapiens cDNA clone IMAGE:5176687.																		tgtgcgcgcatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5000350	5000350	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5000350delA								ZFP3 (682 upstream) : ZNF232 (8489 downstream)																							GGACCTCAGTAAAAGCCCAGT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7775621	7775621	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7775621delT	uc010cno.1	-											Homo sapiens cDNA FLJ35054 fis, clone OCBBF2018380.																		TCACCCACACTTTTTATATCT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	8291384	8291387	+	IGR	DEL	TCTA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8291384_8291387delTCTA								RPL26 (4819 upstream) : RNF222 (2636 downstream)																							Catccatccctctatctatctatc	0.176													3	3	---	---	---	---	
GLP2R	9340	broad.mit.edu	37	17	9773047	9773048	+	Intron	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9773047_9773048delAG	uc002gmd.1	+							NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor						G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				lung(2)|ovary(1)	3					Glucagon recombinant(DB00040)	gagaaacctaagagagagagag	0.000													4	2	---	---	---	---	
MAP2K4	6416	broad.mit.edu	37	17	12028819	12028819	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12028819delA	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron|MAP2K4_uc010vvi.1_Intron|MAP2K4_uc010vvj.1_Intron	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TAAGTTGCTGAAAAAAAAAAA	0.294			D|Mis|N		pancreatic|breast|colorectal								8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13703738	13703740	+	IGR	DEL	TGT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13703738_13703740delTGT								HS3ST3A1 (198494 upstream) : CDRT15P (224075 downstream)																							TCTttgttgctgttgttgttgtt	0.251													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15708451	15708452	+	IGR	DEL	TG	-	-	rs3062448		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15708451_15708452delTG								MEIS3P1 (15434 upstream) : ADORA2B (139779 downstream)																							tttttttttttggcggagtctc	0.020													4	2	---	---	---	---	
MYO15A	51168	broad.mit.edu	37	17	18017054	18017054	+	Intron	DEL	A	-	-	rs72282387		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18017054delA	uc010vxh.1	+							NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV						sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					agactgtctcaaaaaaaaaaa	0.060													4	2	---	---	---	---	
B9D1	27077	broad.mit.edu	37	17	19278136	19278136	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19278136delA	uc002gvl.3	-						B9D1_uc010cqm.1_Intron|MAPK7_uc002gvn.2_5'Flank|MAPK7_uc002gvo.2_5'Flank			Q9UPM9	B9D1_HUMAN	SubName: Full=cDNA FLJ57537;						cilium assembly	centrosome|microtubule basal body	protein binding				0	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					caagaaagtgaaaagacgatc	0.000													4	2	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	19919530	19919531	+	Intron	INS	-	A	A	rs150157650		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19919530_19919531insA	uc002gwq.2	+							NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						gactccatctcaaaaaaaaaaa	0.079													4	4	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	19989108	19989108	+	Intron	DEL	G	-	-	rs79908157		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19989108delG	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_5'Flank|CYTSB_uc002gws.2_5'Flank	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						GAGCAATGGCGGACTCCCGCT	0.493													2	5	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	20097635	20097635	+	Intron	DEL	C	-	-	rs112127857		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20097635delC	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gwt.2_Intron|CYTSB_uc002gwu.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						tctttacttaccccaagtcag	0.000													5	5	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	20130318	20130336	+	Intron	DEL	CTCCCAGGGAAGCACTGCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20130318_20130336delCTCCCAGGGAAGCACTGCT	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron|CYTSB_uc002gwt.2_Intron|CYTSB_uc002gwu.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						GGGCCAGTGCCTCCCAGGGAAGCACTGCTCTCCCAGGGA	0.598											OREG0024242	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20233890	20233892	+	Intron	DEL	TTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20233890_20233892delTTG	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						TTTTGGACttttgttgttgttgt	0.197													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21250516	21250516	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21250516delC								MAP2K3 (31967 upstream) : KCNJ12 (29183 downstream)																							GCCCTTCCCGCCCCCTGGTCC	0.632													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21346007	21346008	+	IGR	DEL	TA	-	-	rs72306824		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21346007_21346008delTA								KCNJ12 (22828 upstream) : C17orf51 (85564 downstream)																							ggctaatttttaaaattttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21347043	21347044	+	IGR	DEL	AG	-	-	rs111380221		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21347043_21347044delAG								KCNJ12 (23864 upstream) : C17orf51 (84528 downstream)																							aagcacaggcagagttaattta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21351164	21351165	+	IGR	INS	-	TG	TG	rs77745849		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21351164_21351165insTG								KCNJ12 (27985 upstream) : C17orf51 (80407 downstream)																							TCCATCATACATGTGCCCTTGG	0.510													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21526254	21526255	+	IGR	INS	-	A	A	rs144707550	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21526254_21526255insA								C17orf51 (48523 upstream) : FAM27L (299115 downstream)																							ATGGTTTCTTTTTTTCCTTTTC	0.183													13	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22253548	22253549	+	IGR	INS	-	C	C	rs138638530		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22253548_22253549insC								FLJ36000 (340478 upstream) : None (None downstream)																							agaatcttcttgtgatgtttgc	0.000													18	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25287370	25287370	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25287370delT								None (None upstream) : WSB1 (333736 downstream)																							CTAAATGCTATTTTTTTTAAA	0.308													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25295543	25295543	+	IGR	DEL	T	-	-	rs78287895		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25295543delT								None (None upstream) : WSB1 (325563 downstream)																							tatttaaaaattttttCCACC	0.244													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27660491	27660491	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27660491delA								NUFIP2 (39325 upstream) : TAOK1 (57452 downstream)																							TTCCATCTCGAAAAAAAAAAA	0.169													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27699329	27699330	+	IGR	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27699329_27699330delTT								NUFIP2 (78163 upstream) : TAOK1 (18613 downstream)																							TCCCATGCTCtttttttttttt	0.213													4	2	---	---	---	---	
GOSR1	9527	broad.mit.edu	37	17	28838551	28838551	+	Intron	DEL	T	-	-	rs5819904		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28838551delT	uc002hfe.2	+						GOSR1_uc002hfd.2_Intron|GOSR1_uc002hff.2_Intron	NM_004871	NP_004862	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1 isoform 1						intra-Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|SNARE complex	SNAP receptor activity				0						aacatttgtattttttttttt	0.144													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36402732	36402732	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36402732delA	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																		actccatcttaaaaaaaaaaa	0.129													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36564025	36564026	+	IGR	INS	-	T	T	rs146717520		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36564025_36564026insT								SOCS7 (8008 upstream) : ARHGAP23 (49618 downstream)																							atgtatttcccttttttttttt	0.000													4	2	---	---	---	---	
SRCIN1	80725	broad.mit.edu	37	17	36755242	36755245	+	Intron	DEL	GTGT	-	-	rs140186252		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36755242_36755245delGTGT	uc002hqd.2	-						SRCIN1_uc002hqh.1_Intron	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein						exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0						TAAGGCATGAgtgtgtgtgtgtat	0.407													3	3	---	---	---	---	
CASC3	22794	broad.mit.edu	37	17	38323195	38323195	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38323195delT	uc010cwt.1	+						CASC3_uc010cws.1_3'UTR|CASC3_uc002hue.2_Intron	NM_007359	NP_031385	O15234	CASC3_HUMAN	metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1						AGATAAGGTCTTTTTtttttt	0.234													3	3	---	---	---	---	
TNS4	84951	broad.mit.edu	37	17	38637223	38637223	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38637223delT	uc010cxb.2	-						TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			TTTGCAACCCTTTTGATCTCT	0.532													4	2	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39789866	39789867	+	Intron	DEL	GT	-	-	rs151010375		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39789866_39789867delGT	uc010wfs.1	-						uc010cxq.1_Intron|uc002hxi.1_Intron	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		gctgtgtgtggtgtgtgtgtgg	0.000													4	3	---	---	---	---	
G6PC	2538	broad.mit.edu	37	17	41057906	41057911	+	Intron	DEL	ACAAAA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41057906_41057911delACAAAA	uc002icb.1	+						G6PC_uc010whf.1_Intron	NM_000151	NP_000142	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit						gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		ataaaaaaatacaaaaacttagccag	0.000									Glycogen_Storage_Disease_type_Ia				1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41383176	41383177	+	Intron	INS	-	A	A	rs113021295		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41383176_41383177insA	uc002ido.2	-											Homo sapiens cDNA clone IMAGE:5169062, partial cds.																		ggagaaaccccatctgtactaa	0.218													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41780665	41780666	+	IGR	DEL	AG	-	-	rs138999628		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41780665_41780666delAG								MEOX1 (41403 upstream) : SOST (50433 downstream)																							AGACAACAAAAGAGAGTCAGAT	0.312													2	6	---	---	---	---	
ASB16	92591	broad.mit.edu	37	17	42250095	42250096	+	Intron	INS	-	TGATTCTCC	TGATTCTCC	rs147039706	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42250095_42250096insTGATTCTCC	uc002ifl.1	+						ASB16_uc002ifm.1_Intron	NM_080863	NP_543139	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box-containing protein						intracellular signal transduction		protein binding			kidney(2)	2		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		ctgggttcaaatgcctcagcct	0.005													6	3	---	---	---	---	
MAP3K14	9020	broad.mit.edu	37	17	43386355	43386355	+	Intron	DEL	T	-	-	rs77912522		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43386355delT	uc002iiw.1	-							NM_003954	NP_003945	Q99558	M3K14_HUMAN	mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|I-kappaB kinase/NF-kappaB cascade|immune response|positive regulation of I-kappaB kinase/NF-kappaB cascade|T cell costimulation	cytosol	ATP binding|MAP kinase kinase kinase activity|NF-kappaB-inducing kinase activity|protein binding			central_nervous_system(3)|breast(2)|lung(1)|ovary(1)|stomach(1)	8						tttaaaaaaattttttttttg	0.000													3	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43711571	43711572	+	Intron	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43711571_43711572delGA	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron|MGC57346_uc010dan.2_Intron|MGC57346_uc002ijj.3_Intron			P34998	CRFR1_HUMAN	SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		atgagcaggggAGAGAGAGAGG	0.198													9	4	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44215233	44215233	+	Intron	DEL	A	-	-	rs75260986		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44215233delA	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				actctgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
NSF	4905	broad.mit.edu	37	17	44785330	44785330	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44785330delT	uc002iku.2	+						NSF_uc010wke.1_Intron|NSF_uc010wkf.1_Intron|NSF_uc010wkg.1_Intron	NM_006178	NP_006169	P46459	NSF_HUMAN	vesicle-fusing ATPase						protein transport|synaptic transmission	cytosol	ATP binding|metal ion binding			ovary(1)	1		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		atccgggaggtggaggttgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46103486	46103487	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46103486_46103487delAC								CDK5RAP3 (44340 upstream) : COPZ2 (48 downstream)																							CCTTATATGAacacacacacac	0.490											OREG0024510	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
UBE2Z	65264	broad.mit.edu	37	17	47001096	47001096	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47001096delT	uc002ioi.2	+							NM_023079	NP_075567	Q9H832	UBE2Z_HUMAN	ubiquitin-conjugating enzyme E2Z						apoptosis	cytoplasm|nucleus	ATP binding|ubiquitin-protein ligase activity				0						CAGTAGCCTCttttttttttt	0.214													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47158423	47158424	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47158423_47158424insA								IGF2BP1 (24918 upstream) : B4GALNT2 (51398 downstream)																							gaaactgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
LUC7L3	51747	broad.mit.edu	37	17	48828354	48828355	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48828354_48828355insT	uc002isr.2	+						LUC7L3_uc010wmw.1_3'UTR|LUC7L3_uc002isq.2_3'UTR|LUC7L3_uc002iss.2_3'UTR|uc002ist.1_5'Flank	NM_006107	NP_006098	O95232	LC7L3_HUMAN	LUC7-like 3						apoptosis|mRNA processing|response to stress|RNA splicing	focal adhesion|nuclear speck	DNA binding|mRNA binding|protein binding				0						GATGTCATTTCTTTTTTTTTTT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50406514	50406515	+	IGR	DEL	AA	-	-	rs2769574	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50406514_50406515delAA								CA10 (169137 upstream) : None (None downstream)																							acacacacacaaacacacacac	0.297													3	4	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54331075	54331075	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54331075delG	uc002iun.1	+							NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						actccagtctggacgacagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	57507203	57507206	+	IGR	DEL	ATTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57507203_57507206delATTG								YPEL2 (28108 upstream) : DHX40 (135680 downstream)																							CTTTTCCCTTattgattgattgat	0.216													3	4	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58311477	58311478	+	Intron	INS	-	T	T	rs151158730		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58311477_58311478insT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|SCARNA20_uc002iyp.1_5'Flank	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			agcatgactaattttttttttt	0.000													4	2	---	---	---	---	
APPBP2	10513	broad.mit.edu	37	17	58575490	58575490	+	Intron	DEL	A	-	-	rs77814808		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58575490delA	uc002iys.1	-						APPBP2_uc010ddl.1_Intron	NM_006380	NP_006371	Q92624	APBP2_HUMAN	amyloid beta precursor protein-binding protein						intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			ccctggctccaaaaaaaaaaa	0.159													3	3	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	58891631	58891632	+	Intron	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58891631_58891632delTG	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			cttggtattttgtgtgtgtgtg	0.000													2	4	---	---	---	---	
BRIP1	83990	broad.mit.edu	37	17	59901119	59901120	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59901119_59901120delAC	uc002izk.1	-							NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1						cacacaataaacacacacacac	0.000			F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60325311	60325311	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60325311delG								MED13 (182668 upstream) : TBC1D3P2 (16758 downstream)																							AGGAAGGTCTGGGTGAAATGA	0.244													4	2	---	---	---	---	
MRC2	9902	broad.mit.edu	37	17	60746447	60746452	+	Intron	DEL	ACACAC	-	-	rs140362106		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60746447_60746452delACACAC	uc002jad.2	+						MRC2_uc002jac.2_Intron	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3						AAATATGGCAacacacacacacacac	0.364													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63391070	63391070	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63391070delA								RGS9 (167251 upstream) : AXIN2 (133615 downstream)																							catctggcccaaggcaacccc	0.109													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64554532	64554532	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64554532delC	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						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)	ggacctttagcagagacttgg	0.050													4	2	---	---	---	---	
CACNG5	27091	broad.mit.edu	37	17	64861386	64861387	+	Intron	INS	-	T	T	rs34773445		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64861386_64861387insT	uc010wqi.1	+							NM_145811	NP_665810	Q9UF02	CCG5_HUMAN	voltage-dependent calcium channel gamma-5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			ctatttttaTGTTTTTTTTTTT	0.193													3	3	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65592598	65592600	+	Intron	DEL	TTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65592598_65592600delTTG	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			CCCTATTTCTttgttgttgttgt	0.177													4	4	---	---	---	---	
LOC651250	651250	broad.mit.edu	37	17	66122028	66122029	+	RNA	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66122028_66122029delAA	uc002jgq.2	+	6		c.1151_1152delAA			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						TTCGTGAGCTaaaaaaaaaaaa	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68917358	68917359	+	IGR	INS	-	TGTG	TGTG	rs34413452		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68917358_68917359insTGTG								KCNJ2 (741177 upstream) : None (None downstream)																							TCTATGTAAATtgtgtgtgtgt	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71319207	71319207	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71319207delT								CDC42EP4 (11064 upstream) : SDK2 (11317 downstream)																							aaactatcacttttttttttt	0.000													4	2	---	---	---	---	
SEC14L1	6397	broad.mit.edu	37	17	75187625	75187626	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75187625_75187626insT	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_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						ATTTGGttttgttttttttttc	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75241907	75241908	+	IGR	DEL	GC	-	-	rs67971549		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75241907_75241908delGC								SEC14L1 (28728 upstream) : SEPT9 (35584 downstream)																							atgtgtgtgtgcgtgtttacgt	0.010													4	2	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75481272	75481273	+	Intron	INS	-	GTA	GTA	rs139055400		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75481272_75481273insGTA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc010wtl.1_Intron|SEPT9_uc002jty.3_Intron|SEPT9_uc010wtm.1_Intron|SEPT9_uc010wtn.1_Intron|SEPT9_uc010dhd.2_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			tgattgtggtggtggtggtgat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76651040	76651041	+	IGR	DEL	TT	-	-	rs145661828		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76651040_76651041delTT								DNAH17 (182184 upstream) : CYTH1 (19090 downstream)																							TTAAATTAGAtttttttttttt	0.183													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77063359	77063360	+	IGR	DEL	AC	-	-	rs58308823		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77063359_77063360delAC								C1QTNF1 (17490 upstream) : ENGASE (7659 downstream)																							accctggcaaacacacacacac	0.000													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77242099	77242099	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77242099delA	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			agcatgtcagaaaaaaaaaaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	79643478	79643479	+	IGR	INS	-	CT	CT	rs138247364		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79643478_79643479insCT								CCDC137 (2544 upstream) : ARL16 (4755 downstream)																							ctctccttctcctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	317977	317978	+	IGR	INS	-	T	T	rs138873298		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:317977_317978insT								THOC1 (49918 upstream) : COLEC12 (1378 downstream)																							TGTCtttattcttttttttttt	0.233													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1187359	1187359	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1187359delA								ADCYAP1 (275188 upstream) : C18orf2 (67031 downstream)																							TATGTGAAAGAAAAAAAAAAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1680543	1680543	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1680543delT								C18orf2 (273362 upstream) : METTL4 (856982 downstream)																							AAGTAAACACTTACAAAAGGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2422722	2422722	+	IGR	DEL	T	-	-	rs111655260		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2422722delT								None (None upstream) : METTL4 (114803 downstream)																							GAAGTCAttcttttttttttt	0.184													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3684776	3684776	+	Intron	DEL	A	-	-	rs76221174		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3684776delA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				ATGAAACAGGAAAAAAAATGT	0.438													2	4	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4100715	4100715	+	Intron	DEL	C	-	-	rs78518516		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4100715delC	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				gccaccttcactagtgacttt	0.000													3	3	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4371746	4371747	+	Intron	INS	-	A	A	rs148563424	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4371746_4371747insA	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				GGCAAAATGGTAAAAAGGCAAA	0.386													4	3	---	---	---	---	
EPB41L3	23136	broad.mit.edu	37	18	5630859	5630860	+	5'Flank	INS	-	ACACAC	ACACAC	rs150116355	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5630859_5630860insACACAC	uc010dkq.1	-						EPB41L3_uc002kmv.1_5'Flank	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						GGGATAGAATTacacacacaca	0.455													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5672379	5672380	+	IGR	INS	-	C	C	rs144672031	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5672379_5672380insC								EPB41L3 (41737 upstream) : TMEM200C (217804 downstream)																							GTAAGTCATATCCCACCATGAT	0.248													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	7186651	7186651	+	IGR	DEL	T	-	-	rs11348974		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7186651delT								LAMA1 (68838 upstream) : LRRC30 (44486 downstream)																							cagctaattcttttttttttt	0.000													4	2	---	---	---	---	
CEP76	79959	broad.mit.edu	37	18	12682162	12682162	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12682162delT	uc002kri.2	-						PSMG2_uc002krg.2_Intron|CEP76_uc002krh.3_Intron|CEP76_uc010wzz.1_Intron|CEP76_uc010xaa.1_Intron	NM_024899	NP_079175	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa						G2/M transition of mitotic cell cycle|regulation of centriole replication	centriole|cytosol	protein binding				0						AAGAAAtttcttttttttttc	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13936434	13936435	+	IGR	INS	-	AC	AC	rs147696593	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13936434_13936435insAC								MC2R (20899 upstream) : ZNF519 (139554 downstream)																							GTGAGAAAGTAACAGAGCTTCT	0.495													1	5	---	---	---	---	
ANKRD30B	374860	broad.mit.edu	37	18	14814786	14814786	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14814786delT	uc010dlo.2	+						ANKRD30B_uc010xak.1_Intron	NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B											ovary(1)|skin(1)	2						TATCCCCTAATAGCTGAAGAA	0.348													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19187290	19187291	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19187290_19187291insT								ESCO1 (6597 upstream) : SNRPD1 (4969 downstream)																							ccggccTATTAttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19926952	19926958	+	IGR	DEL	CCCCTCC	-	-	rs144361320		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19926952_19926958delCCCCTCC								GATA6 (144725 upstream) : CTAGE1 (66606 downstream)																							CTTCCTCTCTCCCCTCCCCCTGGCCGA	0.512													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20406971	20406971	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20406971delA								CTAGE1 (409093 upstream) : RBBP8 (106324 downstream)																							TCCATGCTTTAAAAAAACTTC	0.473													4	2	---	---	---	---	
RBBP8	5932	broad.mit.edu	37	18	20551112	20551112	+	Intron	DEL	A	-	-	rs35208743		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20551112delA	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc002ktx.1_Intron	NM_002894	NP_002885	Q99708	COM1_HUMAN	retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GAGAGTCTTTAAAAAAAAAAA	0.448								Direct_reversal_of_damage|Homologous_recombination					1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	21069822	21069822	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21069822delA								RIOK3 (6725 upstream) : C18orf8 (13640 downstream)																							AATGAAAAAGAAAAAAAAAAA	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	21547039	21547040	+	IGR	DEL	AC	-	-	rs139443515		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21547039_21547040delAC								LAMA3 (12012 upstream) : TTC39C (25697 downstream)																							CAGATTGTATacacacacacac	0.450													3	3	---	---	---	---	
TTC39C	125488	broad.mit.edu	37	18	21624167	21624170	+	Intron	DEL	TCTT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21624167_21624170delTCTT	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1						AAAGTCAGACTCTTTCTAGGATTT	0.490													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22269394	22269395	+	IGR	DEL	AG	-	-	rs33942587		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22269394_22269395delAG								HRH4 (209474 upstream) : ZNF521 (372493 downstream)																							ACAAACAAACagagagagagag	0.292													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22654007	22654008	+	Intron	INS	-	GTGTGCAC	GTGTGCAC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22654007_22654008insGTGTGCAC	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					tgcatgtgtgtgtctgtgcaca	0.287			T	PAX5	ALL								3	5	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22680646	22680646	+	Intron	DEL	A	-	-	rs76038955		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22680646delA	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TTGAAGAATTAAAAAAAAAAA	0.318			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23414585	23414586	+	IGR	INS	-	T	T	rs34695245		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23414585_23414586insT								ZNF521 (482371 upstream) : SS18 (181633 downstream)																							gtgttgttagcttttttttttt	0.035													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23496767	23496768	+	IGR	INS	-	TTTCTTACACATCG	TTTCTTACACATCG	rs142833233	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23496767_23496768insTTTCTTACACATCG								ZNF521 (564553 upstream) : SS18 (99451 downstream)																							ctagctcttgttttcatttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23548185	23548186	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23548185_23548186insT								ZNF521 (615971 upstream) : SS18 (48033 downstream)																							GACCTTTCTAAttttttttttc	0.158													3	3	---	---	---	---	
TAF4B	6875	broad.mit.edu	37	18	23860008	23860008	+	Intron	DEL	A	-	-	rs34693562		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23860008delA	uc002kvu.3	+						TAF4B_uc002kvs.3_Intron|TAF4B_uc002kvt.3_Intron	NM_005640	NP_005631	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding						transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			actctatctcaaaaaaaaaaa	0.000													4	4	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	34947659	34947659	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34947659delT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						cttttctttcttttttttttt	0.348													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35001519	35001520	+	Intron	DEL	GT	-	-	rs151102794		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35001519_35001520delGT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						TGTGTCATGCGTGTGAGTCATG	0.589													4	3	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35102483	35102484	+	Intron	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35102483_35102484delCA	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						TGTGAGCGCGCACACACACACA	0.480													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39299059	39299061	+	IGR	DEL	CTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39299059_39299061delCTG								KC6 (198498 upstream) : PIK3C3 (236138 downstream)																							GACTCTGTATCTGCTGCTGCTGC	0.374													4	2	---	---	---	---	
SIGLEC15	284266	broad.mit.edu	37	18	43422408	43422409	+	3'UTR	DEL	GA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43422408_43422409delGA	uc002lbl.1	+	6					SIGLEC15_uc010xcp.1_RNA	NM_213602	NP_998767	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15 precursor							integral to membrane					0						gtgtgtgtgtgAGAGAGAGAGA	0.401													4	2	---	---	---	---	
PIAS2	9063	broad.mit.edu	37	18	44486311	44486311	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44486311delA	uc002lck.2	-						PIAS2_uc010dnp.2_Intron|PIAS2_uc002lcl.2_Intron|PIAS2_uc010xda.1_Intron|PIAS2_uc002lcm.2_Intron|PIAS2_uc002lcn.1_Intron	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform						androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4						aaaaagaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45564867	45564868	+	Intron	INS	-	AG	AG	rs141102732	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45564867_45564868insAG	uc002lda.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnv.2_Intron|ZBTB7C_uc010dnw.2_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						caacttccagtagtttccaagc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51317048	51317048	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51317048delT								DCC (259266 upstream) : MBD2 (363527 downstream)																							TCCCTCTTCATTTTTTTTGAG	0.318													4	2	---	---	---	---	
ONECUT2	9480	broad.mit.edu	37	18	55134106	55134109	+	Intron	DEL	TGTT	-	-	rs36085545		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55134106_55134109delTGTT	uc002lgo.2	+							NM_004852	NP_004843	O95948	ONEC2_HUMAN	one cut domain, family member 2						organ morphogenesis	nucleus	sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		AGGCTACTCATGTTTGTTAGAGCC	0.505													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55425558	55425558	+	IGR	DEL	C	-	-	rs36067041		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55425558delC								ATP8B1 (26519 upstream) : NEDD4L (286061 downstream)																							ttctgtttatccgtcctgtgt	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57403945	57403945	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57403945delA								CCBE1 (39301 upstream) : PMAIP1 (163247 downstream)																							ctgtgtctacaaaaaaatatt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60683187	60683188	+	IGR	DEL	TT	-	-	rs35871934		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60683187_60683188delTT								PHLPP1 (35522 upstream) : BCL2 (107391 downstream)																							TCTCGCTCTCtttttttttttt	0.213													4	2	---	---	---	---	
BCL2	596	broad.mit.edu	37	18	60865411	60865412	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60865411_60865412delAC	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)	acacagacatacacacacacac	0.178			T	IGH@	NHL|CLL								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62410213	62410214	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62410213_62410214insA								C18orf20 (593953 upstream) : None (None downstream)																							TCAAAGTGCAGAAAAAAAATAG	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65005663	65005677	+	IGR	DEL	CTTCCCTCCTTCCTT	-	-	rs72305925	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65005663_65005677delCTTCCCTCCTTCCTT								CDH19 (734447 upstream) : DSEL (168142 downstream)																							ccctcccttccttccctccttccttcttccctcct	0.028													6	3	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66471333	66471333	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66471333delG	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				tattagagatggagtttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71915536	71915536	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71915536delT								C18orf55 (89332 upstream) : CYB5A (4992 downstream)																							caagccttcctttctgcccaA	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	771607	771608	+	IGR	DEL	CT	-	-	rs113627400		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:771607_771608delCT								C19orf21 (7289 upstream) : PTBP1 (25784 downstream)																							gcccagtcccctctctcctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3342173	3342175	+	IGR	DEL	AAA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3342173_3342175delAAA								CELF5 (45102 upstream) : NFIC (17441 downstream)																							actccatctcaaaaaaaaaaaag	0.246													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3561966	3561967	+	IGR	INS	-	T	T	rs12981321		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3561966_3561967insT								C19orf28 (4395 upstream) : HMG20B (10976 downstream)																							GCCttttcttgttttttttgag	0.168													4	2	---	---	---	---	
ARRDC5	645432	broad.mit.edu	37	19	4902218	4902218	+	Intron	DEL	C	-	-	rs66520973		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4902218delC	uc002mbm.2	-							NM_001080523	NP_001073992	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5						signal transduction						0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CACTGTCTCTCCCCATGAATG	0.279													4	3	---	---	---	---	
PTPRS	5802	broad.mit.edu	37	19	5248400	5248400	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5248400delA	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		aagcaagaagaaaaaaaaaaa	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6581061	6581062	+	IGR	INS	-	T	T	rs116048035		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6581061_6581062insT								TNFSF9 (45122 upstream) : CD70 (2073 downstream)																							ttccttccttcttccctccttc	0.139													4	3	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153025	7153028	+	Intron	DEL	CACA	-	-	rs149041762	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153025_7153028delCACA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	acacacacaccacacacacacacc	0.167													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	7636721	7636722	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7636721_7636722insA								PNPLA6 (10069 upstream) : KIAA1543 (24066 downstream)																							aaattagtcccagctacttggg	0.000													1	5	---	---	---	---	
ZNF44	51710	broad.mit.edu	37	19	12407866	12407866	+	5'Flank	DEL	T	-	-	rs138816905		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12407866delT	uc010xmj.1	-						ZNF44_uc002mtl.2_5'Flank|ZNF44_uc010dyr.1_5'Flank|ZNF44_uc010xmi.1_5'Flank|ZNF44_uc002mtn.3_5'Flank|ZNF44_uc010dys.2_5'Flank|ZNF44_uc002mto.2_5'Flank	NM_001164276	NP_001157748	P15621	ZNF44_HUMAN	zinc finger protein 44 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AGCATGGttgttttttttttg	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13295891	13295892	+	IGR	DEL	GT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13295891_13295892delGT								IER2 (30175 upstream) : CACNA1A (21364 downstream)																							gcatacatacgtgtgtgtatac	0.005													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13686539	13686539	+	IGR	DEL	T	-	-	rs112120332		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13686539delT								CACNA1A (69265 upstream) : CCDC130 (156035 downstream)																							ggtgagaccctcccccccatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13729547	13729548	+	IGR	DEL	AG	-	-	rs112163024		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13729547_13729548delAG								CACNA1A (112273 upstream) : CCDC130 (113026 downstream)																							agacagagacagagagagagag	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14323333	14323333	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14323333delA								LPHN1 (6336 upstream) : CD97 (168880 downstream)																							gactcagtctaaaaaaaaaaa	0.219													6	3	---	---	---	---	
PKN1	5585	broad.mit.edu	37	19	14541210	14541221	+	5'Flank	DEL	CTCTCTCTCTCT	-	-	rs112131776		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14541210_14541221delCTCTCTCTCTCT	uc002myp.2	+							NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8						cccttccttcctctctctctctctctctctct	0.009													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14842459	14842460	+	IGR	INS	-	AA	AA	rs143619378	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14842459_14842460insAA								ZNF333 (10689 upstream) : EMR2 (745 downstream)																							AACTCTACCTTAAAGCCGTATT	0.441													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15209986	15209987	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15209986_15209987insA								OR1I1 (11044 upstream) : SYDE1 (8227 downstream)																							gaagggaagggaagggaaaggg	0.000													3	8	---	---	---	---	
ILVBL	10994	broad.mit.edu	37	19	15237395	15237396	+	5'Flank	INS	-	A	A	rs141870824	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15237395_15237396insA	uc002nam.2	-						ILVBL_uc010dzw.2_5'Flank|ILVBL_uc010dzx.1_5'Flank	NM_006844	NP_006835	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like							integral to membrane	magnesium ion binding|thiamine pyrophosphate binding|transferase activity			ovary(2)	2						agctaaaaaagaaaaaaaaagt	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15593377	15593378	+	IGR	DEL	TC	-	-	rs58633996		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15593377_15593378delTC								PGLYRP2 (3062 upstream) : CYP4F22 (25958 downstream)																							ctttctttcttccttccttcct	0.000													6	4	---	---	---	---	
CYP4F3	4051	broad.mit.edu	37	19	15771529	15771530	+	3'UTR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15771529_15771530insT	uc002nbj.2	+	13					CYP4F3_uc010xok.1_3'UTR|CYP4F3_uc010xol.1_3'UTR|CYP4F3_uc010xom.1_3'UTR|CYP4F3_uc002nbk.2_3'UTR|CYP4F3_uc010xon.1_3'UTR	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,						leukotriene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3						GGGGTGCCTAAttttttttttt	0.124													4	2	---	---	---	---	
C19orf44	84167	broad.mit.edu	37	19	16625198	16625198	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16625198delA	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167												0						ctgtctccagaaaaaaaaaaa	0.284													4	2	---	---	---	---	
JUND	3727	broad.mit.edu	37	19	18393626	18393629	+	5'Flank	DEL	TCTG	-	-	rs41507248		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18393626_18393629delTCTG	uc002nip.2	-							NM_005354	NP_005345	P17535	JUND_HUMAN	jun D proto-oncogene						regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0						GCTCCCCACCTCTGTCTGAATGGA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	18688758	18688758	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18688758delC								UBA52 (489 upstream) : C19orf60 (10737 downstream)																							acgcacttcacccacccttcg	0.030													4	2	---	---	---	---	
CRTC1	23373	broad.mit.edu	37	19	18838059	18838062	+	Intron	DEL	CAAA	-	-	rs71336690		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18838059_18838062delCAAA	uc002nkb.3	+						CRTC1_uc010ebv.2_Intron	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform						interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519						gaccctgtctcaaacaaacaaggc	0.000													4	4	---	---	---	---	
SLC25A42	284439	broad.mit.edu	37	19	19209344	19209344	+	Intron	DEL	G	-	-	rs5827430		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19209344delG	uc002nlf.1	+						SLC25A42_uc010xqn.1_Intron	NM_178526	NP_848621	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			ggtcatggctgcagtgagcta	0.070													2	5	---	---	---	---	
TMEM161A	54929	broad.mit.edu	37	19	19244865	19244866	+	Intron	INS	-	T	T	rs145323190		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19244865_19244866insT	uc002nlg.2	-						TMEM161A_uc010eca.2_Intron|TMEM161A_uc002nlh.2_Intron|TMEM161A_uc002nli.2_Intron|TMEM161A_uc002nlj.2_Intron	NM_017814	NP_060284	Q9NX61	T161A_HUMAN	transmembrane protein 161A precursor						cellular response to oxidative stress|cellular response to UV|negative regulation of apoptosis|positive regulation of DNA repair|response to retinoic acid	integral to membrane				breast(2)	2			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			TCTCTGACGTGTTTTTTTTTTT	0.223													5	4	---	---	---	---	
NCAN	1463	broad.mit.edu	37	19	19342148	19342149	+	Intron	INS	-	TC	TC			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19342148_19342149insTC	uc002nlz.2	+						NCAN_uc010ecc.1_Intron	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor						axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			tcttttttttttttttttgaga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22626546	22626547	+	IGR	INS	-	CT	CT	rs143185518	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22626546_22626547insCT								ZNF98 (21398 upstream) : ZNF492 (190579 downstream)																							ttgtgaaacccgtctctgctaa	0.000													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24019159	24019160	+	IGR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24019159_24019160delAC								RPSAP58 (8242 upstream) : ZNF254 (197087 downstream)																							tagtattccaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24544618	24544619	+	IGR	INS	-	T	T	rs138656558	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24544618_24544619insT								LOC100101266 (198369 upstream) : None (None downstream)																							tggaaacactgtttttttttag	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27846764	27846765	+	IGR	INS	-	T	T	rs149691710	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27846764_27846765insT								None (None upstream) : LOC148189 (434637 downstream)																							gaaaagttcaacgtgtgagacg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27906193	27906194	+	IGR	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27906193_27906194delAA								None (None upstream) : LOC148189 (375208 downstream)																							aaaactgctcaatcaaaagaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29977878	29977881	+	Intron	DEL	AACT	-	-	rs75596598		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29977878_29977881delAACT	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		CAGATTCAAAAACTAACTAAATCA	0.338													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29986593	29986593	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29986593delA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		actccatatcaaaaaaaaaaa	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30004069	30004070	+	Intron	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30004069_30004070insG	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		gaggaaggagagggggatgagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30066393	30066393	+	IGR	DEL	G	-	-	rs57957245		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30066393delG								VSTM2B (11167 upstream) : POP4 (30777 downstream)																							ACCAAGAGTTGTCCTGGTGGC	0.582													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30386878	30386878	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30386878delA								CCNE1 (71660 upstream) : C19orf2 (27673 downstream)																							gtctctactgaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31092718	31092718	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31092718delT								ZNF536 (43753 upstream) : DKFZp566F0947 (548065 downstream)																							AGCCCTGCAGTTTGCTTGTGT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31149447	31149448	+	IGR	DEL	CA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31149447_31149448delCA								ZNF536 (100482 upstream) : DKFZp566F0947 (491335 downstream)																							ctctctctgtcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31321496	31321496	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31321496delT								ZNF536 (272531 upstream) : DKFZp566F0947 (319287 downstream)																							ATAAAGAGTCTTTTTTTTTCC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31852608	31852608	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31852608delT								TSHZ3 (12418 upstream) : ZNF507 (983906 downstream)																							AAATTGGTACttttttttttt	0.134													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32741096	32741096	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32741096delT								TSHZ3 (900906 upstream) : ZNF507 (95418 downstream)																							AAGATCAGTCTTTTTTTTTTT	0.269													3	3	---	---	---	---	
UBA2	10054	broad.mit.edu	37	19	34925730	34925730	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34925730delT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			AGATAACTAATTTTTTTTTTC	0.338													5	3	---	---	---	---	
LSR	51599	broad.mit.edu	37	19	35751737	35751738	+	Intron	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35751737_35751738delAC	uc002nyl.2	+						LSR_uc002nym.2_Intron|LSR_uc002nyn.2_Intron|LSR_uc002nyo.2_Intron|LSR_uc010xsr.1_Intron|LSR_uc002nyp.2_Intron	NM_205834	NP_991403	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor						embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity				0	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			agaaacacaaacacacacacac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36074582	36074583	+	IGR	INS	-	T	T	rs74172750		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36074582_36074583insT								ATP4A (20022 upstream) : HAUS5 (29063 downstream)																							cataggcaaacttttttttttt	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36086794	36086795	+	IGR	INS	-	C	C			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36086794_36086795insC								ATP4A (32234 upstream) : HAUS5 (16851 downstream)																							tactaaaaatacaaaaaattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36463466	36463466	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36463466delA								LRFN3 (27371 upstream) : SDHAF1 (22635 downstream)																							CTCCCAGTTTAAAAAAAAAAA	0.209													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36735041	36735042	+	IGR	INS	-	T	T	rs145401532	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36735041_36735042insT								ZNF146 (5368 upstream) : ZFP14 (92120 downstream)																							GTCTGTGTGTCTGAGTGGCTGG	0.510													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36737103	36737104	+	IGR	INS	-	AT	AT	rs150601550	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36737103_36737104insAT								ZNF146 (7430 upstream) : ZFP14 (90058 downstream)																							tctgtgcgcacgtgtctgcgtg	0.084													3	4	---	---	---	---	
ZFP82	284406	broad.mit.edu	37	19	36885802	36885802	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36885802delA	uc002ody.1	-							NM_133466	NP_597723	Q8N141	ZFP82_HUMAN	zinc finger protein 82 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2						TCTTACCTATAAACCTCCTCA	0.294													4	2	---	---	---	---	
SIPA1L3	23094	broad.mit.edu	37	19	38527917	38527918	+	Intron	DEL	TC	-	-	rs35570244		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38527917_38527918delTC	uc002ohk.2	+							NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			tcagggaacgtctgtcataagg	0.000													3	5	---	---	---	---	
CAPN12	147968	broad.mit.edu	37	19	39227453	39227456	+	Intron	DEL	CTCT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39227453_39227456delCTCT	uc002ojd.1	-						CAPN12_uc010egd.1_5'Flank|CAPN12_uc002ojc.1_5'Flank	NM_144691	NP_653292	Q6ZSI9	CAN12_HUMAN	calpain 12						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			aacccccagcctctctctgtccct	0.162													13	6	---	---	---	---	
CYP2A7	1549	broad.mit.edu	37	19	41410365	41410366	+	Intron	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41410365_41410366delAA	uc002opo.2	-							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)			tgtcttaaggaaaaaaaaaaaa	0.153													5	4	---	---	---	---	
PSG1	5669	broad.mit.edu	37	19	43360107	43360107	+	Intron	DEL	C	-	-	rs138851816		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43360107delC	uc010eio.1	-						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG8_uc002oul.3_5'Flank|PSG8_uc002oum.3_5'Flank|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_5'Flank|PSG10_uc010eip.2_5'Flank|PSG1_uc002our.1_Intron|PSG1_uc002oux.1_Intron|PSG1_uc002ouy.1_Intron	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1						female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				cagacacacaccccccccccc	0.333													4	2	---	---	---	---	
PLAUR	5329	broad.mit.edu	37	19	44166872	44166873	+	Intron	INS	-	T	T	rs112075151		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44166872_44166873insT	uc002oxf.1	-						PLAUR_uc002oxd.1_Intron|PLAUR_uc002oxe.1_Intron|PLAUR_uc002oxg.1_Intron	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor						attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	cctttccactgttttttttttt	0.000													4	2	---	---	---	---	
CEACAM16	388551	broad.mit.edu	37	19	45204407	45204407	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45204407delC	uc010xxd.1	+						CEACAM16_uc002ozq.2_Intron	NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion											ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				CCCTACTTTTCCTCTCTTCTC	0.577													4	2	---	---	---	---	
CCDC61	729440	broad.mit.edu	37	19	46510312	46510312	+	Intron	DEL	T	-	-	rs35425844		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46510312delT	uc002pdw.2	+							NM_001080402	NP_001073871			coiled-coil domain containing 61											ovary(1)	1		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		atgtgttggcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46737275	46737276	+	IGR	DEL	AC	-	-	rs68019601		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46737275_46737276delAC								IGFL1 (2777 upstream) : HIF3A (63029 downstream)																							ACAGAAGCAAacacacacacac	0.332													4	3	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47703191	47703192	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47703191_47703192insT	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TAGATGATGGCttttttttttt	0.248													3	3	---	---	---	---	
CABP5	56344	broad.mit.edu	37	19	48546789	48546790	+	Intron	INS	-	TC	TC	rs139672144	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48546789_48546790insTC	uc002phu.1	-							NM_019855	NP_062829	Q9NP86	CABP5_HUMAN	calcium binding protein 5						signal transduction	cytoplasm	calcium ion binding			skin(1)	1		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		catcaccaccaccaccatcatc	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49286861	49286861	+	IGR	DEL	A	-	-	rs573921		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49286861delA								FGF21 (25279 upstream) : BCAT2 (11459 downstream)																							gacgtgtgccaaaacgcatgc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49949404	49949405	+	5'Flank	INS	-	T	T	rs150242832	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49949404_49949405insT	uc002pnr.1	-											Homo sapiens cDNA clone IMAGE:40119139.																		GGAGGATTAACAAGGGAGACTG	0.426													6	6	---	---	---	---	
FCGRT	2217	broad.mit.edu	37	19	50015239	50015239	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50015239delT	uc002poe.2	+						FCGRT_uc002pod.2_5'Flank|FCGRT_uc002pog.2_5'Flank|FCGRT_uc002pof.1_5'Flank|FCGRT_uc010yax.1_5'Flank|FCGRT_uc002poh.1_5'Flank	NM_001136019	NP_001129491	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha						antigen processing and presentation|female pregnancy|immune response	integral to membrane|MHC class I protein complex	IgG binding|receptor activity			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		AAGGATGTGGttttttttttt	0.308													6	3	---	---	---	---	
IL4I1	259307	broad.mit.edu	37	19	50424720	50424724	+	Intron	DEL	AATCC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50424720_50424724delAATCC	uc002pqu.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|NUP62_uc002pqx.2_Intron|NUP62_uc002pqy.2_Intron|NUP62_uc002pqz.2_Intron|NUP62_uc002pra.2_Intron|NUP62_uc002prb.2_Intron|NUP62_uc002prc.2_Intron	NM_172374	NP_758962	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 2							lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)		TTCACTCTCAAATCCAATTCAGGAT	0.620													4	2	---	---	---	---	
ZNF175	7728	broad.mit.edu	37	19	52080033	52080044	+	Intron	DEL	TCTTGAATCCTT	-	-	rs139192489		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52080033_52080044delTCTTGAATCCTT	uc002pxb.2	+							NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175						response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		gttccttgtgtcttgaatcctttcttgaatcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52284805	52284806	+	IGR	INS	-	C	C	rs148323404	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52284805_52284806insC								FPR2 (11028 upstream) : FPR3 (13605 downstream)																							aagcaggactgtaatgccccag	0.000													3	5	---	---	---	---	
ZNF616	90317	broad.mit.edu	37	19	52642804	52642804	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52642804delC	uc002pym.2	-						ZNF616_uc002pyn.2_Intron	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		TGGTGGGAATCCACCTCGCGA	0.622											OREG0025656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ZNF808	388558	broad.mit.edu	37	19	53066664	53066665	+	RNA	INS	-	AGTA	AGTA	rs151076736	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53066664_53066665insAGTA	uc002pzq.2	+	4		c.3176_3177insAGTA						Q8N4W9	ZN808_HUMAN	Homo sapiens zinc finger protein 808, mRNA (cDNA clone IMAGE:3542548), complete cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		cacatgcctgcagtatcaacta	0.045													4	2	---	---	---	---	
ZNF28	7576	broad.mit.edu	37	19	53306015	53306015	+	Intron	DEL	T	-	-	rs11347464		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53306015delT	uc002qad.2	-						ZNF28_uc002qac.2_Intron|ZNF28_uc010eqe.2_Intron	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28						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)		ACGTTGTGACttttttttttt	0.119													4	2	---	---	---	---	
ZNF331	55422	broad.mit.edu	37	19	54032044	54032044	+	Intron	DEL	T	-	-	rs11295331		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54032044delT	uc002qbx.1	+						ZNF331_uc002qby.1_Intron|ZNF331_uc002qbz.1_Intron	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)		CAGATAtttcttttttttttt	0.129			T	?	follicular thyroid adenoma								2	4	---	---	---	---	
ZNF331	55422	broad.mit.edu	37	19	54061700	54061700	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54061700delT	uc002qbx.1	+						ZNF331_uc002qby.1_Intron|ZNF331_uc002qbz.1_Intron|ZNF331_uc002qca.1_Intron|ZNF331_uc010eqr.1_Intron|ZNF331_uc002qcb.1_Intron|ZNF331_uc002qcc.1_Intron|ZNF331_uc002qcd.1_Intron	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)		ttcttaggccttttatggaga	0.000			T	?	follicular thyroid adenoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54355827	54355829	+	IGR	DEL	CTT	-	-	rs150864923		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54355827_54355829delCTT								NLRP12 (28179 upstream) : MYADM (13782 downstream)																							cgtgcccagccttcttcttcttc	0.015													5	3	---	---	---	---	
TARM1	441864	broad.mit.edu	37	19	54585249	54585249	+	5'Flank	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54585249delT	uc010yei.1	-							NM_001135686	NP_001129158	B6A8C7	TARM1_HUMAN	OSCAR-like transcript-2							integral to membrane					0						TTCATCACCAttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55027933	55027934	+	IGR	DEL	AC	-	-	rs34219955		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55027933_55027934delAC								LAIR2 (6038 upstream) : KIR3DX1 (15975 downstream)																							TGAGAGAGGGacacacacacac	0.332													7	8	---	---	---	---	
PPP1R12C	54776	broad.mit.edu	37	19	55618485	55618485	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55618485delA	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		gactgcctttAAAAAAAAAAA	0.005													6	4	---	---	---	---	
SSC5D	284297	broad.mit.edu	37	19	56001802	56001803	+	Intron	INS	-	CCAAGCAA	CCAAGCAA	rs140569962	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56001802_56001803insCCAAGCAA	uc002qlg.3	+							NM_001144950	NP_001138422	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine-rich glycoprotein							extracellular region|membrane	scavenger receptor activity				0						CTCCCCCGACCCCAAGGCTGGT	0.698													4	2	---	---	---	---	
RFPL4A	342931	broad.mit.edu	37	19	56272452	56272453	+	Intron	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56272452_56272453delTT	uc010yge.1	+							NM_001145014	NP_001138486	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A								zinc ion binding				0						tggtttttcctttttttttttt	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56403754	56403755	+	IGR	INS	-	AC	AC	rs141948919	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56403754_56403755insAC								NLRP4 (10536 upstream) : NLRP13 (3558 downstream)																							tacacacacatacacacacaca	0.015													3	5	---	---	---	---	
ZSCAN5A	79149	broad.mit.edu	37	19	56829488	56829489	+	Intron	DEL	GT	-	-	rs3833262		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56829488_56829489delGT	uc002qmr.2	-							NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						TGTTTGGCTGgtgtgtgtgtgt	0.356													5	3	---	---	---	---	
ZNF667	63934	broad.mit.edu	37	19	56960007	56960008	+	Intron	INS	-	A	A	rs139185818		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56960007_56960008insA	uc002qnd.2	-						ZNF667_uc010etl.2_Intron|ZNF667_uc002qne.2_Intron|ZNF667_uc010etm.2_Intron	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		tcaaccacagtaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57196765	57196767	+	IGR	DEL	ACT	-	-	rs148056160		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57196765_57196767delACT								ZNF835 (12519 upstream) : ZIM2 (89156 downstream)																							gtatcacaccactaagaacagcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57437385	57437386	+	IGR	INS	-	TG	TG	rs139299715	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57437385_57437386insTG								MIMT1 (77463 upstream) : USP29 (194123 downstream)																							Gttttttttttgggtttttttt	0.149													4	2	---	---	---	---	
ZIM3	114026	broad.mit.edu	37	19	57649481	57649484	+	Intron	DEL	AGGG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57649481_57649484delAGGG	uc002qnz.1	-							NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ggaaggaggcagggagggagggag	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	58685248	58685249	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58685248_58685249insT								ZNF329 (18771 upstream) : ZNF274 (9147 downstream)																							ACTCAGTTCCAttttttttttt	0.277													5	3	---	---	---	---	
ZNF544	27300	broad.mit.edu	37	19	58738748	58738748	+	5'Flank	DEL	G	-	-	rs75750997		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58738748delG	uc010euo.2	+						ZNF544_uc010eun.1_5'Flank|ZNF544_uc010yhw.1_5'Flank|ZNF544_uc010yhx.1_5'Flank|ZNF544_uc010yhy.1_5'Flank|ZNF544_uc002qrt.3_5'Flank|ZNF544_uc002qru.3_5'Flank|ZNF544_uc002qrv.2_5'Flank	NM_014480	NP_055295	Q6NX49	ZN544_HUMAN	zinc finger protein 544						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		gctatcttatgtccactttta	0.000													5	5	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3265173	3265179	+	Intron	DEL	GACGAAG	-	-	rs150215605	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3265173_3265179delGACGAAG	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						CCAACTGTATGACGAAGGCAAAAAACT	0.319													4	2	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3562610	3562610	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3562610delG	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						ATTCAggccaggcatggtggc	0.169													4	2	---	---	---	---	
SIGLEC1	6614	broad.mit.edu	37	20	3689086	3689086	+	5'Flank	DEL	A	-	-	rs71331061		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3689086delA	uc002wja.2	-						SIGLEC1_uc002wiz.3_5'Flank|SIGLEC1_uc002wjc.2_5'Flank	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor						cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10						taaaagcacgaaaaaaaaaaa	0.005													4	5	---	---	---	---	
RNF24	11237	broad.mit.edu	37	20	3944108	3944108	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3944108delG	uc002wkh.2	-						RNF24_uc002wki.2_Intron|RNF24_uc002wkj.2_Intron	NM_007219	NP_009150	Q9Y225	RNF24_HUMAN	ring finger protein 24 isoform 1							Golgi membrane|integral to membrane	zinc ion binding				0						ccaaagtgctgggattacagg	0.129													4	2	---	---	---	---	
C20orf30	29058	broad.mit.edu	37	20	5062205	5062205	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5062205delC	uc010gbi.2	-							NM_014145	NP_054864	Q96A57	CT030_HUMAN	hypothetical protein LOC29058 isoform 2							integral to membrane					0						ACCTAAAGCTCCCACATGCCC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6190211	6190212	+	IGR	INS	-	TCTT	TCTT	rs146162295	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6190211_6190212insTCTT								FERMT1 (86020 upstream) : BMP2 (558533 downstream)																							tctttcctCTCTCTTTCAACCC	0.124													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12822980	12822981	+	IGR	DEL	GT	-	-	rs71833259		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12822980_12822981delGT								BTBD3 (915738 upstream) : SPTLC3 (166646 downstream)																							TTGTTTTGGGgtgtgtgtgtgt	0.327													2	4	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15617865	15617866	+	Intron	INS	-	TATTA	TATTA	rs140705478	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15617865_15617866insTATTA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				tttacttgctgtattaattctg	0.084													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20808789	20808790	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20808789_20808790delAG								RALGAPA2 (115523 upstream) : PLK1S1 (297834 downstream)																							gaaggaaggaagggagggaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23522977	23522978	+	IGR	DEL	TT	-	-	rs66894754		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23522977_23522978delTT								CSTT (324 upstream) : CST9L (22394 downstream)																							tgtgtgtgtgtttgtgtgtatg	0.188													4	2	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25831101	25831102	+	Intron	INS	-	C	C	rs147373877	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25831101_25831102insC	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						GAGCAGGACTGTTGTGCTTGCT	0.431													11	5	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25831425	25831426	+	Intron	INS	-	T	T	rs148044070	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25831425_25831426insT	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						agggtgaataatttgctcaTCC	0.248													5	3	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25835766	25835766	+	Intron	DEL	C	-	-	rs77086666		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25835766delC	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						aaagccatcacttgggacatg	0.090													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25903695	25903695	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25903695delA								FAM182B (54909 upstream) : LOC100134868 (86740 downstream)																							TTAAGATGACAAAAAAACACC	0.428													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26204484	26204485	+	IGR	INS	-	T	T	rs145826095		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26204484_26204485insT								MIR663 (15570 upstream) : None (None downstream)																							AAGGTGCCAGGTTTTTTTTTTA	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29422533	29422534	+	IGR	DEL	AA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29422533_29422534delAA								None (None upstream) : FRG1B (189345 downstream)																							CTGGAGACATAAATAGAGGAAG	0.282													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29595617	29595618	+	IGR	INS	-	A	A	rs145720535		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29595617_29595618insA								None (None upstream) : FRG1B (16261 downstream)																							CTATTCCATGTAAAAAAATCAC	0.401													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29605899	29605900	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29605899_29605900insA								None (None upstream) : FRG1B (5979 downstream)																							GGTCCTAAATGAAAAAAAaaag	0.119													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29636672	29636673	+	Intron	INS	-	A	A	rs67210451		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-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													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30048982	30048983	+	IGR	INS	-	GTTT	GTTT	rs143461372	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30048982_30048983insGTTT								DEFB123 (10923 upstream) : DEFB124 (4326 downstream)																							taattttgttcgtttgtttgtt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30078634	30078635	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30078634_30078635insA								NCRNA00028 (3257 upstream) : HM13 (23606 downstream)																							acaatgtttccaaaaaaaaaaa	0.129													6	3	---	---	---	---	
HM13	81502	broad.mit.edu	37	20	30102619	30102620	+	Intron	INS	-	CCT	CCT	rs138291873	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30102619_30102620insCCT	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwb.1_Intron	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			CGGGACAGACACCTCTCCCCGG	0.653													4	2	---	---	---	---	
TPX2	22974	broad.mit.edu	37	20	30334683	30334683	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30334683delT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TCCCCTTCCATTTATCTCTTA	0.353													4	2	---	---	---	---	
EPB41L1	2036	broad.mit.edu	37	20	34761065	34761065	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34761065delC	uc002xfb.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xev.2_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)					GTGGCCAACTCGGGGACTGAG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37282758	37282761	+	IGR	DEL	ATGA	-	-	rs10562731		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37282758_37282761delATGA								ADIG (65654 upstream) : SLC32A1 (70344 downstream)																							aattGGCtggatgaatgaatgaat	0.137													2	4	---	---	---	---	
FAM83D	81610	broad.mit.edu	37	20	37559297	37559298	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37559297_37559298insT	uc002xjg.2	+						FAM83D_uc002xjf.2_Intron	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610						cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)				ctaattttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39566279	39566279	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39566279delT								MAFB (248403 upstream) : TOP1 (91183 downstream)																							gaggacacggttagggtgcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39756017	39756018	+	Intron	DEL	TG	-	-	rs35658382		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39756017_39756018delTG	uc002xjn.1	-											Homo sapiens cDNA clone IMAGE:5260583.																		ATAATTGTACtgtgtgtgtgtg	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41932318	41932318	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41932318delA								PTPRT (113761 upstream) : SFRS6 (154186 downstream)																							cacacgtctcaaagactcagc	0.000													4	2	---	---	---	---	
L3MBTL	26013	broad.mit.edu	37	20	42153755	42153755	+	Intron	DEL	A	-	-	rs66599011		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42153755delA	uc010zwh.1	+						L3MBTL_uc010ggk.1_Intron|L3MBTL_uc002xkl.2_Intron|L3MBTL_uc002xkm.2_Intron|L3MBTL_uc010ggl.2_Intron	NM_015478	NP_056293	Q9Y468	LMBL1_HUMAN	l(3)mbt-like isoform I						chromatin modification|hemopoiesis|negative regulation of transcription, DNA-dependent|regulation of megakaryocyte differentiation|regulation of mitosis	chromatin|condensed chromosome|nucleoplasm	identical protein binding|methylated histone residue binding|nucleosomal histone binding|SAM domain binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ctggggagttaaaaaaaaaaa	0.000													6	3	---	---	---	---	
JPH2	57158	broad.mit.edu	37	20	42814309	42814310	+	Intron	INS	-	GATG	GATG	rs139632440	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42814309_42814310insGATG	uc002xli.1	-						JPH2_uc002xlj.2_Intron	NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			gatggatcatagatggatggat	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46010141	46010141	+	IGR	DEL	A	-	-	rs74574794		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46010141delA								ZMYND8 (24667 upstream) : NCOA3 (120516 downstream)																							actccgtctcaaaaaaaaaaa	0.030													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46976308	46976308	+	IGR	DEL	T	-	-	rs71923261		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46976308delT								SULF2 (560948 upstream) : LOC284749 (12346 downstream)																							gctttcaagatttttttttta	0.000													6	3	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47284685	47284686	+	Intron	DEL	GT	-	-	rs72330220		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47284685_47284686delGT	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGTGTGACACGTGTGTGTGTGT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48579858	48579858	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48579858delT								RNF114 (9438 upstream) : SNAI1 (19669 downstream)																							cggccGTGAAttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49993633	49993634	+	IGR	INS	-	GCGC	GCGC	rs140915264	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49993633_49993634insGCGC								KCNG1 (353958 upstream) : NFATC2 (14132 downstream)																							tgtgtgtgtgtgcgtgtgtgtg	0.158													1	5	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	52036762	52036762	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52036762delG	uc002xwo.2	+						uc002xwp.1_Intron	NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						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)			gccaggtacagggaggatgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52741034	52741035	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52741034_52741035insT								BCAS1 (53730 upstream) : CYP24A1 (28953 downstream)																							ggtctcaaccattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56675926	56675927	+	IGR	INS	-	CATT	CATT	rs139541663	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56675926_56675927insCATT								PMEPA1 (389385 upstream) : C20orf85 (50056 downstream)																							attcattcatgcattcattcat	0.282													4	2	---	---	---	---	
OSBPL2	9885	broad.mit.edu	37	20	60853802	60853802	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60853802delT	uc002yck.1	+						OSBPL2_uc002ycl.1_Intron|OSBPL2_uc011aah.1_Intron|OSBPL2_uc002ycm.1_5'Flank	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform						lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			TGTGTGTGTGTTGCCAACGTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61090744	61090745	+	IGR	DEL	AT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61090744_61090745delAT								GATA5 (39718 upstream) : C20orf200 (50810 downstream)																							GGTCACCCACATGGAGTCGGCA	0.639													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9419053	9419054	+	IGR	INS	-	TTG	TTG			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9419053_9419054insTTG								None (None upstream) : None (None downstream)																							TTCTAATTAAATTGTCGGTGGA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9421602	9421603	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9421602_9421603insA								None (None upstream) : None (None downstream)																							attttttttttatttttattag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9576469	9576469	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9576469delA								None (None upstream) : None (None downstream)																							TAGGCCCCTGAAAAAAAATGT	0.527													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9828644	9828645	+	IGR	DEL	TC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9828644_9828645delTC								None (None upstream) : None (None downstream)																							GGCTCCTAAGTCTCTACCTGGT	0.371													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10567215	10567218	+	Intron	DEL	CTGG	-	-	rs71270918		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10567215_10567218delCTGG	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		AACCACAAAACTGGCTTTTTACTC	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10820616	10820616	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10820616delA								None (None upstream) : TPTE (86127 downstream)																							gacacgaatgaaatggaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10841779	10841779	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10841779delT								None (None upstream) : TPTE (64964 downstream)																							tggaatggactcgaatggaat	0.000													7	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11052980	11052984	+	Intron	DEL	TAATC	-	-	rs148507295		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11052980_11052984delTAATC	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)		AATAAATCATTAATCTAACAATGGA	0.229													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11069677	11069678	+	Intron	INS	-	A	A	rs138292766		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11069677_11069678insA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ttatgctaagcaaaaaaaaggc	0.000													7	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085705	11085707	+	Intron	DEL	ACT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085705_11085707delACT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cactaccaccactaccaccacca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11117942	11117942	+	IGR	DEL	A	-	-	rs60384332		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11117942delA								BAGE (19005 upstream) : None (None downstream)																							atagatagataggtagataga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18060428	18060429	+	IGR	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18060428_18060429insA								C21orf34 (78334 upstream) : CXADR (824901 downstream)																							tctgatcatggaaaaaaattat	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20281034	20281035	+	IGR	INS	-	GTTTT	GTTTT	rs147831579	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20281034_20281035insGTTTT								TMPRSS15 (505064 upstream) : None (None downstream)																							agtgagactccgttttgttttg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20928963	20928963	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20928963delG								None (None upstream) : None (None downstream)																							tgggagcaaaggcacgtctta	0.000													4	2	---	---	---	---	
C21orf131	387486	broad.mit.edu	37	21	22143876	22143877	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22143876_22143877insT	uc002ykz.3	-						C21orf131_uc002yky.3_Intron|C21orf131_uc002yla.3_Intron|C21orf131_uc002ylb.3_Intron|C21orf131_uc002ylc.3_Intron	NR_024090				Homo sapiens cDNA FLJ37207 fis, clone BRALZ2007576.												0						ACTTCACTATCttttttttttt	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25158533	25158533	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25158533delC								None (None upstream) : None (None downstream)																							GAAGGCCCCTCCTCTGAAAAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29312826	29312827	+	IGR	INS	-	TG	TG			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29312826_29312827insTG								NCRNA00113 (189274 upstream) : C21orf94 (72855 downstream)																							GCACACAGGGCtgtgtgtgtgt	0.332													4	2	---	---	---	---	
RNF160	26046	broad.mit.edu	37	21	30332708	30332708	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30332708delA	uc002ymr.2	-							NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294								ligase activity|zinc ion binding				0						aaaagaaaaGAAAAAAAAAAA	0.189													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33658560	33658560	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33658560delG								C21orf45 (7184 upstream) : MRAP (5564 downstream)																							tggaaggggaggggagggaag	0.075													4	2	---	---	---	---	
DONSON	29980	broad.mit.edu	37	21	35266156	35266158	+	Intron	DEL	AAA	-	-	rs5843628		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35266156_35266158delAAA	uc002ysn.1	-									Q9NYP3	DONS_HUMAN	Homo sapiens full length insert cDNA clone ZD90F06.						multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2						TAGGAGCCAGAAAAAAAAAAATC	0.404													1	5	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41669468	41669468	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41669468delT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGCCTATGTGTTACAGGTAGA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46453830	46453830	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46453830delT								NCRNA00162 (29188 upstream) : C21orf122 (37043 downstream)																							TTGGCTGGCCTTTTGCATTCA	0.517													4	2	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46920590	46920592	+	Intron	DEL	GTG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46920590_46920592delGTG	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron|SLC19A1_uc010gpy.1_Intron	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		ggtgtgtagtgtgggggtgtggt	0.000													6	3	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46923834	46923834	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46923834delC	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_5'Flank	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AGAAGGGCCTCAGGCAAACCC	0.373													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17236536	17236536	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17236536delC								psiTPTE22 (57015 upstream) : XKR3 (27777 downstream)																							tttccacacacctACAGTGCA	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17835709	17835709	+	IGR	DEL	T	-	-	rs112722406		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17835709delT								CECR1 (132971 upstream) : CECR2 (5130 downstream)																							cctctttttattttttttttt	0.139													3	3	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18310700	18310701	+	Intron	INS	-	ACAC	ACAC	rs140359300	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18310700_18310701insACAC	uc002zng.3	-						MICAL3_uc011agl.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		TGCACATGTATacacacacaca	0.302													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	18528772	18528773	+	IGR	INS	-	ATAA	ATAA	rs148931717	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18528772_18528773insATAA								FLJ41941 (8038 upstream) : TUBA8 (31913 downstream)																							GTAATTATTACATAAAGTGACA	0.277													2	4	---	---	---	---	
DGCR5	26220	broad.mit.edu	37	22	18984015	18984015	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18984015delA	uc002zon.1	+						uc002zoo.2_5'Flank					Homo sapiens mRNA for KIAA1647 protein, partial cds.												0						accctgtctcaaaaaaaaaaa	0.174													4	3	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19032878	19032879	+	Intron	INS	-	AAAC	AAAC	rs141480434	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19032878_19032879insAAAC	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)					tgactcgtcttaaacaaacaaa	0.000													3	4	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19043048	19043048	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19043048delA	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)					gtgaaaccacatctctaataa	0.000													4	2	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19080411	19080413	+	Intron	DEL	GAG	-	-	rs72183223		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19080411_19080413delGAG	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)					gaaaaatgaagaggaggaggagg	0.054													2	4	---	---	---	---	
CLTCL1	8218	broad.mit.edu	37	22	19190025	19190026	+	Intron	INS	-	C	C	rs67556687		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19190025_19190026insC	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron|CLTCL1_uc011agt.1_Intron|CLTCL1_uc011agu.1_Intron|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpe.2_Intron|CLTCL1_uc002zpd.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)					CCTTCCGCCATCACGGCACCTC	0.653			T	?	ALCL								5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21052399	21052399	+	IGR	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21052399delG								POM121L4P (6390 upstream) : TMEM191A (3003 downstream)																							AGCTGCTGGTGGGGAGGTCTT	0.647													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21591197	21591197	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21591197delA								LOC400891 (172742 upstream) : POM121L8P (45517 downstream)																							cactctatgtaaaaaaaaaaa	0.030													4	3	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22379404	22379405	+	5'Flank	INS	-	AA	AA	rs139471194		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22379404_22379405insAA	uc011aim.1	+						uc002zvu.2_Intron|uc002zvv.2_5'Flank					Parts of antibodies, mostly variable regions.												0						AGCCCATTCTCAAAAACAAAAA	0.233													3	3	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22644316	22644317	+	Intron	DEL	GG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22644316_22644317delGG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						gcaggACCAaggggaagggcca	0.010													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23677935	23677935	+	IGR	DEL	A	-	-	rs140196644		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23677935delA								BCR (17712 upstream) : ZDHHC8P1 (54858 downstream)																							ggagggtcagaatctttagcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23774114	23774115	+	IGR	INS	-	AC	AC	rs78236231		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23774114_23774115insAC								ZDHHC8P1 (29315 upstream) : IGLL1 (141200 downstream)																							CCCAGAATTATAGGCAGCACGG	0.594													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24099880	24099881	+	IGR	DEL	AG	-	-	rs113186766		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24099880_24099881delAG								VPREB3 (3250 upstream) : C22orf15 (5327 downstream)																							ttcttgagacagagtcttgctc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24592175	24592176	+	IGR	DEL	AC	-	-	rs57091777		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24592175_24592176delAC								SUSD2 (7101 upstream) : GGT5 (23447 downstream)																							acacacacatacacacacacac	0.000													4	2	---	---	---	---	
PIWIL3	440822	broad.mit.edu	37	22	25168693	25168693	+	Intron	DEL	G	-	-	rs67559281		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25168693delG	uc003abd.1	-						PIWIL3_uc011ajx.1_Intron|PIWIL3_uc011ajy.1_Intron|PIWIL3_uc010gut.1_Intron	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3						cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4						GTGCTTAGGTGGGTGCACAGC	0.502											OREG0026416	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	7	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26220983	26220984	+	Intron	INS	-	AT	AT	rs146322754	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26220983_26220984insAT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						catgtgcacagatatatatata	0.005													2	4	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26716250	26716250	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26716250delC	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						GTATCATTCTCCCGGGTGTTC	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27192040	27192053	+	IGR	DEL	TGTGTGTGTGTGTG	-	-	rs72099762		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27192040_27192053delTGTGTGTGTGTGTG								MIAT (77091 upstream) : MN1 (952213 downstream)																							tatgcatgcatgtgtgtgtgtgtgtgtgtgtgtg	0.355													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27720865	27720866	+	IGR	INS	-	TGGA	TGGA	rs150647664	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27720865_27720866insTGGA								MIAT (605916 upstream) : MN1 (423400 downstream)																							ggacgggtaggtggatggatgg	0.119													3	3	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	29071723	29071724	+	Intron	INS	-	CA	CA	rs71316854		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29071723_29071724insCA	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						tgaaaccctgtcacacacacac	0.059													4	2	---	---	---	---	
NF2	4771	broad.mit.edu	37	22	30073573	30073574	+	Intron	DEL	GG	-	-	rs35161712		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30073573_30073574delGG	uc003age.3	+						NF2_uc003afy.3_Intron|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_Intron	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						GTGGGCCGGTGGGGAGCCCTTT	0.594			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				2	5	---	---	---	---	
HORMAD2	150280	broad.mit.edu	37	22	30549071	30549072	+	Intron	DEL	AT	-	-	rs5763821	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30549071_30549072delAT	uc003agy.2	+							NM_152510	NP_689723	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)			gtttccccccatctcagcacca	0.000													6	3	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31017457	31017458	+	Intron	INS	-	TTA	TTA	rs8139921	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31017457_31017458insTTA	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTCATTTGTTGttttttgtttg	0.218													3	4	---	---	---	---	
OSBP2	23762	broad.mit.edu	37	22	31276036	31276037	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31276036_31276037insA	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron|OSBP2_uc003ajb.2_5'Flank|OSBP2_uc011ald.1_5'Flank	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						gactctgtctcaaaaaaaaaaa	0.277													4	3	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31950760	31950760	+	Intron	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31950760delT	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						gcccggctaattttttttttg	0.000													4	2	---	---	---	---	
C22orf30	253143	broad.mit.edu	37	22	32100417	32100418	+	Intron	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32100417_32100418insT	uc003alp.3	-						C22orf30_uc003alo.1_Intron|C22orf30_uc010gwj.1_Intron	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143												0						GTGATTTTCACTTTTTTTTTTT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32380674	32380674	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32380674delA								YWHAH (27085 upstream) : SLC5A1 (58363 downstream)																							gccttgagagaaaaaaatggg	0.000													4	2	---	---	---	---	
RFPL2	10739	broad.mit.edu	37	22	32591451	32591452	+	Intron	INS	-	T	T	rs149767574	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32591451_32591452insT	uc003amg.3	-						RFPL2_uc003ame.3_5'Flank|RFPL2_uc003amf.3_Intron|RFPL2_uc003amh.3_Intron	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2								zinc ion binding			skin(1)	1						tttcttttttctttttttttga	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34743947	34743950	+	IGR	DEL	GTGT	-	-	rs71798546		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34743947_34743950delGTGT								LARGE (425363 upstream) : ISX (718179 downstream)																							GGGAAGAGGGgtgtgtgtgtgtgt	0.324													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35358367	35358367	+	IGR	DEL	T	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35358367delT								None (None upstream) : ISX (103762 downstream)																							TAAAAACATATTTTTTTTTTT	0.239													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35411562	35411563	+	IGR	DEL	AA	-	-	rs67733631		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35411562_35411563delAA								None (None upstream) : ISX (50566 downstream)																							CCCAAGGTGGAAAAAAAAAAAA	0.262													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35649594	35649595	+	IGR	DEL	GC	-	-	rs71713395		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35649594_35649595delGC								ISX (166216 upstream) : HMGXB4 (3850 downstream)																							TGGATTTtgtgcgcgcgcgcgc	0.356													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36029740	36029741	+	Intron	DEL	GT	-	-	rs144873500		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36029740_36029741delGT	uc010gwt.1	-											Homo sapiens hypothetical gene supported by BC001801, mRNA (cDNA clone MGC:3170 IMAGE:3355513), complete cds.																		gcgtgtgtcagtgtgtgtgcgt	0.000													3	3	---	---	---	---	
APOL3	80833	broad.mit.edu	37	22	36539184	36539185	+	Intron	INS	-	A	A	rs143776615	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36539184_36539185insA	uc003aot.2	-						APOL3_uc003aoq.2_Intron|APOL3_uc003aor.2_Intron|APOL3_uc003aos.2_Intron|APOL3_uc003aou.2_Intron|APOL3_uc003aov.2_Intron	NM_145640	NP_663615	O95236	APOL3_HUMAN	apolipoprotein L3 isoform 1						inflammatory response|lipoprotein metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	lipid binding|lipid transporter activity|signal transducer activity				0						tcccctgtaacacaatcctgaa	0.010													2	4	---	---	---	---	
MYH9	4627	broad.mit.edu	37	22	36691447	36691448	+	Intron	INS	-	GT	GT	rs146428638	by1000genomes	TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36691447_36691448insGT	uc003apg.2	-							NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						AGAGGGCCACGgtgtgtgtgtg	0.554			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				13	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37194794	37194794	+	IGR	DEL	T	-	-	rs5845299		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37194794delT								IFT27 (22680 upstream) : PVALB (1952 downstream)																							CCCTCACGCCTCCCCACGTGT	0.592													3	3	---	---	---	---	
CSF2RB	1439	broad.mit.edu	37	22	37334735	37334736	+	3'UTR	DEL	AC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37334735_37334736delAC	uc003aqa.3	+	14					CSF2RB_uc003aqc.3_3'UTR	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta						respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	GCTcacacagacacacacacac	0.386													3	3	---	---	---	---	
TMPRSS6	164656	broad.mit.edu	37	22	37468652	37468653	+	Intron	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37468652_37468653insA	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6						gatggatggatgatggacgatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	38684585	38684585	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38684585delA								TMEM184B (15569 upstream) : CSNK1E (2113 downstream)																							actccgtctcaaaaaaaaaaa	0.119													4	2	---	---	---	---	
LOC646851	646851	broad.mit.edu	37	22	39037131	39037132	+	Intron	DEL	GA	-	-	rs149221033		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39037131_39037132delGA	uc011anx.1	-						LOC646851_uc011anw.1_Intron			B7Z7C6	B7Z7C6_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000348086;												0						AGAAAGAGGGGAGAGAAAGGAT	0.228													3	3	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40393990	40393990	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40393990delA	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						acagagaaggaaagagacttg	0.274													4	2	---	---	---	---	
EP300	2033	broad.mit.edu	37	22	41531211	41531211	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41531211delC	uc003azl.3	+							NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						TTTTTTATCTCCCATTCCATG	0.269			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				4	2	---	---	---	---	
EP300	2033	broad.mit.edu	37	22	41533071	41533071	+	Intron	DEL	A	-	-	rs10717148		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41533071delA	uc003azl.3	+							NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						ctcaagaaggaaaaaaaaaTg	0.000			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	42771572	42771573	+	IGR	DEL	TT	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42771572_42771573delTT								TCF20 (160127 upstream) : NFAM1 (4842 downstream)																							ccAGCAGttctttttttttttt	0.015													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43677514	43677515	+	Intron	DEL	CT	-	-	rs67974922		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43677514_43677515delCT	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron|uc003bdv.2_Intron	NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				ctgtcacctcctcctcagccac	0.267													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	43760004	43760004	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43760004delA								SCUBE1 (20649 upstream) : MPPED1 (48016 downstream)																							CTGCTCACTTAAAAAAAAAAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45031655	45031655	+	IGR	DEL	A	-	-	rs143011476		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45031655delA								NCRNA00207 (63326 upstream) : PRR5 (32938 downstream)																							ggaacctgggaggcaaaggtc	0.040													2	4	---	---	---	---	
CERK	64781	broad.mit.edu	37	22	47123347	47123348	+	Intron	INS	-	TTC	TTC	rs140871011		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47123347_47123348insTTC	uc003bia.2	-							NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		cagctgtttctttttttttttt	0.000													4	2	---	---	---	---	
CERK	64781	broad.mit.edu	37	22	47134264	47134265	+	5'Flank	INS	-	G	G			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47134264_47134265insG	uc003bia.2	-							NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		cagggagagacggggggacccg	0.084													4	3	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	48978766	48978772	+	Intron	DEL	CACACAC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48978766_48978772delCACACAC	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		acatgccacacacacaccacacaccac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49467012	49467019	+	IGR	DEL	TTCCTTCC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49467012_49467019delTTCCTTCC								FAM19A5 (319270 upstream) : C22orf34 (341157 downstream)																							ccttccttcgttccttccttccttcctt	0.005													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50346330	50346331	+	IGR	DEL	TG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50346330_50346331delTG								CRELD2 (25144 upstream) : PIM3 (7812 downstream)																							tgtgtgtggttgtgtgtgtgtg	0.322													4	2	---	---	---	---	
MAPK8IP2	23542	broad.mit.edu	37	22	51047328	51047328	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51047328delC	uc003bmx.2	+						MAPK8IP2_uc003bmy.2_Intron|MAPK8IP2_uc011asc.1_Intron	NM_012324	NP_036456	Q13387	JIP2_HUMAN	mitogen-activated protein kinase 8 interacting						behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior	cytoplasm|postsynaptic density	beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding			large_intestine(2)|central_nervous_system(1)	3		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGAAGAATGACCCAAATTTCT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	284694	284696	+	IGR	DEL	CTC	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:284694_284696delCTC								NCRNA00107 (2642 upstream) : PPP2R3B (10276 downstream)																							AACCATCAATCTCCTGGGCTCCT	0.498													4	2	---	---	---	---	
GPM6B	2824	broad.mit.edu	37	X	13843773	13843773	+	Intron	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13843773delA	uc004cvx.2	-						GPM6B_uc011min.1_Intron|GPM6B_uc004cwa.2_Intron	NM_001001994	NP_001001994	Q13491	GPM6B_HUMAN	glycoprotein M6B isoform 4						cell differentiation|nervous system development	integral to membrane					0						ACCACTTTACAGGGGGGCTAC	0.517													4	2	---	---	---	---	
GPR173	54328	broad.mit.edu	37	X	53089762	53089763	+	Intron	INS	-	A	A	rs111798225		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53089762_53089763insA	uc004dru.2	+							NM_018969	NP_061842	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173							integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						gactccgtctcaaaaaaaaaaa	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56051143	56051143	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56051143delA								RRAGB (265937 upstream) : KLF8 (207679 downstream)																							gaacagaaggagaagtttcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	57084812	57084812	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57084812delA								SPIN3 (62824 upstream) : SPIN2B (61304 downstream)																							cgtgtctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	58535719	58535719	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58535719delC								ZXDA (598652 upstream) : None (None downstream)																							atttggagcactttggggcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61749740	61749741	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61749740_61749741insT								None (None upstream) : SPIN4 (817367 downstream)																							agagttgaacctttcttttgat	0.000													4	2	---	---	---	---	
ATRX	546	broad.mit.edu	37	X	77026855	77026855	+	Intron	DEL	A	-	-	rs72378738		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77026855delA	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron|ATRX_uc004ecr.2_Intron|ATRX_uc010nlx.1_Intron|ATRX_uc010nly.1_Intron	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	actccgtctcaaaaaaaaaaa	0.169			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						3	3	---	---	---	---	
HDX	139324	broad.mit.edu	37	X	83640008	83640008	+	Intron	DEL	G	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83640008delG	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2						atttgcccttggctatttagg	0.000													4	2	---	---	---	---	
DACH2	117154	broad.mit.edu	37	X	85660596	85660596	+	Intron	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85660596delC	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.2_Intron	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						tctgagctctccaattctcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	92306214	92306214	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92306214delC								PCDH11X (427988 upstream) : NAP1L3 (619715 downstream)																							tgtctggtttccgttggctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	101437415	101437415	+	IGR	DEL	C	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101437415delC								BEX5 (26429 upstream) : NXF2B (32865 downstream)																							TCTATTCAAGCCCTCCTCTTC	0.498													4	2	---	---	---	---	
CXorf56	63932	broad.mit.edu	37	X	118690546	118690546	+	Intron	DEL	A	-	-	rs72211801		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118690546delA	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384	Q9H5V9	CX056_HUMAN	hypothetical protein LOC63932								protein binding				0						actccgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	120363051	120363052	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120363051_120363052insT								GLUD2 (179257 upstream) : None (None downstream)																							tcttttgaatatttttttttgt	0.000													4	3	---	---	---	---	
RP1-177G6.2	286411	broad.mit.edu	37	X	139791614	139791615	+	5'Flank	INS	-	A	A			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139791614_139791615insA	uc004fbe.2	+							NM_001126492	NP_001119964			SubName: Full=Novel protein;												0						ACCACTGCAGGAAAAAAAAAAA	0.421													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	149700543	149700543	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149700543delA								MAMLD1 (18097 upstream) : MTM1 (36504 downstream)																							TCATGATCCTACATTGCCAAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150164961	150164962	+	IGR	DEL	AG	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150164961_150164962delAG								HMGB3 (5715 upstream) : GPR50 (180097 downstream)																							aagggagggaagagagagagag	0.337													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9943660	9943660	+	IGR	DEL	G	-	-	rs112143371		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9943660delG								TTTY22 (292806 upstream) : None (None downstream)																							gagaacttaaggggcagtcta	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9958887	9958891	+	IGR	DEL	TAATT	-	-	rs147545322		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9958887_9958891delTAATT								TTTY22 (308033 upstream) : None (None downstream)																							tagtcaaaaataatttaattccaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10061087	10061087	+	IGR	DEL	A	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10061087delA								TTTY22 (410233 upstream) : None (None downstream)																							ctgctcaatcaaaagtgtggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10066700	10066701	+	IGR	INS	-	T	T			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10066700_10066701insT								TTTY22 (415846 upstream) : None (None downstream)																							cttctgtctagtttttatgtga	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13843067	13843071	+	IGR	DEL	ATACA	-	-			TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13843067_13843071delATACA								None (None upstream) : TTTY15 (931227 downstream)																							aatggaatggatacaaatgttatgg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59024002	59024007	+	IGR	DEL	AAAAAA	-	-	rs3036473		TCGA-18-3411-01A-01D-0983-08	TCGA-18-3411-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59024002_59024007delAAAAAA								None (None upstream) : None (None downstream)																							aaactgtctcaaaaaaaaaaaaaaaa	0.010													4	3	---	---	---	---	
