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
TMEM82	388595	broad.mit.edu	37	1	16074138	16074138	+	3'UTR	SNP	G	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16074138G>C	uc001axc.2	+	6						NM_001013641	NP_001013663	A0PJX8	TMM82_HUMAN	transmembrane protein 82							integral to membrane				breast(1)|central_nervous_system(1)	2		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCTGCCTCAGGGAGGATCTGG	0.642													10	43	---	---	---	---	PASS
POMGNT1	55624	broad.mit.edu	37	1	46662429	46662429	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46662429C>A	uc001cpe.2	-	4	492	c.328G>T	c.(328-330)GTA>TTA	p.V110L	POMGNT1_uc010olx.1_Missense_Mutation_p.V88L|POMGNT1_uc010oly.1_RNA|POMGNT1_uc010olz.1_5'UTR|POMGNT1_uc001cpg.2_Missense_Mutation_p.V110L|POMGNT1_uc001cpf.2_5'UTR|POMGNT1_uc001cpj.2_Intron	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose	110	Lumenal (Potential).				protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GCCACATATACTTTGCTGCGA	0.617													8	31	---	---	---	---	PASS
GBP2	2634	broad.mit.edu	37	1	89578232	89578232	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89578232C>A	uc001dmz.1	-	8	1556	c.1285G>T	c.(1285-1287)GGA>TGA	p.G429*	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	429					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		CGGTAACCTCCTGGTTTAGAA	0.443													6	233	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142621039	142621039	+	Intron	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142621039C>T	uc001eiw.1	+						uc001eix.1_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		CCAAGAGCAACAGGAAACGAA	0.393													3	15	---	---	---	---	PASS
CELF3	11189	broad.mit.edu	37	1	151679697	151679697	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151679697G>T	uc001eys.1	-	8	1640	c.846C>A	c.(844-846)TAC>TAA	p.Y282*	CELF3_uc010pdh.1_Nonsense_Mutation_p.Y90*|CELF3_uc001eyr.2_Nonsense_Mutation_p.Y281*|CELF3_uc009wmy.2_Intron|CELF3_uc009wmx.1_Nonsense_Mutation_p.Y282*	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4	282					nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						GCACCGGGCTGTAGCCGTTGA	0.672													3	5	---	---	---	---	PASS
ALDH9A1	223	broad.mit.edu	37	1	165652237	165652237	+	Silent	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165652237G>T	uc001gdh.1	-	3	543	c.438C>A	c.(436-438)GGC>GGA	p.G146G	ALDH9A1_uc010pky.1_Silent_p.G52G|ALDH9A1_uc010pkz.1_Silent_p.G136G|ALDH9A1_uc010pla.1_Silent_p.G52G	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1	122					carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)	ATGCAGCCAAGCCCGCATAAT	0.403													24	61	---	---	---	---	PASS
NMNAT2	23057	broad.mit.edu	37	1	183230359	183230359	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183230359G>T	uc001gqc.1	-	9	1066	c.731C>A	c.(730-732)TCC>TAC	p.S244Y	NMNAT2_uc009wye.1_RNA|NMNAT2_uc001gqb.1_Missense_Mutation_p.S239Y	NM_015039	NP_055854	Q9BZQ4	NMNA2_HUMAN	nicotinamide mononucleotide adenylyltransferase	244					water-soluble vitamin metabolic process	Golgi membrane|nucleus	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity			skin(1)	1						GAGTATTGAGGAGTGATTCAT	0.522													50	187	---	---	---	---	PASS
ZNF678	339500	broad.mit.edu	37	1	227842449	227842449	+	Silent	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227842449A>T	uc001hqw.1	+	4	843	c.498A>T	c.(496-498)TCA>TCT	p.S166S	ZNF678_uc009xet.1_Intron|ZNF678_uc009xeu.1_Intron	NM_178549	NP_848644	F5GXA7	F5GXA7_HUMAN	zinc finger protein 678	221					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			pancreas(1)	1		Prostate(94;0.0885)				ATTGGTGGTCACAACTAACTA	0.338													9	82	---	---	---	---	PASS
C1orf101	257044	broad.mit.edu	37	1	244803349	244803349	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244803349T>C	uc001iam.2	+	22	2881	c.2822T>C	c.(2821-2823)CTT>CCT	p.L941P	C1orf101_uc001ial.2_3'UTR|C1orf101_uc010pym.1_Missense_Mutation_p.L790P|C1orf101_uc010pyn.1_Missense_Mutation_p.L874P	NM_001130957	NP_001124429	Q5SY80	CA101_HUMAN	hypothetical protein LOC257044 isoform 1	941	Cytoplasmic (Potential).					integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			TATGAACCACTTCACAAACCT	0.333													8	550	---	---	---	---	PASS
CAD	790	broad.mit.edu	37	2	27465207	27465207	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27465207C>G	uc002rji.2	+	40	6296	c.6134C>G	c.(6133-6135)GCT>GGT	p.A2045G	CAD_uc010eyw.2_Missense_Mutation_p.A1982G	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	2045	ATCase (Aspartate transcarbamylase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	GTGATCAATGCTGGGGATGGG	0.612													10	27	---	---	---	---	PASS
GALM	130589	broad.mit.edu	37	2	38956797	38956797	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38956797A>T	uc002rqy.2	+	5	986	c.734A>T	c.(733-735)AAT>ATT	p.N245I		NM_138801	NP_620156	Q96C23	GALM_HUMAN	galactose mutarotase	245					hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)				TTTGACCACAATTTCTGTCTG	0.448													26	113	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89185365	89185365	+	Intron	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89185365G>A	uc010ytr.1	-						uc002stl.2_RNA					Parts of antibodies, mostly variable regions.																		GGTGCCTACGGGGACATCGTG	0.448													39	143	---	---	---	---	PASS
DYNC1I2	1781	broad.mit.edu	37	2	172586347	172586347	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172586347A>G	uc002uha.1	+	15	1685	c.1520A>G	c.(1519-1521)AAG>AGG	p.K507R	DYNC1I2_uc002uhc.2_Missense_Mutation_p.K481R|DYNC1I2_uc002uhb.1_Missense_Mutation_p.K481R|DYNC1I2_uc010zds.1_Missense_Mutation_p.K499R|DYNC1I2_uc002uhe.1_Missense_Mutation_p.K507R|DYNC1I2_uc002uhf.1_Missense_Mutation_p.K481R|DYNC1I2_uc010zdt.1_Missense_Mutation_p.K499R|DYNC1I2_uc002uhg.1_Missense_Mutation_p.K422R|DYNC1I2_uc010zdu.1_Missense_Mutation_p.K230R	NM_001378	NP_001369	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	507	WD 5.				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)			TGGACAGTAAAGCTTTGGACA	0.413													6	264	---	---	---	---	PASS
CFLAR	8837	broad.mit.edu	37	2	202006265	202006265	+	Intron	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202006265T>C	uc002uxb.3	+						CFLAR_uc002uwz.2_3'UTR|CFLAR_uc002uxa.3_Intron|CFLAR_uc010zhk.1_Intron|CFLAR_uc002uxc.3_Intron|CFLAR_uc010zhl.1_Intron|CFLAR_uc010fsw.1_Intron|CFLAR_uc002uxd.3_Intron|CFLAR_uc002uxe.2_3'UTR|CFLAR_uc002uxf.2_Intron|CFLAR_uc010fsy.2_Intron|CFLAR_uc010fsx.2_Intron|CFLAR_uc010zhm.1_Intron|CFLAR_uc010fsz.2_Intron|CFLAR_uc002uxg.2_Intron|uc002uxh.1_Intron	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						gtttagatgctttccaatctt	0.045													5	135	---	---	---	---	PASS
ALS2CR4	65062	broad.mit.edu	37	2	202494503	202494503	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202494503T>C	uc002uyh.1	-	9	727	c.626A>G	c.(625-627)AAG>AGG	p.K209R	ALS2CR4_uc002uyg.1_Missense_Mutation_p.K201R|ALS2CR4_uc010zho.1_Missense_Mutation_p.K4R|ALS2CR4_uc010zhp.1_RNA	NM_001044385	NP_001037850	Q96Q45	TM237_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	233						integral to membrane	protein binding				0						CCAGGAAGGCTTCACGTCCAT	0.428													5	219	---	---	---	---	PASS
ACCN4	55515	broad.mit.edu	37	2	220402025	220402025	+	Silent	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220402025C>A	uc002vma.2	+	7	1721	c.1707C>A	c.(1705-1707)ATC>ATA	p.I569I	ACCN4_uc002vlz.2_Silent_p.I588I|ACCN4_uc002vmb.2_Silent_p.I242I	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	569	Cytoplasmic (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)		TGCTGGAGATCCTCGACTACA	0.652													6	22	---	---	---	---	PASS
SCG2	7857	broad.mit.edu	37	2	224463522	224463522	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224463522T>C	uc002vnm.2	-	2	612	c.479A>G	c.(478-480)AAG>AGG	p.K160R		NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	160					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space|stored secretory granule	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		GTGCTTAAGCTTTCTTTCTGG	0.398													6	371	---	---	---	---	PASS
C2orf57	165100	broad.mit.edu	37	2	232457795	232457795	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232457795G>A	uc002vrz.2	+	1	184	c.133G>A	c.(133-135)GAC>AAC	p.D45N		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	45										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		CGCATCCACTGACTGGCAGGA	0.562													20	55	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238233432	238233432	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238233432A>T	uc002vwl.2	-	44	9804	c.9519T>A	c.(9517-9519)AGT>AGA	p.S3173R	COL6A3_uc002vwo.2_Missense_Mutation_p.S2967R|COL6A3_uc010znj.1_Missense_Mutation_p.S2566R|COL6A3_uc002vwj.2_Missense_Mutation_p.S554R	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	3173	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCCCATCACACTGATGACTC	0.552													10	73	---	---	---	---	PASS
PER2	8864	broad.mit.edu	37	2	239180147	239180147	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239180147A>G	uc002vyc.2	-	6	815	c.578T>C	c.(577-579)TTT>TCT	p.F193S	PER2_uc010znv.1_Missense_Mutation_p.F193S|PER2_uc010znw.1_Missense_Mutation_p.F193S|PER2_uc010fyx.1_Missense_Mutation_p.F193S	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	193	PAS 1.				circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		GGCCACCGCAAACATATCCTG	0.552													15	52	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242168842	242168842	+	3'UTR	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242168842C>A	uc002waz.2	-	28					HDLBP_uc002wba.2_3'UTR|HDLBP_uc002wbb.2_3'UTR	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CACGGCCAGGCCTGGAGGAGC	0.622													6	27	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242168992	242168992	+	3'UTR	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242168992A>G	uc002waz.2	-	28					HDLBP_uc002wba.2_3'UTR|HDLBP_uc002wbb.2_3'UTR	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		AGCAGGCTGGAGAGGGTTCTG	0.552													6	328	---	---	---	---	PASS
THAP4	51078	broad.mit.edu	37	2	242545863	242545863	+	Silent	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242545863C>A	uc002wbt.2	-	3	1489	c.1266G>T	c.(1264-1266)GTG>GTT	p.V422V	THAP4_uc002wbs.2_Silent_p.V10V	NM_015963	NP_057047	Q8WY91	THAP4_HUMAN	THAP domain containing 4 isoform 1	422							DNA binding|metal ion binding				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		ACAGTGGCTCCACCACTGGGT	0.587													9	24	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47144868	47144868	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47144868G>A	uc003cqs.2	-	7	4938	c.4885C>T	c.(4885-4887)CAC>TAC	p.H1629Y	SETD2_uc003cqv.2_Missense_Mutation_p.H1696Y	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1629	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding	p.R1629fs*15(1)		kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCACAGCTGTGATTCATGAAA	0.333			N|F|S|Mis		clear cell renal carcinoma								120	346	---	---	---	---	PASS
NMD3	51068	broad.mit.edu	37	3	160939777	160939777	+	Intron	SNP	A	T	T	rs35246182		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160939777A>T	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_5'UTR	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			ttttttttttAAAAGAACTTA	0.368													4	40	---	---	---	---	PASS
FGF12	2257	broad.mit.edu	37	3	192445062	192445062	+	5'UTR	SNP	G	A	A	rs11544864		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192445062G>A	uc003fsy.2	-	2						NM_004113	NP_004104	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		CCAAATCTGGGAAGCCAATCT	0.507													8	68	---	---	---	---	PASS
EVC2	132884	broad.mit.edu	37	4	5642374	5642374	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5642374T>C	uc003gij.2	-	10	1391	c.1337A>G	c.(1336-1338)GAG>GGG	p.E446G	EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_Missense_Mutation_p.E366G	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	446						integral to membrane				large_intestine(3)|ovary(2)	5						CCGATCGTACTCCTCTTGTAT	0.333													7	375	---	---	---	---	PASS
QDPR	5860	broad.mit.edu	37	4	17488607	17488607	+	3'UTR	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17488607A>G	uc003gpd.2	-	7					uc010ief.1_5'Flank|QDPR_uc003gpe.2_3'UTR|QDPR_uc003gpf.2_RNA	NM_000320	NP_000311	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase						dihydrobiopterin metabolic process|L-phenylalanine catabolic process|tetrahydrobiopterin biosynthetic process	cytosol	6,7-dihydropteridine reductase activity|binding|electron carrier activity			ovary(1)	1					NADH(DB00157)	GTCCTAGGAGAGCAAATGCAT	0.443													4	42	---	---	---	---	PASS
KIAA1239	57495	broad.mit.edu	37	4	37444977	37444977	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37444977C>T	uc011bxz.1	+	7	1367	c.1367C>T	c.(1366-1368)ACG>ATG	p.T456M		NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495	456											0						TTTCTAGGAACGACAGACATG	0.453													4	201	---	---	---	---	PASS
SLC39A8	64116	broad.mit.edu	37	4	103184147	103184147	+	3'UTR	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103184147A>T	uc003hwb.1	-	8					SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_3'UTR|SLC39A8_uc003hwc.2_3'UTR	NM_022154	NP_071437	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TCCTTTTTGGAGATGTTTTTA	0.313													7	238	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82836753	82836753	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82836753C>T	uc003kii.3	+	8	8287	c.7931C>T	c.(7930-7932)GCT>GTT	p.A2644V	VCAN_uc003kij.3_Missense_Mutation_p.A1657V|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.A1308V	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2644	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		GATGTTCTGGCTAGCTACACT	0.438													37	126	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127637113	127637113	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127637113C>T	uc003kuu.2	-	47	6446	c.6007G>A	c.(6007-6009)GAA>AAA	p.E2003K		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2003	EGF-like 33; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCATAACCTTCGTTACATAGA	0.343													92	360	---	---	---	---	PASS
FSTL4	23105	broad.mit.edu	37	5	132939626	132939626	+	Silent	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132939626G>A	uc003kyn.1	-	2	267	c.49C>T	c.(49-51)CTG>TTG	p.L17L		NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	17						extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGCCGGCAGGGAGGCTCCG	0.532													8	84	---	---	---	---	PASS
KIFC1	3833	broad.mit.edu	37	6	33371689	33371689	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33371689C>A	uc003oef.3	+	6	989	c.539C>A	c.(538-540)GCC>GAC	p.A180D	KIFC1_uc011drf.1_Missense_Mutation_p.A172D	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	180	Potential.				blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						CAGGTCAAGGCCCTGGGGACA	0.572													4	67	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38758105	38758105	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38758105G>A	uc003ooe.1	+	18	2654	c.2054G>A	c.(2053-2055)TGG>TAG	p.W685*		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GTGTTAACATGGTCGTCTTTA	0.358													105	370	---	---	---	---	PASS
TJAP1	93643	broad.mit.edu	37	6	43469319	43469319	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43469319C>A	uc003ovd.2	+	6	560	c.184C>A	c.(184-186)CGC>AGC	p.R62S	TJAP1_uc003ovf.2_Missense_Mutation_p.R62S|TJAP1_uc003ove.2_Missense_Mutation_p.R62S|TJAP1_uc003ovc.2_Missense_Mutation_p.R62S|TJAP1_uc010jyp.2_Missense_Mutation_p.R21S|TJAP1_uc011dvh.1_Missense_Mutation_p.R62S|TJAP1_uc003ovg.2_5'UTR|TJAP1_uc010jyq.2_Missense_Mutation_p.R62S|TJAP1_uc011dvi.1_Missense_Mutation_p.R62S|TJAP1_uc011dvj.1_5'UTR|TJAP1_uc003ovi.2_5'Flank	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a	62	Potential.					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)			CGCCACCAGACGCACTGAGGC	0.592													5	21	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90572531	90572531	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572531T>G	uc003pnr.2	+	7	1299	c.1103T>G	c.(1102-1104)GTT>GGT	p.V368G	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.V368G|CASP8AP2_uc011dzz.1_Missense_Mutation_p.V368G	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	368					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GAAAGAAAAGTTGATCAAAAA	0.323													27	61	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90572532	90572532	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572532T>C	uc003pnr.2	+	7	1300	c.1104T>C	c.(1102-1104)GTT>GTC	p.V368V	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Silent_p.V368V|CASP8AP2_uc011dzz.1_Silent_p.V368V	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	368					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AAAGAAAAGTTGATCAAAAAC	0.318													27	61	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90573344	90573344	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90573344T>C	uc003pnr.2	+	7	2112	c.1916T>C	c.(1915-1917)CTA>CCA	p.L639P	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.L639P|CASP8AP2_uc011dzz.1_Missense_Mutation_p.L639P	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	639					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTTGCTCTTCTAGCAGTGACT	0.438													4	111	---	---	---	---	PASS
RTN4IP1	84816	broad.mit.edu	37	6	107067108	107067108	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107067108C>A	uc003prj.2	-	4	1066	c.589G>T	c.(589-591)GGC>TGC	p.G197C	RTN4IP1_uc010kdd.2_Missense_Mutation_p.G197C|RTN4IP1_uc003prk.2_Missense_Mutation_p.G97C	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	197						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)		TCATTCAGGCCACCAACTTTG	0.443													84	264	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	132014640	132014640	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132014640C>T	uc003qcu.3	+	16	1635	c.1288C>T	c.(1288-1290)CGA>TGA	p.R430*	ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Nonsense_Mutation_p.R430*	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	430	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TTTTCAGTGCCGAAAACCTGA	0.338													4	285	---	---	---	---	PASS
KIF25	3834	broad.mit.edu	37	6	168443302	168443302	+	Silent	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168443302G>A	uc003qwk.1	+	8	1153	c.891G>A	c.(889-891)GCG>GCA	p.A297A	KIF25_uc003qwl.1_Intron	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	297					microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCAGCCTTGCGGCCCTGGCAG	0.657													6	36	---	---	---	---	PASS
ZNF727	442319	broad.mit.edu	37	7	63537854	63537854	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63537854A>T	uc011kdm.1	+	4	606	c.427A>T	c.(427-429)AAA>TAA	p.K143*		NM_001159522	NP_001152994	A8MUV8	ZN727_HUMAN	zinc finger protein 727	143	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TACCCGTAGCAAAACCTGTCA	0.368													31	331	---	---	---	---	PASS
MLXIPL	51085	broad.mit.edu	37	7	73008146	73008146	+	3'UTR	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73008146G>T	uc003tyn.1	-	17					MLXIPL_uc003tyj.1_3'UTR|MLXIPL_uc003tyk.1_3'UTR|MLXIPL_uc003tyl.1_3'UTR|MLXIPL_uc003tym.1_3'UTR|MLXIPL_uc003tyo.1_RNA|MLXIPL_uc003typ.1_3'UTR	NM_032951	NP_116569	Q9NP71	WBS14_HUMAN	Williams Beuren syndrome chromosome region 14						anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				CCGTGCCCAGGGAAAGCAGCC	0.647													11	26	---	---	---	---	PASS
LMTK2	22853	broad.mit.edu	37	7	97766745	97766745	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97766745A>G	uc003upd.1	+	2	515	c.222A>G	c.(220-222)ATA>ATG	p.I74M		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	74					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					ACCCAGAAATAGACTTTAAGG	0.358													5	302	---	---	---	---	PASS
PVRIG	79037	broad.mit.edu	37	7	99818579	99818579	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99818579T>C	uc003uue.2	+	7	1058	c.686T>C	c.(685-687)CTT>CCT	p.L229P	GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uuf.1_Missense_Mutation_p.L229P	NM_024070	NP_076975	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin	229						integral to membrane				skin(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CAGGCTGCTCTTCACGTCCCT	0.682													4	43	---	---	---	---	PASS
FIS1	51024	broad.mit.edu	37	7	100883107	100883107	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100883107C>T	uc003uyj.3	-	5	525	c.439G>A	c.(439-441)GTG>ATG	p.V147M	CLDN15_uc003uyg.1_5'Flank|CLDN15_uc003uyh.1_5'Flank|CLDN15_uc003uyi.2_5'Flank|FIS1_uc010lht.2_RNA|FIS1_uc010lhu.2_RNA	NM_016068	NP_057152	Q9Y3D6	FIS1_HUMAN	tetratricopeptide repeat domain 11	147	Mitochondrial intermembrane (Potential).				apoptosis|mitochondrial fission|peroxisome fission	integral to mitochondrial outer membrane|integral to peroxisomal membrane	protein binding				0	Lung NSC(181;0.168)|all_lung(186;0.215)					GACTTGGACACAGCAAGTCCG	0.637													3	16	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113519158	113519158	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113519158T>C	uc010ljy.1	-	4	2020	c.1989A>G	c.(1987-1989)GGA>GGG	p.G663G		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	663					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						CTCTTGATTTTCCCTGACTTT	0.368													13	488	---	---	---	---	PASS
ARHGEF35	445328	broad.mit.edu	37	7	143884368	143884368	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143884368G>A	uc003wdz.1	-	2	1227	c.1109C>T	c.(1108-1110)CCA>CTA	p.P370L		NM_001003702	NP_001003702	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF)	370	Glu-rich.										0						CCCGCTGACTGGGACCCCTTT	0.537													40	125	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52361653	52361653	+	Silent	SNP	G	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52361653G>C	uc003xqu.3	-	11	1376	c.1275C>G	c.(1273-1275)CCC>CCG	p.P425P		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	425	Ig-like C2-type 3.				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)				CTTGATCCTTGGGGGTTACTG	0.383													22	152	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53537286	53537286	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53537286T>C	uc003xre.3	-	23	5256	c.4698A>G	c.(4696-4698)CAA>CAG	p.Q1566Q	RB1CC1_uc003xrf.3_Silent_p.Q1563Q	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	1566					autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CCTTTTTGGCTTGACAGTATT	0.333													8	765	---	---	---	---	PASS
ZNF707	286075	broad.mit.edu	37	8	144776493	144776493	+	Silent	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144776493C>T	uc003yze.3	+	7	1224	c.909C>T	c.(907-909)CTC>CTT	p.L303L	ZNF707_uc010mfh.2_Silent_p.L303L|ZNF707_uc010mfi.2_Silent_p.L303L|ZNF707_uc003yzf.3_Silent_p.L303L|ZNF707_uc003yzh.3_Silent_p.L230L|ZNF707_uc011lkq.1_RNA|BREA2_uc010mfj.1_5'Flank	NM_173831	NP_776192	Q96C28	ZN707_HUMAN	zinc finger protein 707	303	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AGGAGAACCTCAGCCACCACC	0.647													3	18	---	---	---	---	PASS
CNTLN	54875	broad.mit.edu	37	9	17298419	17298419	+	Intron	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17298419G>T	uc003zmz.2	+						CNTLN_uc003zmx.3_3'UTR|CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		ATAGAATTCAGATTTTTTCAA	0.239													26	69	---	---	---	---	PASS
RGP1	9827	broad.mit.edu	37	9	35749857	35749857	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35749857T>C	uc011lpf.1	+	2	246	c.105T>C	c.(103-105)ACT>ACC	p.T35T	GBA2_uc011lpb.1_5'Flank|GBA2_uc003zxw.2_5'Flank|GBA2_uc011lpc.1_5'Flank|GBA2_uc011lpd.1_5'UTR|RGP1_uc011lpe.1_Silent_p.T75T	NM_001080496	NP_001073965	Q92546	RGP1_HUMAN	RGP1 retrograde golgi transport homolog	35										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)			CCACGGCCACTTCTGCATCCA	0.597													4	54	---	---	---	---	PASS
SVIL	6840	broad.mit.edu	37	10	29752498	29752498	+	Missense_Mutation	SNP	T	C	C	rs150671744	byFrequency	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29752498T>C	uc001iut.1	-	35	6953	c.6200A>G	c.(6199-6201)AAG>AGG	p.K2067R	LOC387647_uc001iuo.1_Intron|LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.K981R|SVIL_uc001iuu.1_Missense_Mutation_p.K1641R	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	2067	Gelsolin-like 5.				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				ACCAGTGATCTTGTTCTCGAT	0.587													14	35	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37488676	37488676	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37488676C>G	uc001iza.1	+	30	2669	c.2570C>G	c.(2569-2571)TCA>TGA	p.S857*		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	913						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						CCTTCAGAATCAAAACAAAAG	0.264													14	752	---	---	---	---	PASS
PBLD	64081	broad.mit.edu	37	10	70056040	70056040	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70056040A>C	uc001jns.1	-	4	469	c.266T>G	c.(265-267)GTG>GGG	p.V89G	PBLD_uc001jnr.1_Missense_Mutation_p.V56G|PBLD_uc001jnt.1_Missense_Mutation_p.V89G|PBLD_uc001jnu.1_Missense_Mutation_p.V89G|PBLD_uc001jnv.1_Intron	NM_022129	NP_071412	P30039	PBLD_HUMAN	MAWD binding protein isoform a	89					biosynthetic process		isomerase activity			skin(2)|ovary(1)	3						GTGAAACAGCACAGCTGCAGA	0.423													17	63	---	---	---	---	PASS
PLCE1	51196	broad.mit.edu	37	10	96076377	96076377	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96076377C>A	uc001kjk.2	+	29	6840	c.6206C>A	c.(6205-6207)TCT>TAT	p.S2069Y	PLCE1_uc010qnx.1_Missense_Mutation_p.S2053Y|PLCE1_uc001kjm.2_Missense_Mutation_p.S1761Y|PLCE1_uc001kjp.2_Missense_Mutation_p.S427Y	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	2069	Ras-associating 1.				activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				TATTTTATATCTAAAGAAAAG	0.358													14	257	---	---	---	---	PASS
ARHGAP19	84986	broad.mit.edu	37	10	99006064	99006064	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99006064A>T	uc001knb.2	-	7	987	c.958T>A	c.(958-960)TTG>ATG	p.L320M	ARHGAP19_uc001kmy.2_RNA|ARHGAP19_uc001kna.2_Missense_Mutation_p.L311M|ARHGAP19_uc009xvi.2_RNA|ARHGAP19_uc009xvj.2_Missense_Mutation_p.L291M|ARHGAP19_uc009xvk.2_Missense_Mutation_p.L114M	NM_032900	NP_116289	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	320					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		AAATAGTGCAATCTCGCACAC	0.428													69	192	---	---	---	---	PASS
DCLRE1A	9937	broad.mit.edu	37	10	115610067	115610067	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115610067T>C	uc001law.2	-	2	1715	c.797A>G	c.(796-798)GAG>GGG	p.E266G		NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	266					cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)		TTTGTCATTCTCAACAAAATC	0.383								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					6	183	---	---	---	---	PASS
SEC23IP	11196	broad.mit.edu	37	10	121680583	121680583	+	Intron	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121680583G>A	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron|SEC23IP_uc009xzk.1_RNA	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TACTACTATGGTTAGGTAAGC	0.393													8	64	---	---	---	---	PASS
C10orf88	80007	broad.mit.edu	37	10	124697369	124697369	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124697369T>A	uc001lgw.2	-	5	1180	c.955A>T	c.(955-957)AAA>TAA	p.K319*	C10orf88_uc001lgx.2_Nonsense_Mutation_p.K221*	NM_024942	NP_079218	Q9H8K7	CJ088_HUMAN	hypothetical protein LOC80007	319											0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)		TCACTTACTTTCTTTGGTAAG	0.368													7	378	---	---	---	---	PASS
DOCK1	1793	broad.mit.edu	37	10	129160369	129160369	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129160369A>T	uc001ljt.2	+	33	3326	c.3262A>T	c.(3262-3264)ATA>TTA	p.I1088L	DOCK1_uc010qun.1_Missense_Mutation_p.I1109L|DOCK1_uc009yaq.2_Missense_Mutation_p.I83L	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1088					apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GGTGGGCCCAATATTAGAAAT	0.393													31	133	---	---	---	---	PASS
CTR9	9646	broad.mit.edu	37	11	10789686	10789686	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10789686T>G	uc001mja.2	+	15	2087	c.1938T>G	c.(1936-1938)AAT>AAG	p.N646K		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	646	TPR 13.				histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ATGCAAAGAATCTGTATGCTG	0.348													21	220	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	56143438	56143438	+	IGR	SNP	G	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56143438G>C								OR8J1 (14767 upstream) : OR5R1 (41298 downstream)																							CAGAATCCTTGCTACTGGCTT	0.408													57	308	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	56143439	56143439	+	IGR	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56143439C>T								OR8J1 (14768 upstream) : OR5R1 (41297 downstream)																							AGAATCCTTGCTACTGGCTTC	0.408													57	306	---	---	---	---	PASS
PC	5091	broad.mit.edu	37	11	66616396	66616396	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66616396C>T	uc001ojn.1	-	21	3560	c.3511G>A	c.(3511-3513)GAC>AAC	p.D1171N	PC_uc001ojo.1_Missense_Mutation_p.D1171N|PC_uc001ojp.1_Missense_Mutation_p.D1171N|PC_uc001ojm.1_Missense_Mutation_p.D160N	NM_022172	NP_071504	P11498	PYC_HUMAN	pyruvate carboxylase precursor	1171	Biotinyl-binding.				gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	ATGAGGTCGTCACCTTCCAGT	0.592													6	21	---	---	---	---	PASS
RNF121	55298	broad.mit.edu	37	11	71693807	71693807	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71693807A>T	uc001ora.2	+	4	584	c.244A>T	c.(244-246)ATG>TTG	p.M82L	RNF121_uc001ord.2_Missense_Mutation_p.M1L|RNF121_uc001orb.2_Missense_Mutation_p.M50L|RNF121_uc009yst.2_Missense_Mutation_p.M50L	NM_018320	NP_060790	Q9H920	RN121_HUMAN	ring finger protein 121	82	Helical; (Potential).					integral to membrane	zinc ion binding				0						TGTGTTTCAGATGGTGACCCT	0.458													43	525	---	---	---	---	PASS
ALG8	79053	broad.mit.edu	37	11	77817939	77817939	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77817939T>C	uc001oza.1	-	10	1157	c.1092A>G	c.(1090-1092)CGA>CGG	p.R364R	ALG8_uc001oyz.1_Silent_p.R364R|ALG8_uc009yux.1_Silent_p.R262R	NM_024079	NP_076984	Q9BVK2	ALG8_HUMAN	dolichyl pyrophosphate Glc1Man9GlcNAc2	364					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GAGTTAGACATCGGAGAAAGC	0.423													19	228	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103091360	103091360	+	Silent	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103091360C>A	uc001pho.2	+	57	9099	c.8955C>A	c.(8953-8955)GTC>GTA	p.V2985V	DYNC2H1_uc001phn.1_Silent_p.V2985V|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2985	Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AGCCTTTAGTCAATGAAGCTA	0.308													38	168	---	---	---	---	PASS
SDHD	6392	broad.mit.edu	37	11	111965721	111965721	+	3'UTR	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111965721T>C	uc001pmz.2	+	4						NM_003002	NP_002993	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D						respiratory electron transport chain|transport|tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain complex II	electron carrier activity|heme binding|succinate dehydrogenase activity|ubiquinone binding				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Succinic acid(DB00139)	CTTTGAAGAATTGATGTATGC	0.418			Mis|N|F|S			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				5	17	---	---	---	---	PASS
DDX6	1656	broad.mit.edu	37	11	118639000	118639000	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118639000T>C	uc001pub.2	-	5	791	c.430A>G	c.(430-432)ACA>GCA	p.T144A	DDX6_uc001puc.2_Missense_Mutation_p.T144A	NM_004397	NP_004388	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	144	ATP (By similarity).|Helicase ATP-binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		CTCTTGCCTGTTCCATTTTTT	0.373			T	IGH@	B-NHL								6	254	---	---	---	---	PASS
VPS26B	112936	broad.mit.edu	37	11	134109913	134109913	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134109913C>T	uc001qhe.2	+	3	865	c.409C>T	c.(409-411)CGC>TGC	p.R137C		NM_052875	NP_443107	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B	137					protein transport|vacuolar transport	cytosol|retromer complex					0	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		CATCAGCCGCCGCCTCAATGA	0.463													8	163	---	---	---	---	PASS
LOC100288778	100288778	broad.mit.edu	37	12	88906	88906	+	Silent	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88906A>T	uc010scy.1	+	7	882	c.327A>T	c.(325-327)CCA>CCT	p.P109P	LOC100288778_uc010scz.1_RNA|LOC100288778_uc010sdc.1_RNA|LOC100288778_uc010sdd.1_Silent_p.P109P|LOC100288778_uc010sde.1_Silent_p.P109P|LOC100288778_uc010sdf.1_Silent_p.P109P|LOC100288778_uc010sdg.1_Silent_p.P109P|LOC100288778_uc010sdh.1_RNA					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						ccccaccaccacccccaGCTC	0.512													4	7	---	---	---	---	PASS
PTPN6	5777	broad.mit.edu	37	12	7069507	7069507	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7069507T>C	uc001qsb.2	+	14	1824	c.1582T>C	c.(1582-1584)TCG>CCG	p.S528P	PTPN6_uc001qsa.1_Missense_Mutation_p.S530P|PTPN6_uc010sfr.1_Missense_Mutation_p.S489P|PTPN6_uc009zfl.1_Missense_Mutation_p.S528P|PTPN6_uc010sfs.1_Missense_Mutation_p.S516P	NM_002831	NP_002822	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type	528					apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1						CTGCCCACAGTCGCAGAAGGG	0.667													4	40	---	---	---	---	PASS
PPFIBP1	8496	broad.mit.edu	37	12	27844837	27844837	+	Silent	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27844837A>G	uc001ric.1	+	27	3236	c.2859A>G	c.(2857-2859)GAA>GAG	p.E953E	PPFIBP1_uc010sjr.1_Silent_p.E784E|PPFIBP1_uc001rib.1_Silent_p.E947E|PPFIBP1_uc001ria.2_Silent_p.E922E|PPFIBP1_uc001rid.1_Silent_p.E800E|PPFIBP1_uc001rif.1_Silent_p.E460E	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	953					cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					TGTATGAGGAAGATGATTTGG	0.403													7	605	---	---	---	---	PASS
ITGB7	3695	broad.mit.edu	37	12	53589227	53589227	+	Silent	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53589227A>G	uc009zmv.2	-	8	1163	c.1092T>C	c.(1090-1092)CCT>CCC	p.P364P	ITGB7_uc001scc.2_Silent_p.P364P|ITGB7_uc010snz.1_RNA	NM_000889	NP_000880	P26010	ITB7_HUMAN	integrin, beta 7 precursor	364	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|breast(1)	8						CTGCAGACTTAGGAATCAGTT	0.532													5	203	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59276667	59276667	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59276667T>C	uc001sqr.2	-	12	1710	c.1464A>G	c.(1462-1464)CCA>CCG	p.P488P	LRIG3_uc009zqh.2_Silent_p.P428P|LRIG3_uc010ssh.1_RNA	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	488	LRRCT.					integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			CAAAGCCATCTGGGCTAACAG	0.413													37	93	---	---	---	---	PASS
E2F7	144455	broad.mit.edu	37	12	77444477	77444477	+	Silent	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77444477C>T	uc001sym.3	-	4	653	c.417G>A	c.(415-417)AGG>AGA	p.R139R	E2F7_uc001syn.2_Silent_p.R139R	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	139					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						TTCTGCTTGGCCTTTGCTTTT	0.453													75	294	---	---	---	---	PASS
C12orf12	196477	broad.mit.edu	37	12	91347603	91347603	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91347603T>C	uc001tbj.2	-	1	1351	c.917A>G	c.(916-918)GAG>GGG	p.E306G		NM_152638	NP_689851	Q8TC90	CL012_HUMAN	hypothetical protein LOC196477	306	Potential.|Glu-rich.									central_nervous_system(1)|pancreas(1)	2						atcttcgacctcttcttcctc	0.095													7	474	---	---	---	---	PASS
SLC25A3	5250	broad.mit.edu	37	12	98989101	98989101	+	Intron	SNP	T	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98989101T>A	uc001tfo.2	+						SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_Intron|SLC25A3_uc001tfr.2_Intron|SLC25A3_uc001tfs.2_5'UTR|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron	NM_005888	NP_005879	Q00325	MPCP_HUMAN	solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		TGGCCAAAGCTATTCAGCTGT	0.323													22	57	---	---	---	---	PASS
GIT2	9815	broad.mit.edu	37	12	110421492	110421492	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110421492T>A	uc001tps.2	-	5	578	c.413A>T	c.(412-414)CAT>CTT	p.H138L	GIT2_uc001tpq.2_Missense_Mutation_p.H138L|GIT2_uc001tpv.2_Missense_Mutation_p.H138L|GIT2_uc001tpu.2_Missense_Mutation_p.H138L|GIT2_uc001tpt.2_Missense_Mutation_p.H138L|GIT2_uc010sxu.1_Missense_Mutation_p.H76L|GIT2_uc001tpw.2_Missense_Mutation_p.H138L|GIT2_uc010sxv.1_Missense_Mutation_p.H138L	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting	138	ANK 1.				regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1						CACGCTCGAATGGAGTTGCTG	0.388													41	150	---	---	---	---	PASS
CCDC60	160777	broad.mit.edu	37	12	119926644	119926644	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119926644A>G	uc001txe.2	+	5	995	c.530A>G	c.(529-531)AAG>AGG	p.K177R	uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	177										ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CACACCATGAAGCCTGTGATC	0.557													6	237	---	---	---	---	PASS
WDR66	144406	broad.mit.edu	37	12	122389391	122389391	+	Silent	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122389391A>G	uc009zxk.2	+	9	1417	c.1275A>G	c.(1273-1275)GAA>GAG	p.E425E		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	425	WD 3.						calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		ATCAGTATGAAGAGAGGGATA	0.338													9	724	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32721987	32721987	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32721987C>A	uc001utx.2	+	13	1791	c.1295C>A	c.(1294-1296)ACC>AAC	p.T432N	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	432					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGACTTATAACCATCATCACA	0.438													49	484	---	---	---	---	PASS
ESD	2098	broad.mit.edu	37	13	47345584	47345584	+	Silent	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47345584G>A	uc001vbn.2	-	10	999	c.816C>T	c.(814-816)CAC>CAT	p.H272H	ESD_uc001vbo.2_3'UTR	NM_001984	NP_001975	P10768	ESTD_HUMAN	esterase D/formylglutathione hydrolase	272						cytoplasmic membrane-bounded vesicle	carboxylesterase activity|S-formylglutathione hydrolase activity			ovary(1)	1		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	GATGTCTGATGTGGTCAGTAA	0.338													134	602	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76432183	76432183	+	3'UTR	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76432183A>T	uc001vjv.2	+	27					LMO7_uc010thv.1_3'UTR|LMO7_uc010thw.1_3'UTR|LMO7_uc001vjx.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CTTTTTTTTTAAAAAAAAGAA	0.313													6	226	---	---	---	---	PASS
RNASE3	6037	broad.mit.edu	37	14	21359845	21359845	+	5'UTR	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21359845C>T	uc001vyj.2	+	2						NM_002935	NP_002926	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3 (eosinophil						defense response to bacterium|RNA catabolic process	extracellular region|soluble fraction	nucleic acid binding|pancreatic ribonuclease activity				0	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TTACAGGAAACATGGTTCCAA	0.502													5	36	---	---	---	---	PASS
SDCCAG1	9147	broad.mit.edu	37	14	50298067	50298067	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50298067A>C	uc001wxc.2	-	11	963	c.895T>G	c.(895-897)TTT>GTT	p.F299V	SDCCAG1_uc010anj.1_Missense_Mutation_p.F299V|SDCCAG1_uc010tqi.1_Missense_Mutation_p.F299V|SDCCAG1_uc001wxe.2_Missense_Mutation_p.F257V|SDCCAG1_uc001wxd.1_5'UTR|SDCCAG1_uc010anq.1_Missense_Mutation_p.F70V	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1	299						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)		TTGGAATAAAATTCATCCACC	0.299													76	581	---	---	---	---	PASS
SOS2	6655	broad.mit.edu	37	14	50597307	50597307	+	Silent	SNP	T	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50597307T>A	uc001wxs.3	-	20	3347	c.3249A>T	c.(3247-3249)CCA>CCT	p.P1083P	SOS2_uc010ans.2_5'UTR|SOS2_uc010tql.1_Silent_p.P1050P	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	1083					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					TTGGAGAGGTTGGTGCTGACA	0.418													41	247	---	---	---	---	PASS
TXNDC16	57544	broad.mit.edu	37	14	52922174	52922174	+	Silent	SNP	G	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52922174G>C	uc001wzs.2	-	18	2159	c.1710C>G	c.(1708-1710)ACC>ACG	p.T570T	TXNDC16_uc010tqu.1_Silent_p.T565T|TXNDC16_uc010aoe.2_RNA	NM_020784	NP_065835	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16 isoform 1	570					cell redox homeostasis	extracellular region					0	Breast(41;0.0716)					CAGCATATTTGGTTGACCTAT	0.443													42	373	---	---	---	---	PASS
DNAL1	83544	broad.mit.edu	37	14	74156076	74156076	+	Splice_Site	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74156076A>G	uc001xoq.3	+	7	557	c.392_splice	c.e7-2	p.A131_splice	DNAL1_uc010aru.2_Splice_Site_p.A92_splice|DNAL1_uc010arv.2_Splice_Site	NM_031427	NP_113615	Q4LDG9	DNAL1_HUMAN	axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		TTTTACTTGTAGCTGAGTTTG	0.279													4	178	---	---	---	---	PASS
TMEM63C	57156	broad.mit.edu	37	14	77723017	77723017	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77723017C>T	uc001xtf.2	+	24	2581	c.2369C>T	c.(2368-2370)TCG>TTG	p.S790L	TMEM63C_uc010asq.1_Missense_Mutation_p.S790L	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C	790						integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		GAGCTAGACTCGGCCCAGTTC	0.627													10	56	---	---	---	---	PASS
ZNF770	54989	broad.mit.edu	37	15	35275034	35275034	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35275034G>A	uc001ziw.2	-	3	913	c.602C>T	c.(601-603)ACT>ATT	p.T201I		NM_014106	NP_054825	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	201	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		TTTTAAGTGAGTTGACTGTCG	0.338													59	286	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42454278	42454278	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42454278T>C	uc001zpd.2	-	24	2596	c.2445A>G	c.(2443-2445)AAA>AAG	p.K815K	VPS39_uc001zpc.2_Silent_p.K804K|VPS39_uc001zpb.2_Silent_p.K150K	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	815					protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		GATTGAACCGTTTCTTTTGTG	0.458													7	479	---	---	---	---	PASS
PRTG	283659	broad.mit.edu	37	15	55965850	55965850	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55965850C>T	uc002adg.2	-	10	1619	c.1571G>A	c.(1570-1572)AGT>AAT	p.S524N	PRTG_uc002adh.2_Missense_Mutation_p.S26N	NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor	524	Fibronectin type-III 2.				multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ACTTGTCAAACTAATTTCAGG	0.448													23	80	---	---	---	---	PASS
NARG2	79664	broad.mit.edu	37	15	60740178	60740178	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60740178T>C	uc002agp.2	-	11	2521	c.2286A>G	c.(2284-2286)AAA>AAG	p.K762K	NARG2_uc002ago.2_Silent_p.K625K|NARG2_uc002agq.3_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a	762						nucleus				ovary(1)|lung(1)	2						CTCTTCTGATTTTCTTCCGTT	0.348													6	344	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70343760	70343760	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70343760C>T	uc002asm.2	-	19	3300	c.2181G>A	c.(2179-2181)TGG>TGA	p.W727*	TLE3_uc002ask.2_Nonsense_Mutation_p.W654*|TLE3_uc002asl.2_Nonsense_Mutation_p.W727*|TLE3_uc010ukd.1_Nonsense_Mutation_p.W717*|TLE3_uc010bik.1_Nonsense_Mutation_p.W308*|TLE3_uc010bil.1_Nonsense_Mutation_p.W724*|TLE3_uc002asn.2_Nonsense_Mutation_p.W715*|TLE3_uc002asp.2_Nonsense_Mutation_p.W719*|TLE3_uc002aso.2_Nonsense_Mutation_p.W722*	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a	727	WD 6.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						AAGGCGTCCTCCAGGCGTTGA	0.542													4	103	---	---	---	---	PASS
IGF1R	3480	broad.mit.edu	37	15	99192822	99192822	+	Silent	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99192822C>T	uc002bul.2	+	1	62	c.12C>T	c.(10-12)GGC>GGT	p.G4G	IGF1R_uc010urq.1_Silent_p.G4G|IGF1R_uc010bon.2_Silent_p.G4G	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor	4					anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	TGAAGTCTGGCTCCGGAGGAG	0.443													5	27	---	---	---	---	PASS
RBL2	5934	broad.mit.edu	37	16	53493512	53493512	+	Silent	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53493512A>G	uc002ehi.3	+	9	1447	c.1329A>G	c.(1327-1329)AAA>AAG	p.K443K	RBL2_uc010vgv.1_Silent_p.K369K|RBL2_uc002ehj.2_Silent_p.K153K|RBL2_uc010vgw.1_Silent_p.K227K	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	443	Domain A.|Pocket; binds E1A.				cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						CAAGTGAGAAACTGGAACAGA	0.423													4	78	---	---	---	---	PASS
KCNG4	93107	broad.mit.edu	37	16	84270394	84270394	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84270394G>T	uc010voc.1	-	2	819	c.698C>A	c.(697-699)ACC>AAC	p.T233N	KCNG4_uc002fhu.1_Missense_Mutation_p.T233N	NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,	233						voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3						GACGGCTGTGGTGGCCACGAA	0.632													3	16	---	---	---	---	PASS
ITGAE	3682	broad.mit.edu	37	17	3618235	3618235	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3618235C>G	uc002fwo.3	-	31	3545	c.3446G>C	c.(3445-3447)TGT>TCT	p.C1149S	ITGAE_uc002fwn.3_RNA	NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	1149	Cytoplasmic (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		AAAAAAGCCACACTGAAACAA	0.428													10	275	---	---	---	---	PASS
CLEC10A	10462	broad.mit.edu	37	17	6981408	6981408	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6981408A>G	uc002gek.2	-	3	395	c.92T>C	c.(91-93)CTG>CCG	p.L31P	CLEC10A_uc002gej.2_Missense_Mutation_p.L31P|CLEC10A_uc002gel.2_Missense_Mutation_p.L31P|CLEC10A_uc010clv.1_Missense_Mutation_p.L31P	NM_182906	NP_878910	Q8IUN9	CLC10_HUMAN	C-type lectin, superfamily member 14 isoform 1	31	Cytoplasmic (Potential).				endocytosis|innate immune response	integral to membrane|plasma membrane	sugar binding				0						GAGACGCTGCAGGAGGGACTG	0.627													9	57	---	---	---	---	PASS
CNTD1	124817	broad.mit.edu	37	17	40963557	40963557	+	3'UTR	SNP	T	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40963557T>A	uc002ibm.3	+	7					CNTD1_uc010wha.1_3'UTR|BECN1_uc002ibo.3_Intron|BECN1_uc010whb.1_Intron|BECN1_uc010whc.1_Intron|BECN1_uc002ibn.2_Intron	NM_173478	NP_775749	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1											central_nervous_system(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CATGTGATTCTGTGCCATTTT	0.428													4	28	---	---	---	---	PASS
MAP3K14	9020	broad.mit.edu	37	17	43347888	43347888	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43347888A>T	uc002iiw.1	-	12	1973	c.1864T>A	c.(1864-1866)TGC>AGC	p.C622S	MAP3K14_uc002iiu.1_Missense_Mutation_p.C152S|MAP3K14_uc010daj.1_RNA|MAP3K14_uc002iiv.1_Missense_Mutation_p.C206S	NM_003954	NP_003945	Q99558	M3K14_HUMAN	mitogen-activated protein kinase kinase kinase	622	Interaction with ZFP91.|Protein 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						AGAGGGGCGCAGGAGGGTGGG	0.642													6	23	---	---	---	---	PASS
LRRC46	90506	broad.mit.edu	37	17	45909254	45909254	+	5'UTR	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45909254T>C	uc002ima.2	+	1					MRPL10_uc010wky.1_5'Flank|MRPL10_uc002ilz.2_5'Flank|MRPL10_uc002ily.2_5'Flank|LRRC46_uc002imb.2_5'UTR	NM_033413	NP_219481	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46											ovary(1)	1						TCTGAGTTTCTCTCTCCTCCT	0.498													27	65	---	---	---	---	PASS
CUEDC1	404093	broad.mit.edu	37	17	55948719	55948719	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55948719A>G	uc002ivd.1	-	6	1515	c.796T>C	c.(796-798)TAC>CAC	p.Y266H	CUEDC1_uc002ive.1_Missense_Mutation_p.Y266H	NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1	266										skin(2)	2						TGGGATTCGTATTTCAATCGA	0.532													28	152	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60782793	60782793	+	Intron	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60782793G>T	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_3'UTR|uc002jaj.1_5'Flank|uc002jak.2_5'Flank	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						TTTGCCTCTGGGTGGTGGTCA	0.483													10	68	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2784571	2784571	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2784571T>C	uc002klm.3	+	45	5860	c.5671T>C	c.(5671-5673)TTT>CTT	p.F1891L	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_RNA	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	1891					chromosome organization		ATP binding				0						GGGAATGGTATTTGGAGCTCC	0.378													14	253	---	---	---	---	PASS
GREB1L	80000	broad.mit.edu	37	18	19085476	19085476	+	Silent	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19085476G>A	uc010xam.1	+	24	4447	c.4176G>A	c.(4174-4176)AAG>AAA	p.K1392K	GREB1L_uc010xan.1_Silent_p.K808K|GREB1L_uc010dlr.1_Silent_p.K503K	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast	1392						integral to membrane					0						ATGACCCCAAGTACAGTTTGA	0.507													4	242	---	---	---	---	PASS
TTC39C	125488	broad.mit.edu	37	18	21646078	21646078	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21646078A>G	uc002kuw.2	+	3	771	c.319A>G	c.(319-321)ACA>GCA	p.T107A	TTC39C_uc002kuu.2_Missense_Mutation_p.T46A	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1	107							binding			ovary(1)	1						AGTAATTGAAACAATCAAGAA	0.348													9	595	---	---	---	---	PASS
MYO1F	4542	broad.mit.edu	37	19	8601836	8601836	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8601836T>C	uc002mkg.2	-	17	1910	c.1796A>G	c.(1795-1797)AAC>AGC	p.N599S		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	599	Myosin head-like.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3						GGATCACCTGTTCTCCTCCCA	0.517													5	125	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9049695	9049695	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9049695G>T	uc002mkp.2	-	5	32140	c.31936C>A	c.(31936-31938)CCT>ACT	p.P10646T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10648	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						AGTTCACTAGGTGAGATATTT	0.473													10	331	---	---	---	---	PASS
UBL5	59286	broad.mit.edu	37	19	9939534	9939534	+	Silent	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9939534C>T	uc002mmi.1	+	4	266	c.162C>T	c.(160-162)CAC>CAT	p.H54H	FBXL12_uc002mmh.2_5'Flank|UBL5_uc002mmj.1_Silent_p.H54H	NM_001048241	NP_001041706	Q9BZL1	UBL5_HUMAN	ubiquitin-like 5	54	Ubiquitin-like.					cytoplasm					0						TTAAGGACCACGTGTCTCTGG	0.423													5	352	---	---	---	---	PASS
ZNF738	148203	broad.mit.edu	37	19	21563808	21563808	+	3'UTR	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21563808G>T	uc002nps.3	+	5						NR_027130				SubName: Full=cDNA FLJ14673 fis, clone NT2RP2003714, moderately similar to Zinc finger protein 430;												0						AATGATCCAAGGAGAGTGATG	0.378													3	8	---	---	---	---	PASS
DPY19L3	147991	broad.mit.edu	37	19	32954279	32954279	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32954279A>G	uc002ntg.2	+	13	1506	c.1330A>G	c.(1330-1332)ACA>GCA	p.T444A	DPY19L3_uc002nth.1_Missense_Mutation_p.T444A|DPY19L3_uc002nti.1_RNA	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3	444						integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)					CAGTGATTCTACAAATCAACA	0.338													6	322	---	---	---	---	PASS
ZNF570	148268	broad.mit.edu	37	19	37967302	37967302	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37967302G>A	uc002ogk.1	+	4	751	c.222G>A	c.(220-222)ATG>ATA	p.M74I	ZNF570_uc010efl.1_Missense_Mutation_p.M130I|ZNF570_uc010xtr.1_5'UTR	NM_144694	NP_653295	Q96NI8	ZN570_HUMAN	zinc finger protein 570	74	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CACCCTGGATGGTGAAGAGAG	0.408													55	266	---	---	---	---	PASS
WDR87	83889	broad.mit.edu	37	19	38385942	38385942	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38385942C>T	uc010efu.2	-	4	509	c.284G>A	c.(283-285)GGG>GAG	p.G95E	WDR87_uc002ohj.2_Missense_Mutation_p.G134E	NM_031951	NP_114157	Q6ZQQ6	WDR87_HUMAN	NYD-SP11 protein	95											0						AAAGTGGTCCCCAAAGAGTCG	0.542													4	173	---	---	---	---	PASS
GRIK5	2901	broad.mit.edu	37	19	42563630	42563630	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42563630C>A	uc002osj.1	-	5	593	c.558G>T	c.(556-558)GAG>GAT	p.E186D	GRIK5_uc010eib.1_Missense_Mutation_p.E105D	NM_002088	NP_002079	Q16478	GRIK5_HUMAN	glutamate receptor KA2 precursor	186	Extracellular (Potential).					cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)	CTGACAGCGTCTCCTTGGAGA	0.607													15	50	---	---	---	---	PASS
ZNF175	7728	broad.mit.edu	37	19	52090388	52090388	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52090388G>T	uc002pxb.2	+	5	1182	c.804G>T	c.(802-804)AAG>AAT	p.K268N		NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175	268					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)		AGTCACTCAAGCAACATCAAA	0.428													8	57	---	---	---	---	PASS
KIR3DX1	90011	broad.mit.edu	37	19	55049203	55049203	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55049203T>C	uc010erm.2	+	2	281	c.269T>C	c.(268-270)CTC>CCC	p.L90P	KIR3DX1_uc010yfa.1_RNA|KIR3DX1_uc010yfb.1_RNA|KIR3DX1_uc010yfc.1_RNA|KIR3DX1_uc010yfd.1_RNA					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		AGAGTACTCCTCTGTCATTCA	0.343													6	350	---	---	---	---	PASS
CST2	1470	broad.mit.edu	37	20	23804525	23804525	+	3'UTR	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23804525G>A	uc002wtq.1	-	3						NM_001322	NP_001313	P09228	CYTT_HUMAN	cystatin SA precursor							extracellular region	cysteine-type endopeptidase inhibitor activity				0						GCCTCCTGCAGCCTTCTCTGT	0.612													6	35	---	---	---	---	PASS
TPX2	22974	broad.mit.edu	37	20	30345350	30345350	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30345350A>G	uc002wwp.1	+	3	769	c.71A>G	c.(70-72)GAT>GGT	p.D24G	TPX2_uc010gdv.1_Missense_Mutation_p.D24G	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog	24					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)			TCCTTGGATGATGAAGGAGAT	0.408													7	513	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31016216	31016216	+	Silent	SNP	T	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31016216T>C	uc002wxs.2	+	5	888	c.462T>C	c.(460-462)GCT>GCC	p.A154A	ASXL1_uc002wxr.1_RNA|ASXL1_uc010geb.2_Silent_p.A96A	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	154					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						GCTACAGAGCTTCCTCACAGG	0.488			F|N|Mis		MDS|CMML								5	210	---	---	---	---	PASS
ITCH	83737	broad.mit.edu	37	20	33026360	33026360	+	Silent	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33026360A>G	uc010geu.1	+	9	918	c.726A>G	c.(724-726)TCA>TCG	p.S242S	ITCH_uc002xak.2_Silent_p.S201S|ITCH_uc010zuj.1_Silent_p.S91S	NM_031483	NP_113671	Q96J02	ITCH_HUMAN	itchy homolog E3 ubiquitin protein ligase	242					apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6						ATTCTCCATCACTCTCAAATG	0.478													39	257	---	---	---	---	PASS
KRTAP19-2	337969	broad.mit.edu	37	21	31859596	31859596	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31859596G>T	uc011acy.1	-	1	72	c.72C>A	c.(70-72)TGC>TGA	p.C24*		NM_181608	NP_853639	Q3LHN2	KR192_HUMAN	keratin associated protein 19-2	24						intermediate filament					0						AACCATATCTGCATCCTTCAT	0.542													6	52	---	---	---	---	PASS
DSCR3	10311	broad.mit.edu	37	21	38610801	38610801	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38610801A>G	uc002ywf.1	-	4	550	c.311T>C	c.(310-312)GTT>GCT	p.V104A	DSCR3_uc010gnm.1_RNA|DSCR3_uc010gnn.1_Missense_Mutation_p.V62A|DSCR3_uc010gnl.2_Missense_Mutation_p.V104A|DSCR3_uc011aeg.1_Intron|DSCR3_uc011aeh.1_Intron	NM_006052	NP_006043	O14972	DSCR3_HUMAN	Down syndrome critical region protein 3	104					vacuolar transport	nucleus|retromer complex					0						CTCATACAGAACTTTGTTACC	0.443													66	188	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	33780246	33780246	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33780246C>T	uc003and.3	-	9	1516	c.937G>A	c.(937-939)GAG>AAG	p.E313K	LARGE_uc011amd.1_Missense_Mutation_p.E112K|LARGE_uc003ane.3_Missense_Mutation_p.E313K|LARGE_uc010gwp.2_Missense_Mutation_p.E313K|LARGE_uc011ame.1_Missense_Mutation_p.E245K|LARGE_uc011amf.1_Missense_Mutation_p.E313K|LARGE_uc010gwq.1_RNA	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	313	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)				CACATCTGCTCCCATTTCATC	0.488													27	115	---	---	---	---	PASS
RANGAP1	5905	broad.mit.edu	37	22	41650402	41650402	+	Silent	SNP	C	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41650402C>T	uc003azs.2	-	10	2640	c.1170G>A	c.(1168-1170)GAG>GAA	p.E390E	RANGAP1_uc003azt.2_Silent_p.E390E|RANGAP1_uc003azu.2_Silent_p.E390E|RANGAP1_uc003azr.2_5'Flank|RANGAP1_uc010gyk.2_5'Flank|RANGAP1_uc011aoz.1_Silent_p.E335E	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	390	Asp/Glu-rich (highly acidic).|Asp/Glu-rich (highly acidic).				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						cctcctcctcctcttcttcct	0.264													4	121	---	---	---	---	PASS
MLC1	23209	broad.mit.edu	37	22	50518347	50518347	+	Silent	SNP	G	A	A	rs121908343		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50518347G>A	uc003bjg.1	-	5	696	c.423C>T	c.(421-423)AAC>AAT	p.N141N	MLC1_uc011arl.1_Intron|MLC1_uc003bjh.1_Silent_p.N141N|MLC1_uc011arm.1_Silent_p.N111N|MLC1_uc011arn.1_Silent_p.N62N|MLC1_uc011aro.1_Intron	NM_139202	NP_631941	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with	141			N -> S (in MLC1).|N -> K (in MLC1).			basolateral plasma membrane|endosome|integral to membrane|integral to membrane of membrane fraction	ion channel activity			pancreas(1)	1		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GTGAACTCACGTTTATTGCTG	0.463													66	261	---	---	---	---	PASS
KLHL4	56062	broad.mit.edu	37	X	86921522	86921522	+	Silent	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86921522G>T	uc004efb.2	+	11	2327	c.2145G>T	c.(2143-2145)GTG>GTT	p.V715V	KLHL4_uc004efa.2_Intron	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	715	Kelch 6.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						TTGTAGTGGTGAAGCTACCCT	0.343													216	299	---	---	---	---	PASS
RBMXL3	139804	broad.mit.edu	37	X	114424200	114424200	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114424200G>T	uc011mte.1	+	1	238	c.196G>T	c.(196-198)GCC>TCC	p.A66S	LRCH2_uc010nqe.2_Intron|LRCH2_uc004epz.2_Intron	NM_001145346	NP_001138818	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	66	RRM.						nucleotide binding|RNA binding				0						CAAGGCTGCCGCCAGAGATAT	0.567													12	20	---	---	---	---	PASS
ZFY	7544	broad.mit.edu	37	Y	2829189	2829189	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:2829189G>A	uc004fqj.2	+	3	457	c.136G>A	c.(136-138)GTG>ATG	p.V46M	ZFY_uc010nwd.1_Missense_Mutation_p.V46M|ZFY_uc011nan.1_Intron|ZFY_uc010nwe.2_Missense_Mutation_p.V20M	NM_003411	NP_003402	P08048	ZFY_HUMAN	zinc finger protein, Y-linked isoform 1	46					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTCTAATATTGTGGATTCTGA	0.358													171	283	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11711	11711	+	RNA	SNP	G	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11711G>A	uc004cov.3	+	1		c.1134G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		TTCTCATAATCGCCCACGGAC	0.483													100	32	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5532620	5532621	+	IGR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5532620_5532621delGT								AJAP1 (688770 upstream) : NPHP4 (390249 downstream)																							gagcttgcacgtgtgtgtgtgt	0.416													3	3	---	---	---	---	
TAS1R2	80834	broad.mit.edu	37	1	19178265	19178265	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19178265delT	uc001bba.1	-							NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2 precursor						detection of chemical stimulus involved in sensory perception of sweet taste	plasma membrane	protein heterodimerization activity|taste receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	TCATCGCCCCTGAGTCCTGTC	0.547													4	2	---	---	---	---	
GMEB1	10691	broad.mit.edu	37	1	29007649	29007649	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29007649delG	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTTGTGACGGGGGTACTGC	0.393													4	2	---	---	---	---	
PTP4A2	8073	broad.mit.edu	37	1	32375887	32375887	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32375887delT	uc001bty.1	-						PTP4A2_uc010ogs.1_Intron|PTP4A2_uc001btz.1_Intron	NM_080391	NP_536316	Q12974	TP4A2_HUMAN	protein tyrosine phosphatase type IVA, member 2							early endosome|plasma membrane	prenylated protein tyrosine phosphatase activity|protein binding|protein tyrosine/serine/threonine phosphatase activity				0		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)				AATTCTATGAttttttttttt	0.159													8	4	---	---	---	---	
CCDC30	728621	broad.mit.edu	37	1	43013678	43013678	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43013678delA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc010oju.1_Intron|CCDC30_uc001chp.2_Intron	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30												0						ggggccaagcaaaaagatggg	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	50245607	50245607	+	Intron	DEL	A	-	-	rs113055427		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50245607delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		tcaaaagcagaaaaaaaaaat	0.000													4	9	---	---	---	---	
FAM159A	348378	broad.mit.edu	37	1	53124751	53124751	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53124751delT	uc001cug.1	+						FAM159A_uc001cuh.2_Intron	NM_001042693		Q6UWV7	F159A_HUMAN	hypothetical protein LOC348378							integral to membrane					0						TATTTCAGCAttttttttttg	0.149													4	2	---	---	---	---	
ZYG11A	440590	broad.mit.edu	37	1	53347540	53347540	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53347540delT	uc001cuk.2	+						ZYG11A_uc001cul.2_Intron	NM_001004339	NP_001004339	Q6WRX3	ZY11A_HUMAN	zyg-11 homolog A								binding				0						TCTCATCAGCTTTTTTTTTTT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	63424290	63424290	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63424290delT								ATG4C (94241 upstream) : FOXD3 (364440 downstream)																							ttcTTTAAGATTTTTTTTGTG	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84940824	84940824	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84940824delA								DNASE2B (60133 upstream) : RPF1 (4096 downstream)																							TACAATAAACAAAAAAAAGAA	0.333													4	2	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86259179	86259180	+	Intron	DEL	GA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86259179_86259180delGA	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		aaagagaggggagagagagagc	0.178													4	2	---	---	---	---	
LOC400759	400759	broad.mit.edu	37	1	89887469	89887469	+	Intron	DEL	G	-	-	rs67428662		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89887469delG	uc009wcy.1	+							NR_003133				Homo sapiens cDNA, FLJ17004.												0						ctgtatttctgaaaaaaaaaa	0.129													3	4	---	---	---	---	
TGFBR3	7049	broad.mit.edu	37	1	92263681	92263682	+	Intron	DEL	AA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92263681_92263682delAA	uc001doh.2	-						TGFBR3_uc009wde.2_Intron|TGFBR3_uc010osy.1_Intron|TGFBR3_uc001doi.2_Intron|TGFBR3_uc001doj.2_Intron	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		GTCAAGCCTTAAATCCTAAATC	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108646149	108646149	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108646149delG								VAV3 (138604 upstream) : SLC25A24 (31300 downstream)																							tacagaataaggcaagggaga	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116907015	116907015	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116907015delT								C1orf161 (229154 upstream) : ATP1A1 (7989 downstream)																							ATAAGCCTCATTTTTTTTGTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120031419	120031420	+	IGR	DEL	AG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120031419_120031420delAG								HSD3B2 (42299 upstream) : HSD3B1 (18406 downstream)																							gaaggaagaaagagagagagag	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145077808	145077809	+	Intron	INS	-	C	C	rs771108		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145077808_145077809insC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_5'Flank|PDE4DIP_uc001emh.2_5'Flank|PDE4DIP_uc001emk.2_5'Flank			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AAAAAAAAAAAAAAAAACCTGT	0.391													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145292408	145292408	+	5'Flank	DEL	C	-	-	rs59280816		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145292408delC	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001emq.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATATAAATGACTTTGATCACT	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148904610	148904611	+	IGR	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148904610_148904611insT								NBPF16 (146299 upstream) : LOC645166 (23675 downstream)																							TCAAGCCCAGATTTTTTTTTTC	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149032494	149032494	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149032494delA								LOC645166 (79440 upstream) : LOC388692 (246982 downstream)																							CAGAGAATTCATCACTGACTT	0.294													3	3	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154711863	154711863	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154711863delC	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			attcttagtgccccccacccc	0.000													4	2	---	---	---	---	
OR10T2	128360	broad.mit.edu	37	1	158369426	158369427	+	5'Flank	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158369426_158369427insA	uc010pih.1	-							NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					ATGATTTTTCCAAAAAATTATT	0.282													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	171873802	171873802	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171873802delT	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						AGATGGCCTGTTTTTTTTGCG	0.453													4	2	---	---	---	---	
ABL2	27	broad.mit.edu	37	1	179095931	179095931	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179095931delT	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Intron|ABL2_uc001gmh.3_Intron|ABL2_uc010pne.1_Intron|ABL2_uc009wxf.1_Intron|ABL2_uc001gmk.2_Intron	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TTATGCCAAATTTTTTTTTTA	0.289			T	ETV6	AML								10	5	---	---	---	---	
GLT25D2	23127	broad.mit.edu	37	1	183901232	183901233	+	Intron	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183901232_183901233delTG	uc010poj.1	-							NM_015101	NP_055916	Q8IYK4	GT252_HUMAN	glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2						TGTATCAGGCTGTGTGTGTGTG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201920750	201920750	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201920750delC								LMOD1 (5034 upstream) : TIMM17A (3869 downstream)																							TAAGCTAAAACCCCTCTGTCT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	202015273	202015273	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202015273delA								ELF3 (28967 upstream) : GPR37L1 (76756 downstream)																							TGACCTGCCTAAAATAAATCC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222400811	222400811	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222400811delG								DUSP10 (485350 upstream) : HHIPL2 (294791 downstream)																							GGCAGAGTCAGGAGTCTATGC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	227562759	227562760	+	IGR	DEL	TC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227562759_227562760delTC								CDC42BPA (56933 upstream) : ZNF678 (188484 downstream)																							ttccttcctttctctctctctc	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232504843	232504844	+	IGR	DEL	TG	-	-	rs63744362		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232504843_232504844delTG								DISC1 (327827 upstream) : SIPA1L2 (28870 downstream)																							CAtctctctctgtctctgtctc	0.376													5	3	---	---	---	---	
MTR	4548	broad.mit.edu	37	1	237065771	237065771	+	3'UTR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237065771delA	uc001hyi.3	+	33					MTR_uc010pxw.1_3'UTR|MTR_uc010pxx.1_3'UTR|MTR_uc010pxy.1_3'UTR	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	tatggcgtctaaaatagtgct	0.174													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246086999	246086999	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246086999delT	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)		ctccactccctccccttacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249236585	249236586	+	IGR	DEL	TT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249236585_249236586delTT								PGBD2 (23241 upstream) : None (None downstream)																							tttgttagcattttttttttca	0.000													4	2	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	1866498	1866499	+	Intron	DEL	AG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1866498_1866499delAG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		CAAAGAGGGCAGAGAGAGAGGT	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4312648	4312648	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4312648delT								ALLC (562390 upstream) : None (None downstream)																							taatTGGCTATTTTTTTAATG	0.139													4	2	---	---	---	---	
RNF144A	9781	broad.mit.edu	37	2	7061370	7061370	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7061370delC	uc002qys.2	+						RNF144A_uc002qyt.2_Intron|uc002qyr.1_5'Flank	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		GTGCTTACTTCCTGGATGTTC	0.478													4	2	---	---	---	---	
PDIA6	10130	broad.mit.edu	37	2	10948573	10948573	+	Intron	DEL	C	-	-	rs76231534		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10948573delC	uc002rau.2	-						PDIA6_uc010yjg.1_Intron|PDIA6_uc002rav.2_Intron|PDIA6_uc010yjh.1_Intron|PDIA6_uc002raw.2_Intron	NM_005742	NP_005733	Q15084	PDIA6_HUMAN	protein disulfide isomerase A6 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		attatagagaccagaggcagg	0.000													4	2	---	---	---	---	
PQLC3	130814	broad.mit.edu	37	2	11318191	11318192	+	3'UTR	INS	-	AGA	AGA	rs148190616	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11318191_11318192insAGA	uc002rbc.2	+	7					PQLC3_uc010yjk.1_3'UTR	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor							integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		CTGCAGTGTTGAGGCCAGTCAC	0.406													6	6	---	---	---	---	
PQLC3	130814	broad.mit.edu	37	2	11318225	11318235	+	3'UTR	DEL	CCATTTTGAGG	-	-	rs3832137		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11318225_11318235delCCATTTTGAGG	uc002rbc.2	+	7					PQLC3_uc010yjk.1_3'UTR	NM_152391	NP_689604	Q8N755	PQLC3_HUMAN	PQ loop repeat containing 3 precursor							integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)		TCCAAGAAGCCCATTTTGAGGCCATTTTGAG	0.412													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13031049	13031049	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13031049delA								TRIB2 (148193 upstream) : None (None downstream)																							TGGCTTCTGCAAAAAAAAAAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18158595	18158595	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18158595delT								KCNS3 (44371 upstream) : NT5C1B (577396 downstream)																							GTTTTCCTCCTTTTTTTTTCC	0.413													4	2	---	---	---	---	
EFR3B	22979	broad.mit.edu	37	2	25268123	25268123	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25268123delT	uc010eyh.2	+						EFR3B_uc002rfw.2_Intron	NM_014971	NP_055786	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B								binding				0						GCCACTTCCCTTTCTCAGACT	0.557													4	2	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26865963	26865963	+	5'Flank	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26865963delG	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aaaaaaaaaagaaaTGTGTGC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26967444	26967444	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26967444delA								KCNK3 (13378 upstream) : C2orf18 (19698 downstream)																							CGGAGTCGCTAAAAATCACAC	0.502													4	2	---	---	---	---	
XDH	7498	broad.mit.edu	37	2	31596399	31596402	+	Intron	DEL	GTTT	-	-	rs139496928		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31596399_31596402delGTTT	uc002rnv.1	-							NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	CAGATAGATGgtttgtttgtttgt	0.196													1	5	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32823206	32823206	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32823206delT	uc010ezu.2	+							NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					CCTCCCCCCCttttttttttg	0.239													3	3	---	---	---	---	
TTC27	55622	broad.mit.edu	37	2	33042314	33042315	+	Intron	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33042314_33042315insA	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						ccctgtatcttaaaaaaaaaaa	0.119													4	2	---	---	---	---	
ABCG5	64240	broad.mit.edu	37	2	44065648	44065650	+	Intron	DEL	AGC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44065648_44065650delAGC	uc002rtn.2	-						ABCG5_uc002rto.2_5'UTR|ABCG5_uc002rtp.2_5'UTR|ABCG8_uc002rtq.2_5'Flank|ABCG8_uc010yoa.1_5'Flank	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTCCTGGGGGAGCAGCAGCAGCA	0.660													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48188478	48188479	+	IGR	INS	-	A	A	rs146460833	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48188478_48188479insA								FBXO11 (55664 upstream) : FOXN2 (353316 downstream)																							ctatcctaagcaaaataataaa	0.000													4	2	---	---	---	---	
C1D	10438	broad.mit.edu	37	2	68281138	68281138	+	5'Flank	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68281138delT	uc002sea.3	-						C1D_uc002seb.2_Intron|C1D_uc002sec.2_Intron|C1D_uc010fdc.2_Intron	NM_173177	NP_775269	Q13901	C1D_HUMAN	nuclear DNA-binding protein						apoptosis|maturation of 5.8S rRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear exosome (RNase complex)|nucleolus	DNA binding|RNA binding				0						tcttaatgtatttttatttac	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72087009	72087012	+	IGR	DEL	GTGT	-	-	rs144814313		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72087009_72087012delGTGT								DYSF (173117 upstream) : CYP26B1 (269355 downstream)																							atgtatgtgagtgtgtgtgcatga	0.162													4	2	---	---	---	---	
NOTO	344022	broad.mit.edu	37	2	73435901	73435901	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73435901delA	uc010yrd.1	+							NM_001134462	NP_001127934	A8MTQ0	NOTO_HUMAN	notochord homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CTATATAATGAAAAAAAAAAG	0.398													4	2	---	---	---	---	
CCT7	10574	broad.mit.edu	37	2	73474707	73474707	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73474707delA	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						TGTGTTATTTAAAAAAAAAAA	0.373													7	4	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80011157	80011157	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80011157delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						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						TAAGTTTTTCTTCTGCTCATA	0.343													4	2	---	---	---	---	
KDM3A	55818	broad.mit.edu	37	2	86683244	86683244	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86683244delT	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A						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						CAATCATACATTTTTTTTCTG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96524700	96524701	+	Intron	DEL	AG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96524700_96524701delAG	uc002sva.1	-						uc002suz.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		TCTACATAACAGAGAGAGAGAG	0.238													3	4	---	---	---	---	
LOC729234	729234	broad.mit.edu	37	2	96679935	96679937	+	Intron	DEL	AAC	-	-	rs113830014		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96679935_96679937delAAC	uc010fht.2	+							NR_003698				Homo sapiens fumarylacetoacetate hydrolase domain containing 2 pseudogene (LOC729234), non-coding RNA.												0						ggaggtgattaacaatttgaagg	0.207													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105474220	105474221	+	IGR	INS	-	A	A	rs145392763	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105474220_105474221insA								POU3F3 (750 upstream) : MRPS9 (180262 downstream)																							CAGTCTCCAAGAAAAAAATAAT	0.386													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107845181	107845182	+	IGR	DEL	TT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107845181_107845182delTT								ST6GAL2 (341618 upstream) : LOC729121 (594338 downstream)																							GGTTGTGCCATTTTACAATGCT	0.213													4	2	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	114013024	114013024	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114013024delA	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_RNA|LOC654433_uc010fks.2_RNA|LOC654433_uc010fkt.2_RNA|LOC654433_uc002tjr.3_RNA|LOC654433_uc002tjs.3_RNA	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						TCCACAGTCCAAAAAAAAAAG	0.408			T	PPARG	follicular thyroid		Thyroid dysgenesis 						7	8	---	---	---	---	
WASH2P	375260	broad.mit.edu	37	2	114355774	114355784	+	Intron	DEL	GAGGTGGCTGG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114355774_114355784delGAGGTGGCTGG	uc002tkh.2	+						WASH2P_uc002tka.2_Intron|WASH2P_uc002tkb.2_Intron|WASH2P_uc002tkd.2_Intron	NM_182905	NP_878908			WAS protein family homolog 1												0						ccctgtccccgaggtggctgggaggTGGCTC	0.261													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129658053	129658054	+	IGR	DEL	TT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129658053_129658054delTT								HS6ST1 (581882 upstream) : None (None downstream)																							CTTTTTTAGCTTTTTTTTTTCA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130199602	130199602	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130199602delT								None (None upstream) : LOC389033 (480833 downstream)																							gaggctcctctttttgctgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132769521	132769521	+	IGR	DEL	T	-	-	rs141619696	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132769521delT								C2orf27B (210287 upstream) : NCRNA00164 (135643 downstream)																							gggattatagttttgaggcac	0.060													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132892026	132892026	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132892026delT								C2orf27B (332792 upstream) : NCRNA00164 (13138 downstream)																							Attttttttcttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133074008	133074009	+	Intron	INS	-	T	T	rs144826258	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133074008_133074009insT	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		TCTTGTGACCCTTGTGTCCCTT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133103684	133103684	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133103684delT								NCRNA00164 (88142 upstream) : GPR39 (70463 downstream)																							TTTCCTTTCATTTTTTTCAAA	0.264													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133709694	133709694	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133709694delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						ATGCTCTGTGAAAAAAAACAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134608110	134608110	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134608110delA								NCKAP5 (282079 upstream) : MGAT5 (403720 downstream)																							TGATGACTCCAAAATGAATAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139126360	139126360	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139126360delG								HNMT (352427 upstream) : SPOPL (132990 downstream)																							agctctttgtggccatattaa	0.060													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141570691	141570691	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141570691delT	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACCTAGCACCTTTTTTTCCCT	0.313										TSP Lung(27;0.18)			4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	145077967	145077967	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145077967delC	uc010fnn.2	-						GTDC1_uc002tvq.2_5'Flank|GTDC1_uc002tvr.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TATAATGTTTCCCTGTCTTAC	0.358													4	2	---	---	---	---	
RAPGEF4	11069	broad.mit.edu	37	2	173756254	173756254	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173756254delA	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc002uhw.3_Intron|RAPGEF4_uc010zec.1_Intron|RAPGEF4_uc010zed.1_Intron|RAPGEF4_uc010zee.1_Intron|RAPGEF4_uc010fqo.2_Intron	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)			GTATTGAGCTAAAAGGTTCAT	0.403													4	2	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179537655	179537655	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179537655delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'Flank|TTN_uc002una.1_Intron|TTN_uc010frf.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)			TGTGCCATTCTTTTTTTTTTC	0.303													7	4	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179656290	179656291	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179656290_179656291insT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron|TTN_uc010frg.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTGAAGGAATTTTTTTTTTT	0.386													3	3	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	198076747	198076748	+	Intron	DEL	CT	-	-	rs72297664		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198076747_198076748delCT	uc002uuc.2	-						ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron|ANKRD44_uc002uud.1_Intron	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTCACTGAGCctctctctctct	0.381													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	212184809	212184809	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212184809delA								CPS1 (640980 upstream) : ERBB4 (55633 downstream)																							tcactgaagtaattacaactt	0.000													4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	215044890	215044890	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215044890delG	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCCTGCAACTGGGGAGTAATT	0.368													4	2	---	---	---	---	
TMEM198	130612	broad.mit.edu	37	2	220413076	220413076	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220413076delG	uc002vme.2	+						TMEM198_uc002vmf.2_Intron	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198							integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		attcaaggcaggcaggagaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	223685048	223685048	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223685048delT								MOGAT1 (110399 upstream) : ACSL3 (40684 downstream)																							atTACATCTCTTTTCCGGCAT	0.244													4	2	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	232940157	232940157	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232940157delC	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CTTGTTGAAACCCCATTATTT	0.378													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240169881	240169881	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240169881delT	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CCTCTTGCACttttttttttt	0.279													7	4	---	---	---	---	
FBLN2	2199	broad.mit.edu	37	3	13659079	13659082	+	Intron	DEL	CCAT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13659079_13659082delCCAT	uc011avb.1	+						FBLN2_uc011auz.1_Intron|FBLN2_uc011ava.1_Intron|FBLN2_uc011avc.1_Intron	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			acccatccacccatccatccatcc	0.000													8	4	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27393303	27393304	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27393303_27393304insT	uc003cdt.1	-							NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						AGTGTCTGCTATTTTCATTATT	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	30317725	30317725	+	IGR	DEL	A	-	-	rs61005881	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30317725delA								RBMS3 (271106 upstream) : TGFBR2 (330269 downstream)																							gaatgagaggaaaaaaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	39249646	39249646	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39249646delT								XIRP1 (15569 upstream) : CX3CR1 (55340 downstream)																							aaacttcatcttttttccctg	0.065													4	2	---	---	---	---	
FLNB	2317	broad.mit.edu	37	3	58141433	58141434	+	Intron	DEL	GA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58141433_58141434delGA	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		tttccccattgaagtccatgga	0.208													4	2	---	---	---	---	
SENP7	57337	broad.mit.edu	37	3	101078046	101078046	+	Intron	DEL	A	-	-	rs11337184		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101078046delA	uc003dut.2	-						SENP7_uc003duu.2_Intron|SENP7_uc003duv.2_Intron|SENP7_uc003duw.2_Intron|SENP7_uc003dux.2_Intron	NM_020654	NP_065705	Q9BQF6	SENP7_HUMAN	sentrin/SUMO-specific protease 7 isoform 1						proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5						CTGTGCTTACACCTTATTTCA	0.284													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112395743	112395744	+	IGR	DEL	AC	-	-	rs72409085		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112395743_112395744delAC								CCDC80 (35766 upstream) : CD200R1L (138812 downstream)																							CTCACCCGTAACACACACACAC	0.460													4	2	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119748921	119748921	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119748921delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATCTAGTTGGAAAAAAAAAAT	0.259													7	4	---	---	---	---	
PARP15	165631	broad.mit.edu	37	3	122354250	122354250	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122354250delT	uc003efm.2	+						PARP15_uc003efn.2_Intron|PARP15_uc003efo.1_Intron|PARP15_uc003efp.1_Intron|PARP15_uc011bjt.1_Intron	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		TAACGTGCAGtttttttttta	0.189													4	2	---	---	---	---	
PDIA5	10954	broad.mit.edu	37	3	122847727	122847728	+	Intron	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122847727_122847728delTG	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801	Q14554	PDIA5_HUMAN	protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)		TATTAGCAAATGTGAATAAGTA	0.322													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124341035	124341036	+	Intron	INS	-	CAAGA	CAAGA	rs141303413	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124341035_124341036insCAAGA	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc003ehj.2_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						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						TGGAGCTAAAGCAAAAGAACAG	0.371													1	5	---	---	---	---	
UMPS	7372	broad.mit.edu	37	3	124459144	124459144	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124459144delA	uc003ehl.3	+						UMPS_uc003ehm.3_Intron|UMPS_uc011bka.1_Intron|UMPS_uc011bkb.1_Intron|UMPS_uc011bkc.1_Intron|UMPS_uc003ehn.3_Intron|UMPS_uc011bkd.1_Intron	NM_000373	NP_000364	P11172	UMPS_HUMAN	uridine monophosphate synthase						'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)		AACCTCTGCCAAAAAAAAAAT	0.438													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127257232	127257232	+	5'Flank	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127257232delA	uc003ejk.2	-											Homo sapiens cDNA FLJ25806 fis, clone TST07194.																		TGAATTTAAGAaaaaaaaaat	0.234													3	3	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	128121145	128121145	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128121145delT	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						GATTGCTGCATTTTTTTTGAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137509718	137509718	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137509718delT								SOX14 (25322 upstream) : CLDN18 (207940 downstream)																							GCTTACAGCATTTTTTTTGTT	0.388													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140251449	140251449	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140251449delA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						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						TACCCCTTACAAAAAAAAATT	0.294										HNSCC(16;0.037)			10	5	---	---	---	---	
RASA2	5922	broad.mit.edu	37	3	141299673	141299674	+	Intron	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141299673_141299674insA	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.1_Intron	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						ATGAGAACATTAAAAAAAAAAA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154228889	154228889	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154228889delT								GPR149 (81385 upstream) : MME (513024 downstream)																							CTGTCTCACATTCTTAGAATA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155812148	155812148	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155812148delT								GMPS (156630 upstream) : KCNAB1 (26189 downstream)																							GCATTTGCAATTTTTTTTTTC	0.393													1	5	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169009022	169009022	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169009022delC	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						tccttcatttcccccacttga	0.144													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170875606	170875606	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170875606delC	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CAATCATTCACCCCAAAGAAA	0.502													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170981040	170981041	+	Intron	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170981040_170981041insA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ATGCTACTTGTAAAAAAAACTC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177208971	177208971	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177208971delA								TBL1XR1 (293923 upstream) : None (None downstream)																							TGGAGAAGTTAAAAAAATGCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178733192	178733193	+	IGR	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178733192_178733193insT								KCNMB2 (170976 upstream) : ZMAT3 (8334 downstream)																							TAGAGAACAGATTTTTTTAAAC	0.312													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179506682	179506683	+	3'UTR	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179506682_179506683insT	uc003fkh.2	+	21						NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CAGAAAGCAGATTTTTTTTTTC	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184243554	184243555	+	IGR	DEL	GG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184243554_184243555delGG								CHRD (135935 upstream) : EPHB3 (36032 downstream)																							tgaggaagtcgggaagggagga	0.238													4	2	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184578135	184578135	+	Intron	DEL	A	-	-	rs11478298		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184578135delA	uc003fpb.1	+						VPS8_uc010hyd.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)			cctgtctcttaaaaaaaaaaa	0.005													5	3	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189526459	189526460	+	Intron	DEL	AG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189526459_189526460delAG	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_Intron|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Intron	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)		ATACTGAACCAGAGAGAGAGAA	0.475									Hay-Wells_syndrome	HNSCC(45;0.13)			4	2	---	---	---	---	
ACAP2	23527	broad.mit.edu	37	3	195068495	195068495	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195068495delG	uc003fun.3	-						ACAP2_uc003fuo.2_Intron	NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						ccattactttgggagcccaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195353385	195353386	+	IGR	DEL	CG	-	-	rs111429267		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195353385_195353386delCG								APOD (42309 upstream) : SDHAP2 (31524 downstream)																							catgcacacacgcgcacacaca	0.030													2	7	---	---	---	---	
SDHAP2	727956	broad.mit.edu	37	3	195410263	195410263	+	Intron	DEL	T	-	-	rs151050676		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195410263delT	uc003fuw.2	+						SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						agcgagaccctgtctcaaaag	0.149													2	5	---	---	---	---	
TNK2	10188	broad.mit.edu	37	3	195626940	195626940	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195626940delT	uc003fvu.1	-						TNK2_uc010hzx.1_Intron	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1						positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	AGCAACTCAGTCCCCCAAAGC	0.552													4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3134126	3134126	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3134126delT	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ATCCTGAAACTTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9240444	9240445	+	5'Flank	INS	-	AA	AA			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9240444_9240445insAA	uc011bwo.1	+											RecName: Full=Ubiquitin carboxyl-terminal hydrolase 17-like protein 2;          EC=3.1.2.15; AltName: Full=Ubiquitin thioesterase 17-like protein 2; AltName: Full=Ubiquitin-specific-processing protease 17-like protein 2; AltName: Full=Deubiquitinating enzyme 17-like protein 2; AltName: Full=Deubiquitinating protein 3;          Short=DUB-3;																		cacacacacacgcacacGGTTT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24231582	24231582	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24231582delT								PPARGC1A (339882 upstream) : MIR573 (290233 downstream)																							GCTGAAGGCATTTTTGGAAAT	0.458													4	2	---	---	---	---	
ARAP2	116984	broad.mit.edu	37	4	36177863	36177863	+	Intron	DEL	A	-	-	rs11287090		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36177863delA	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH						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						tacaaaacatagacaaaaatg	0.040													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49155704	49155705	+	IGR	INS	-	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49155704_49155705insC								CWH43 (91611 upstream) : None (None downstream)																							tccattccattcattccattcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49515125	49515126	+	IGR	DEL	CG	-	-	rs4066485		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49515125_49515126delCG								CWH43 (451032 upstream) : None (None downstream)																							gacacacacacgcacacacacg	0.238													4	3	---	---	---	---	
IGFBP7	3490	broad.mit.edu	37	4	57935830	57935830	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57935830delA	uc003hcn.2	-						IGFBP7_uc011cag.1_Intron	NM_001553	NP_001544	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7						cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			lung(2)|central_nervous_system(1)	3	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ccctatctctaaaaaaacaaa	0.159													4	2	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62903222	62903223	+	Intron	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62903222_62903223delGT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						gtgtgtataagtgtgtgtgtgt	0.262													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67935084	67935084	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67935084delT								MIR1269 (792438 upstream) : CENPC1 (402905 downstream)																							ATGATTTCCCTTTTTTATTAT	0.348													4	2	---	---	---	---	
UGT2B7	7364	broad.mit.edu	37	4	69972578	69972578	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69972578delT	uc003heg.3	+						UGT2B7_uc010ihq.2_Intron	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2						agcttttttcttttttttttt	0.040													4	2	---	---	---	---	
HERC3	8916	broad.mit.edu	37	4	89614349	89614350	+	Intron	INS	-	C	C			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89614349_89614350insC	uc003hrw.1	+						HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron	NM_014606	NP_055421	Q15034	HERC3_HUMAN	hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TTTTTTCTCTTCCCCCCCACCA	0.332													4	2	---	---	---	---	
AP1AR	55435	broad.mit.edu	37	4	113187238	113187238	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113187238delA	uc003iaj.3	+						AP1AR_uc003iak.3_Intron	NM_018569	NP_061039	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0						TTCCCTTTCCAAAAAAAAGAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125385145	125385145	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125385145delT								LOC285419 (533627 upstream) : ANKRD50 (200323 downstream)																							ACTTTCTTAATTTTTTTTTTG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126822794	126822794	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126822794delT								MIR2054 (394332 upstream) : None (None downstream)																							tgcttacaagtttttttaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139652899	139652899	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139652899delT								SLC7A11 (489396 upstream) : CCRN4L (284044 downstream)																							GGAGTGTTCATTTTTTTTTGC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	148275599	148275599	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148275599delT								MIR548G (9730 upstream) : EDNRA (126308 downstream)																							TTTCTTCCCCTTTCCCGCCTC	0.408													4	2	---	---	---	---	
DCLK2	166614	broad.mit.edu	37	4	151160754	151160754	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151160754delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					ccgtgtcttcaaaaaaaaaaa	0.169													8	4	---	---	---	---	
SH3D19	152503	broad.mit.edu	37	4	152100224	152100224	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152100224delA	uc010ipl.1	-						SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				CATTTCTCTGAAGCAGTTACA	0.313													4	2	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159794620	159794621	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159794620_159794621insT	uc003iqe.3	+							NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ctcattctcccaagtagacagg	0.099													4	2	---	---	---	---	
ENPP6	133121	broad.mit.edu	37	4	185025175	185025175	+	Intron	DEL	C	-	-	rs7662087	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185025175delC	uc003iwc.2	-							NM_153343	NP_699174	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		cttttcttttctttttttGAA	0.502													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185418826	185418826	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185418826delT								IRF2 (23100 upstream) : CASP3 (130026 downstream)																							tgtttgtttgttttttttaac	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190596438	190596439	+	IGR	INS	-	TCCTTGG	TCCTTGG	rs140220951		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190596438_190596439insTCCTTGG								None (None upstream) : FRG1 (265535 downstream)																							GTGCTGAGATAAAATTAAATTC	0.332													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190622268	190622268	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190622268delG								None (None upstream) : FRG1 (239706 downstream)																							CTAACTCTATGGTGGTGAAGG	0.348													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190676820	190676820	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190676820delA								None (None upstream) : FRG1 (185154 downstream)																							taaataatgtaaaaaaacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190840895	190840895	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190840895delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		tttttgcattgaaaaggagaa	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2967042	2967043	+	IGR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2967042_2967043delGT								C5orf38 (211530 upstream) : IRX1 (629125 downstream)																							GCTGGGGCTGGTGTGTGTGTGT	0.545													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5504962	5504962	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5504962delT								KIAA0947 (14625 upstream) : FLJ33360 (805592 downstream)																							ctcaaagagctgaaaggatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10924458	10924458	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10924458delT								DAP (163071 upstream) : CTNND2 (47494 downstream)																							ACATGCCTACTTTCAGATATA	0.259													3	5	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22305646	22305647	+	Intron	INS	-	TTCA	TTCA	rs149772610	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22305646_22305647insTTCA	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						aatgacccatcttcagatggtc	0.000										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36535551	36535551	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36535551delC								RANBP3L (233540 upstream) : SLC1A3 (70906 downstream)																							GCCACCCTCTCCCCAGGCAAT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52646227	52646227	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52646227delC								MOCS2 (240629 upstream) : FST (130368 downstream)																							CATCATGCCTCCTCCAACGCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67964585	67964585	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67964585delA								PIK3R1 (366938 upstream) : SLC30A5 (425233 downstream)																							AATAAATCTTAAAAAAAAAAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	68261447	68261448	+	IGR	DEL	CA	-	-	rs143783701		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68261447_68261448delCA								PIK3R1 (663800 upstream) : SLC30A5 (128370 downstream)																							cacatcctctcacacacacaca	0.099													4	3	---	---	---	---	
HEXB	3074	broad.mit.edu	37	5	73963243	73963243	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73963243delA	uc003kdd.2	+							NM_000521	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B preproprotein						cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		aaactctctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
ATG10	83734	broad.mit.edu	37	5	81443521	81443521	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81443521delG	uc003khs.2	+						ATG10_uc003khq.2_3'UTR|ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500	Q9H0Y0	ATG10_HUMAN	APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		catagaatctggggttgtcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91944109	91944109	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91944109delC								None (None upstream) : FLJ42709 (800956 downstream)																							CATCAGGCTTCTTGATAAATA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	98734905	98734905	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98734905delA								CHD1 (472667 upstream) : LOC100133050 (980304 downstream)																							ATCAGTCAGGAAAAAAAAGCT	0.398													4	2	---	---	---	---	
WDR36	134430	broad.mit.edu	37	5	110429252	110429252	+	Intron	DEL	G	-	-	rs116618688	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110429252delG	uc003kpd.2	+						WDR36_uc010jbu.2_Intron	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36						response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TGGTAATGGAGACAGGGTGGG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120079871	120079872	+	IGR	INS	-	C	C	rs140512511	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120079871_120079872insC								PRR16 (56909 upstream) : None (None downstream)																							gtctcttcaatctggggcctgg	0.000													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127859153	127859155	+	Intron	DEL	ACA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127859153_127859155delACA	uc003kuu.2	-						FBN2_uc003kuv.2_Intron|FBN2_uc003kuw.3_Intron|FBN2_uc003kux.1_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ttctttagctacaacaacttcct	0.000													4	2	---	---	---	---	
LARS	51520	broad.mit.edu	37	5	145540213	145540214	+	Intron	INS	-	ATTT	ATTT	rs140796536	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145540213_145540214insATTT	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CAATTACTTTAATTTACTTAAA	0.208													3	4	---	---	---	---	
STK32A	202374	broad.mit.edu	37	5	146680508	146680508	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146680508delG	uc010jgn.1	+						STK32A_uc003lol.3_Intron|STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTGGCACaggggccaaggg	0.075													4	2	---	---	---	---	
CSF1R	1436	broad.mit.edu	37	5	149473844	149473844	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149473844delT	uc003lrm.2	-							NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor						cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	agagcttcaGTTTTTTTTTCC	0.234													4	2	---	---	---	---	
SLC36A2	153201	broad.mit.edu	37	5	150713094	150713099	+	Intron	DEL	AGGAAT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150713094_150713099delAGGAAT	uc003lty.2	-						GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_Intron|SLC36A2_uc003lua.2_Intron|SLC36A2_uc010jhv.2_Intron	NM_181776	NP_861441	Q495M3	S36A2_HUMAN	solute carrier family 36, member 2						cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAAGTACTGAAGGAATAGTATTTCAT	0.291													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157154456	157154456	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157154456delT								C5orf52 (47296 upstream) : THG1L (3867 downstream)																							tacccatcccttttttttttc	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157541878	157541878	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157541878delT								CLINT1 (255710 upstream) : EBF1 (581046 downstream)																							AAGATCTTTATTTTTTTTTTC	0.363													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165282833	165282833	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165282833delA								None (None upstream) : None (None downstream)																							TTTGTGGCTGAAAAAAAAATG	0.348													4	2	---	---	---	---	
ZNF354A	6940	broad.mit.edu	37	5	178153248	178153248	+	Intron	DEL	A	-	-	rs138546234		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178153248delA	uc003mjj.2	-							NM_005649	NP_005640	O60765	Z354A_HUMAN	zinc finger protein 354A						regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		gaatggtgggaaaaaaaaaga	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179787439	179787439	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179787439delA								GFPT2 (7124 upstream) : CNOT6 (133978 downstream)																							TCCTGGTACCAAAAAAAAGGC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	1223024	1223026	+	IGR	DEL	AGA	-	-	rs76620606		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1223024_1223026delAGA								LOC285768 (121457 upstream) : FOXQ1 (89649 downstream)																							AATCTGAAGGAGAAGGTGTGTGG	0.557													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3783186	3783186	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3783186delT								C6orf145 (30940 upstream) : FAM50B (66446 downstream)																							GTGTTTGTTCTTTTTATAAAT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11169057	11169058	+	IGR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11169057_11169058delGT								LOC221710 (30093 upstream) : NEDD9 (14473 downstream)																							ATAAGGAGCAGTGTGTGTGTGT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34121893	34121894	+	IGR	DEL	CA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34121893_34121894delCA								GRM4 (8024 upstream) : HMGA1 (82683 downstream)																							CAGCCGTATTCAGCCTGGGCTG	0.386													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38414083	38414083	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38414083delT	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						AAACAACTAGTTTTTTTTTTT	0.199													3	3	---	---	---	---	
LRFN2	57497	broad.mit.edu	37	6	40521793	40521793	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40521793delC	uc003oph.1	-							NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCCCCTTCTTCCCCCACCCAT	0.572													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57373990	57373990	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57373990delT	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)		tatttctttatttttcctttc	0.204													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57411089	57411089	+	Intron	DEL	G	-	-	rs11293899		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57411089delG	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)		AGGGGAAAATGACAATAAAAT	0.279													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415403	57415404	+	Intron	INS	-	A	A	rs151310189		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415403_57415404insA	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)		ACAAATGGACTAAAAATAATGT	0.302													2	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57492883	57492883	+	Intron	DEL	T	-	-	rs63666464		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57492883delT	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)		AAAGATTGAGTTTTTTTAGGA	0.348													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57563226	57563226	+	IGR	DEL	T	-	-	rs11350954		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57563226delT								PRIM2 (49851 upstream) : GUSBL2 (682933 downstream)																							cccttaagacttttcttgaca	0.164													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57565371	57565372	+	IGR	INS	-	CTA	CTA	rs149489760		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57565371_57565372insCTA								PRIM2 (51996 upstream) : GUSBL2 (680787 downstream)																							GAATCTGGACCCTACTAGTCAG	0.208													4	2	---	---	---	---	
GUSBL2	375513	broad.mit.edu	37	6	58287268	58287269	+	Intron	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58287268_58287269insA	uc011dxq.1	-						GUSBL2_uc011dxp.1_Intron|GUSBL2_uc003peb.3_Intron|GUSBL2_uc003pec.3_Intron|GUSBL2_uc003ped.3_Intron|GUSBL2_uc003pee.3_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0						TTCCAACGGATACGCAGAATAG	0.431											OREG0017520	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58535034	58535035	+	IGR	DEL	TT	-	-	rs67190761		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58535034_58535035delTT								GUSBL2 (247310 upstream) : None (None downstream)																							TTTGTTTTTGTTTTTTTTCCCA	0.376													4	2	---	---	---	---	
SMAP1	60682	broad.mit.edu	37	6	71457330	71457330	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71457330delA	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770	Q8IYB5	SMAP1_HUMAN	stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0						cttttggcagaagaggggaga	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77703751	77703751	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77703751delT								IMPG1 (921416 upstream) : HTR1B (468197 downstream)																							TCTTGAGATATTTTATTTGCT	0.328													4	2	---	---	---	---	
SESN1	27244	broad.mit.edu	37	6	109323220	109323222	+	Intron	DEL	TGT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109323220_109323222delTGT	uc003pst.3	-						SESN1_uc003psu.2_Intron	NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		TATAAGCAGATGTTGTATCACTG	0.350													4	3	---	---	---	---	
C6orf186	728464	broad.mit.edu	37	6	110639247	110639247	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110639247delA	uc010kdu.1	-						C6orf186_uc003pub.2_Intron	NM_001123364	NP_001116836	Q5JXM2	CF186_HUMAN	chromosome 6 open reading frame 186 precursor							extracellular region					0						CTTTAAACTGAAAACATCAGC	0.478													4	2	---	---	---	---	
STXBP5	134957	broad.mit.edu	37	6	147648594	147648594	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147648594delT	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron|STXBP5_uc003qma.2_Intron	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b						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)		GTGGttttgctttttttttga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156919752	156919754	+	IGR	DEL	TTG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156919752_156919754delTTG								MIR1202 (651739 upstream) : ARID1B (179332 downstream)																							GTGAAATGCCTTGTTGTTGTTGT	0.522													4	2	---	---	---	---	
IGF2R	3482	broad.mit.edu	37	6	160445269	160445272	+	Intron	DEL	TAGC	-	-	rs79145362		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160445269_160445272delTAGC	uc003qta.2	+							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)		catgagatgatagctaggggaatg	0.000													4	3	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	166921570	166921571	+	Intron	DEL	CA	-	-	rs80026073	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166921570_166921571delCA	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.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)		cacacacccccacacacacaca	0.317													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	50056	50062	+	IGR	DEL	ACACCGG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50056_50062delACACCGG								None (None upstream) : FAM20C (142907 downstream)																							tggggctcgaacaccggaccagattga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6921712	6921713	+	IGR	INS	-	GG	GG	rs139821239	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6921712_6921713insGG								C7orf28B (55851 upstream) : C1GALT1 (300533 downstream)																							CTCGAAGTCCCGGGTACTATAC	0.347													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7362252	7362252	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7362252delA								C1GALT1 (78273 upstream) : COL28A1 (35992 downstream)																							TTCCACTTCGAAAAAGAGGCC	0.488													4	2	---	---	---	---	
ANKMY2	57037	broad.mit.edu	37	7	16668752	16668752	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16668752delA	uc003sti.2	-						ANKMY2_uc010ktz.2_Intron	NM_020319	NP_064715	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2							cilium	zinc ion binding			central_nervous_system(1)	1	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CGTCTCATTTAAAAAAAATTT	0.378													4	2	---	---	---	---	
CDCA7L	55536	broad.mit.edu	37	7	21944850	21944850	+	Intron	DEL	T	-	-	rs11331068		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21944850delT	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						GCTTAAACCATTAACAGTTAC	0.353													4	2	---	---	---	---	
HOXA11	3207	broad.mit.edu	37	7	27223950	27223950	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27223950delA	uc003syx.2	-						HOXA11_uc003syy.2_Intron|HOXA11AS_uc003syz.1_5'Flank	NM_005523	NP_005514	P31270	HXA11_HUMAN	homeobox A11						branching involved in ureteric bud morphogenesis|cartilage development involved in endochondral bone morphogenesis|developmental growth|dorsal/ventral pattern formation|mesodermal cell fate specification|positive regulation of cell development|positive regulation of chondrocyte differentiation	protein-DNA complex|transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)	2						GGCCCTTCATAAACCTTATAT	0.458			T	NUP98	CML								4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30891616	30891616	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30891616delT	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_5'Flank	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						TTTCCATTTCTTTTTTTTTTC	0.438													7	4	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43429218	43429219	+	Intron	INS	-	TGT	TGT	rs145783879	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43429218_43429219insTGT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						Attgttgttgctgttgttgttg	0.178													4	3	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43572330	43572330	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43572330delA	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						tccctggcacattcagaagga	0.139													4	2	---	---	---	---	
ADCY1	107	broad.mit.edu	37	7	45613283	45613283	+	5'Flank	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45613283delT	uc003tne.3	+						ADCY1_uc003tnd.2_5'Flank	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCACACCTTCTTCCCGGGACA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51048396	51048396	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51048396delA								GRB10 (187237 upstream) : COBL (35514 downstream)																							GGTTTTTTTGAAATGGATTGC	0.423													4	2	---	---	---	---	
LOC493754	493754	broad.mit.edu	37	7	66018297	66018297	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66018297delT	uc010lac.1	-						LOC493754_uc010lad.2_Intron|LOC493754_uc011kdx.1_Intron					Homo sapiens cDNA FLJ14309 fis, clone PLACE3000221.												0						aaaaGCATTCTTTTTTTTTTT	0.214													7	7	---	---	---	---	
POM121C	100101267	broad.mit.edu	37	7	75092825	75092825	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75092825delT	uc003udk.3	-						POM121C_uc003udl.1_Intron	NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						accgcacatgtaaaagaagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77319733	77319733	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77319733delT	uc003ugj.1	-											Homo sapiens clone 124-1V1, mRNA sequence.																		AACTGCTTTCTTTATACAAGG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84479448	84479448	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84479448delA								SEMA3A (655231 upstream) : SEMA3D (145426 downstream)																							GTAACTTAAGAAAAAAAAATG	0.159													4	2	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87172296	87172297	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87172296_87172297insT	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	CATTCTCGGAATTTTTTCAACA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96391626	96391626	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96391626delA								SHFM1 (52423 upstream) : DLX6AS (206202 downstream)																							tttgagttctaaaaaaaaatc	0.035													4	2	---	---	---	---	
TECPR1	25851	broad.mit.edu	37	7	97875582	97875583	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97875582_97875583insT	uc003upg.2	-						TECPR1_uc003uph.1_Intron	NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1						ttctttttctcttttttttttt	0.252													8	5	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105102889	105102889	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105102889delA	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						aaaaaaaaccaaaaaaaaaac	0.000													16	7	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110727782	110727782	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110727782delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		ttataataccaaaaaaatggt	0.070													4	2	---	---	---	---	
AHCYL2	23382	broad.mit.edu	37	7	129019300	129019300	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129019300delA	uc011kov.1	+						AHCYL2_uc003vot.2_Intron|AHCYL2_uc003vov.2_Intron|AHCYL2_uc011kow.1_Intron|AHCYL2_uc011kox.1_Intron	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						atctctatttaaaaaaaaaaa	0.144													4	4	---	---	---	---	
NRF1	4899	broad.mit.edu	37	7	129395139	129395140	+	3'UTR	DEL	TT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129395139_129395140delTT	uc003voz.2	+	11					NRF1_uc003vpa.2_3'UTR|NRF1_uc011kpa.1_3'UTR|NRF1_uc003vpb.2_3'UTR	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1						generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1						TTTGTTAACCTTTTTTTTTTTA	0.337													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151850225	151850227	+	Intron	DEL	AAG	-	-	rs72392332		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151850225_151850227delAAG	uc003wla.2	-						MLL3_uc003wkz.2_Intron|MLL3_uc003wkx.2_Intron|MLL3_uc003wky.2_Intron	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)		TATCCAAAAAAAGAAATTTATAA	0.271			N		medulloblastoma								5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2198248	2198248	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2198248delC								MYOM2 (104869 upstream) : CSMD1 (594628 downstream)																							CTTCTATGGTCCCCGTGTTCA	0.567													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4685578	4685578	+	Intron	DEL	T	-	-	rs78827772		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4685578delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CGTAGTGGGATTTTTTTTTAC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15713940	15713940	+	IGR	DEL	T	-	-	rs33921281		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15713940delT								TUSC3 (91947 upstream) : MSR1 (251448 downstream)																							ATTTTCTCTCTTTTTTTTTTA	0.358													2	5	---	---	---	---	
SLC25A37	51312	broad.mit.edu	37	8	23429448	23429449	+	3'UTR	INS	-	T	T	rs145581404	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23429448_23429449insT	uc003xdo.2	+	4					SLC25A37_uc003xdp.2_RNA|SLC25A37_uc010ltz.2_RNA|SLC25A37_uc003xdq.2_RNA|uc003xds.2_5'Flank	NM_016612	NP_057696	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25, member 37						ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CACGTAGATCATTTTTTTTTTG	0.535													3	3	---	---	---	---	
CCDC25	55246	broad.mit.edu	37	8	27606401	27606401	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27606401delT	uc003xgc.2	-						CCDC25_uc003xgd.2_Intron|CCDC25_uc011lan.1_Intron|CCDC25_uc011lao.1_Intron|CCDC25_uc003xge.2_Intron|CCDC25_uc003xgf.1_Intron	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25												0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		tatcattgagtttttttttca	0.075													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32300038	32300038	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32300038delA	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)		CCCTGGAAGGAAAGGCTTGCA	0.408													4	2	---	---	---	---	
ADAM9	8754	broad.mit.edu	37	8	38896479	38896480	+	Intron	INS	-	T	T	rs139240981	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38896479_38896480insT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TACTTTTTTTGTTTTTTTTGGT	0.356													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42030874	42030874	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42030874delT								AP3M2 (2172 upstream) : PLAT (1362 downstream)																							GTCCTCAGTGTTTTTTttttt	0.279													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	56449151	56449152	+	IGR	INS	-	AG	AG	rs140550448	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56449151_56449152insAG								XKR4 (10443 upstream) : TMEM68 (202168 downstream)																							TCTGGATAGACAGACTGCTCCG	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62115585	62115585	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62115585delA								CHD7 (336122 upstream) : CLVS1 (84940 downstream)																							AGAATCTTTCAAAAAACAGGA	0.338													4	2	---	---	---	---	
CYP7B1	9420	broad.mit.edu	37	8	65620249	65620249	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65620249delT	uc003xvj.2	-							NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				ATTCAATTAGTTTTTTTTTTC	0.323													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68417751	68417751	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68417751delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TAACTATTTCTTTTTTTTTAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88950408	88950408	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88950408delA								DCAF4L2 (64112 upstream) : MMP16 (99054 downstream)																							ctctgtctccaaaaaaaaaga	0.000													3	4	---	---	---	---	
CALB1	793	broad.mit.edu	37	8	91094033	91094034	+	Intron	DEL	TC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91094033_91094034delTC	uc003yel.1	-						CALB1_uc003yem.1_Intron|CALB1_uc011lge.1_5'Flank	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1							nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)			gtccctcccttctctctctctc	0.193													7	4	---	---	---	---	
RUNX1T1	862	broad.mit.edu	37	8	93042036	93042037	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93042036_93042037insT	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)			TGTTTCACTCATTTTTTTTAAA	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111872025	111872025	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111872025delT								KCNV1 (883949 upstream) : None (None downstream)																							TGTTCTAGCCTTTTTGGTAGG	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	113047713	113047713	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113047713delA								None (None upstream) : CSMD3 (187448 downstream)																							gatgttggttaaaaaatacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120138021	120138021	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120138021delC								COLEC10 (18826 upstream) : MAL2 (82589 downstream)																							CTGTGATTGTCCCCAAGTTGC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130829955	130829955	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130829955delT								GSDMC (30821 upstream) : FAM49B (23763 downstream)																							gtttgttttctttttttggtt	0.000													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140924807	140924807	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140924807delG	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						ttcaggctcagaggccgagtc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143150066	143150066	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143150066delA								MIR1302-7 (282392 upstream) : NCRNA00051 (129651 downstream)																							gatgtactggaaaaaaaaaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1322679	1322679	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1322679delT								DMRT2 (265126 upstream) : SMARCA2 (692663 downstream)																							TGGGGATGACTTTTTTTCCAG	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7809423	7809423	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7809423delT								C9orf123 (9624 upstream) : PTPRD (504824 downstream)																							TGGTTGTTTATTTTTTTTTCC	0.338													4	2	---	---	---	---	
C9orf72	203228	broad.mit.edu	37	9	27565219	27565220	+	Intron	DEL	AG	-	-	rs150509184		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27565219_27565220delAG	uc003zqq.2	-						C9orf72_uc003zqr.1_Intron	NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a											ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		AGTACCTTAAAGAACATATCAG	0.366													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	30022479	30022479	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30022479delT								None (None upstream) : None (None downstream)																							AACATGTTTGTTTTTTTTCTt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68402732	68402733	+	IGR	INS	-	AT	AT			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68402732_68402733insAT								FAM27B (608543 upstream) : MIR1299 (599506 downstream)																							ATCTCACATGATGAAGACTAAA	0.287													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69063223	69063223	+	5'Flank	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69063223delG	uc004afe.1	+						uc010mnq.1_5'Flank					Homo sapiens cDNA, FLJ18209.																		TTTTCAAAAAGCAAAGACTCT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	73110376	73110376	+	IGR	DEL	T	-	-	rs34038992		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73110376delT								KLF9 (80803 upstream) : TRPM3 (39592 downstream)																							ttctaatgtctttggctaaga	0.050													4	2	---	---	---	---	
C9orf85	138241	broad.mit.edu	37	9	74526496	74526496	+	5'UTR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74526496delG	uc004ain.2	+	1					C9orf85_uc004aio.2_RNA|C9orf85_uc010mou.2_RNA|C9orf85_uc010mov.2_RNA|FAM108B1_uc004ail.2_5'Flank|FAM108B1_uc004aim.1_5'Flank	NM_182505	NP_872311	Q96MD7	CI085_HUMAN	hypothetical protein LOC138241												0						CCTCCCAGAAGAGTCACGTGG	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76232891	76232891	+	IGR	DEL	T	-	-	rs78601245		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76232891delT								ANXA1 (447584 upstream) : RORB (879361 downstream)																							GTAAGTGGGATTTTTTTTTTT	0.338													4	3	---	---	---	---	
RORB	6096	broad.mit.edu	37	9	77112628	77112628	+	5'UTR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77112628delT	uc004ajh.2	+	1						NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						AGCCAGAACATTTTTTTTTCA	0.388													4	2	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94367107	94367107	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94367107delA	uc004ari.1	-							NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						GTAAGGCTTGAAAAAAAAATT	0.363													4	2	---	---	---	---	
ECM2	1842	broad.mit.edu	37	9	95271425	95271425	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95271425delG	uc004ash.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Intron|ECM2_uc011lty.1_Intron|ECM2_uc004asg.2_Intron|ECM2_uc010mqz.1_5'Flank	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor						cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2						CACAGAACATGGGGCACGCTC	0.512													4	2	---	---	---	---	
MRPL50	54534	broad.mit.edu	37	9	104152596	104152596	+	3'UTR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104152596delA	uc004bbe.2	-	2					MRPL50_uc011lvj.1_Intron	NM_019051	NP_061924	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50							mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)				GTAATATGAGAAAAAAAAAGA	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104576652	104576652	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104576652delA								GRIN3A (75790 upstream) : None (None downstream)																							ATGATTACTGAAAAAAAAAAA	0.299													3	4	---	---	---	---	
FSD1L	83856	broad.mit.edu	37	9	108230789	108230789	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108230789delT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron|FSD1L_uc004bcp.2_Intron	NM_001145313	NP_001138785	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing												0						CTCTTAACCAttttttttttt	0.134													6	3	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127911822	127911822	+	3'UTR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127911822delA	uc004bpg.3	-	7					PPP6C_uc010mwv.2_3'UTR|PPP6C_uc010mww.2_3'UTR|PPP6C_uc011lzr.1_3'UTR	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						tttaaaatttaaaaaaaaaaa	0.348													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136184772	136184774	+	IGR	DEL	CTG	-	-	rs72449624		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136184772_136184774delCTG								ABO (34142 upstream) : SURF6 (12779 downstream)																							GAGGCTGAGACTGCTGGATGAAG	0.621													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137037535	137037535	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137037535delG								RNU6ATAC (7849 upstream) : RXRA (171409 downstream)																							TCAGGGCTCAGGGGCCTCTAT	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137197380	137197382	+	IGR	DEL	TGA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137197380_137197382delTGA								RNU6ATAC (167694 upstream) : RXRA (11562 downstream)																							GCCatgagggtgatgatgatggt	0.128													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1683147	1683147	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1683147delA	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTACAATTGCAAGATCCGAAA	0.408													4	2	---	---	---	---	
C10orf18	54906	broad.mit.edu	37	10	5793932	5793933	+	Intron	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5793932_5793933delTG	uc001iij.2	+						C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2						ctcagtgttttgacttattGTC	0.277													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27301407	27301407	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27301407delT	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						CATAAGTCAATTAAACAACTC	0.209													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27332107	27332107	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27332107delA	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						aattaaaatgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33925702	33925704	+	IGR	DEL	ATA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33925702_33925704delATA								NRP1 (301696 upstream) : PARD3 (474394 downstream)																							CTAAGCTTTTATATCAAAAAGCG	0.369													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36163770	36163770	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36163770delC								FZD8 (233408 upstream) : None (None downstream)																							TCGCCACCCTCCCACCAGGGG	0.493													4	2	---	---	---	---	
LOC100129055	100129055	broad.mit.edu	37	10	38498330	38498331	+	Intron	DEL	AA	-	-	rs66650613		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38498330_38498331delAA	uc001izn.2	+							NR_024524				Homo sapiens cDNA clone IMAGE:4825074.												0						TCTGAAGTGTAAAGAGTATTCC	0.411													2	4	---	---	---	---	
SGMS1	259230	broad.mit.edu	37	10	52343106	52343106	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52343106delC	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron|SGMS1_uc009xou.1_Intron	NM_147156	NP_671512	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2						cctcccagcacccccaatcct	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54314791	54314791	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54314791delA								DKK1 (237375 upstream) : MBL2 (210350 downstream)																							gaagcagaggaaaaaatggtc	0.055													4	2	---	---	---	---	
SLC29A3	55315	broad.mit.edu	37	10	73096087	73096087	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73096087delG	uc001jrr.3	+						SLC29A3_uc001jrs.3_Intron|SLC29A3_uc010qjq.1_Intron|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Intron	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0						catgaattttgggggcatgaa	0.239													4	2	---	---	---	---	
AGAP5	729092	broad.mit.edu	37	10	75477008	75477008	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75477008delA	uc001juu.3	-						BMS1P4_uc001juv.3_Intron|BMS1P4_uc010qkm.1_Intron	NM_001144000	NP_001137472	A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						GCTAATCTAGAAATGGCAATA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85946455	85946456	+	IGR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85946455_85946456delGT								C10orf99 (1406 upstream) : CDHR1 (8061 downstream)																							ggtatgtatggtgtgtgtgtgg	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86609901	86609901	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86609901delC								FAM190B (331625 upstream) : GRID1 (749411 downstream)																							ACCAGTCATTCATTCCAATTT	0.373													4	2	---	---	---	---	
PIK3AP1	118788	broad.mit.edu	37	10	98406653	98406653	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98406653delA	uc001kmq.2	-						PIK3AP1_uc001kmp.2_Intron	NM_152309	NP_689522	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1							cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		ATCAACCCACAAAAATCCTCA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111404267	111404267	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111404267delA								None (None upstream) : XPNPEP1 (220257 downstream)																							aaacaatcagaaaaaaagtca	0.080													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115154465	115154466	+	IGR	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115154465_115154466insT								TCF7L2 (227031 upstream) : HABP2 (158312 downstream)																							AGTCCTGCTACTTTTTCCTCAT	0.322													4	2	---	---	---	---	
VWA2	340706	broad.mit.edu	37	10	116050482	116050482	+	Intron	DEL	A	-	-	rs35482716		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116050482delA	uc001lbl.1	+							NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		cagtagatccagggtacaggg	0.015													4	4	---	---	---	---	
GFRA1	2674	broad.mit.edu	37	10	118028752	118028752	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118028752delA	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)		TTTAATGTGGAAAAAAAAAAA	0.398													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135461246	135461247	+	IGR	INS	-	G	G	rs140694261		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135461246_135461247insG								FRG2B (20947 upstream) : LOC653544 (29032 downstream)																							atttattgcaaaaaaaaagaat	0.000													5	5	---	---	---	---	
SCGB1C1	147199	broad.mit.edu	37	11	190325	190326	+	5'Flank	DEL	CA	-	-	rs77529988		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:190325_190326delCA	uc001loa.1	+							NM_145651	NP_663626	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1 precursor							extracellular region	binding			skin(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		gtcagagcgccagttattaagc	0.000													4	2	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7265175	7265175	+	Intron	DEL	T	-	-	rs34724330		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7265175delT	uc001mfd.2	+							NM_175733		Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		GCAGAAAGCATTTTTTTTTTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	11240036	11240036	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11240036delC								ZBED5 (360416 upstream) : GALNTL4 (52385 downstream)																							TTGGCTCCAGCCACACCTGTG	0.488													4	2	---	---	---	---	
ABCC8	6833	broad.mit.edu	37	11	17460187	17460187	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17460187delA	uc001mnc.2	-						ABCC8_uc010rcy.1_Intron	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	TTCCACAAGGAAAAAAAGATT	0.468													4	2	---	---	---	---	
SLC6A5	9152	broad.mit.edu	37	11	20675762	20675762	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20675762delT	uc001mqd.2	+						SLC6A5_uc009yic.2_Intron	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter						synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	TGGGGTTGGATTTTTTTTTTC	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29143907	29143907	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29143907delC								METT5D1 (788853 upstream) : KCNA4 (887859 downstream)																							CTAAATAACACCCCCCCTGAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29865705	29865705	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29865705delA								None (None upstream) : KCNA4 (166061 downstream)																							GATGCACCCCAAGAGTATTCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34862391	34862391	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34862391delG								EHF (179310 upstream) : APIP (34323 downstream)																							CCCAGAAGGAGGCAGTGGTGT	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49428325	49428326	+	IGR	INS	-	TC	TC	rs58823494		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49428325_49428326insTC								FOLH1 (198103 upstream) : LOC440040 (151754 downstream)																							tctatcatctatatctgtatat	0.173													5	3	---	---	---	---	
SPTBN2	6712	broad.mit.edu	37	11	66485296	66485297	+	Intron	DEL	AC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66485296_66485297delAC	uc001ojd.2	-							NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2						actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						CTAGATCCTTACACACACACAC	0.495													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74456592	74456592	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74456592delA								CHRDL2 (14406 upstream) : RNF169 (3321 downstream)																							ttatggcactaaaaaaaaaaa	0.104													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82045193	82045193	+	Intron	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82045193delG	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		GGTATTCAGTGGAAGACAATA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90171676	90171677	+	IGR	INS	-	AC	AC	rs142340059	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90171676_90171677insAC								CHORDC1 (215144 upstream) : MIR1261 (430612 downstream)																							aacacacagagacacacacaca	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93333317	93333318	+	IGR	DEL	CC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93333317_93333318delCC								C11orf75 (56771 upstream) : KIAA1731 (61498 downstream)																							atagctcattccaaggctgaca	0.000													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95980376	95980376	+	Intron	DEL	A	-	-	rs75115900		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95980376delA	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGACCATGCAAAAAAAAAAT	0.378			T	MECT1|CRTC3	salivary gland mucoepidermoid								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	104787879	104787882	+	Intron	DEL	TAAC	-	-	rs145338506		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104787879_104787882delTAAC	uc001phz.2	-						uc001pia.1_Intron					Homo sapiens mRNA; cDNA DKFZp667O0320 (from clone DKFZp667O0320).																		CAGAGACAGGTAACTAACTGACTG	0.328													3	3	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108183414	108183415	+	Intron	DEL	CT	-	-	rs147088513		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108183414_108183415delCT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron|ATM_uc009yxt.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ctaatactgactctgccacttC	0.178			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			3	5	---	---	---	---	
NCAM1	4684	broad.mit.edu	37	11	113147816	113147818	+	3'UTR	DEL	GAT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113147816_113147818delGAT	uc001pns.2	+	6					NCAM1_uc001pnt.2_3'UTR			P13591	NCAM1_HUMAN	SubName: Full=cDNA FLJ52974, highly similar to Neural cell adhesion molecule 1, 140 kDa isoform;						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		ATGAAATACAgatgatgatgatg	0.335													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114924009	114924009	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114924009delT								FAM55B (346357 upstream) : CADM1 (115944 downstream)																							tgTAAACCCCTTTACAATCAG	0.229													4	2	---	---	---	---	
TECTA	7007	broad.mit.edu	37	11	121060084	121060085	+	Intron	INS	-	T	T	rs11459448		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121060084_121060085insT	uc010rzo.1	+							NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor						cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TTGTCCTCCTCttttttttttt	0.203													4	2	---	---	---	---	
CDON	50937	broad.mit.edu	37	11	125871412	125871413	+	Intron	DEL	AG	-	-	rs34580130		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125871412_125871413delAG	uc009zbw.2	-						CDON_uc001qdb.3_Intron|CDON_uc001qdc.3_Intron	NM_016952	NP_058648	Q4KMG0	CDON_HUMAN	surface glycoprotein, Ig superfamily member						cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|skin(2)|breast(1)	6	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		ATTTTGAGTCAGAGTTAATGAA	0.238													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127807145	127807146	+	IGR	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127807145_127807146insA								KIRREL3 (933790 upstream) : ETS1 (521510 downstream)																							TAGTTTAGTTGAAGCAAATGAA	0.277													4	2	---	---	---	---	
EFCAB4B	84766	broad.mit.edu	37	12	3778692	3778692	+	Intron	DEL	A	-	-	rs147095622		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3778692delA	uc001qmj.2	-						EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron|EFCAB4B_uc001qmi.1_Intron	NM_032680	NP_116069	Q9BSW2	EFC4B_HUMAN	EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			AAATTTCTTCAACCTCTGTGC	0.478													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31361558	31361559	+	5'Flank	INS	-	GTGAACGCTGTG	GTGAACGCTGTG	rs142162402	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31361558_31361559insGTGAACGCTGTG	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		TAGGCCAAAGAGtgtaccctct	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32046793	32046794	+	IGR	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32046793_32046794insT								H3F3C (101618 upstream) : C12orf35 (65559 downstream)																							gtggtggcacgcacttgtaatc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32046797	32046797	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32046797delT								H3F3C (101622 upstream) : C12orf35 (65556 downstream)																							tggcacgcacttgtaatccca	0.000													4	3	---	---	---	---	
HDAC7	51564	broad.mit.edu	37	12	48176636	48176637	+	3'UTR	INS	-	CCTCA	CCTCA			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48176636_48176637insCCTCA	uc010slo.1	-	26					HDAC7_uc009zku.2_RNA|HDAC7_uc001rqe.2_3'UTR|HDAC7_uc001rqj.3_3'UTR|HDAC7_uc001rqk.3_3'UTR	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|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 kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		tcacacacacgctcacacacac	0.292													6	3	---	---	---	---	
PA2G4	5036	broad.mit.edu	37	12	56505493	56505494	+	Intron	INS	-	AT	AT	rs143474707	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56505493_56505494insAT	uc001sjm.2	+						PA2G4_uc009zol.2_Intron|PA2G4_uc009zom.2_Intron	NM_006191	NP_006182	Q9UQ80	PA2G4_HUMAN	ErbB3-binding protein 1						cell cycle arrest|cell proliferation|negative regulation of transcription, DNA-dependent|regulation of translation|rRNA processing	cytoplasm|nucleolus|ribonucleoprotein complex	DNA binding|RNA binding|sequence-specific DNA binding transcription factor activity|ubiquitin protein ligase binding				0			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			tggattttaaaatatatataTA	0.035													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58514147	58514148	+	IGR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58514147_58514148delGT								XRCC6BP1 (163096 upstream) : LRIG3 (751790 downstream)																							tctagttgtcgtgTGTGTGTGT	0.163													4	2	---	---	---	---	
C12orf56	115749	broad.mit.edu	37	12	64669019	64669019	+	Intron	DEL	T	-	-	rs5798743		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64669019delT	uc001ssa.3	-						uc001srx.2_Intron|C12orf56_uc001sry.2_Intron|C12orf56_uc001srz.2_Intron	NM_001099676	NP_001093146	Q8IXR9	CL056_HUMAN	hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		taatatataatagtcatgtaa	0.174													11	20	---	---	---	---	
TMBIM4	51643	broad.mit.edu	37	12	66539381	66539381	+	Intron	DEL	T	-	-	rs75009871		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66539381delT	uc001stc.2	-						LLPH_uc010ssx.1_Intron|TMBIM4_uc001std.2_Intron|TMBIM4_uc009zqr.2_Intron|TMBIM4_uc001ste.2_Intron|TMBIM4_uc001stf.2_Intron|TMBIM4_uc009zqs.2_Intron	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4							integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)		GGAAAGCTTATTTTTTTTTTT	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68337634	68337635	+	IGR	DEL	GA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68337634_68337635delGA								DYRK2 (281191 upstream) : IFNG (210915 downstream)																							GAGAAGGAATGAGAACCAGGGG	0.356													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81735235	81735236	+	Intron	INS	-	AA	AA	rs146469031	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81735235_81735236insAA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						GTTTGATTAATAAACACCATAG	0.129													4	4	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495246	92495247	+	Intron	INS	-	G	G			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495246_92495247insG	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron			P62324	BTG1_HUMAN	Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				aaagaaagaaagaaagaaagaa	0.114			T	MYC	BCLL								3	5	---	---	---	---	
GOLGA2B	55592	broad.mit.edu	37	12	100553648	100553648	+	5'Flank	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100553648delT	uc001tgs.2	-						GOLGA2B_uc001tgt.2_RNA|GOLGA2B_uc001tgu.2_5'UTR	NM_017600	NP_060070			golgi autoantigen, golgin subfamily a, 2-like 1												0						ccattttctgttttttttgca	0.000													4	2	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	111950105	111950105	+	Intron	DEL	T	-	-	rs112796017		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111950105delT	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						AGAAAAAGTGTtttttttgtt	0.224													4	2	---	---	---	---	
RASAL1	8437	broad.mit.edu	37	12	113566146	113566149	+	Intron	DEL	ACAC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113566146_113566149delACAC	uc001tum.1	-						RASAL1_uc010syp.1_Intron|RASAL1_uc001tul.2_Intron|RASAL1_uc001tun.1_Intron|RASAL1_uc010syq.1_Intron|RASAL1_uc001tuo.3_Intron|RASAL1_uc010syr.1_Intron	NM_004658	NP_004649	O95294	RASL1_HUMAN	RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4						AGAGGCCCAGACACACACACACAC	0.382													4	2	---	---	---	---	
RBM19	9904	broad.mit.edu	37	12	114355948	114355948	+	Intron	DEL	A	-	-	rs66790437		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114355948delA	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AAAAAAAAAGAAAAAAAAAAG	0.388													4	6	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116401523	116401523	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116401523delA	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GGAAAAAAACAAAAAAAAAGC	0.328													4	2	---	---	---	---	
NOS1	4842	broad.mit.edu	37	12	117722892	117722892	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117722892delA	uc001twm.1	-							NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal						multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	aaTAAAAAATAAAAAAAAAAG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127915576	127915576	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127915576delT								LOC100128554 (958246 upstream) : TMEM132C (983715 downstream)																							AAGGCTCCCATTTTTTTGCCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	133035977	133035977	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133035977delC								GALNT9 (130072 upstream) : FBRSL1 (31180 downstream)																							TGGAGACAGGCCCTGCGAAGG	0.602													4	2	---	---	---	---	
TNFRSF19	55504	broad.mit.edu	37	13	24206710	24206710	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24206710delT	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron	NM_018647	NP_061117	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		CTTGGTTTTCTTTACTGTATC	0.363													4	2	---	---	---	---	
FLT1	2321	broad.mit.edu	37	13	28888537	28888537	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28888537delA	uc001usb.3	-						FLT1_uc010aap.2_Intron|FLT1_uc010aaq.2_Intron|FLT1_uc001usa.3_Intron	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	AAATGAAAAGAAAAAAAAAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29474434	29474435	+	IGR	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29474434_29474435delTG								SLC46A3 (181284 upstream) : MTUS2 (124313 downstream)																							tacctgtagctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30317853	30317853	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30317853delC								SLC7A1 (148028 upstream) : UBL3 (20693 downstream)																							CAGGGACTTTCCAGCAATTAA	0.388													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32699817	32699817	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32699817delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACAATTTATCAAAAAAACAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	39054867	39054867	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39054867delG								UFM1 (117725 upstream) : FREM2 (206306 downstream)																							ccttcagcatgggtagaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40886862	40886863	+	IGR	INS	-	GC	GC	rs35967008		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40886862_40886863insGC								COG6 (521060 upstream) : LOC646982 (34410 downstream)																							tgtgtgtgtgtgCACTCTTCAT	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43725626	43725626	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43725626delC								DNAJC15 (42322 upstream) : ENOX1 (62054 downstream)																							GACAGCAATGCCCAGGCTTTA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55699189	55699190	+	IGR	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55699189_55699190insA								MIR1297 (813006 upstream) : None (None downstream)																							TAGTTCCGTAGAAAACTATGAT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58438185	58438185	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58438185delA								PCDH17 (135120 upstream) : None (None downstream)																							agccacctggaaattgcaaaa	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68485591	68485591	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68485591delT								PCDH9 (681123 upstream) : None (None downstream)																							TTTTGTTGTCTTTTTTTTTTT	0.423													4	2	---	---	---	---	
RBM26	64062	broad.mit.edu	37	13	79945699	79945699	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79945699delA	uc001vkz.2	-						RBM26_uc001vky.2_Intron|RBM26_uc001vla.2_Intron|RBM26_uc001vkx.2_5'Flank|RBM26_uc001vlb.1_5'Flank	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26						mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		AACAGCAGGCAAAAAAAAAAC	0.279													5	4	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92680214	92680214	+	Intron	DEL	T	-	-	rs11363751		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92680214delT	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)				ATGACTGATATATAACAAAAC	0.328													2	6	---	---	---	---	
DOCK9	23348	broad.mit.edu	37	13	99549376	99549377	+	Intron	INS	-	T	T			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99549376_99549377insT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron|DOCK9_uc010afu.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)					CCCAGTCATCGTATCTCTTTGG	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105479225	105479225	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105479225delT								None (None upstream) : DAOA (638991 downstream)																							catccatgcattttttagatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112333267	112333267	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112333267delA								C13orf16 (336674 upstream) : SOX1 (388646 downstream)																							TAAGGCCGGCAAAGGGCTTGC	0.592													4	2	---	---	---	---	
TUBGCP3	10426	broad.mit.edu	37	13	113180923	113180924	+	Intron	INS	-	CAC	CAC			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113180923_113180924insCAC	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					atcatcatcatcaccatcatca	0.000													6	3	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114795108	114795108	+	Intron	DEL	T	-	-	rs34468499		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114795108delT	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron|RASA3_uc010tkl.1_Intron|RASA3_uc010aha.1_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			GTCATCCTGGTGGGCCAGGAC	0.582													4	5	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114840450	114840450	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114840450delA	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron|RASA3_uc010tkl.1_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TCCATTCTGTAAAAAAAACGC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19113832	19113832	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19113832delG								None (None upstream) : OR11H12 (263762 downstream)																							aaatgtacttgtaataaataa	0.060													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19826354	19826354	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19826354delC								POTEG (241412 upstream) : P704P (157600 downstream)																							GATACCTAGGCCCCTAGTAAA	0.542													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23703369	23703369	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23703369delT								SLC7A8 (50520 upstream) : HOMEZ (39475 downstream)																							TGTTGGTCTCTTTTTTTTTTC	0.219													4	2	---	---	---	---	
SCFD1	23256	broad.mit.edu	37	14	31175238	31175238	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31175238delT	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)		GTTCTCCTGGTTTTTTTTTTC	0.209													9	4	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76419245	76419245	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76419245delT	uc001xrx.2	+						TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		atggggtttatttttggggtc	0.000													4	2	---	---	---	---	
VIPAR	63894	broad.mit.edu	37	14	77907716	77907716	+	Intron	DEL	T	-	-	rs34716621		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77907716delT	uc001xtt.1	-						VIPAR_uc001xtu.1_Intron|VIPAR_uc010tvj.1_Intron|VIPAR_uc001xtv.1_Intron	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894						endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1						TTGGTTGTTGTTTTTTTTTTT	0.358													7	4	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	81039047	81039047	+	Intron	DEL	A	-	-	rs34430507		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81039047delA	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)		TGAAAACAACAAAAAAAAACA	0.413													3	3	---	---	---	---	
C14orf102	55051	broad.mit.edu	37	14	90784178	90784178	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90784178delA	uc001xyi.1	-						C14orf102_uc001xyj.1_Intron	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1								protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)		CAAAGCAAAGAAAAAAAAAAG	0.353													9	4	---	---	---	---	
TC2N	123036	broad.mit.edu	37	14	92258466	92258466	+	Intron	DEL	G	-	-	rs6575218		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92258466delG	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)		ccatctcaaagaaaaaaagaa	0.134													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92432407	92432407	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92432407delT								FBLN5 (18361 upstream) : TRIP11 (3055 downstream)																							ATTTGGAGTATTTTTTTGCCT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100660773	100660773	+	IGR	DEL	T	-	-	rs36018069		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100660773delT								DEGS2 (34761 upstream) : YY1 (44329 downstream)																							TGCCGCTGACTTAGACAACAC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20857994	20857995	+	IGR	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20857994_20857995insA								GOLGA8C (76968 upstream) : BCL8 (12061 downstream)																							tgtccaatattaagatcatgat	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21167769	21167769	+	Intron	DEL	T	-	-	rs145671489		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21167769delT	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																		AGTTGTTTCATTTTTTTTGAG	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31555450	31555450	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31555450delG								TRPM1 (161526 upstream) : KLF13 (63633 downstream)																							ACATAAACTTGGGGGGATTTG	0.557													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33229025	33229025	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33229025delT	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TGTGAAAAGGTGAAACACTAG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39796441	39796441	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39796441delA								C15orf54 (249393 upstream) : THBS1 (76839 downstream)																							CTCTCAATTCAAAAAAGTAGG	0.348													4	2	---	---	---	---	
THBS1	7057	broad.mit.edu	37	15	39881651	39881651	+	Intron	DEL	A	-	-	rs111526810		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39881651delA	uc001zkh.2	+						THBS1_uc010bbi.2_Intron	NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor						activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			ovary(3)|central_nervous_system(3)	6		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)	ACCCTTCACCAAAAAAAAAAG	0.418													4	2	---	---	---	---	
C15orf21	283651	broad.mit.edu	37	15	45848231	45848231	+	RNA	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45848231delT	uc010beg.1	+	6		c.1226delT			C15orf21_uc010beh.1_RNA|C15orf21_uc010bei.1_RNA|C15orf21_uc010bej.1_RNA|C15orf21_uc001zvm.1_RNA|C15orf21_uc001zvn.1_RNA					Homo sapiens cDNA FLJ39426 fis, clone PROST2000505.												0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;3.03e-17)|GBM - Glioblastoma multiforme(94;7.36e-07)		TTTGTTTAGCTTTTTTTTTTT	0.323			T	ETV1	prostate								3	4	---	---	---	---	
IGDCC4	57722	broad.mit.edu	37	15	65697905	65697906	+	Intron	DEL	TT	-	-	rs150498839		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65697905_65697906delTT	uc002aou.1	-							NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member							integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3						cctgaccctcttattgtgtttt	0.050													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	69421297	69421297	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69421297delA								TMEM84 (33136 upstream) : GLCE (31676 downstream)																							CAACAAAATGAAAATGCCAAC	0.483													4	2	---	---	---	---	
PML	5371	broad.mit.edu	37	15	74314975	74314975	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74314975delT	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron|PML_uc002awx.2_5'Flank|PML_uc002awy.2_5'Flank	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|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 resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						CTGTAGTAACTTTTTATACTC	0.368			T	RARA|PAX5	APL|ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79953632	79953635	+	IGR	DEL	CAGC	-	-	rs79679028		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79953632_79953635delCAGC								KIAA1024 (188990 upstream) : MTHFS (183685 downstream)																							AGACCAGAGGCAGCCAGGACTGAC	0.422													2	4	---	---	---	---	
KIAA1199	57214	broad.mit.edu	37	15	81152802	81152802	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81152802delA	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						GCATCACTCCAAAAGGATTAG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81290042	81290042	+	IGR	DEL	A	-	-	rs66644181		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81290042delA								MESDC2 (7837 upstream) : MESDC1 (3253 downstream)																							AACATCCattaaaaaaaaaaa	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82361974	82361975	+	IGR	INS	-	G	G	rs148071343	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82361974_82361975insG								MEX3B (23613 upstream) : EFTUD1 (60586 downstream)																							CAAAAGCAGTTGGTTCTGCAGC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96231252	96231252	+	IGR	DEL	A	-	-	rs11332823		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96231252delA								LOC145820 (180178 upstream) : NR2F2 (637905 downstream)																							GGATGGTCTTAACGTCAGAGC	0.448													9	5	---	---	---	---	
LMF1	64788	broad.mit.edu	37	16	943317	943318	+	Intron	INS	-	T	T	rs148163704	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:943317_943318insT	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				CAGTGGCTTCCTTTGCGCCTTC	0.525													4	5	---	---	---	---	
LOC342346	342346	broad.mit.edu	37	16	4621857	4621857	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4621857delT	uc010uxn.1	+							NM_001145011	NP_001138483	C9JH24	C9JH24_HUMAN	hypothetical protein LOC342346												0						ttttcttttcttttttttttt	0.254													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8057121	8057121	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8057121delT								A2BP1 (293781 upstream) : TMEM114 (562382 downstream)																							atttgctttatttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18303290	18303290	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18303290delT								XYLT1 (738552 upstream) : NOMO2 (207893 downstream)																							ATTACTATGATTTTTTTTTTA	0.184													4	2	---	---	---	---	
CSNK2A2	1459	broad.mit.edu	37	16	58202835	58202835	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58202835delT	uc002enc.2	-							NM_001896	NP_001887	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide						axon guidance|Wnt receptor signaling pathway	cytosol|nucleus	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						GGAAGAtttcttttttttttt	0.244													4	2	---	---	---	---	
CNOT1	23019	broad.mit.edu	37	16	58584792	58584792	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58584792delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron|CNOT1_uc010vik.1_Intron|SNORA46_uc002eny.1_5'Flank	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGACTAGTACAAATGAAACTT	0.303													4	2	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71126932	71126933	+	Intron	INS	-	AT	AT	rs139360305		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71126932_71126933insAT	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron|HYDIN_uc002ezw.3_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				gattagaAATcacacacacaca	0.158													2	4	---	---	---	---	
CDYL2	124359	broad.mit.edu	37	16	80683061	80683061	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80683061delA	uc002ffs.2	-							NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1						tgaaagaaataaagggcttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80950259	80950259	+	IGR	DEL	A	-	-	rs79967920		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80950259delA								CDYL2 (112084 upstream) : C16orf61 (59442 downstream)																							tctcaaaaacaaaaaaaaGGA	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	82458971	82458973	+	IGR	DEL	CAA	-	-	rs76081425	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82458971_82458973delCAA								MPHOSPH6 (255142 upstream) : CDH13 (201605 downstream)																							TAGGAATGGCCAAAGATTGGAAA	0.369													4	2	---	---	---	---	
SLC38A8	146167	broad.mit.edu	37	16	84065775	84065776	+	Intron	DEL	TT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84065775_84065776delTT	uc002fhg.1	-							NM_001080442	NP_001073911	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8						amino acid transport|sodium ion transport	integral to membrane					0						AGATGTAGAGTTttgttgttgt	0.129													4	4	---	---	---	---	
SLC38A8	146167	broad.mit.edu	37	16	84065782	84065793	+	Intron	DEL	GTTGTTGTTTTG	-	-	rs2326156	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84065782_84065793delGTTGTTGTTTTG	uc002fhg.1	-							NM_001080442	NP_001073911	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8						amino acid transport|sodium ion transport	integral to membrane					0						GAGTTttgttgttgttgttttgttgttgttgt	0.123													4	4	---	---	---	---	
COTL1	23406	broad.mit.edu	37	16	84644477	84644483	+	Intron	DEL	ATCTTCA	-	-	rs67301390		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84644477_84644483delATCTTCA	uc002fid.2	-						COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_Intron	NM_021149	NP_066972	Q14019	COTL1_HUMAN	coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1						CCAACCAAGCATCTTCATGATGCTGCC	0.459													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84833982	84833982	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84833982delT								USP10 (20457 upstream) : CRISPLD2 (19605 downstream)																							cattcaatcatttaatcctcc	0.129													3	7	---	---	---	---	
MTHFSD	64779	broad.mit.edu	37	16	86564386	86564386	+	3'UTR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86564386delC	uc002fjn.2	-	8					MTHFSD_uc010voo.1_3'UTR|MTHFSD_uc002fjo.2_3'UTR|MTHFSD_uc002fjm.2_3'UTR|MTHFSD_uc010vop.1_3'UTR|MTHFSD_uc010voq.1_3'UTR|MTHFSD_uc010vor.1_3'UTR	NM_001159377	NP_001152849	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain						folic acid-containing compound biosynthetic process		5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|RNA binding				0						ACCAGCCGTGCGGGCGGGGGC	0.587													4	2	---	---	---	---	
ACSF3	197322	broad.mit.edu	37	16	89162644	89162645	+	Intron	INS	-	TGA	TGA	rs145110748	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89162644_89162645insTGA	uc002fmp.2	+						ACSF3_uc010cig.1_Intron|ACSF3_uc010cih.1_Intron|ACSF3_uc002fmq.1_5'Flank	NM_174917	NP_777577	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3 precursor						fatty acid metabolic process	mitochondrion	acid-thiol ligase activity|ATP binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0281)		ATGAAGCTGGCTGAGGGTGGAA	0.609													3	4	---	---	---	---	
ABR	29	broad.mit.edu	37	17	966801	966801	+	Intron	DEL	T	-	-	rs72294527		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:966801delT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CTAGACACTGTTATGTGAACT	0.463													4	2	---	---	---	---	
PRPSAP2	5636	broad.mit.edu	37	17	18833655	18833655	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18833655delC	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron|PRPSAP2_uc002guq.1_Intron	NM_002767	NP_002758	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1						tcactgcactccaggctgagc	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21234377	21234378	+	IGR	INS	-	CG	CG	rs138103866		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21234377_21234378insCG								MAP2K3 (15828 upstream) : KCNJ12 (45321 downstream)																							TGTGGAAGTCATATTgagagga	0.282													3	4	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21310887	21310890	+	Intron	DEL	CCAT	-	-	rs141253420		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21310887_21310890delCCAT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	cacccattacccatccatccatcc	0.000										Prostate(3;0.18)			4	2	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21310898	21310898	+	Intron	DEL	T	-	-	rs61143113		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21310898delT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	catccatccatccacccatcc	0.000										Prostate(3;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25274220	25274220	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25274220delT								None (None upstream) : WSB1 (346886 downstream)																							aaatgtaaagtttaggatata	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	28569084	28569084	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28569084delT								SLC6A4 (6130 upstream) : BLMH (6139 downstream)																							AAGCAGGACATTTTTTTTTCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34295168	34295168	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34295168delT								LYZL6 (24497 upstream) : CCL16 (8368 downstream)																							tctttctttcttttttttttc	0.030													5	3	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39735060	39735061	+	Intron	DEL	TC	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39735060_39735061delTC	uc010wfs.1	-							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)		cctctccctttctctctctctc	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58634381	58634381	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58634381delA								APPBP2 (30801 upstream) : PPM1D (43173 downstream)																							TTCTTAAGGGAAAAAAAATAT	0.388													4	2	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59045928	59045928	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59045928delT	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.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)			agttgttgccttttttttttg	0.000													6	3	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64801916	64801917	+	3'UTR	DEL	GT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64801916_64801917delGT	uc002jfp.1	+	17						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)	TTGTGTGTGCGTGTGTGTGTGT	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74646994	74646995	+	IGR	INS	-	TTTTG	TTTTG	rs139084267	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74646994_74646995insTTTTG								ST6GALNAC1 (7100 upstream) : MXRA7 (24814 downstream)																							GCTGACCCTAACAATATGTGCA	0.149													3	3	---	---	---	---	
AFMID	125061	broad.mit.edu	37	17	76202664	76202665	+	Intron	INS	-	T	T	rs138402622	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76202664_76202665insT	uc002jva.3	+						AFMID_uc002jvb.3_Intron|AFMID_uc002juz.3_Intron	NM_001010982	NP_001010982	Q63HM1	AFMID_HUMAN	arylformamidase isoform 1							cytosol|nucleus	arylformamidase activity			large_intestine(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)			attattcaatgttttgtagaga	0.035													6	5	---	---	---	---	
TIMP2	7077	broad.mit.edu	37	17	76872995	76872996	+	Intron	INS	-	A	A	rs149985577	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76872995_76872996insA	uc002jwf.2	-						TIMP2_uc002jwe.2_5'Flank|TIMP2_uc010wty.1_Intron	NM_003255	NP_003246	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2 precursor								metal ion binding|metalloendopeptidase inhibitor activity			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			ccagctaaaatagcccttttcT	0.248													2	4	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80156546	80156546	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80156546delT	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			caggatacaattaaaaaaaaa	0.030													4	2	---	---	---	---	
B3GNTL1	146712	broad.mit.edu	37	17	80959302	80959302	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80959302delA	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			aactgtgaagaAAAAAGGAAG	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	111052	111052	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:111052delC	uc002kke.2	+											Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		ctaggttcagcctacaggagc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11639098	11639098	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11639098delT								FAM38B (937119 upstream) : GNAL (50038 downstream)																							TGTCTGGTTGTTTTTCTTTAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32471841	32471841	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32471841delA								DTNA (33 upstream) : MAPRE2 (85051 downstream)																							AGCTAGTGATAAAGGAGGATC	0.338													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37597287	37597287	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37597287delG								LOC647946 (217005 upstream) : None (None downstream)																							ACATGGAGGCGTGCTAATGGC	0.433													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	40103424	40103424	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40103424delA	uc002lat.2	+						uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		ATCAGGCCCTAAGGAAAACAG	0.438													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50021724	50021724	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50021724delC	uc002lfe.1	+							NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		gtttctctatccccacccata	0.000													4	2	---	---	---	---	
MBD2	8932	broad.mit.edu	37	18	51732219	51732219	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51732219delT	uc002lfg.1	-						MBD2_uc002lfh.1_Intron	NM_003927	NP_003918	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2 isoform 1						transcription, DNA-dependent		C2H2 zinc finger domain binding|methyl-CpG binding|satellite DNA binding				0				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)	Hexobarbital(DB01355)	TTTGAAATGCTTTTTTTTTCC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64125165	64125166	+	IGR	DEL	CA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64125165_64125166delCA								CDH7 (576991 upstream) : CDH19 (46155 downstream)																							agcaaatacccacacacacaca	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76536601	76536601	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76536601delA								None (None upstream) : SALL3 (203674 downstream)																							CAGGTATAATAAAAAAATATT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4603451	4603454	+	IGR	DEL	GATG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4603451_4603454delGATG								SEMA6B (43680 upstream) : TNFAIP8L1 (36076 downstream)																							tggatgagtagatggatggatgga	0.000													3	3	---	---	---	---	
MLLT1	4298	broad.mit.edu	37	19	6224725	6224725	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6224725delT	uc002mek.2	-							NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1						GGCACTACGAtttttttgttt	0.294			T	MLL	AL								4	2	---	---	---	---	
NWD1	284434	broad.mit.edu	37	19	16872616	16872616	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16872616delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7						TGATGTAAGGAAAAAAAAAAC	0.269													3	3	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17991503	17991504	+	Intron	INS	-	CAAAA	CAAAA	rs144134876	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17991503_17991504insCAAAA	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						agatcttttctcaaaacaaaac	0.005													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23289875	23289876	+	IGR	INS	-	T	T	rs113497339		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23289875_23289876insT								ZNF99 (337091 upstream) : ZNF91 (231543 downstream)																							GCATGtttttgttttttttttt	0.173													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24065805	24065805	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24065805delT								RPSAP58 (54888 upstream) : ZNF254 (150442 downstream)																							ccattttctgttttttttttt	0.000													3	3	---	---	---	---	
LIG1	3978	broad.mit.edu	37	19	48661623	48661624	+	Intron	INS	-	CCT	CCT	rs141917338	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48661623_48661624insCCT	uc002pia.1	-						LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|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	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	cacagaggaagcctgggcctct	0.223								NER					3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57448733	57448733	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57448733delC								MIMT1 (88811 upstream) : USP29 (182776 downstream)																							TTTTTGTGTGCACGCTGCAGA	0.468													4	2	---	---	---	---	
SLC27A5	10998	broad.mit.edu	37	19	59021942	59021942	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59021942delA	uc002qtc.2	-							NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid						bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		ctctgcctcgaaaaaaaaaac	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22407038	22407038	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22407038delA								LOC284788 (5757 upstream) : C20orf56 (134156 downstream)																							CAGCATAACCAAAAAAAAAAA	0.428													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26202319	26202319	+	IGR	DEL	C	-	-	rs74486893		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26202319delC								MIR663 (13405 upstream) : None (None downstream)																							attacagaatctttatatctg	0.005													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26228625	26228625	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26228625delA								MIR663 (39711 upstream) : None (None downstream)																							CTACAATGACAAAAAAAAATT	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26250583	26250583	+	IGR	DEL	T	-	-	rs75043991		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26250583delT								MIR663 (61669 upstream) : None (None downstream)																							ttattttggcttttttttctt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29455506	29455506	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29455506delT								None (None upstream) : FRG1B (156373 downstream)																							ATAGGTTTTATTTCAGTGATT	0.124													4	2	---	---	---	---	
RALGAPB	57148	broad.mit.edu	37	20	37169993	37169993	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37169993delT	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron|RALGAPB_uc002xja.1_Intron	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						AAAATCTCTATTTTTTTTTTA	0.343													6	4	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41331860	41331861	+	Intron	DEL	AG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41331860_41331861delAG	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						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)				agagagacacagagagagagag	0.327													3	3	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45562998	45562999	+	Intron	INS	-	CG	CG	rs1360612		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45562998_45562999insCG	uc002xsm.2	+						EYA2_uc010ghp.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				gccagcttccttgtcgtggtgg	0.000													4	2	---	---	---	---	
NCOA3	8202	broad.mit.edu	37	20	46191283	46191283	+	Intron	DEL	T	-	-	rs75850932		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46191283delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5						tctgtcttGATTTTTTTTTTT	0.159													3	3	---	---	---	---	
ZNF831	128611	broad.mit.edu	37	20	57786834	57786835	+	Intron	INS	-	TGTG	TGTG	rs141763800	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57786834_57786835insTGTG	uc002yan.2	+							NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831							intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					GGAGCTGACCTtgtgtgtgtgt	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10130988	10130989	+	IGR	DEL	AT	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10130988_10130989delAT								None (None upstream) : TPTE (775754 downstream)																							AGTTAAAAACATAAAATCCAGT	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10714105	10714106	+	IGR	INS	-	AG	AG	rs148942212		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10714105_10714106insAG								None (None upstream) : TPTE (192637 downstream)																							tctacaagaacagtttcctgac	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10751362	10751362	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10751362delT								None (None upstream) : TPTE (155381 downstream)																							aactcctttgtgatgtgtgca	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10775714	10775715	+	IGR	INS	-	GG	GG	rs55946795		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10775714_10775715insGG								None (None upstream) : TPTE (131028 downstream)																							tggaatggaatagaatggaatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10775715	10775716	+	IGR	INS	-	ATG	ATG	rs55946795		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10775715_10775716insATG								None (None upstream) : TPTE (131027 downstream)																							ggaatggaatagaatggaatgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10809119	10809123	+	IGR	DEL	GGAAA	-	-	rs79536468		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10809119_10809123delGGAAA								None (None upstream) : TPTE (97620 downstream)																							ggaatggaatggaaaggaatggaaa	0.000													3	3	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10996562	10996562	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10996562delC	uc002yis.1	-									P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaaattcccaccacatacaga	0.010													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11032608	11032608	+	Intron	DEL	T	-	-	rs2257758		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11032608delT	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCTTAAATTCTTTTTAGTCAA	0.289													8	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11043382	11043382	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11043382delA	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)		aattctgaggaaaagcaagat	0.000													4	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11093710	11093711	+	Intron	INS	-	A	A	rs141963528		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11093710_11093711insA	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)		tcAAAACCTCCAAAAAACACTG	0.193													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11096043	11096044	+	Intron	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11096043_11096044insA	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)		AGGCAGTTTGCAAAAAAAAATG	0.178													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11126866	11126867	+	IGR	INS	-	G	G	rs71931427		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11126866_11126867insG								BAGE (27929 upstream) : None (None downstream)																							tttgtttgtttttttgtttttg	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11126867	11126868	+	IGR	INS	-	TTG	TTG	rs71931427		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11126867_11126868insTTG								BAGE (27930 upstream) : None (None downstream)																							ttgtttgtttttttgtttttgt	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11187952	11187954	+	IGR	DEL	ATA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11187952_11187954delATA								BAGE (89015 upstream) : None (None downstream)																							gaagcacagcataataatatgtg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14361245	14361247	+	IGR	DEL	TAT	-	-	rs146270343	by1000genomes	TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14361245_14361247delTAT								None (None upstream) : C21orf99 (49240 downstream)																							ttctgtcttgtatttatgtgaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23650293	23650293	+	IGR	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23650293delA								NCAM2 (739079 upstream) : None (None downstream)																							GTCTTTTTTTAAAACATCCTA	0.269													4	2	---	---	---	---	
ITSN1	6453	broad.mit.edu	37	21	35022702	35022703	+	Intron	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35022702_35022703delTG	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						CCATTCGTTTtgtgtgtgtgtg	0.342													4	2	---	---	---	---	
HIRA	7290	broad.mit.edu	37	22	19417866	19417867	+	Intron	DEL	GA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19417866_19417867delGA	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron|MRPL40_uc002zpg.2_5'Flank|MRPL40_uc002zph.2_5'Flank	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					AAGATGGAAGGAGAGAGAGGTG	0.446													4	2	---	---	---	---	
LOC91316	91316	broad.mit.edu	37	22	24025806	24025806	+	Intron	DEL	C	-	-	rs34936243		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24025806delC	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						GTTGCAGAGACAAGGGGCACA	0.577													4	5	---	---	---	---	
POM121L9P	29774	broad.mit.edu	37	22	24660701	24660701	+	RNA	DEL	A	-	-	rs71320760		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24660701delA	uc002zzs.3	+	7		c.4433delA			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						AGATTGTTTGAAAAAAAAAAA	0.363													4	2	---	---	---	---	
ADRBK2	157	broad.mit.edu	37	22	26093827	26093827	+	Intron	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26093827delC	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	agatgaATCTCCCCCACTAGG	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35331738	35331738	+	IGR	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35331738delT								None (None upstream) : ISX (130391 downstream)																							accaaccttcttttagttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	43182074	43182074	+	IGR	DEL	A	-	-	rs76813882		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43182074delA								A4GALT (64788 upstream) : ARFGAP3 (10458 downstream)																							tgTAGCCCTCAACGTGAAATG	0.458													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	15901912	15901913	+	IGR	INS	-	A	A			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15901912_15901913insA								AP1S2 (28812 upstream) : GRPR (239511 downstream)																							cctcccctctgaaaaaaaaaaa	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	43379040	43379040	+	IGR	DEL	C	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43379040delC								PPP1R2P9 (741554 upstream) : MAOA (136369 downstream)																							aaactgattgccactctgact	0.040													4	2	---	---	---	---	
RP2	6102	broad.mit.edu	37	X	46719736	46719736	+	Intron	DEL	T	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46719736delT	uc004dgw.3	+							NM_006915	NP_008846	O75695	XRP2_HUMAN	XRP2 protein						cell morphogenesis|CTP biosynthetic process|GTP biosynthetic process|protein folding|UTP biosynthetic process|visual perception	cytoplasm|plasma membrane	ATP binding|GTP binding|GTPase activator activity|nucleoside diphosphate kinase activity|unfolded protein binding				0						TTAGGCATTCTTTTTTTTTCC	0.279													4	2	---	---	---	---	
FAM120C	54954	broad.mit.edu	37	X	54162190	54162195	+	Intron	DEL	AAATTA	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54162190_54162195delAAATTA	uc004dsz.3	-						FAM120C_uc011moh.1_Intron	NM_017848	NP_060318	Q9NX05	F120C_HUMAN	hypothetical protein LOC54954											ovary(1)|central_nervous_system(1)	2						aaccttacataaattatttcatctga	0.073													8	11	---	---	---	---	
ATP1B4	23439	broad.mit.edu	37	X	119510565	119510565	+	Intron	DEL	A	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119510565delA	uc004esr.2	+						ATP1B4_uc004esq.2_Intron|ATP1B4_uc011mtx.1_Intron|ATP1B4_uc011mty.1_Intron	NM_001142447	NP_001135919	Q9UN42	AT1B4_HUMAN	ATPase, (Na+)/K+ transporting, beta 4						ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2						aacttcagctaagggccacag	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9945223	9945224	+	IGR	INS	-	T	T	rs147580695		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9945223_9945224insT								TTTY22 (294369 upstream) : None (None downstream)																							tatcagataaatttaacaatga	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9961116	9961116	+	IGR	DEL	G	-	-	rs149972693		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9961116delG								TTTY22 (310262 upstream) : None (None downstream)																							CTGAAAAAAAGAATTGTCTTG	0.358													4	5	---	---	---	---	
HSFY2	159119	broad.mit.edu	37	Y	20931854	20931855	+	Intron	DEL	TG	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:20931854_20931855delTG	uc004ftv.2	-						HSFY2_uc004ftu.2_Intron	NM_152584	NP_689797	Q96LI6	HSFY1_HUMAN	heat shock transcription factor, Y-linked 1							cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TTCACATACAtgtgtgtgtgtg	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28796861	28796861	+	IGR	DEL	G	-	-			TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28796861delG								None (None upstream) : None (None downstream)																							GAACGGTTTTGAATGTCAGTG	0.124													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58979107	58979108	+	IGR	INS	-	CACTCCA	CACTCCA	rs10449120		TCGA-CJ-5671-01A-11D-1534-10	TCGA-CJ-5671-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58979107_58979108insCACTCCA								None (None upstream) : None (None downstream)																							attgcattcccttccattccat	0.000													4	2	---	---	---	---	
